From matt.mccormick at kitware.com  Tue Jul  1 10:42:18 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 1 Jul 2014 10:42:18 -0400
Subject: [ITK-users] [ITK]  make: path to ITK build unknown
In-Reply-To: <1404163146356-34178.post@n7.nabble.com>
References: <1404156895729-34171.post@n7.nabble.com>
 <CALzTN-T8TWDwAjHR2NsLX_cO5ZaasymPpoAJEfQDgERur9viqg@mail.gmail.com>
 <1404158799755-34173.post@n7.nabble.com>
 <CALzTN-TA=B0Dk4MuzMS2+4=VuvX_E0kQeLjU7L_O9fbbFxyW2A@mail.gmail.com>
 <1404160568558-34175.post@n7.nabble.com>
 <CALzTN-SeVZKh0Ko32MqFq4x8jta+Koiho1fyFc37FvGOoMfUuA@mail.gmail.com>
 <1404161490890-34177.post@n7.nabble.com>
 <1404163146356-34178.post@n7.nabble.com>
Message-ID: <CALzTN-Sp-hnZeGd1tXadPYEFDdp7ZDHosgr8PcOOe+TeGGZKKw@mail.gmail.com>

After testing on Ubuntu 12.04, I confirmed that even without adjusting
CMAKE_INSTALL_PREFIX, a 'make install' is sufficient for cmake to
automatically find ITK_DIR.

This error:

  fatal error: itkBinaryThresholdImageFilter.h: No such file or directory
compilation terminated.

Is probably related to an issue in your project's CMakeLists.txt.
Please download and unpack the tarball for this example [1], test to
verify it builds, and use it as an example for your project.

Hope this helps,
Matt

[1] http://itk.org/ITKExamples/src/Filtering/Thresholding/ThresholdAnImageUsingBinary/Documentation.html

On Mon, Jun 30, 2014 at 5:19 PM, donelron <donelron at web.de> wrote:
> I just ran
> cmake  -DCMAKE_INSTALL_PREFIX=/usr . /home/ron/vtk_itk/ITK
> make
> sudo make install, but the problem is still there - same errror message:
> --------------------------------------------------------------------------------
> fatal error: itkBinaryThresholdImageFilter.h: No such file or directory
> compilation terminated.
> etc..
> --------------------------------------------------------------------------------
>
>
>
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/make-path-to-ITK-build-unknown-tp34171p34178.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

From e.heim at dkfz-heidelberg.de  Tue Jul  1 11:35:45 2014
From: e.heim at dkfz-heidelberg.de (Heim, Eric)
Date: Tue, 1 Jul 2014 17:35:45 +0200
Subject: [ITK-users] ITK Python Wrapping vs. SimpleITK
Message-ID: <57EE86D11538B44096C712532DBB6C5A0109F25B2D6D@DKFZEX01.ad.dkfz-heidelberg.de>

Dear all,

I'm currently embedding python into a C/C++ application and want to access ITK through python.
The ITK python wrapping requires CableSwig to work, but I can't compile it under newer Visual Studio versions.
After looking at the git repository I noticed that the last commit in CableSwig was done ~2 years ago.
Some open source projects, like 3DSlicer, are now using SimpleITK in their python wrapping.

What are the future development plans of ITK python wrapping, CableSwig and SimpleITK?
Would it be more future-proof to embed SimpleITK into an application than ITK?  Are there maybe plans
to fully integrate SimpleITK into ITK, so there is no need for additional toolkit dependencies except ITK?

Cheers,
Eric
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140701/f823df17/attachment.html>

From matt.mccormick at kitware.com  Tue Jul  1 12:14:00 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 1 Jul 2014 12:14:00 -0400
Subject: [ITK-users] [ITK]  ITK Python Wrapping vs. SimpleITK
In-Reply-To: <57EE86D11538B44096C712532DBB6C5A0109F25B2D6D@DKFZEX01.ad.dkfz-heidelberg.de>
References: <57EE86D11538B44096C712532DBB6C5A0109F25B2D6D@DKFZEX01.ad.dkfz-heidelberg.de>
Message-ID: <CALzTN-QpARtDGSUv1VxjBo3GNMD0gT=JEPUX+PTC-R3bKK7YKg@mail.gmail.com>

Hi Eric,

ITK no longer requires CableSwig for wrapping.  However, it currently
does not build on Visual Studio newer that 2008. This due to GCCXML
limitations.  We have investigated a GCCXML replacement, but it still
needs work.

SimpleITK is also a good option. It has no dependencies other than ITK.

Hope this helps,
Matt

On Tue, Jul 1, 2014 at 11:35 AM, Heim, Eric <e.heim at dkfz-heidelberg.de> wrote:
> Dear all,
>
>
>
> I?m currently embedding python into a C/C++ application and want to access
> ITK through python.
>
> The ITK python wrapping requires CableSwig to work, but I can?t compile it
> under newer Visual Studio versions.
>
> After looking at the git repository I noticed that the last commit in
> CableSwig was done ~2 years ago.
>
> Some open source projects, like 3DSlicer, are now using SimpleITK in their
> python wrapping.
>
>
>
> What are the future development plans of ITK python wrapping, CableSwig and
> SimpleITK?
>
> Would it be more future-proof to embed SimpleITK into an application than
> ITK?  Are there maybe plans
>
> to fully integrate SimpleITK into ITK, so there is no need for additional
> toolkit dependencies except ITK?
>
>
>
> Cheers,
>
> Eric
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From donelron at web.de  Tue Jul  1 17:09:24 2014
From: donelron at web.de (donelron)
Date: Tue, 1 Jul 2014 14:09:24 -0700 (PDT)
Subject: [ITK-users] [ITK]  make: path to ITK build unknown
In-Reply-To: <CALzTN-Sp-hnZeGd1tXadPYEFDdp7ZDHosgr8PcOOe+TeGGZKKw@mail.gmail.com>
References: <1404156895729-34171.post@n7.nabble.com>
 <CALzTN-T8TWDwAjHR2NsLX_cO5ZaasymPpoAJEfQDgERur9viqg@mail.gmail.com>
 <1404158799755-34173.post@n7.nabble.com>
 <CALzTN-TA=B0Dk4MuzMS2+4=VuvX_E0kQeLjU7L_O9fbbFxyW2A@mail.gmail.com>
 <1404160568558-34175.post@n7.nabble.com>
 <CALzTN-SeVZKh0Ko32MqFq4x8jta+Koiho1fyFc37FvGOoMfUuA@mail.gmail.com>
 <1404161490890-34177.post@n7.nabble.com>
 <1404163146356-34178.post@n7.nabble.com>
 <CALzTN-Sp-hnZeGd1tXadPYEFDdp7ZDHosgr8PcOOe+TeGGZKKw@mail.gmail.com>
Message-ID: <1404248964241-34182.post@n7.nabble.com>

My CMakeLists.txt  looks like:
-------------------------------------------------------------------------------------------------
cmake_minimum_required(VERSION 2.4)

if(COMMAND cmake_policy)
      cmake_policy(SET CMP0003 NEW)
endif(COMMAND cmake_policy)

SET(DITK_DIR /home/ron/vtk_itk/ITK)

project(BinaryThresholdFilter)
include_regular_expression("^.*$")

# Find ITK.
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

add_executable(BinaryThresholdImageFilter BinaryThresholdImageFilter.cxx )
target_link_libraries(BinaryThresholdImageFilter ${ITK_LIBRARIES})


if(BUILD_TESTING)
  add_subdirectory(test)
endif()
-------------------------------------------------------------------------------------------------


I downloaded and compiled the code you mentioned with 
cmake  ../BinaryThresholding/
make
and the result here is similar as with the project I was talking about in my
initial post:


fatal error: itkImageFileReader.h: No such file or directory
compilation terminated.
make[2]: ***
[CMakeFiles/BinaryThresholdImageFilter.dir/BinaryThresholdImageFilter.o]
Error 1
make[1]: *** [CMakeFiles/BinaryThresholdImageFilter.dir/all] Error 2
make: *** [all] Error 2


However, if I  
cmake -DITK_DIR=/home/ron/vtk_itk/ITK  ../BinaryThresholding/
make
it successfully compiles.




--
View this message in context: http://itk-users.7.n7.nabble.com/make-path-to-ITK-build-unknown-tp34171p34182.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From franciscolopezdelafranca at gmail.com  Wed Jul  2 09:19:41 2014
From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=)
Date: Wed, 2 Jul 2014 06:19:41 -0700 (PDT)
Subject: [ITK-users] Surface extraction problem
Message-ID: <1404307181365-7585840.post@n2.nabble.com>

Hi everybody.
I've created a 3D cylinder by using the class CylinderSpatialObject. After
that, I pass the cylinder object to an object of class
SpatialObjectToImageFilter in order to prepare the spatial object to be
written to file.
I've set both the cylinder object and the image filter a value of 0 for
background and 255 for foreground.
Finally, I pass, as input, the image filter output to an image file writer
(ImageFileWriter) object to save it to file (Nifti format, for instance).
The result is the attached "cilindro.jpg" figure.

Up to here, all is ok. The problem comes next.
What I want is to extract the surface of the 3D cylinder. I search for the
web and found an example, from which I followed the implementation.
I copy below my code and attach the result of the surface extraction
("cilindro_superficie.jpg"), hoping that anyone see if I am committing any
error. I expected just the boundary of the 3D cylinder (with no inside
points), and it seems like the bounding box of the cylinder what I've got
including the inside points.

Thank you very much and my best regards.

My code is (I've erased the obvious code):


    typedef itk::Image< PixelType, Dimension > ImageType;
    typedef itk::Mesh<double, 3> MeshType;

    typedef itk::ImageFileReader< ImageType > ReaderType;
    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(
inputFileName);

        reader->Update();

    typedef itk::BinaryMask3DMeshSource< ImageType, MeshType >
MeshSourceType;
    MeshSourceType::Pointer meshSource = MeshSourceType::New();

    meshSource->SetObjectValue( 255);

    meshSource->SetInput( reader->GetOutput() );

        meshSource->Update();

    typedef itk::MeshSpatialObject<MeshType> SpatialObjectType;
    SpatialObjectType::Pointer mesh = SpatialObjectType::New();
    mesh->SetMesh(meshSource->GetOutput());

    typedef itk::SpatialObjectToImageFilter<SpatialObjectType, ImageType>
MeshFilterType;
    MeshFilterType::Pointer meshFilter = MeshFilterType::New();

    meshFilter->SetSize(size);
    meshFilter->SetOutsideValue(0);
    meshFilter->SetInsideValue(255);
    meshFilter->SetInput(mesh);

        meshFilter->Update();

    typedef itk::ImageFileWriter<ImageType> ImageWriterType;
    ImageWriterType::Pointer imageWriter = ImageWriterType::New();

    imageWriter->SetFileName(outputFileName);
    imageWriter->SetInput(meshFilter->GetOutput());

        imageWriter->Update();

<http://itk-insight-users.2283740.n2.nabble.com/file/n7585840/cilindro.jpg> 
<http://itk-insight-users.2283740.n2.nabble.com/file/n7585840/cilindro_superficie.jpg> 



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Surface-extraction-problem-tp7585840.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From mrguilfoyle at gmail.com  Wed Jul  2 12:14:03 2014
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Wed, 2 Jul 2014 17:14:03 +0100
Subject: [ITK-users] [ITK] Resampling after SetDirection() and
	SetOrigin()
In-Reply-To: <CALzTN-Q--_ih8u3GOH8B55Ny_a6Dx6Bd5HC8pjL5ySo5mCyZoQ@mail.gmail.com>
References: <CAC5Ld0CRDrNp4iiJEFb+2ztwXNWXG+k_racPYzRqHDZ1oQm8pg@mail.gmail.com>
 <CALzTN-QS4yvbmcfHxVi7QncoXSWtj6Hv59bqNsMkxUOzbpTgfA@mail.gmail.com>
 <CAC5Ld0AWvfwoi66nbXrJqkNBOBhXN1SupgLy_=Kpu55vh=PNNA@mail.gmail.com>
 <CALzTN-Q--_ih8u3GOH8B55Ny_a6Dx6Bd5HC8pjL5ySo5mCyZoQ@mail.gmail.com>
Message-ID: <CAC5Ld0Cqtv2ZaFPCrqG12UxeB0wAbDrfAnvvq3c2O09Cqowh-Q@mail.gmail.com>

Hi Matt

Sorry to labour this point but I'm still confused as to what is going on;
my misunderstanding may well be to do with how the pipelines work.

As an example:

import itk

fileNameIn = '/route/to/input.nii'
fileNameOut = '/route/to/output.nii'
image_type = itk.Image[itk.F, 3]
reader = itk.ImageFileReader[image_type].New()
reader.SetFileName(fileNameIn)
reader.Update()

image = reader.GetOutput()
#image.GetOrigin() gives [-148, -153,  55]
#image.GetDirection().GetVnlMatrix().get(0,0)....(2,2)
#gives matrix:  1.0     0       0
#               0       0.95    0.3
#               0       -0.3    0.95

image.GetOrigin().Fill(0)
image.GetDirection().SetIdentity()
#image.GetOrigin() gives [0, 0, 0]
#image.GetDirection().GetVnlMatrix().get(0,0)....(2,2)
#gives matrix:  1.0     0       0
#               0       1.0     0
#               0       0       1.0

writer = itk.ImageFileWriter[image_type].New()
writer.SetFileName(fileNameOut)
writer.SetInput(image)
writer.Update()

*#output image volume is unchanged when viewed in (e.g.) ImageJ*
resampler = itk.ResampleImageFilter[image_type, image_type].New()
resampler.SetInput(image)
resampler.SetSize(image.GetLargestPossibleRegion().GetSize())
resampler.SetOutputOrigin(image.GetOrigin())
resampler.SetOutputSpacing(image.GetSpacing())
resampler.SetOutputDirection(image.GetDirection())
resampler.Update()

writer.SetInput(resampler.GetOutput())
writer.Update()




*#now output is translated and rotated by the (inverse) values of the
original#origin vector and direction matrix##However,
resampler.GetInput().GetOrigin() gives [0,0,0]#and similarly the direction
of the input is a 3x3 identity matrix*

I don't understand why the resampler changes the image volume since it
should not be 'aware' of the original origin/direction.

>From your previous reply you suggest that the call to resampler.Update()
might cause the reader to re-import the file from disk.  Is this the case
even when the reader and resampler are not connected in a pipeline (as
here).  Further, if the reader does re-import the original image and
origin/direction parameters why does resampler.GetInput().GetOrigin()
report [0, 0, 0] and  the input direction matrix is an identity?

I want to understand why this is happening as it is clearly important for
ensuring I set up more complex pipelines correctly.

Many thanks
Mathew


On 30 June 2014 03:28, Matt McCormick <matt.mccormick at kitware.com> wrote:

> Hi Mathew,
>
> The image does not retain the original parameters somewhere.  However,
> can must be take, because if the image is generated by a filter in a
> pipeline, that filter will reset the original value when the pipeline
> is re-run. ChangeInformationImageFilter will ensure this reset does
> not happen during a pipeline update.
>
> The Set methods doo reorient/reposition the whole image volume in
> world space.  The resampling filter does not select a subregion or
> rotates the images -- to get the same out, the  sampling locations of
> the output image for the ResampleImageFilter must be set as desired.
> Set SetOutputOrigin [1], SetOutputDirection [2], etc.
>
> Hope this helps to clarify.
>
> I checked by wrapped install, and I have ChangeInformationImageFilter
> instantiations for float images.
>
> Hope this helps,
> Matt
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html#ac4b197ddefd3b3344bd9c9471acd5b00
>
> [2]
> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html#a9fdd6b862ab6cbaa03702da393bd0474
>
>
> On Sun, Jun 29, 2014 at 10:01 PM, Mathew Guilfoyle
> <mrguilfoyle at gmail.com> wrote:
> > Matt, thanks for the reply.
> >
> > I would be grateful if you could you explain why this is the desired
> > behaviour.  If I use the SetDirection() or SetOrigin() methods does the
> > image object retain the original parameters somewhere?  Subsequently
> calling
> > GetDirection() or GetOrigin() reports the changed parameters.
> >
> > Intuitively you would expect both Set methods to reorient/reposition the
> > whole image volume in world space, and on the face of it that is what
> they
> > seem to do.  However, on passing the image to a resampling filter they
> act
> > to select a subregion or to rotate the image. I would have thought that
> > rotations and region selections should be options passed to the filter
> and
> > not set in the image itself?
> >
> > How does the ChangeInformationImageFilter do it differently?
>  Incidentally I
> > have wrapped for float but don't get this as an option for this filter.
> >
> > Thanks
> > Mathew
> >
> >
> >
> > On 30 June 2014 01:45, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
> >>
> >> Hi Mathew,
> >>
> >> Yes, that is the correct and expected behavior. I do not know if
> >> ImageJ is using the actual location in world space.
> >>
> >> It sounds like ChangeInformationImageFilter is what you are looking
> >> for.  It will be wrapped for float images if wrapped for float images
> >> is enabled in you CMake configuration (ITK_WRAP_float).
> >>
> >> Hope this helps,
> >> Matt
> >>
> >>
> >> On Sat, Jun 28, 2014 at 9:55 PM, Mathew Guilfoyle <
> mrguilfoyle at gmail.com>
> >> wrote:
> >> > If I change an image's direction and origin using SetDirection() and
> >> > SetOrigin() methods and then write the image back to a file, the
> volume
> >> > stack viewed in (e.g.) ImageJ is unchanged.  This is the behaviour I
> >> > would
> >> > expect as changing the direction and origin shouldn't alter the array
> of
> >> > image pixels, just its location and orientation in 'world space'?
> >> >
> >> > However, if I take the same image, adjust the origin and direction as
> >> > before, and then input it to ResampleImageFilter with an identity
> >> > transform
> >> > (and set spacing, origin, direction, and size to those of the input
> >> > image)
> >> > the output is a translated and rotated image.
> >> >
> >> > It seems the difference between the original and adjusted origin and
> >> > direction are applied as a translation and rotation during resampling,
> >> > even
> >> > though GetOrigin() and GetDirection() on the input image to the
> >> > resampler
> >> > return the adjusted parameters.
> >> >
> >> > Is this the expected behaviour? Is there another image parameter that
> >> > needs
> >> > to be changed to correctly alter origin and direction?
> >> >
> >> > (ChangeInformationImageFilter is not wrapped for float images so I
> can't
> >> > use
> >> > it for my application)
> >> >
> >> > Thanks
> >> >
> >> > _____________________________________
> >> > Powered by www.kitware.com
> >> >
> >> > Visit other Kitware open-source projects at
> >> > http://www.kitware.com/opensource/opensource.html
> >> >
> >> > Kitware offers ITK Training Courses, for more information visit:
> >> > http://www.kitware.com/products/protraining.php
> >> >
> >> > Please keep messages on-topic and check the ITK FAQ at:
> >> > http://www.itk.org/Wiki/ITK_FAQ
> >> >
> >> > Follow this link to subscribe/unsubscribe:
> >> > http://public.kitware.com/mailman/listinfo/insight-users
> >> >
> >> > _______________________________________________
> >> > Community mailing list
> >> > Community at itk.org
> >> > http://public.kitware.com/mailman/listinfo/community
> >> >
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140702/148f2957/attachment-0001.html>

From gabrielgimenez85 at gmail.com  Wed Jul  2 17:43:53 2014
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Wed, 2 Jul 2014 14:43:53 -0700 (PDT)
Subject: [ITK-users] MattesMutualInformationImageToImageMetric: Joint PDF
	summed to zero
Message-ID: <1404337433182-7585842.post@n2.nabble.com>

Hi everyone, first of all, sorry for my bad English.

I modified the ImageRegistration8 example for use the
itkOnePlusOneEvolutionaryOptimize and
itkMattesMutualInformationImageToImageMetric like in the ImageRegistration11
example.
Can help me with this error ?

Thanks.

1   -0.536085   [0, 0, 0, 2.4210718274608496, -15.626697762130291,
0.24074437575656304]
2   -0.536085   [0, 0, 0, 2.4210718274608496, -15.626697762130291,
0.24074437575656304]
3   -0.536085   [0, 0, 0, 2.4210718274608496, -15.626697762130291,
0.24074437575656304]
ExceptionObject caught !

itk::ExceptionObject (0xa23c098)
Location: "itk::MattesMutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::MeasureType
itk::MattesMutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::GetValue(itk::MattesMutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::ParametersType&) const [with TFixedImage = itk::Image<float,
3u>, TMovingImage = itk::Image<float, 3u>,
itk::MattesMutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::MeasureType = double,
itk::MattesMutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::ParametersType = itk::OptimizerParameters<double>]" 
File:
/media/datos/FP-UNA/tesis/implementacion/qtCreator/InsightToolkit-4.5.1/Modules/Registration/Common/include/itkMattesMutualInformationImageToImageMetric.hxx
Line: 546
Description: itk::ERROR:
MattesMutualInformationImageToImageMetric(0xa22f070): Joint PDF summed to
zero
Image (0xa23bc10)
  RTTI typeinfo:   itk::Image<double, 2u>
  Reference Count: 2
  Modified Time: 437
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 0
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 2
    Index: [0, 0]
    Size: [20, 20]
  BufferedRegion: 
    Dimension: 2
    Index: [0, 0]
    Size: [20, 20]
  RequestedRegion: 
    Dimension: 2
    Index: [0, 0]
    Size: [20, 20]
  Spacing: [15.9375, 15.625]
  Origin: [0, 0]
  Direction: 
1 0
0 1

  IndexToPointMatrix: 
15.9375 0
0 15.625

  PointToIndexMatrix: 
0.0627451 0
0 0.064

  Inverse Direction: 
1 0
0 1

  PixelContainer: 
    ImportImageContainer (0xa23bd58)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 438
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0xa4b4880
      Container manages memory: true
      Size: 400
      Capacity: 400




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MattesMutualInformationImageToImageMetric-Joint-PDF-summed-to-zero-tp7585842.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Wed Jul  2 17:50:37 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 2 Jul 2014 17:50:37 -0400
Subject: [ITK-users] [ITK] MattesMutualInformationImageToImageMetric:
	Joint PDF	summed to zero
In-Reply-To: <1404337433182-7585842.post@n2.nabble.com>
References: <1404337433182-7585842.post@n2.nabble.com>
Message-ID: <D88B608B-50BF-40E3-9E4A-9C99EAE6FF79@mail.nih.gov>

Hello,

This is likely caused by the images no longer overlapping sufficiently.

You didn't indicate how you modified the example. So it's difficult to specifically help.

Check your transform, parameter, scales, and initalRadius for the optimizer or similar optimizer parameter.

Brad


On Jul 2, 2014, at 5:43 PM, Gabriel A. Gim?nez <gabrielgimenez85 at gmail.com> wrote:

> Hi everyone, first of all, sorry for my bad English.
> 
> I modified the ImageRegistration8 example for use the
> itkOnePlusOneEvolutionaryOptimize and
> itkMattesMutualInformationImageToImageMetric like in the ImageRegistration11
> example.
> Can help me with this error ?
> 
> Thanks.
> 
> 1   -0.536085   [0, 0, 0, 2.4210718274608496, -15.626697762130291,
> 0.24074437575656304]
> 2   -0.536085   [0, 0, 0, 2.4210718274608496, -15.626697762130291,
> 0.24074437575656304]
> 3   -0.536085   [0, 0, 0, 2.4210718274608496, -15.626697762130291,
> 0.24074437575656304]
> ExceptionObject caught !
> 
> itk::ExceptionObject (0xa23c098)
> Location: "itk::MattesMutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::MeasureType
> itk::MattesMutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::GetValue(itk::MattesMutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::ParametersType&) const [with TFixedImage = itk::Image<float,
> 3u>, TMovingImage = itk::Image<float, 3u>,
> itk::MattesMutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::MeasureType = double,
> itk::MattesMutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::ParametersType = itk::OptimizerParameters<double>]" 
> File:
> /media/datos/FP-UNA/tesis/implementacion/qtCreator/InsightToolkit-4.5.1/Modules/Registration/Common/include/itkMattesMutualInformationImageToImageMetric.hxx
> Line: 546
> Description: itk::ERROR:
> MattesMutualInformationImageToImageMetric(0xa22f070): Joint PDF summed to
> zero
> Image (0xa23bc10)
>  RTTI typeinfo:   itk::Image<double, 2u>
>  Reference Count: 2
>  Modified Time: 437
>  Debug: Off
>  Object Name: 
>  Observers: 
>    none
>  Source: (none)
>  Source output name: (none)
>  Release Data: Off
>  Data Released: False
>  Global Release Data: Off
>  PipelineMTime: 0
>  UpdateMTime: 0
>  RealTimeStamp: 0 seconds 
>  LargestPossibleRegion: 
>    Dimension: 2
>    Index: [0, 0]
>    Size: [20, 20]
>  BufferedRegion: 
>    Dimension: 2
>    Index: [0, 0]
>    Size: [20, 20]
>  RequestedRegion: 
>    Dimension: 2
>    Index: [0, 0]
>    Size: [20, 20]
>  Spacing: [15.9375, 15.625]
>  Origin: [0, 0]
>  Direction: 
> 1 0
> 0 1
> 
>  IndexToPointMatrix: 
> 15.9375 0
> 0 15.625
> 
>  PointToIndexMatrix: 
> 0.0627451 0
> 0 0.064
> 
>  Inverse Direction: 
> 1 0
> 0 1
> 
>  PixelContainer: 
>    ImportImageContainer (0xa23bd58)
>      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
>      Reference Count: 1
>      Modified Time: 438
>      Debug: Off
>      Object Name: 
>      Observers: 
>        none
>      Pointer: 0xa4b4880
>      Container manages memory: true
>      Size: 400
>      Capacity: 400
> 
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MattesMutualInformationImageToImageMetric-Joint-PDF-summed-to-zero-tp7585842.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From j.plumat at auckland.ac.nz  Wed Jul  2 19:29:20 2014
From: j.plumat at auckland.ac.nz (Jerome Plumat)
Date: Thu, 03 Jul 2014 11:29:20 +1200
Subject: [ITK-users] 3D Affine Registration - no rotation found
Message-ID: <53B495D0.4080500@auckland.ac.nz>

Hi everyone,
I'm facing to a problem with 3D affine multi resolution registration.
The pipeline registers two 3D MRI head and necks volumes (600x400x40). 
These are scans of the same patient at two times. Due to the protocol, 
volumes are similar expect for MRI artifacts. In fine the algorithm 
would be used to registered an atlas defined on the fixed image on 
moving image.

The main elements of the pipeline are listed below. It's implemented 
with itk4 and is mostly based on MutliResImageRegistration2.cxx, I use 
the Mutual Information metric, linear interpolator, the optimizer is 
RegularStepGradientDescentOptimizer and CenteredTransformInitializer.

The registration is performed without any error and the translation is 
correctly found but the algorithm can't provide any rotation and I can't 
figure why.
The final results are
versor X = [1.00007, 0.000485777, 1.5912e-05]
versor Y = [-0.000126483, 0.999922, 1.34996e-05]
versor Z = [2.35376e-05, -8.28481e-05, 0.999986]
Translation X = 1.35204
Translation Y = 0.647584
Translation Z = -0.132708
Iterations = 96
Metric value = -0.738412

Following 
http://www.cmake.org/pipermail/insight-users/2006-August/019025.html the 
final rotation is 0.0003 along axis [-0.155456, -0.0122989, -0.987766].
Moreover, visual validation clearly highlight the fact the rotation is 
not sufficient.

Hope any one has advices.
Thanks in advances.

Jerome.


Part of code:

....

// transform
typedef itk::AffineTransform< double, Dimension> TransformType;
typedef itk::CenteredTransformInitializer< TransformType, 
FixedImageType, MovingImageType > TransformInitializerType;
// optimizer
typedef itk::RegularStepGradientDescentOptimizer OptimizerType;

// metric
typedef itk::MattesMutualInformationImageToImageMetric<
MovingImageType,
MovingImageType > MetricType;
// interpolator
typedef itk:: LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;

// registration
typedef itk::MultiResolutionImageRegistrationMethod<
FixedImageType,
MovingImageType > RegistrationType;


typedef itk::MultiResolutionPyramidImageFilter<
FixedImageType,
FixedImageType > FixedImagePyramidType;
typedef itk::MultiResolutionPyramidImageFilter<
MovingImageType,
MovingImageType > MovingImagePyramidType;


...

metric->SetNumberOfHistogramBins( 256 );
metric->SetNumberOfSpatialSamples( 50000 );
metric->ReinitializeSeed( 76926294 );

....

// connect the inputs
registration->SetFixedImage( fixedImage );
registration->SetMovingImage( movingImage );


// set the regions
registration->SetFixedImageRegion( fixedImage->GetLargestPossibleRegion() );

// configure the initializer
initializer->SetTransform( transform );
initializer->SetFixedImage( fixedImage );
initializer->SetMovingImage( movingImage );
initializer->MomentsOn();
initializer->InitializeTransform();

registration->SetInitialTransformParameters( transform->GetParameters() );

// optimizer scales
typedef OptimizerType::ScalesType OptimizerScalesType;
OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
const double momentScale = 1;
const double translationScale = 1.0 / 1e7;

//number of dimensions: N*(N+1)
for(unsigned int i=0; i<(Dimension*Dimension); i++ )
{
optimizerScales[i] = momentScale;
}

for( unsigned int i=(Dimension*Dimension);
i<((Dimension+1)*Dimension); i++ )
{
optimizerScales[i] = translationScale;
}
optimizer->SetScales( optimizerScales );


// performed registration
...

//
// deformed the moving image and save it
//
typedef itk::ResampleImageFilter<
MovingImageType,
FixedImageType > ResampleFilterType;
typedef itk::CastImageFilter<
MovingImageType,
OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;

ResampleFilterType::Pointer resampler = ResampleFilterType::New();
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();

TransformType::Pointer finalTransform = TransformType::New();

finalTransform->SetParameters(
registration->GetLastTransformParameters() );
finalTransform->SetFixedParameters(
transform->GetFixedParameters() );

// set transform and initial moving image
resampler->SetTransform( finalTransform );
resampler->SetInput( movingImage );

resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
resampler->SetOutputOrigin( fixedImage->GetOrigin() );
resampler->SetOutputSpacing( fixedImage->GetSpacing() );
resampler->SetOutputDirection( fixedImage->GetDirection() );
resampler->SetDefaultPixelValue( defaultOutputPixel );

writer->SetFileName( argv[argvOutputImageFile] );
caster->SetInput( resampler->GetOutput() );
writer->SetInput( caster->GetOutput() );

...

-- 

Jerome
-------
School of Medical Sciences
University of Auckland

If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? ? Hillel HaZaken


From gabrielgimenez85 at gmail.com  Wed Jul  2 19:48:49 2014
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Wed, 2 Jul 2014 16:48:49 -0700 (PDT)
Subject: [ITK-users] [ITK] MattesMutualInformationImageToImageMetric:
 Joint PDF	summed to zero
In-Reply-To: <D88B608B-50BF-40E3-9E4A-9C99EAE6FF79@mail.nih.gov>
References: <1404337433182-7585842.post@n2.nabble.com>
 <D88B608B-50BF-40E3-9E4A-9C99EAE6FF79@mail.nih.gov>
Message-ID: <1404344929836-7585845.post@n2.nabble.com>

Basically (enclosed please find my code) , I used the ImageRegistration8.cxx
as the
major code but replaced the image metric and optimizer part with
corresponding code in
ImageRegistration11.cxx.

What do you recommend? Something to read about this?

Thanks! ImageRegistration8Modificado.cxx
<http://itk-insight-users.2283740.n2.nabble.com/file/n7585845/ImageRegistration8Modificado.cxx>  



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MattesMutualInformationImageToImageMetric-Joint-PDF-summed-to-zero-tp7585842p7585845.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From nicgallego at gmail.com  Thu Jul  3 04:12:59 2014
From: nicgallego at gmail.com (Nicolas Gallego)
Date: Thu, 3 Jul 2014 10:12:59 +0200
Subject: [ITK-users] [ITK]  3D Affine Registration - no rotation found
In-Reply-To: <53B495D0.4080500@auckland.ac.nz>
References: <53B495D0.4080500@auckland.ac.nz>
Message-ID: <CAHFTQh51-0HCDi-1jVtUCcQLqBEvi8Se2-psMFF8xrGD7sDf5A@mail.gmail.com>

Hi J?r?me,

Have you tried changing the optimizer scales?
That parameter changes the sensitivity of the optimization process between
the translation and rotation of the transform, it seams to me that the
value 1.0/1e7 is probably too small and the optimizer is not sensitive
enough to rotations.

For test purposes you can also set the mutual information metric to compute
histograms on the whole image, that may give you a much detailed metric map
for the optimizer as well.

metric->SetNumberOfSpatialSamples( <some value> );

Hope that helps,

Nicol?s Gallego-Ortiz
Universit? catholique de Louvain, Belgium


2014-07-03 1:29 GMT+02:00 Jerome Plumat <j.plumat at auckland.ac.nz>:

> Hi everyone,
> I'm facing to a problem with 3D affine multi resolution registration.
> The pipeline registers two 3D MRI head and necks volumes (600x400x40).
> These are scans of the same patient at two times. Due to the protocol,
> volumes are similar expect for MRI artifacts. In fine the algorithm would
> be used to registered an atlas defined on the fixed image on moving image.
>
> The main elements of the pipeline are listed below. It's implemented with
> itk4 and is mostly based on MutliResImageRegistration2.cxx, I use the
> Mutual Information metric, linear interpolator, the optimizer is
> RegularStepGradientDescentOptimizer and CenteredTransformInitializer.
>
> The registration is performed without any error and the translation is
> correctly found but the algorithm can't provide any rotation and I can't
> figure why.
> The final results are
> versor X = [1.00007, 0.000485777, 1.5912e-05]
> versor Y = [-0.000126483, 0.999922, 1.34996e-05]
> versor Z = [2.35376e-05, -8.28481e-05, 0.999986]
> Translation X = 1.35204
> Translation Y = 0.647584
> Translation Z = -0.132708
> Iterations = 96
> Metric value = -0.738412
>
> Following http://www.cmake.org/pipermail/insight-users/2006-
> August/019025.html the final rotation is 0.0003 along axis [-0.155456,
> -0.0122989, -0.987766].
> Moreover, visual validation clearly highlight the fact the rotation is not
> sufficient.
>
> Hope any one has advices.
> Thanks in advances.
>
> Jerome.
>
>
> Part of code:
>
> ....
>
> // transform
> typedef itk::AffineTransform< double, Dimension> TransformType;
> typedef itk::CenteredTransformInitializer< TransformType, FixedImageType,
> MovingImageType > TransformInitializerType;
> // optimizer
> typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
>
> // metric
> typedef itk::MattesMutualInformationImageToImageMetric<
> MovingImageType,
> MovingImageType > MetricType;
> // interpolator
> typedef itk:: LinearInterpolateImageFunction<
> MovingImageType,
> double > InterpolatorType;
>
> // registration
> typedef itk::MultiResolutionImageRegistrationMethod<
> FixedImageType,
> MovingImageType > RegistrationType;
>
>
> typedef itk::MultiResolutionPyramidImageFilter<
> FixedImageType,
> FixedImageType > FixedImagePyramidType;
> typedef itk::MultiResolutionPyramidImageFilter<
> MovingImageType,
> MovingImageType > MovingImagePyramidType;
>
>
> ...
>
> metric->SetNumberOfHistogramBins( 256 );
> metric->SetNumberOfSpatialSamples( 50000 );
> metric->ReinitializeSeed( 76926294 );
>
> ....
>
> // connect the inputs
> registration->SetFixedImage( fixedImage );
> registration->SetMovingImage( movingImage );
>
>
> // set the regions
> registration->SetFixedImageRegion( fixedImage->GetLargestPossibleRegion()
> );
>
> // configure the initializer
> initializer->SetTransform( transform );
> initializer->SetFixedImage( fixedImage );
> initializer->SetMovingImage( movingImage );
> initializer->MomentsOn();
> initializer->InitializeTransform();
>
> registration->SetInitialTransformParameters( transform->GetParameters() );
>
> // optimizer scales
> typedef OptimizerType::ScalesType OptimizerScalesType;
> OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
> const double momentScale = 1;
> const double translationScale = 1.0 / 1e7;
>
> //number of dimensions: N*(N+1)
> for(unsigned int i=0; i<(Dimension*Dimension); i++ )
> {
> optimizerScales[i] = momentScale;
> }
>
> for( unsigned int i=(Dimension*Dimension);
> i<((Dimension+1)*Dimension); i++ )
> {
> optimizerScales[i] = translationScale;
> }
> optimizer->SetScales( optimizerScales );
>
>
> // performed registration
> ...
>
> //
> // deformed the moving image and save it
> //
> typedef itk::ResampleImageFilter<
> MovingImageType,
> FixedImageType > ResampleFilterType;
> typedef itk::CastImageFilter<
> MovingImageType,
> OutputImageType > CastFilterType;
> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>
> ResampleFilterType::Pointer resampler = ResampleFilterType::New();
> WriterType::Pointer writer = WriterType::New();
> CastFilterType::Pointer caster = CastFilterType::New();
>
> TransformType::Pointer finalTransform = TransformType::New();
>
> finalTransform->SetParameters(
> registration->GetLastTransformParameters() );
> finalTransform->SetFixedParameters(
> transform->GetFixedParameters() );
>
> // set transform and initial moving image
> resampler->SetTransform( finalTransform );
> resampler->SetInput( movingImage );
>
> resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
> resampler->SetOutputOrigin( fixedImage->GetOrigin() );
> resampler->SetOutputSpacing( fixedImage->GetSpacing() );
> resampler->SetOutputDirection( fixedImage->GetDirection() );
> resampler->SetDefaultPixelValue( defaultOutputPixel );
>
> writer->SetFileName( argv[argvOutputImageFile] );
> caster->SetInput( resampler->GetOutput() );
> writer->SetInput( caster->GetOutput() );
>
> ...
>
> --
>
> Jerome
> -------
> School of Medical Sciences
> University of Auckland
>
> If I am not for myself, who will be for me? And if I am only for myself,
> then what an I? And if not now when? ? Hillel HaZaken
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140703/fc0aeaa0/attachment.html>

From elena.bresciani87 at gmail.com  Thu Jul  3 10:16:49 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Thu, 3 Jul 2014 16:16:49 +0200
Subject: [ITK-users] Rotate image
Message-ID: <CACxk=Wy35t4jWqbZfY3fYSCPwt9aZ-dYmJqECjviEfgy3g+VDQ@mail.gmail.com>

Hello guys,

I need help on image rotation. I have two questions:

1 - how can I modify the code in ResampleImageFilter4.cxx to make the size
of the output image following the rotation? More specifically: if image
size is Size X >> Size Y and I want a 90? rotation the result (using the
code in the example without modifications) is cropped because the new image
has now Size Y >> Size X but in the example this is not taken into account.
I know I could use Permute Axis but I would like to write something that
works both for 90 and 180 degrees rotations.

2 - I would like to do something like in the scheme attached. Actually, as
shown I've reached my goal only partially using AutoCropLabelMapFilter.
There is a simple way of doing what I want or I have to compute the angle
of inclination of my region of interest and rotate and crop accordingly?
Images are not binary!

Thanks in advance!

Elena
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140703/fe734b45/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Scheme.pdf
Type: application/pdf
Size: 15310 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140703/fe734b45/attachment.pdf>

From matt.mccormick at kitware.com  Thu Jul  3 12:24:47 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 3 Jul 2014 12:24:47 -0400
Subject: [ITK-users] [ITK] Resampling after SetDirection() and
	SetOrigin()
In-Reply-To: <CAC5Ld0Cqtv2ZaFPCrqG12UxeB0wAbDrfAnvvq3c2O09Cqowh-Q@mail.gmail.com>
References: <CAC5Ld0CRDrNp4iiJEFb+2ztwXNWXG+k_racPYzRqHDZ1oQm8pg@mail.gmail.com>
 <CALzTN-QS4yvbmcfHxVi7QncoXSWtj6Hv59bqNsMkxUOzbpTgfA@mail.gmail.com>
 <CAC5Ld0AWvfwoi66nbXrJqkNBOBhXN1SupgLy_=Kpu55vh=PNNA@mail.gmail.com>
 <CALzTN-Q--_ih8u3GOH8B55Ny_a6Dx6Bd5HC8pjL5ySo5mCyZoQ@mail.gmail.com>
 <CAC5Ld0Cqtv2ZaFPCrqG12UxeB0wAbDrfAnvvq3c2O09Cqowh-Q@mail.gmail.com>
Message-ID: <CALzTN-SptoJY_ygY=2Wd2qi90EnOJyY2P_7kr0gNL7kMpXUMhA@mail.gmail.com>

Hi Mathew,

The reader and the resampler are connected in a pipeline by default.
The Update() on the writer or the resampler will nullify your
modification on "image". To disconnect the pipeline,

  reader.Update()
  image = reader.GetOutput()
  image.DisconnectPipeline()

See also [1].

Hope this helps,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1DataObject.html#a8a70b06ebb65da85628342f3e992bc4c

On Wed, Jul 2, 2014 at 12:14 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> Hi Matt
>
> Sorry to labour this point but I'm still confused as to what is going on; my
> misunderstanding may well be to do with how the pipelines work.
>
> As an example:
>
> import itk
>
> fileNameIn = '/route/to/input.nii'
> fileNameOut = '/route/to/output.nii'
> image_type = itk.Image[itk.F, 3]
> reader = itk.ImageFileReader[image_type].New()
> reader.SetFileName(fileNameIn)
> reader.Update()
>
> image = reader.GetOutput()
> #image.GetOrigin() gives [-148, -153,  55]
> #image.GetDirection().GetVnlMatrix().get(0,0)....(2,2)
> #gives matrix:  1.0     0       0
> #               0       0.95    0.3
> #               0       -0.3    0.95
>
> image.GetOrigin().Fill(0)
> image.GetDirection().SetIdentity()
> #image.GetOrigin() gives [0, 0, 0]
> #image.GetDirection().GetVnlMatrix().get(0,0)....(2,2)
> #gives matrix:  1.0     0       0
> #               0       1.0     0
> #               0       0       1.0
>
> writer = itk.ImageFileWriter[image_type].New()
> writer.SetFileName(fileNameOut)
> writer.SetInput(image)
> writer.Update()
> #output image volume is unchanged when viewed in (e.g.) ImageJ
>
> resampler = itk.ResampleImageFilter[image_type, image_type].New()
> resampler.SetInput(image)
> resampler.SetSize(image.GetLargestPossibleRegion().GetSize())
> resampler.SetOutputOrigin(image.GetOrigin())
> resampler.SetOutputSpacing(image.GetSpacing())
> resampler.SetOutputDirection(image.GetDirection())
> resampler.Update()
>
> writer.SetInput(resampler.GetOutput())
> writer.Update()
> #now output is translated and rotated by the (inverse) values of the
> original
> #origin vector and direction matrix
> #
> #However, resampler.GetInput().GetOrigin() gives [0,0,0]
> #and similarly the direction of the input is a 3x3 identity matrix
>
> I don't understand why the resampler changes the image volume since it
> should not be 'aware' of the original origin/direction.
>
> From your previous reply you suggest that the call to resampler.Update()
> might cause the reader to re-import the file from disk.  Is this the case
> even when the reader and resampler are not connected in a pipeline (as
> here).  Further, if the reader does re-import the original image and
> origin/direction parameters why does resampler.GetInput().GetOrigin() report
> [0, 0, 0] and  the input direction matrix is an identity?
>
> I want to understand why this is happening as it is clearly important for
> ensuring I set up more complex pipelines correctly.
>
> Many thanks
> Mathew
>
>
> On 30 June 2014 03:28, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>
>> Hi Mathew,
>>
>> The image does not retain the original parameters somewhere.  However,
>> can must be take, because if the image is generated by a filter in a
>> pipeline, that filter will reset the original value when the pipeline
>> is re-run. ChangeInformationImageFilter will ensure this reset does
>> not happen during a pipeline update.
>>
>> The Set methods doo reorient/reposition the whole image volume in
>> world space.  The resampling filter does not select a subregion or
>> rotates the images -- to get the same out, the  sampling locations of
>> the output image for the ResampleImageFilter must be set as desired.
>> Set SetOutputOrigin [1], SetOutputDirection [2], etc.
>>
>> Hope this helps to clarify.
>>
>> I checked by wrapped install, and I have ChangeInformationImageFilter
>> instantiations for float images.
>>
>> Hope this helps,
>> Matt
>>
>> [1]
>> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html#ac4b197ddefd3b3344bd9c9471acd5b00
>>
>> [2]
>> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html#a9fdd6b862ab6cbaa03702da393bd0474
>>
>>
>> On Sun, Jun 29, 2014 at 10:01 PM, Mathew Guilfoyle
>> <mrguilfoyle at gmail.com> wrote:
>> > Matt, thanks for the reply.
>> >
>> > I would be grateful if you could you explain why this is the desired
>> > behaviour.  If I use the SetDirection() or SetOrigin() methods does the
>> > image object retain the original parameters somewhere?  Subsequently
>> > calling
>> > GetDirection() or GetOrigin() reports the changed parameters.
>> >
>> > Intuitively you would expect both Set methods to reorient/reposition the
>> > whole image volume in world space, and on the face of it that is what
>> > they
>> > seem to do.  However, on passing the image to a resampling filter they
>> > act
>> > to select a subregion or to rotate the image. I would have thought that
>> > rotations and region selections should be options passed to the filter
>> > and
>> > not set in the image itself?
>> >
>> > How does the ChangeInformationImageFilter do it differently?
>> > Incidentally I
>> > have wrapped for float but don't get this as an option for this filter.
>> >
>> > Thanks
>> > Mathew
>> >
>> >
>> >
>> > On 30 June 2014 01:45, Matt McCormick <matt.mccormick at kitware.com>
>> > wrote:
>> >>
>> >> Hi Mathew,
>> >>
>> >> Yes, that is the correct and expected behavior. I do not know if
>> >> ImageJ is using the actual location in world space.
>> >>
>> >> It sounds like ChangeInformationImageFilter is what you are looking
>> >> for.  It will be wrapped for float images if wrapped for float images
>> >> is enabled in you CMake configuration (ITK_WRAP_float).
>> >>
>> >> Hope this helps,
>> >> Matt
>> >>
>> >>
>> >> On Sat, Jun 28, 2014 at 9:55 PM, Mathew Guilfoyle
>> >> <mrguilfoyle at gmail.com>
>> >> wrote:
>> >> > If I change an image's direction and origin using SetDirection() and
>> >> > SetOrigin() methods and then write the image back to a file, the
>> >> > volume
>> >> > stack viewed in (e.g.) ImageJ is unchanged.  This is the behaviour I
>> >> > would
>> >> > expect as changing the direction and origin shouldn't alter the array
>> >> > of
>> >> > image pixels, just its location and orientation in 'world space'?
>> >> >
>> >> > However, if I take the same image, adjust the origin and direction as
>> >> > before, and then input it to ResampleImageFilter with an identity
>> >> > transform
>> >> > (and set spacing, origin, direction, and size to those of the input
>> >> > image)
>> >> > the output is a translated and rotated image.
>> >> >
>> >> > It seems the difference between the original and adjusted origin and
>> >> > direction are applied as a translation and rotation during
>> >> > resampling,
>> >> > even
>> >> > though GetOrigin() and GetDirection() on the input image to the
>> >> > resampler
>> >> > return the adjusted parameters.
>> >> >
>> >> > Is this the expected behaviour? Is there another image parameter that
>> >> > needs
>> >> > to be changed to correctly alter origin and direction?
>> >> >
>> >> > (ChangeInformationImageFilter is not wrapped for float images so I
>> >> > can't
>> >> > use
>> >> > it for my application)
>> >> >
>> >> > Thanks
>> >> >
>> >> > _____________________________________
>> >> > Powered by www.kitware.com
>> >> >
>> >> > Visit other Kitware open-source projects at
>> >> > http://www.kitware.com/opensource/opensource.html
>> >> >
>> >> > Kitware offers ITK Training Courses, for more information visit:
>> >> > http://www.kitware.com/products/protraining.php
>> >> >
>> >> > Please keep messages on-topic and check the ITK FAQ at:
>> >> > http://www.itk.org/Wiki/ITK_FAQ
>> >> >
>> >> > Follow this link to subscribe/unsubscribe:
>> >> > http://public.kitware.com/mailman/listinfo/insight-users
>> >> >
>> >> > _______________________________________________
>> >> > Community mailing list
>> >> > Community at itk.org
>> >> > http://public.kitware.com/mailman/listinfo/community
>> >> >
>> >
>> >
>
>

From nicgallego at gmail.com  Thu Jul  3 12:52:04 2014
From: nicgallego at gmail.com (Nicolas Gallego)
Date: Thu, 3 Jul 2014 18:52:04 +0200
Subject: [ITK-users] [ITK]  Rotate image
In-Reply-To: <CACxk=Wy35t4jWqbZfY3fYSCPwt9aZ-dYmJqECjviEfgy3g+VDQ@mail.gmail.com>
References: <CACxk=Wy35t4jWqbZfY3fYSCPwt9aZ-dYmJqECjviEfgy3g+VDQ@mail.gmail.com>
Message-ID: <CAHFTQh7dq7sN9sxhZ1=JYLx7hN36g6uZtzGGs9CNxLYcHZ96Mg@mail.gmail.com>

Hi Elena,

If I understand well your task, you have the rotation angle and translation
parameters and you would like to transform your image parallel to the
cartesian coordinate system and crop/resample it?

Conceptually then you could proceed as follows:

1. Create a rigid transformation with given angle and translation in 2D
[1]  or 3D [2]

2. Apply the transformation to your image via an interpolator and a
resampler, like illustrated in the Software Guide Section 8.2 [3]

3. The resampler interface lets you specifiy all the image information for
the output:
region( start, size)
spacing
origin
direction

Connect everything and update and that should do the job,

Pay attention to the center of rotation, the example you cite uses the
center of the image as center of rotation, that should be fine.

I would proceed like that, I am not aware of a filter to do this
automatically.

If you don't know a priori the rigid transformation parameters to apply,
then a registration algorithm can be used to estimate them.

[1] http://www.itk.org/Doxygen45/html/classitk_1_1Rigid2DTransform.html
[2] http://www.itk.org/Doxygen45/html/classitk_1_1Rigid3DTransform.html
[3] http://www.itk.org/ItkSoftwareGuide.pdf

hope that helps

Nicol?s Gallego-Ortiz
Universit? catholique de Louvain, Belgium


2014-07-03 16:16 GMT+02:00 elena bresciani <elena.bresciani87 at gmail.com>:

> Hello guys,
>
> I need help on image rotation. I have two questions:
>
> 1 - how can I modify the code in ResampleImageFilter4.cxx to make the size
> of the output image following the rotation? More specifically: if image
> size is Size X >> Size Y and I want a 90? rotation the result (using the
> code in the example without modifications) is cropped because the new image
> has now Size Y >> Size X but in the example this is not taken into account.
> I know I could use Permute Axis but I would like to write something that
> works both for 90 and 180 degrees rotations.
>
> 2 - I would like to do something like in the scheme attached. Actually, as
> shown I've reached my goal only partially using AutoCropLabelMapFilter.
> There is a simple way of doing what I want or I have to compute the angle
> of inclination of my region of interest and rotate and crop accordingly?
> Images are not binary!
>
> Thanks in advance!
>
> Elena
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140703/89a25695/attachment.html>

From matt.mccormick at kitware.com  Thu Jul  3 13:35:05 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 3 Jul 2014 13:35:05 -0400
Subject: [ITK-users] [ANNOUNCE] ITK 4.6 Release Candidate 2 has been tagged!
Message-ID: <CALzTN-Sk_yPBp23Jtiy9XU2YHONWSayn_ags+DNZkijES8qJqA@mail.gmail.com>

On behalf of the Insight Toolkit community, we are proud to announce
that ITK 4.6.0 release candidate 2 has been tagged and is available
for testing!


To obtain the source code,

  git clone http://itk.org/ITK.git
  cd ITK
  git checkout -q --detach v4.6rc02

For more details, please see the Git documentation [1].


Please test the release candidate and share your experiences on the
mailing list, issue tracker, and Gerrit Code Review. Please help
identify issues submitting an Experimental build to the dashboard [2]
with:

  ctest -M Experimental  -T Configure -T Build -T Test -T Submit

and notifying the mailing list.  Testing your own applications against
the RC is also appreciated.

Those community members wishing to contribute by cleaning up the
dashboard can find a list potential candidates on the issue tracker
[3]. Please do not hesitate to ask about any aspect of the
contribution process.

One of the issues that arose in this release candidate phase was
warnings generate by unused typedefs on newer compilers. Assistance
working on these warnings is welcome as is testing to ensure that
removed typedefs does not break code that builts against the toolkit..

Congratulations and well done to everyone that has contributed to this
release. Release candidates are tagged every week.  The final release
is scheduled for July 14th.


[1] http://www.itk.org/Wiki/ITK/Git

[2] http://open.cdash.org/index.php?project=Insight

[3] https://issues.itk.org/jira/issues/?jql=project%20%3D%20ITK%20AND%20fixVersion%20%3D%20%2220140714_ITKv4.6.0_FINAL%22%20AND%20status%20in%20(Open%2C%20%22In%20Progress%22%2C%20Reopened)

New Features
------------------

* CMake improvements
  - Improved Remote Module support
  - Add ITK_FORBID_DOWNLOADS for package maintainers
  - ITK_USE_SYSTEM_EXPAT available

* Filtering Improvements
  - Moved TransformToDisplacementField out of Review
  - An entire noise image generation module
    - http://hdl.handle.net/10380/3158
  - Better pipeline support for ResampleImageFilter
  - Move MagnitudeAndPhaseToComplexImageFilter out of Review
  - Setters for LabelMap overlay filters
  - More consistent filter progress reporting

* ImageO improvements
  - Register the GE image formats by default
  - More IO modules are built as shared libraries
  - OpenFileForReading/Writing methods in ImageIO
  - Support for system tiff 4.0.0-4.0.2 (e.g. some Ubuntu versions)
  - Mangling to internal OpenJPEG
  - SCIFIO improvements

* Infrastructure improvements
  - MetaDataObject print specialization for common types
  - Improvements to ResourceProbe and RealTimeClock
  - More Solve methods for VNLSparseLUSolverTraits
  - Output stream operator for LightObject exposed
  - FFTW bump to 3.3.3

* New Remote Modules
  - Skull stripper
    - http://hdl.handle.net/10380/3353
  - Wiki examples
  - Sphinx examples
  - Variational registration
    - http://hdl.handle.net/10380/3460
  - AnalyzeObjectMapIO
    - http://hdl.handle.net/1926/593
  - FDFImageIO
  - SplitComponents
    - http://hdl.handle.net/10380/320

* Registrationv4 improvements
  - v4 regular step gradient descent optimizer
  - v4 amoeba optimizer
  - v4 exhaustive optimizer
  - v4 Powell optimizer
  - v4 one-plus-one-evolutionary optimizer
  - v4 LBFGS optimizer improvements
  - Use registration method classes as pipeline filters

* Performance improvements
  - Registrationv4
  - Histogram computation
  - Improved SmartPointer copy
  - CompositeTransform
  - Registration Jacobian re-use

* Wrapping improvements
  - pygccxml 1.0.0
  - .pth symlink usable in a virtualenv
  - Cleaner CMake configuration
  - SWIG and PCRE updated to 3.0.2, 8.34
  - Latest GCCXML, which works with GCC 4.9
  - Sweeping wrapping generation cleanup

* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- some measures put us over 85%!

* *Lots* of important bug fixes

* And more! See details in the log below.


List of changes since v4.6rc01
---------------------------------------

Bradley Lowekamp (3):
      BUG: Do not ENABLED_SHARED for GDCMIO
      DOC: Add break in brief description of Canny edge filter
      BUG: Add additional MetaDataObject explicit instantiation.

Jean-Christophe Fillion-Robin (2):
      COMP: Fix "unused-local-typedefs" warnings
      COMP: Fix "unused-local-typedefs" warning in
LandmarkBasedTransformInitializer

Kent Williams (1):
      COMP: Fix typo in ReflectiveImageRegionConstIterator.

Matthew McCormick (4):
      DOC: CMake warning BRANWEB -> BRAINWEB.
      BUG: Remove -Wno-unused-local-typedefs flag.
      COMP: Fix IOSTL Doxygen group and Windows shared build.
      BUG: Use Remote repository explicitly on git fetch.

Michka Popoff (6):
      COMP: Move itkMatrixCoefficients wrapping to Filtering module
      COMP: Fix wrapping with Core only
      STYLE: Pep8 cleanup for generators
      COMP: Fix default wrapping with all modules
      ENH: Use open() instead of file() for python 3 compatibility
      ENH: Allow to use methods which pass std::string by reference from python

Nick Tustison (1):
      ENH:  Adding generic computation type.

From blowekamp at mail.nih.gov  Thu Jul  3 13:51:20 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 3 Jul 2014 13:51:20 -0400
Subject: [ITK-users] [ITK]  Rotate image
In-Reply-To: <CAHFTQh7dq7sN9sxhZ1=JYLx7hN36g6uZtzGGs9CNxLYcHZ96Mg@mail.gmail.com>
References: <CACxk=Wy35t4jWqbZfY3fYSCPwt9aZ-dYmJqECjviEfgy3g+VDQ@mail.gmail.com>
 <CAHFTQh7dq7sN9sxhZ1=JYLx7hN36g6uZtzGGs9CNxLYcHZ96Mg@mail.gmail.com>
Message-ID: <1ADBF0ED-8053-46E5-8063-D66ED3B29C64@mail.nih.gov>

Hello Elena,

After looking at your images, I realized you may be interested in Oriented Bounding Box computation.

I have an external ITK module[1] which computes OBBs in the LabelMap infrastructure. One way it presents the OBB is as an origin and Direction[2]. This information is then passed to the Resample filter to extract the OBB[3].

You may be able to re-use the code in this module or find another way to compute your origin and direction based on information specific for you application.

Hope this helps,
Brad


[1] https://github.com/blowekamp/itkOBBLabelMap
[2] https://github.com/blowekamp/itkOBBLabelMap/blob/master/include/itkOrientedBoundingBoxLabelObject.h#L91-L111
[3] https://github.com/blowekamp/itkOBBLabelMap/blob/master/test/itkOrientedBoundingBoxLabelMapFilterTest2.cxx#L94-L113

On Jul 3, 2014, at 12:52 PM, Nicolas Gallego <nicgallego at gmail.com> wrote:

> Hi Elena,
> 
> If I understand well your task, you have the rotation angle and translation parameters and you would like to transform your image parallel to the cartesian coordinate system and crop/resample it?
> 
> Conceptually then you could proceed as follows:
> 
> 1. Create a rigid transformation with given angle and translation in 2D [1]  or 3D [2]
> 
> 2. Apply the transformation to your image via an interpolator and a resampler, like illustrated in the Software Guide Section 8.2 [3]
> 
> 3. The resampler interface lets you specifiy all the image information for the output:
> region( start, size)
> spacing
> origin
> direction
> 
> Connect everything and update and that should do the job, 
> 
> Pay attention to the center of rotation, the example you cite uses the center of the image as center of rotation, that should be fine.
> 
> I would proceed like that, I am not aware of a filter to do this automatically. 
> 
> If you don't know a priori the rigid transformation parameters to apply, then a registration algorithm can be used to estimate them.
> 
> [1] http://www.itk.org/Doxygen45/html/classitk_1_1Rigid2DTransform.html
> [2] http://www.itk.org/Doxygen45/html/classitk_1_1Rigid3DTransform.html
> [3] http://www.itk.org/ItkSoftwareGuide.pdf
> 
> hope that helps
> 
> Nicol?s Gallego-Ortiz
> Universit? catholique de Louvain, Belgium
> 
> 
> 2014-07-03 16:16 GMT+02:00 elena bresciani <elena.bresciani87 at gmail.com>:
> Hello guys,
> 
> I need help on image rotation. I have two questions:
> 
> 1 - how can I modify the code in ResampleImageFilter4.cxx to make the size of the output image following the rotation? More specifically: if image size is Size X >> Size Y and I want a 90? rotation the result (using the code in the example without modifications) is cropped because the new image has now Size Y >> Size X but in the example this is not taken into account. I know I could use Permute Axis but I would like to write something that works both for 90 and 180 degrees rotations. 
> 
> 2 - I would like to do something like in the scheme attached. Actually, as shown I've reached my goal only partially using AutoCropLabelMapFilter. There is a simple way of doing what I want or I have to compute the angle of inclination of my region of interest and rotate and crop accordingly? Images are not binary!
> 
> Thanks in advance!
> 
> Elena
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> 
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140703/7ce6a473/attachment-0001.html>

From j.plumat at auckland.ac.nz  Thu Jul  3 19:23:08 2014
From: j.plumat at auckland.ac.nz (Jerome Plumat)
Date: Fri, 04 Jul 2014 11:23:08 +1200
Subject: [ITK-users] [ITK]  3D Affine Registration - no rotation found
In-Reply-To: <CAHFTQh51-0HCDi-1jVtUCcQLqBEvi8Se2-psMFF8xrGD7sDf5A@mail.gmail.com>
References: <53B495D0.4080500@auckland.ac.nz>
 <CAHFTQh51-0HCDi-1jVtUCcQLqBEvi8Se2-psMFF8xrGD7sDf5A@mail.gmail.com>
Message-ID: <53B5E5DC.7040500@auckland.ac.nz>

Hi Nicol?s,
Thank for the answer and advices. Indeed you are right: the value 1/1E7 
is too small. I set it to 1/1E2 and the registration is better 
performed. I also increased the number of samples but the scale value 
has a huge influence on the results.

However, I don't understand why this value has such an impact on the 
rotation optimization. If I understand well the user guide section 8.7.2 
top of page 359 the first optimizerScales[0] to 
optimizerScales[Dimension*Dimension-1] are relative to the moments of 
the affine transform while optimizerScales[Dimension*Dimension] to 
optimizerScales[(Dimensions+1)*Dimension-1] should influence the 
translations.

Any light?
Cheers,


Jerome Plumat
-------
School of Medical Sciences
University of Auckland


If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? ? Hillel HaZaken

On 03/07/14 20:12, Nicolas Gallego wrote:
> Hi J?r?me,
>
> Have you tried changing the optimizer scales?
> That parameter changes the sensitivity of the optimization process 
> between the translation and rotation of the transform, it seams to me 
> that the value 1.0/1e7 is probably too small and the optimizer is not 
> sensitive enough to rotations.
>
> For test purposes you can also set the mutual information metric to 
> compute histograms on the whole image, that may give you a much 
> detailed metric map for the optimizer as well.
>
> metric->SetNumberOfSpatialSamples(<some value>);
>
> Hope that helps,
>
> Nicol?s Gallego-Ortiz
> Universit? catholique de Louvain, Belgium
>
>
> 2014-07-03 1:29 GMT+02:00 Jerome Plumat <j.plumat at auckland.ac.nz 
> <mailto:j.plumat at auckland.ac.nz>>:
>
>     Hi everyone,
>     I'm facing to a problem with 3D affine multi resolution registration.
>     The pipeline registers two 3D MRI head and necks volumes
>     (600x400x40). These are scans of the same patient at two times.
>     Due to the protocol, volumes are similar expect for MRI artifacts.
>     In fine the algorithm would be used to registered an atlas defined
>     on the fixed image on moving image.
>
>     The main elements of the pipeline are listed below. It's
>     implemented with itk4 and is mostly based on
>     MutliResImageRegistration2.cxx, I use the Mutual Information
>     metric, linear interpolator, the optimizer is
>     RegularStepGradientDescentOptimizer and CenteredTransformInitializer.
>
>     The registration is performed without any error and the
>     translation is correctly found but the algorithm can't provide any
>     rotation and I can't figure why.
>     The final results are
>     versor X = [1.00007, 0.000485777, 1.5912e-05]
>     versor Y = [-0.000126483, 0.999922, 1.34996e-05]
>     versor Z = [2.35376e-05, -8.28481e-05, 0.999986]
>     Translation X = 1.35204
>     Translation Y = 0.647584
>     Translation Z = -0.132708
>     Iterations = 96
>     Metric value = -0.738412
>
>     Following
>     http://www.cmake.org/pipermail/insight-users/2006-August/019025.html
>     the final rotation is 0.0003 along axis [-0.155456, -0.0122989,
>     -0.987766].
>     Moreover, visual validation clearly highlight the fact the
>     rotation is not sufficient.
>
>     Hope any one has advices.
>     Thanks in advances.
>
>     Jerome.
>
>
>     Part of code:
>
>     ....
>
>     // transform
>     typedef itk::AffineTransform< double, Dimension> TransformType;
>     typedef itk::CenteredTransformInitializer< TransformType,
>     FixedImageType, MovingImageType > TransformInitializerType;
>     // optimizer
>     typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
>
>     // metric
>     typedef itk::MattesMutualInformationImageToImageMetric<
>     MovingImageType,
>     MovingImageType > MetricType;
>     // interpolator
>     typedef itk:: LinearInterpolateImageFunction<
>     MovingImageType,
>     double > InterpolatorType;
>
>     // registration
>     typedef itk::MultiResolutionImageRegistrationMethod<
>     FixedImageType,
>     MovingImageType > RegistrationType;
>
>
>     typedef itk::MultiResolutionPyramidImageFilter<
>     FixedImageType,
>     FixedImageType > FixedImagePyramidType;
>     typedef itk::MultiResolutionPyramidImageFilter<
>     MovingImageType,
>     MovingImageType > MovingImagePyramidType;
>
>
>     ...
>
>     metric->SetNumberOfHistogramBins( 256 );
>     metric->SetNumberOfSpatialSamples( 50000 );
>     metric->ReinitializeSeed( 76926294 <tel:%28%2076926294> );
>
>     ....
>
>     // connect the inputs
>     registration->SetFixedImage( fixedImage );
>     registration->SetMovingImage( movingImage );
>
>
>     // set the regions
>     registration->SetFixedImageRegion(
>     fixedImage->GetLargestPossibleRegion() );
>
>     // configure the initializer
>     initializer->SetTransform( transform );
>     initializer->SetFixedImage( fixedImage );
>     initializer->SetMovingImage( movingImage );
>     initializer->MomentsOn();
>     initializer->InitializeTransform();
>
>     registration->SetInitialTransformParameters(
>     transform->GetParameters() );
>
>     // optimizer scales
>     typedef OptimizerType::ScalesType OptimizerScalesType;
>     OptimizerScalesType optimizerScales(
>     transform->GetNumberOfParameters() );
>     const double momentScale = 1;
>     const double translationScale = 1.0 / 1e7;
>
>     //number of dimensions: N*(N+1)
>     for(unsigned int i=0; i<(Dimension*Dimension); i++ )
>     {
>     optimizerScales[i] = momentScale;
>     }
>
>     for( unsigned int i=(Dimension*Dimension);
>     i<((Dimension+1)*Dimension); i++ )
>     {
>     optimizerScales[i] = translationScale;
>     }
>     optimizer->SetScales( optimizerScales );
>
>
>     // performed registration
>     ...
>
>     //
>     // deformed the moving image and save it
>     //
>     typedef itk::ResampleImageFilter<
>     MovingImageType,
>     FixedImageType > ResampleFilterType;
>     typedef itk::CastImageFilter<
>     MovingImageType,
>     OutputImageType > CastFilterType;
>     typedef itk::ImageFileWriter< OutputImageType > WriterType;
>
>     ResampleFilterType::Pointer resampler = ResampleFilterType::New();
>     WriterType::Pointer writer = WriterType::New();
>     CastFilterType::Pointer caster = CastFilterType::New();
>
>     TransformType::Pointer finalTransform = TransformType::New();
>
>     finalTransform->SetParameters(
>     registration->GetLastTransformParameters() );
>     finalTransform->SetFixedParameters(
>     transform->GetFixedParameters() );
>
>     // set transform and initial moving image
>     resampler->SetTransform( finalTransform );
>     resampler->SetInput( movingImage );
>
>     resampler->SetSize(
>     fixedImage->GetLargestPossibleRegion().GetSize() );
>     resampler->SetOutputOrigin( fixedImage->GetOrigin() );
>     resampler->SetOutputSpacing( fixedImage->GetSpacing() );
>     resampler->SetOutputDirection( fixedImage->GetDirection() );
>     resampler->SetDefaultPixelValue( defaultOutputPixel );
>
>     writer->SetFileName( argv[argvOutputImageFile] );
>     caster->SetInput( resampler->GetOutput() );
>     writer->SetInput( caster->GetOutput() );
>
>     ...
>
>     -- 
>
>     Jerome
>     -------
>     School of Medical Sciences
>     University of Auckland
>
>     If I am not for myself, who will be for me? And if I am only for
>     myself, then what an I? And if not now when? ? Hillel HaZaken
>
>     _____________________________________
>     Powered by www.kitware.com <http://www.kitware.com>
>
>     Visit other Kitware open-source projects at
>     http://www.kitware.com/opensource/opensource.html
>
>     Kitware offers ITK Training Courses, for more information visit:
>     http://www.kitware.com/products/protraining.php
>
>     Please keep messages on-topic and check the ITK FAQ at:
>     http://www.itk.org/Wiki/ITK_FAQ
>
>     Follow this link to subscribe/unsubscribe:
>     http://public.kitware.com/mailman/listinfo/insight-users
>     _______________________________________________
>     Community mailing list
>     Community at itk.org <mailto:Community at itk.org>
>     http://public.kitware.com/mailman/listinfo/community
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140704/98556415/attachment.html>

From wsales at gmail.com  Fri Jul  4 17:41:50 2014
From: wsales at gmail.com (Wagner Sales)
Date: Fri, 4 Jul 2014 18:41:50 -0300
Subject: [ITK-users] Fail to execute TransformReadWrite example
Message-ID: <CA+5pysjCb933hKxi8+nb9PZoE+1j5AuvnpOSXJD5v0VQjXgUjw@mail.gmail.com>

Hi all,

I'm trying to save transforms and catching an strange error. I tried to
execute the simple example on IO directory to validate this, and:

--> checking permission
wsales at wsales-desktop:/tmp/trf$ touch ihavepermission
wsales at wsales-desktop:/tmp/trf$ ls -la
total 28464
drwxrwxr-x  2 wsales wsales     4096 Jul  4 17:52 .
drwxrwxrwt 31 root   root      12288 Jul  4 17:52 ..
-rw-rw-r--  1 wsales wsales        0 Jul  4 17:52 ihavepermission
-rwxrwxr-x  1 wsales wsales 29128152 Jul  4 17:52 TransformReadWrite

wsales at wsales-desktop:/tmp/trf$ ./TransformReadWrite test
Error while saving the transforms

itk::ExceptionObject (0x2af4c30)
Location: "void itk::TransformFileWriterTemplate<ScalarType>::Update()
[with ScalarType = double]"
File:
/home/wsales/Sources/InsightToolkit-4.5.2/Modules/IO/TransformBase/include/itkTransformFileWriter.hxx
Line: 200
Description: itk::ERROR: TransformFileWriterTemplate(0x2ae6300): Can't
Create IO object for file Transforms.meta

Since I can create the file, problem with permissions is not the issue.
About my system ( latest Ubuntu, 'll update today ):
uname  -a
Linux wsales-desktop 3.13.0-27-generic #50-Ubuntu SMP Thu May 15 18:06:16
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Compiler:
clang --version
Ubuntu clang version 3.4-1ubuntu3 (tags/RELEASE_34/final) (based on LLVM
3.4)
Target: x86_64-pc-linux-gnu
Thread model: posix

Some idea about this?
This example was worked fine to me on ITK 3.20, before my version upgrade.

Regards,

Wagner Sales
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140704/a60da9f0/attachment.html>

From wsales at gmail.com  Fri Jul  4 18:43:28 2014
From: wsales at gmail.com (Wagner Sales)
Date: Fri, 4 Jul 2014 19:43:28 -0300
Subject: [ITK-users] Fail to execute TransformReadWrite example
In-Reply-To: <CA+5pysjCb933hKxi8+nb9PZoE+1j5AuvnpOSXJD5v0VQjXgUjw@mail.gmail.com>
References: <CA+5pysjCb933hKxi8+nb9PZoE+1j5AuvnpOSXJD5v0VQjXgUjw@mail.gmail.com>
Message-ID: <CA+5pysiPrrTs+rDpnsmNGKiNtqJYSnMJ85MGyWhAOsBSZAQkTA@mail.gmail.com>

Hi,
I've found the problem. The class HDF5TransformIOTemplate makes an
extension check. After change the transform output file to Transforms.hdf,
works fine.
I think this needs to be changed on Example and on book, since explicity
talks:

  // Then we set the filename using the SetFileName() function. The file's
extension
  // does not matter for the transform reader/writer. Then we call the
Update()
  // function to write the transform(s) onto the disk.

The changed code are above:

template< typename TInternalComputationValueType >

bool

HDF5TransformIOTemplate< TInternalComputationValueType >

::CanWriteFile(const char *fileName)

{

  //

  // all extensions mentioned in wikipedia + 'hd5'

  // actually HDF doesn't care about extensions at

  // all and this is just by convention.

  const char *extensions[] =

  {

    ".hdf",".h4",".hdf4",".h5",".hdf5",".he4",".he5",".hd5",0,

  };

  std::string ext

    (itksys::SystemTools::GetFilenameLastExtension(fileName));

  for(unsigned i = 0; extensions[i] != 0; i++)

    {

    if(ext == extensions[i])

      {

      return true;

      }

    }

  return false;

}

Regards,

Wagner Sales


2014-07-04 18:41 GMT-03:00 Wagner Sales <wsales at gmail.com>:

> Hi all,
>
> I'm trying to save transforms and catching an strange error. I tried to
> execute the simple example on IO directory to validate this, and:
>
> --> checking permission
> wsales at wsales-desktop:/tmp/trf$ touch ihavepermission
> wsales at wsales-desktop:/tmp/trf$ ls -la
> total 28464
> drwxrwxr-x  2 wsales wsales     4096 Jul  4 17:52 .
> drwxrwxrwt 31 root   root      12288 Jul  4 17:52 ..
> -rw-rw-r--  1 wsales wsales        0 Jul  4 17:52 ihavepermission
> -rwxrwxr-x  1 wsales wsales 29128152 Jul  4 17:52 TransformReadWrite
>
> wsales at wsales-desktop:/tmp/trf$ ./TransformReadWrite test
> Error while saving the transforms
>
> itk::ExceptionObject (0x2af4c30)
> Location: "void itk::TransformFileWriterTemplate<ScalarType>::Update()
> [with ScalarType = double]"
> File:
> /home/wsales/Sources/InsightToolkit-4.5.2/Modules/IO/TransformBase/include/itkTransformFileWriter.hxx
> Line: 200
> Description: itk::ERROR: TransformFileWriterTemplate(0x2ae6300): Can't
> Create IO object for file Transforms.meta
>
> Since I can create the file, problem with permissions is not the issue.
> About my system ( latest Ubuntu, 'll update today ):
> uname  -a
> Linux wsales-desktop 3.13.0-27-generic #50-Ubuntu SMP Thu May 15 18:06:16
> UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>
> Compiler:
> clang --version
> Ubuntu clang version 3.4-1ubuntu3 (tags/RELEASE_34/final) (based on LLVM
> 3.4)
> Target: x86_64-pc-linux-gnu
> Thread model: posix
>
> Some idea about this?
> This example was worked fine to me on ITK 3.20, before my version upgrade.
>
> Regards,
>
> Wagner Sales
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140704/24b4c0f8/attachment.html>

From matt.mccormick at kitware.com  Sun Jul  6 02:58:38 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 6 Jul 2014 02:58:38 -0400
Subject: [ITK-users] [ITK]  Fail to execute TransformReadWrite example
In-Reply-To: <CA+5pysiPrrTs+rDpnsmNGKiNtqJYSnMJ85MGyWhAOsBSZAQkTA@mail.gmail.com>
References: <CA+5pysjCb933hKxi8+nb9PZoE+1j5AuvnpOSXJD5v0VQjXgUjw@mail.gmail.com>
 <CA+5pysiPrrTs+rDpnsmNGKiNtqJYSnMJ85MGyWhAOsBSZAQkTA@mail.gmail.com>
Message-ID: <CALzTN-RMsc_hvg32YLhn49WDkJi08ZN_R+XS2mVERoPcxDC5Sg@mail.gmail.com>

Hi Wagner,

Here is a patch that addresses the example [1]. Please review [2].
However, test appears to have uncovered a gap in testing coverage,
because it fails to write the CompositeTransform.  We'll have to look
into the issue further.

Thanks,
Matt

[1] http://review.source.kitware.com/#/c/16048/

[2] http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html

On Fri, Jul 4, 2014 at 6:43 PM, Wagner Sales <wsales at gmail.com> wrote:
> Hi,
> I've found the problem. The class HDF5TransformIOTemplate makes an extension
> check. After change the transform output file to Transforms.hdf, works fine.
> I think this needs to be changed on Example and on book, since explicity
> talks:
>
>   // Then we set the filename using the SetFileName() function. The file's
> extension
>   // does not matter for the transform reader/writer. Then we call the
> Update()
>   // function to write the transform(s) onto the disk.
>
> The changed code are above:
>
> template< typename TInternalComputationValueType >
>
> bool
>
> HDF5TransformIOTemplate< TInternalComputationValueType >
>
> ::CanWriteFile(const char *fileName)
>
> {
>
>   //
>
>   // all extensions mentioned in wikipedia + 'hd5'
>
>   // actually HDF doesn't care about extensions at
>
>   // all and this is just by convention.
>
>   const char *extensions[] =
>
>   {
>
>     ".hdf",".h4",".hdf4",".h5",".hdf5",".he4",".he5",".hd5",0,
>
>   };
>
>   std::string ext
>
>     (itksys::SystemTools::GetFilenameLastExtension(fileName));
>
>   for(unsigned i = 0; extensions[i] != 0; i++)
>
>     {
>
>     if(ext == extensions[i])
>
>       {
>
>       return true;
>
>       }
>
>     }
>
>   return false;
>
> }
>
> Regards,
>
> Wagner Sales
>
>
> 2014-07-04 18:41 GMT-03:00 Wagner Sales <wsales at gmail.com>:
>
>> Hi all,
>>
>> I'm trying to save transforms and catching an strange error. I tried to
>> execute the simple example on IO directory to validate this, and:
>>
>> --> checking permission
>> wsales at wsales-desktop:/tmp/trf$ touch ihavepermission
>> wsales at wsales-desktop:/tmp/trf$ ls -la
>> total 28464
>> drwxrwxr-x  2 wsales wsales     4096 Jul  4 17:52 .
>> drwxrwxrwt 31 root   root      12288 Jul  4 17:52 ..
>> -rw-rw-r--  1 wsales wsales        0 Jul  4 17:52 ihavepermission
>> -rwxrwxr-x  1 wsales wsales 29128152 Jul  4 17:52 TransformReadWrite
>>
>> wsales at wsales-desktop:/tmp/trf$ ./TransformReadWrite test
>> Error while saving the transforms
>>
>> itk::ExceptionObject (0x2af4c30)
>> Location: "void itk::TransformFileWriterTemplate<ScalarType>::Update()
>> [with ScalarType = double]"
>> File:
>> /home/wsales/Sources/InsightToolkit-4.5.2/Modules/IO/TransformBase/include/itkTransformFileWriter.hxx
>> Line: 200
>> Description: itk::ERROR: TransformFileWriterTemplate(0x2ae6300): Can't
>> Create IO object for file Transforms.meta
>>
>> Since I can create the file, problem with permissions is not the issue.
>> About my system ( latest Ubuntu, 'll update today ):
>> uname  -a
>> Linux wsales-desktop 3.13.0-27-generic #50-Ubuntu SMP Thu May 15 18:06:16
>> UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>>
>> Compiler:
>> clang --version
>> Ubuntu clang version 3.4-1ubuntu3 (tags/RELEASE_34/final) (based on LLVM
>> 3.4)
>> Target: x86_64-pc-linux-gnu
>> Thread model: posix
>>
>> Some idea about this?
>> This example was worked fine to me on ITK 3.20, before my version upgrade.
>>
>> Regards,
>>
>> Wagner Sales
>>
>>
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From stackoverflowabder at gmail.com  Sun Jul  6 11:05:06 2014
From: stackoverflowabder at gmail.com (stack overflow)
Date: Sun, 6 Jul 2014 17:05:06 +0200
Subject: [ITK-users] What does this statement mean?
Message-ID: <CAOBx-5ZcjO3kqbtM0FpkZqAGNHGbTfyMUf6+HsqCxFi8S3KA=w@mail.gmail.com>

Hello,

Say that we have the following statements:

typedef itk::Image<double, 2>  FloatImageType;

void CreateF(FloatImageType::Pointer image)
{
...
}

I know what :: means in the function. But, in this case, do we read it as
follows?

*class Pointer is a member of the class FloatImageType*

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140706/376740a0/attachment.html>

From vincent.ngai at gmail.com  Sun Jul  6 22:36:15 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Mon, 7 Jul 2014 10:36:15 +0800
Subject: [ITK-users] What does this statement mean?
In-Reply-To: <CAOBx-5ZcjO3kqbtM0FpkZqAGNHGbTfyMUf6+HsqCxFi8S3KA=w@mail.gmail.com>
References: <CAOBx-5ZcjO3kqbtM0FpkZqAGNHGbTfyMUf6+HsqCxFi8S3KA=w@mail.gmail.com>
Message-ID: <CAC3nAP3UZf7=POsE0PMDrtFsMnUqdrNBvCg3newdZG55ugTNpw@mail.gmail.com>

Hi, It reads as: Pointer is a type scoped within FloatImageType, it simply
means Pointer is something(in this case type) found within FloatImageType.
Members usually refers to variables or functions.


On Sun, Jul 6, 2014 at 11:05 PM, stack overflow <
stackoverflowabder at gmail.com> wrote:

> Hello,
>
> Say that we have the following statements:
>
> typedef itk::Image<double, 2>  FloatImageType;
>
> void CreateF(FloatImageType::Pointer image)
> {
> ...
> }
>
> I know what :: means in the function. But, in this case, do we read it as
> follows?
>
> *class Pointer is a member of the class FloatImageType*
>
> Thanks.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>


-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140707/66b6a008/attachment.html>

From noreply at insightsoftwareconsortium.org  Mon Jul  7 12:12:34 2014
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Mon,  7 Jul 2014 12:12:34 -0400 (EDT)
Subject: [ITK-users] New Submission: Reproducible Research Training at Scipy
	2014
Message-ID: <20140707161234.031773D6C070@insightsoftwareconsortium.org>

Hello,

A new submission has been added to the Insight Journal.

Title: Reproducible Research Training at Scipy 2014
Authors: Ibanez L., McCormick M., Fillon J., Chaudri A., Nelson A., Smith S.
Abstract: This article illustrates the process of performing reproducible research with existing open source tools.

Download and review this publication at: http://hdl.handle.net/10380/3465

Generated by the Insight Journal

You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ .

From noreply at insightsoftwareconsortium.org  Mon Jul  7 13:03:59 2014
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Mon,  7 Jul 2014 13:03:59 -0400 (EDT)
Subject: [ITK-users] New Submission: Test
Message-ID: <20140707170359.828B33D6C1A5@insightsoftwareconsortium.org>

Hello,

A new submission has been added to the Insight Journal.

Title: Test
Authors: Ibanez L.
Abstract: this is a test

Download and review this publication at: http://hdl.handle.net/10380/3466

Generated by the Insight Journal

You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://www.insight-journal.org/ .

From sureerat.r at gmail.com  Mon Jul  7 16:24:53 2014
From: sureerat.r at gmail.com (Sureerat Reaungamornrat)
Date: Mon, 7 Jul 2014 16:24:53 -0400
Subject: [ITK-users] MeanSquaresImageToImageMetricv4 with Vector images
Message-ID: <CABQWK6qv9v+8TSYqh0c3oudXGoKdJWusRwT7Da_GEpEnrRPvnw@mail.gmail.com>

Dear All,

   I tested MeanSquaresImageToImageMetricv4 with vector images using
following file.
...\Modules\Registration\Metricsv4\test\itkMeanSquaresImageToImageMetricv4OnVectorTest.cxx

   First, I changed the vector image declaration to
const unsigned int vectorLength = 25;
typedef itk::Vector<double, vectorLength>                     VectorType;
typedef itk::Image< VectorType, imageDimensionality > ImageType;

And I got the following compilation error:
error LNK2001: unresolved external symbol "public: static class
itk::Vector<double,25> const itk::NumericTraits<class
itk::Vector<double,25> >::Zero".

  Would anyone know what the source of this compilation error or how to fix
this? If I commented out 'New()' as follow
MetricType::Pointer metric;// = MetricType::New();
The program can be compiled.

   Second, I tested the metric with itk::VectorImage whose elements are
itk::VariableLengthVector.
typedef itk::VectorImage<double, imageDimensionality> ImageType;
typedef ImageType::PixelType VectorType;

 I got compilation error as follow
error : 'Length': is not a member of itk::VariableLengthVector<TValueType>
error : 'Length': undeclared identifier
Both are from itkPixelTraits.h
   Where does the ImageToImageMetricv4 use PixelTraits? Is there a way to
fix this?

Thank you very much for time and help,

Best regards,

Ja
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140707/0c580f30/attachment.html>

From franciscolopezdelafranca at gmail.com  Tue Jul  8 01:44:05 2014
From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=)
Date: Mon, 7 Jul 2014 22:44:05 -0700 (PDT)
Subject: [ITK-users] Surface extraction problem
In-Reply-To: <1404307181365-7585840.post@n2.nabble.com>
References: <1404307181365-7585840.post@n2.nabble.com>
Message-ID: <1404798245092-7585861.post@n2.nabble.com>

Hi.
I've found what the problem was.
The solution is simply to use the MeshFileWriter class to save the mesh that
the BinaryMask3DMeshSource class instance outputs. Though the file format
cannot be Nifti as it was the format I was using in my application. It must
be, for instance, VTK format.
Regards.




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Surface-extraction-problem-tp7585840p7585861.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From franciscolopezdelafranca at gmail.com  Tue Jul  8 06:51:20 2014
From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=)
Date: Tue, 8 Jul 2014 03:51:20 -0700 (PDT)
Subject: [ITK-users] Surface extraction problem
In-Reply-To: <1404307181365-7585840.post@n2.nabble.com>
References: <1404307181365-7585840.post@n2.nabble.com>
Message-ID: <1404816680878-7585863.post@n2.nabble.com>

Hi again.
Another way by which you can save the mesh in Nifti format. It is like this:

1. Read a Nifti file with the 3D object.
2. Create a BinaryMask3DMeshSource object to generate the surface of the
object.
3. Create a TriangleMeshToBinaryImageFilter object that receives as input
the output of the mesh source object.
4. Save the output of triangle mesh with an ImageFileWriter.

Regards.



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Surface-extraction-problem-tp7585840p7585863.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From marco.ulge at gmail.com  Wed Jul  9 04:58:18 2014
From: marco.ulge at gmail.com (Marco Ulge)
Date: Wed, 9 Jul 2014 01:58:18 -0700 (PDT)
Subject: [ITK-users] [Itk-users]
Message-ID: <1404896298882-34206.post@n7.nabble.com>

Good morning,

i was looking at the guide, page 641 about
itkImageLinearConstIteratorWithIndex. I found that the example is
incomplete, could someone post the full example please?

Regards,
Marco



--
View this message in context: http://itk-users.7.n7.nabble.com/Itk-users-tp34206.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From jhlegarreta at vicomtech.org  Wed Jul  9 05:15:34 2014
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 9 Jul 2014 11:15:34 +0200
Subject: [ITK-users] [Itk-users]
In-Reply-To: <1404896298882-34206.post@n7.nabble.com>
References: <1404896298882-34206.post@n7.nabble.com>
Message-ID: <CAAKhGh-bi0qORZOMvzD7PJmy53_EOKH6GPpctoz=G3tuh41RNg@mail.gmail.com>

Dear Marco,
as pointed in page 640 of the SW guide, the referred example is an excerpt
of the
ImageLineaerIteratorWithIndex2.cxx example, found in
PATH_TO_SOURCE\Examples\Iterators.

Otherwise, you may find it on github [1].

Nearly all (may be even all) examples found in the SW guide are excerpts of
examples that you can find in the ITK source tree. The guide just shows the
relevant piece of code to understand how the filter works. The guide
usually mentions the name of the example at issue.

The code excerpts in the SW guide and many parts of the guide itself are
extracted automatically from the ITK source code by some sophisticated
scripts the people at kitware and other colleagues have developed.

HTH,
JON HAITZ

[1]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Iterators/ImageLinearIteratorWithIndex2.cxx


On 9 July 2014 10:58, Marco Ulge <marco.ulge at gmail.com> wrote:

> Good morning,
>
> i was looking at the guide, page 641 about
> itkImageLinearConstIteratorWithIndex. I found that the example is
> incomplete, could someone post the full example please?
>
> Regards,
> Marco
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/Itk-users-tp34206.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140709/df1ffefd/attachment.html>

From marco.ulge at gmail.com  Wed Jul  9 05:32:22 2014
From: marco.ulge at gmail.com (Marco Ulge)
Date: Wed, 9 Jul 2014 02:32:22 -0700 (PDT)
Subject: [ITK-users] [Itk-users]
In-Reply-To: <CAAKhGh-bi0qORZOMvzD7PJmy53_EOKH6GPpctoz=G3tuh41RNg@mail.gmail.com>
References: <CAAKhGh-bi0qORZOMvzD7PJmy53_EOKH6GPpctoz=G3tuh41RNg@mail.gmail.com>
Message-ID: <1404898342364-34208.post@n7.nabble.com>

Thanks for the reply, by i figured it out immediatly after posting, which is
the reason i deleted it but you were too fast in replying me. 

By the way, instead of opening a new one i'm having a doubt about this
iterator (ImageLinearIteratorWithIndex):

in the guide it is reported that the NextLine() method "Moves the iterator
to the last valid pixel location in the previous line. The origin of the
previous line is determined by decrementing the current origin along the
fastest increasing dimension of the subspace of the image that excludes the
selected dimension."

So let's say i have a 3d image and let's assume that this image has three
layers each one with 3 lines.

1st layer: line1, line2, line3
2nd layer: line 4, line5, line6
3rd layer: line7, line 8, line9

Following the example in the documentation, how does this iterator walks
through the image (i mean which order it processes the lines)?

Thank a lot,

Marco



--
View this message in context: http://itk-users.7.n7.nabble.com/Re-ITK-users-Itk-users-tp34207p34208.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From nicgallego at gmail.com  Wed Jul  9 05:51:09 2014
From: nicgallego at gmail.com (Nicolas Gallego)
Date: Wed, 9 Jul 2014 11:51:09 +0200
Subject: [ITK-users] [ITK]  [Itk-users]
In-Reply-To: <1404896298882-34206.post@n7.nabble.com>
References: <1404896298882-34206.post@n7.nabble.com>
Message-ID: <CAHFTQh7O3s4q8V1q=RThtH81vCkX8+FGMeOBbN8OUjPuNa9zcw@mail.gmail.com>

Hi Marco,

Refer to your source code examples folder for the complete code of the
examples. In this case

~ \InsightToolkit-4.5.0\Examples\Iterators\ImageLinearIteratorWithIndex2.cxx



Nicol?s Gallego-Ortiz
Universit? catholique de Louvain, Belgium


2014-07-09 10:58 GMT+02:00 Marco Ulge <marco.ulge at gmail.com>:

> Good morning,
>
> i was looking at the guide, page 641 about
> itkImageLinearConstIteratorWithIndex. I found that the example is
> incomplete, could someone post the full example please?
>
> Regards,
> Marco
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/Itk-users-tp34206.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140709/a63ae6c1/attachment.html>

From grothausmann.roman at mh-hannover.de  Wed Jul  9 07:21:33 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Wed, 09 Jul 2014 13:21:33 +0200
Subject: [ITK-users] Surface extraction problem
In-Reply-To: <1404307181365-7585840.post@n2.nabble.com>
References: <1404307181365-7585840.post@n2.nabble.com>
Message-ID: <53BD25BD.1010802@mh-hannover.de>

Hi Francisco,


What You try to achieve is related to this publication:
http://hdl.handle.net/10380/3391
A paraview plugin is also planned.

Regards
Roman


On 02/07/14 15:19, Francisco L?pez-Franca wrote:
> Hi everybody.
> I've created a 3D cylinder by using the class CylinderSpatialObject. After
> that, I pass the cylinder object to an object of class
> SpatialObjectToImageFilter in order to prepare the spatial object to be
> written to file.
> I've set both the cylinder object and the image filter a value of 0 for
> background and 255 for foreground.
> Finally, I pass, as input, the image filter output to an image file writer
> (ImageFileWriter) object to save it to file (Nifti format, for instance).
> The result is the attached "cilindro.jpg" figure.
>
> Up to here, all is ok. The problem comes next.
> What I want is to extract the surface of the 3D cylinder. I search for the
> web and found an example, from which I followed the implementation.
> I copy below my code and attach the result of the surface extraction
> ("cilindro_superficie.jpg"), hoping that anyone see if I am committing any
> error. I expected just the boundary of the 3D cylinder (with no inside
> points), and it seems like the bounding box of the cylinder what I've got
> including the inside points.
>
> Thank you very much and my best regards.
>
> My code is (I've erased the obvious code):
>
>
>      typedef itk::Image< PixelType, Dimension > ImageType;
>      typedef itk::Mesh<double, 3> MeshType;
>
>      typedef itk::ImageFileReader< ImageType > ReaderType;
>      ReaderType::Pointer reader = ReaderType::New();
>      reader->SetFileName(
> inputFileName);
>
>          reader->Update();
>
>      typedef itk::BinaryMask3DMeshSource< ImageType, MeshType >
> MeshSourceType;
>      MeshSourceType::Pointer meshSource = MeshSourceType::New();
>
>      meshSource->SetObjectValue( 255);
>
>      meshSource->SetInput( reader->GetOutput() );
>
>          meshSource->Update();
>
>      typedef itk::MeshSpatialObject<MeshType> SpatialObjectType;
>      SpatialObjectType::Pointer mesh = SpatialObjectType::New();
>      mesh->SetMesh(meshSource->GetOutput());
>
>      typedef itk::SpatialObjectToImageFilter<SpatialObjectType, ImageType>
> MeshFilterType;
>      MeshFilterType::Pointer meshFilter = MeshFilterType::New();
>
>      meshFilter->SetSize(size);
>      meshFilter->SetOutsideValue(0);
>      meshFilter->SetInsideValue(255);
>      meshFilter->SetInput(mesh);
>
>          meshFilter->Update();
>
>      typedef itk::ImageFileWriter<ImageType> ImageWriterType;
>      ImageWriterType::Pointer imageWriter = ImageWriterType::New();
>
>      imageWriter->SetFileName(outputFileName);
>      imageWriter->SetInput(meshFilter->GetOutput());
>
>          imageWriter->Update();
>
> <http://itk-insight-users.2283740.n2.nabble.com/file/n7585840/cilindro.jpg>
> <http://itk-insight-users.2283740.n2.nabble.com/file/n7585840/cilindro_superficie.jpg>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Surface-extraction-problem-tp7585840.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

From jerome.velut at kitware.com  Wed Jul  9 08:57:18 2014
From: jerome.velut at kitware.com (Jerome Velut)
Date: Wed, 9 Jul 2014 14:57:18 +0200
Subject: [ITK-users] ANN: ITK course in Lyon, France - October 2nd
Message-ID: <CAG8ZUkFgz4GtqkTAP2Tjiir_FcU2kkATdKq02rg68HDg7eczTQ@mail.gmail.com>

Kitware will be holding a developers training course on October 2nd 2014 in
Lyon, France. This course will cover the features of ITKv4 :
- Overview/Architecture
- Segmentation
- Registration
- Using ITK in your applications

Please visit our web site for more information and registration details at :

http://formations.kitware.fr/browse/50
<http://formations.kitware.fr/browse/65>

Note that the course will be taught in English. If you have any questions,
please contact us at courses[at]kitware.com or formations[at]kitware.fr.


Best regards,

-- 
J?r?me Velut
Research and Development
Kitware SAS
26 rue Louis Gu?rin
69100 Villeurbanne, France
F: +33 (0)4.37.45.04.15
http://www.kitware.fr
http://www.kitware.fr/company/team/velut.html
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140709/ec37bf0b/attachment.html>

From julien.jomier at kitware.com  Wed Jul  9 09:40:32 2014
From: julien.jomier at kitware.com (Julien Jomier)
Date: Wed, 09 Jul 2014 15:40:32 +0200
Subject: [ITK-users] ANN: CMake Course - September 29 in Lyon, France
Message-ID: <53BD4650.6070909@kitware.com>

Kitware will be holding a CMake training course on September 29, 2014 at 
Kitware's office in Lyon, France. This one-day course will cover CMake, 
CTest, CPack and CDash.

Visit our website for more information and registration details (early 
registration and student discounts available):

    http://training.kitware.fr/browse/46

Note that the course will be taught in English. If you have any 
questions, please contact us at training at kitware.fr.

We are looking forward to seeing you in Lyon,
Julien
-- 
Kitware SAS
26 rue Louis Gu?rin
69100 Villeurbanne, France
http://www.kitware.eu

From jhlegarreta at vicomtech.org  Wed Jul  9 12:24:24 2014
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 9 Jul 2014 18:24:24 +0200
Subject: [ITK-users] [Itk-users]
In-Reply-To: <1404898342364-34208.post@n7.nabble.com>
References: <CAAKhGh-bi0qORZOMvzD7PJmy53_EOKH6GPpctoz=G3tuh41RNg@mail.gmail.com>
 <1404898342364-34208.post@n7.nabble.com>
Message-ID: <CAAKhGh-O6f_LxeJiaKDP24Bo44AivW1_490Mm3My_iO0LGpeXA@mail.gmail.com>

Could the fastest increasing dimension be the lowest dimension?

If that's OK, if you have an image whose dimensions are organized as x,y,z,
the fastest increasing dimension would be x.

JON HAITZ





On 9 July 2014 11:32, Marco Ulge <marco.ulge at gmail.com> wrote:

> Thanks for the reply, by i figured it out immediatly after posting, which
> is
> the reason i deleted it but you were too fast in replying me.
>
> By the way, instead of opening a new one i'm having a doubt about this
> iterator (ImageLinearIteratorWithIndex):
>
> in the guide it is reported that the NextLine() method "Moves the iterator
> to the last valid pixel location in the previous line. The origin of the
> previous line is determined by decrementing the current origin along the
> fastest increasing dimension of the subspace of the image that excludes the
> selected dimension."
>
> So let's say i have a 3d image and let's assume that this image has three
> layers each one with 3 lines.
>
> 1st layer: line1, line2, line3
> 2nd layer: line 4, line5, line6
> 3rd layer: line7, line 8, line9
>
> Following the example in the documentation, how does this iterator walks
> through the image (i mean which order it processes the lines)?
>
> Thank a lot,
>
> Marco
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/Re-ITK-users-Itk-users-tp34207p34208.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140709/5294691b/attachment.html>

From anja.ende at googlemail.com  Thu Jul 10 06:43:42 2014
From: anja.ende at googlemail.com (Anja Ende)
Date: Thu, 10 Jul 2014 11:43:42 +0100
Subject: [ITK-users] deformation, displacement and velocity field transforms
Message-ID: <CAA7ZVg4+GpRoyXxwvd6NPHz0sAECQo7GtjtWvYikMhwB4Rmrxg@mail.gmail.com>

Hello,

I am slightly confused by some terminology in ITK and I was wondering if
someone would be kind enough to help me out on this.

As far as I understand, a deformation field is the vector field which
describes the new <position> of a given point.

A displacement field, on the other hand, the distance and the direction
that the point has moved.

ITK has this ConstantVelocityFieldTransform object. My question is what
does the velocity field in ITK encode? If I integrate the velocity field
over unit time would I get a deformation or a displacement field?

Thanks for any help you can give me.

-- 
Cheers,

Anja
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140710/bbc14d86/attachment.html>

From nicgallego at gmail.com  Thu Jul 10 10:07:28 2014
From: nicgallego at gmail.com (Nicolas Gallego)
Date: Thu, 10 Jul 2014 16:07:28 +0200
Subject: [ITK-users] [ITK]  deformation,
	displacement and velocity field transforms
In-Reply-To: <CAA7ZVg4+GpRoyXxwvd6NPHz0sAECQo7GtjtWvYikMhwB4Rmrxg@mail.gmail.com>
References: <CAA7ZVg4+GpRoyXxwvd6NPHz0sAECQo7GtjtWvYikMhwB4Rmrxg@mail.gmail.com>
Message-ID: <CAHFTQh4KuHbNbBT_3p16=Bgieb69_Y6+p9uQWe=9SbVyDRfCeg@mail.gmail.com>

Hi Anja,

Yes, as far as I understand the concept, the velocity field lives in the
tangent space of the manifold, while the displacement field is the actual
manifold, arbitrarily curved. In practice the transformation between the
velocity field (tanget space) and the displacement field (curved manifold)
is done via the exponential chart, and the inverse via the logaritmic.

The exponential is a k times recursive composition of the field with itself
starting from a scaled version of it by 2^(-K), such that the initial field
is small enough [1]. That is the equivalent of integrating over the unit
interval.

[1]
http://www.itk.org/Doxygen45/html/classitk_1_1ExponentialDisplacementFieldImageFilter.html

hope that helps


Nicol?s Gallego-Ortiz
Universit? catholique de Louvain, Belgium


2014-07-10 12:43 GMT+02:00 Anja Ende <anja.ende at googlemail.com>:

> Hello,
>
> I am slightly confused by some terminology in ITK and I was wondering if
> someone would be kind enough to help me out on this.
>
> As far as I understand, a deformation field is the vector field which
> describes the new <position> of a given point.
>
> A displacement field, on the other hand, the distance and the direction
> that the point has moved.
>
> ITK has this ConstantVelocityFieldTransform object. My question is what
> does the velocity field in ITK encode? If I integrate the velocity field
> over unit time would I get a deformation or a displacement field?
>
> Thanks for any help you can give me.
>
> --
> Cheers,
>
> Anja
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140710/758e1422/attachment.html>

From vishwanath.somashekar at gmail.com  Thu Jul 10 11:01:21 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Thu, 10 Jul 2014 10:01:21 -0500
Subject: [ITK-users] Using MattesMutualMetric in V4 registration framework.
Message-ID: <CAN9DaKaUVZFo6Q5vdGsy1gvXNVCdO6gdkVjshXB6OR8de88fMg@mail.gmail.com>

Hi All,
I am trying to register two 3d images, both OCT's from different patients.
Currently, I do the translation to roughly overlap the two volumes of
interest, then do the affine transform in 3 levels, and finally do the
BSpline transform based registration in just one level.

My Volume size is 200 x 200 x 600. I am using  a machine with 64GB of
memory and 8 core processor.

Am using Conjugate gradient line search optimizer for the Affine
registration with MMIv4 metric, and using LBFGSBv4 optimizer for the
BSpline registration, again using MMIv4 metric. The Bspline grid is 5 x 5 x
5.

It takes about 12 hours for the process to complete. Is this normal?

Also, in the previous MMIv3 version, I could set the number samples used to
calculate the metric. I am not sure how to do that here or whether it even
matters in the v4 framework.

I see that there is something like setusefixedsamplepointset function for
the metric, which is currently set to false. Does it mean it is using all
the voxels in the metric calculation?

I appreciate anyone helping me out here.

Best regards,
Vishwa
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140710/9a8f867e/attachment.html>

From anja.ende at googlemail.com  Thu Jul 10 12:58:04 2014
From: anja.ende at googlemail.com (Anja Ende)
Date: Thu, 10 Jul 2014 17:58:04 +0100
Subject: [ITK-users] [ITK]  deformation,
	displacement and velocity field transforms
In-Reply-To: <CAHFTQh4KuHbNbBT_3p16=Bgieb69_Y6+p9uQWe=9SbVyDRfCeg@mail.gmail.com>
References: <CAA7ZVg4+GpRoyXxwvd6NPHz0sAECQo7GtjtWvYikMhwB4Rmrxg@mail.gmail.com>
 <CAHFTQh4KuHbNbBT_3p16=Bgieb69_Y6+p9uQWe=9SbVyDRfCeg@mail.gmail.com>
Message-ID: <CAA7ZVg5bFF5xDLtqnRWdG9otZko4=rKO_9FAa0NYKe=H949PQw@mail.gmail.com>

Thanks Nicolas!

So, the transformation through the exponentiation is to the actual
displacement/translation of the point rather than the point's new position.


On 10 July 2014 15:07, Nicolas Gallego <nicgallego at gmail.com> wrote:

> Hi Anja,
>
> Yes, as far as I understand the concept, the velocity field lives in the
> tangent space of the manifold, while the displacement field is the actual
> manifold, arbitrarily curved. In practice the transformation between the
> velocity field (tanget space) and the displacement field (curved manifold)
> is done via the exponential chart, and the inverse via the logaritmic.
>
> The exponential is a k times recursive composition of the field with
> itself starting from a scaled version of it by 2^(-K), such that the
> initial field is small enough [1]. That is the equivalent of integrating
> over the unit interval.
>
> [1]
> http://www.itk.org/Doxygen45/html/classitk_1_1ExponentialDisplacementFieldImageFilter.html
>
> hope that helps
>
>
> Nicol?s Gallego-Ortiz
> Universit? catholique de Louvain, Belgium
>
>
> 2014-07-10 12:43 GMT+02:00 Anja Ende <anja.ende at googlemail.com>:
>
>> Hello,
>>
>> I am slightly confused by some terminology in ITK and I was wondering if
>> someone would be kind enough to help me out on this.
>>
>> As far as I understand, a deformation field is the vector field which
>> describes the new <position> of a given point.
>>
>> A displacement field, on the other hand, the distance and the direction
>> that the point has moved.
>>
>> ITK has this ConstantVelocityFieldTransform object. My question is what
>> does the velocity field in ITK encode? If I integrate the velocity field
>> over unit time would I get a deformation or a displacement field?
>>
>> Thanks for any help you can give me.
>>
>> --
>> Cheers,
>>
>> Anja
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>


-- 
Cheers,

Anja
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140710/ad41c449/attachment.html>

From anja.ende at googlemail.com  Thu Jul 10 13:40:07 2014
From: anja.ende at googlemail.com (Anja Ende)
Date: Thu, 10 Jul 2014 18:40:07 +0100
Subject: [ITK-users] itk exponential displacement field image filter
Message-ID: <CAA7ZVg4g2fkWJE6ss0seGxLB9n3iWDNZnJy0TyAPDmBGwVvaQA@mail.gmail.com>

Hello,

I have another question about the itk::
ExponentialDisplacementFieldImageFilter. Looking at the implementation, it
performs the exponentiation using the scaling and squaring approach.

The initial exponential is computed by doing a first order approximation.
However, it is done simply by dividing the input velocity field by the
factor 2^N

ie. exp(v_0) = v/2^N

However, I thought that the linear approximation of exponential of 'x'
where x is close to 0 is: 1+x. So, i thought that the expression should be:

ie. exp(v_0) = 1 + v/2^N

I saw the original Arsigny paper but could not figure this out. I am sure
this is a mistake in understanding on my part and would be very grateful if
someone can explain why this intercept term is not there?

Thanks,

Anja
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140710/2e62952b/attachment.html>

From nicgallego at gmail.com  Fri Jul 11 04:33:05 2014
From: nicgallego at gmail.com (Nicolas Gallego)
Date: Fri, 11 Jul 2014 10:33:05 +0200
Subject: [ITK-users] [ITK]  deformation,
	displacement and velocity field transforms
In-Reply-To: <CAA7ZVg5bFF5xDLtqnRWdG9otZko4=rKO_9FAa0NYKe=H949PQw@mail.gmail.com>
References: <CAA7ZVg4+GpRoyXxwvd6NPHz0sAECQo7GtjtWvYikMhwB4Rmrxg@mail.gmail.com>
 <CAHFTQh4KuHbNbBT_3p16=Bgieb69_Y6+p9uQWe=9SbVyDRfCeg@mail.gmail.com>
 <CAA7ZVg5bFF5xDLtqnRWdG9otZko4=rKO_9FAa0NYKe=H949PQw@mail.gmail.com>
Message-ID: <CAHFTQh7sScGN9hSSbHGHfwfKy9nL5r=okZUfCuchRDB7nAr=DA@mail.gmail.com>

Hi Anja,

Yes, the displacement field is to be applied to the image to warp it to the
fixed image grid, so it is actually the displacement field is used in the
inverse way, it tells the warper for every pixel of the new image where to
look and interpolate from the input image space [1].

The terminology used in actual version is DisplacementField, I saw that the
ExponentialDeformationFieldImageFilter class is being depreciated.


[1]
http://www.itk.org/Doxygen45/html/classitk_1_1WarpImageFilter.html#a75c959bf6fe0d4108a8912723b6337da

Nicol?s Gallego-Ortiz
Universit? catholique de Louvain, Belgium


2014-07-10 18:58 GMT+02:00 Anja Ende <anja.ende at googlemail.com>:

> Thanks Nicolas!
>
> So, the transformation through the exponentiation is to the actual
> displacement/translation of the point rather than the point's new position.
>
>
> On 10 July 2014 15:07, Nicolas Gallego <nicgallego at gmail.com> wrote:
>
>> Hi Anja,
>>
>> Yes, as far as I understand the concept, the velocity field lives in the
>> tangent space of the manifold, while the displacement field is the actual
>> manifold, arbitrarily curved. In practice the transformation between the
>> velocity field (tanget space) and the displacement field (curved manifold)
>> is done via the exponential chart, and the inverse via the logaritmic.
>>
>> The exponential is a k times recursive composition of the field with
>> itself starting from a scaled version of it by 2^(-K), such that the
>> initial field is small enough [1]. That is the equivalent of integrating
>> over the unit interval.
>>
>> [1]
>> http://www.itk.org/Doxygen45/html/classitk_1_1ExponentialDisplacementFieldImageFilter.html
>>
>> hope that helps
>>
>>
>> Nicol?s Gallego-Ortiz
>> Universit? catholique de Louvain, Belgium
>>
>>
>> 2014-07-10 12:43 GMT+02:00 Anja Ende <anja.ende at googlemail.com>:
>>
>>>  Hello,
>>>
>>> I am slightly confused by some terminology in ITK and I was wondering if
>>> someone would be kind enough to help me out on this.
>>>
>>> As far as I understand, a deformation field is the vector field which
>>> describes the new <position> of a given point.
>>>
>>> A displacement field, on the other hand, the distance and the direction
>>> that the point has moved.
>>>
>>> ITK has this ConstantVelocityFieldTransform object. My question is what
>>> does the velocity field in ITK encode? If I integrate the velocity field
>>> over unit time would I get a deformation or a displacement field?
>>>
>>> Thanks for any help you can give me.
>>>
>>> --
>>> Cheers,
>>>
>>> Anja
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>>
>
>
> --
> Cheers,
>
> Anja
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140711/15fc85cd/attachment.html>

From grothausmann.roman at mh-hannover.de  Fri Jul 11 07:53:36 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Fri, 11 Jul 2014 13:53:36 +0200
Subject: [ITK-users] itkMeanImageFilter on RGB (how to adjust example
	MedianFilteringOfAnRGBImage?)
Message-ID: <53BFD040.8070009@mh-hannover.de>

Dear mailing list members,


How would I need to extend/modify the example for MedianFilteringOfAnRGBImage

http://itk.org/ITKExamples/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.html

to work with itkMeanImageFilter?

I modified myRGBPixel like this:

namespace itk{
   template<typename TComponent>
   class myRGBPixel : public RGBPixel<TComponent>{
   public:
     typedef myRGBPixel     Self;
     typedef RGBPixel<TComponent> Superclass;

     myRGBPixel():Superclass() {} //avoid candidate expects 1 argument, 0 provided
     myRGBPixel(int i):Superclass(i) {} //avoid candidate expects 0 arguments, 1 
provided

     using RGBPixel<TComponent>::operator=;

     bool operator<=(const Self & r) const{
       return (this->GetLuminance() <= r.GetLuminance());
     }
     bool operator>=(const Self & r) const{
       return (this->GetLuminance() >= r.GetLuminance());
     }
     bool operator<(const Self & r) const{
       return (this->GetLuminance() < r.GetLuminance());
     }
     bool operator>(const Self & r) const{
       return (this->GetLuminance() > r.GetLuminance());
     }
   };
}


However gcc still yields this error:


In file included from /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.h:115:0,
                  from /net/home/ghky/itk/simple/mean-CPU_02.cxx:8:
/opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx: In instantiation of ?void 
itk::MeanImageFilter<TInputImage, TOutputImage>::ThreadedGenerateData(const 
OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = 
itk::Image<itk::myRGBPixel<unsigned char>, 3u>; TOutputImage = 
itk::Image<itk::myRGBPixel<unsigned char>, 3u>; 
itk::MeanImageFilter<TInputImage, TOutputImage>::OutputImageRegionType = 
itk::ImageRegion<3u>; itk::ThreadIdType = unsigned int]?:
/net/home/ghky/itk/simple/mean-CPU_02.cxx:335:5:   required from here
/opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx:81:9: error: invalid 
static_cast from type 
?itk::ConstNeighborhoodIterator<itk::Image<itk::myRGBPixel<unsigned char>, 3u>, 
itk::ZeroFluxNeumannBoundaryCondition<itk::Image<itk::myRGBPixel<unsigned char>, 
3u>, itk::Image<itk::myRGBPixel<unsigned char>, 3u> > >::PixelType {aka 
itk::myRGBPixel<unsigned char>}? to type 
?itk::MeanImageFilter<itk::Image<itk::myRGBPixel<unsigned char>, 3u>, 
itk::Image<itk::myRGBPixel<unsigned char>, 3u> >::InputRealType {aka double}?
make[3]: *** [CMakeFiles/mean-CPU_02.dir/mean-CPU_02.cxx.o] Error 1
make[2]: *** [CMakeFiles/mean-CPU_02.dir/all] Error 2
make[1]: *** [CMakeFiles/mean-CPU_02.dir/rule] Error 2
make: *** [mean-CPU_02] Error 2


What am I missing in myRGBPixel?

Any help or hints are very much appreciated
Roman

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

From bill.lorensen at gmail.com  Fri Jul 11 11:26:31 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 11 Jul 2014 11:26:31 -0400
Subject: [ITK-users] itkMeanImageFilter on RGB (how to adjust example
	MedianFilteringOfAnRGBImage?)
In-Reply-To: <53BFD040.8070009@mh-hannover.de>
References: <53BFD040.8070009@mh-hannover.de>
Message-ID: <CADZJ4hNWVyp-QLcV-JzxHm0acaka8pBoSp+Adr_ZpP5+8k4Z6Q@mail.gmail.com>

You need to define a cast operator. SOmething like:
  operator TComponent()
  {
    return this->GetLuminance();
  }

But I don't think you will get the result you want.

Bill

On Fri, Jul 11, 2014 at 7:53 AM, Dr. Roman Grothausmann
<grothausmann.roman at mh-hannover.de> wrote:
> Dear mailing list members,
>
>
> How would I need to extend/modify the example for
> MedianFilteringOfAnRGBImage
>
> http://itk.org/ITKExamples/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.html
>
> to work with itkMeanImageFilter?
>
> I modified myRGBPixel like this:
>
> namespace itk{
>   template<typename TComponent>
>   class myRGBPixel : public RGBPixel<TComponent>{
>   public:
>     typedef myRGBPixel     Self;
>     typedef RGBPixel<TComponent> Superclass;
>
>     myRGBPixel():Superclass() {} //avoid candidate expects 1 argument, 0
> provided
>     myRGBPixel(int i):Superclass(i) {} //avoid candidate expects 0
> arguments, 1 provided
>
>     using RGBPixel<TComponent>::operator=;
>
>     bool operator<=(const Self & r) const{
>       return (this->GetLuminance() <= r.GetLuminance());
>     }
>     bool operator>=(const Self & r) const{
>       return (this->GetLuminance() >= r.GetLuminance());
>     }
>     bool operator<(const Self & r) const{
>       return (this->GetLuminance() < r.GetLuminance());
>     }
>     bool operator>(const Self & r) const{
>       return (this->GetLuminance() > r.GetLuminance());
>     }
>   };
> }
>
>
> However gcc still yields this error:
>
>
> In file included from
> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.h:115:0,
>                  from /net/home/ghky/itk/simple/mean-CPU_02.cxx:8:
> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx: In instantiation of
> ?void itk::MeanImageFilter<TInputImage,
> TOutputImage>::ThreadedGenerateData(const OutputImageRegionType&,
> itk::ThreadIdType) [with TInputImage = itk::Image<itk::myRGBPixel<unsigned
> char>, 3u>; TOutputImage = itk::Image<itk::myRGBPixel<unsigned char>, 3u>;
> itk::MeanImageFilter<TInputImage, TOutputImage>::OutputImageRegionType =
> itk::ImageRegion<3u>; itk::ThreadIdType = unsigned int]?:
> /net/home/ghky/itk/simple/mean-CPU_02.cxx:335:5:   required from here
> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx:81:9: error: invalid
> static_cast from type
> ?itk::ConstNeighborhoodIterator<itk::Image<itk::myRGBPixel<unsigned char>,
> 3u>,
> itk::ZeroFluxNeumannBoundaryCondition<itk::Image<itk::myRGBPixel<unsigned
> char>, 3u>, itk::Image<itk::myRGBPixel<unsigned char>, 3u> > >::PixelType
> {aka itk::myRGBPixel<unsigned char>}? to type
> ?itk::MeanImageFilter<itk::Image<itk::myRGBPixel<unsigned char>, 3u>,
> itk::Image<itk::myRGBPixel<unsigned char>, 3u> >::InputRealType {aka
> double}?
> make[3]: *** [CMakeFiles/mean-CPU_02.dir/mean-CPU_02.cxx.o] Error 1
> make[2]: *** [CMakeFiles/mean-CPU_02.dir/all] Error 2
> make[1]: *** [CMakeFiles/mean-CPU_02.dir/rule] Error 2
> make: *** [mean-CPU_02] Error 2
>
>
> What am I missing in myRGBPixel?
>
> Any help or hints are very much appreciated
> Roman
>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>
> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
>
> Tel. +49 511 532-9574
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users



-- 
Unpaid intern in BillsBasement at noware dot com

From donelron at web.de  Fri Jul 11 12:26:17 2014
From: donelron at web.de (donelron)
Date: Fri, 11 Jul 2014 09:26:17 -0700 (PDT)
Subject: [ITK-users] How to get the image intensity with the highest
 frequency count from the histogram of a single-channel grayscale image
Message-ID: <1405095977090-34222.post@n7.nabble.com>

Hi everybody,

I have a simple question with regard to histograms:

Consider the following lines of code that calculate the histogram of an ITK
grayscale image:
-------------------------------------------------------------------------------------------------
		const unsigned int MeasurementVectorSize = 1; // Grayscale
		const unsigned int binsPerDimension = 255;

		typedef itk::Statistics::ImageToHistogramFilter< GrayscaleImageType >
			ImageToHistogramFilterType;

		ImageToHistogramFilterType::HistogramType::MeasurementVectorType
			lowerBound(binsPerDimension);
		lowerBound.Fill(0);

		ImageToHistogramFilterType::HistogramType::MeasurementVectorType
			upperBound(binsPerDimension);
		upperBound.Fill(255) ;

		ImageToHistogramFilterType::HistogramType::SizeType
			size(MeasurementVectorSize);
		size.Fill(binsPerDimension);

		ImageToHistogramFilterType::Pointer imageToHistogramFilter =
			ImageToHistogramFilterType::New();
		imageToHistogramFilter->SetInput( pConnectedComponentFilter->GetOutput()
);
		imageToHistogramFilter->SetHistogramBinMinimum( lowerBound );
		imageToHistogramFilter->SetHistogramBinMaximum( upperBound );
		imageToHistogramFilter->SetHistogramSize( size );

		try
		{
			imageToHistogramFilter->Update();
		}
		catch( itk::ExceptionObject & error )
		{
			std::cerr << "Error: " << error << std::endl;
			system("pause");
		}


		ImageToHistogramFilterType::HistogramType* histogram =
			imageToHistogramFilter->GetOutput();

		std::cout << "Frequency = [ ";
		for(unsigned int i = 0; i < histogram->GetSize()[0]; ++i)
		{
			std::cout << histogram->GetFrequency(i);

			if( i != histogram->GetSize()[0] - 1 )
			{
				std::cout << "," << std::endl;
			}
		}

		std::cout << " ]" << std::endl;
-------------------------------------------------------------------------------------------------

Is there a way to get the intensity with the highest frequency count from
the histogram?
I am aware that this is probably included in the Doxygen documentation, but
since I am neither an experienced ITK user nor C++ programmer, I couldn't
figure it out from the documentation how to do it.
Also, none of the code snippets I found, could answer my question or give me
a hint.

So, if someone could please provide a short code snippet that solves my
problem, that would be really nice:)
Or else, all hints / clues are also very very welcome.
Thank you for your help in advance!!!



--
View this message in context: http://itk-users.7.n7.nabble.com/How-to-get-the-image-intensity-with-the-highest-frequency-count-from-the-histogram-of-a-single-channe-tp34222.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From mat.roscoe at gmail.com  Fri Jul 11 19:33:33 2014
From: mat.roscoe at gmail.com (badrobot)
Date: Fri, 11 Jul 2014 16:33:33 -0700 (PDT)
Subject: [ITK-users] NeighborhoodOperatorImageFilter RunTime Error
Message-ID: <1405121613174-34225.post@n7.nabble.com>

HI I am fairly new to ITK I have created the following: 

	typedef itk::Image<unsigned char, 2> ScalarImage;
	typedef ScalarImage::Pointer ScalarImagePointer;

	typedef itk::Image<itk::CovariantVector&lt;float, 2>, 2> GradientImage;
	typedef GradientImage::Pointer GradientImagePointer;

	typedef itk::NeighborhoodOperatorImageFilter<ScalarImage, ScalarImage,
float> NeighborhoodImageFilter;
	typedef itk::ForwardDifferenceOperator<float, 2> DerivativeOperator;
	itk::Size<2> derivative_kernel_radius;
	derivative_kernel_radius.Fill( 1 );

	DLOG(INFO) << "Creating X Derivative Operator";
	// Compute the derivative in the X direction.
	DerivativeOperator DerivativeX;
	DerivativeX.SetDirection( 0 );
	DerivativeX.CreateToRadius( derivative_kernel_radius );

	DLOG(INFO) << "Computing X Derivative";
	typename NeighborhoodImageFilter::Pointer DerivativeXFilter =
NeighborhoodImageFilter::New();
	DerivativeXFilter->SetOperator( DerivativeX );
	DerivativeXFilter->SetInput( input_depth_map );
	DerivativeXFilter->Update();

Everything in this works fine until I run the update command when I get the
following output: 

I0711 20:09:07.657845  4045 DepthDerivative.cpp:62] Creating X Derivative
Operator
I0711 20:09:07.657874  4045 DepthDerivative.cpp:68] Computing X Derivative
terminate called after throwing an instance of 'itk::ExceptionObject'
  what(): 
/home/badrobit/InsightToolkit-4.5.2/Modules/Core/Common/src/itkProcessObject.cxx:1370:
itk::ERROR: NeighborhoodOperatorImageFilter(0x1c01500): Input Primary is
required but not set.
Aborted (core dumped)


This looks like it should be a fairly simply problem to catch but I am
unable to figure it out. I was hoping someone here could help me.



--
View this message in context: http://itk-users.7.n7.nabble.com/NeighborhoodOperatorImageFilter-RunTime-Error-tp34225.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From mat.roscoe at unb.ca  Sat Jul 12 00:58:02 2014
From: mat.roscoe at unb.ca (Matthew Roscoe)
Date: Sat, 12 Jul 2014 01:58:02 -0300
Subject: [ITK-users] Run Time Errors with NeighborhoodOperatorImageFilter
Message-ID: <CAAnihgi3QX+vkNE6NO2y3TG6oxW2hVL+8zHLapgN=Kdy90sSeg@mail.gmail.com>

Hello,

I am currently trying to get a derivative filter working. I have
implemented the following function:

void
DepthDerivative::ForwardDifferenceDerivative( const ScalarImage::Pointer
input_depth_map, GradientImage* const gradient_image )
{
DLOG(INFO) << "Setting up Forward Difference Derivative";
// Setup the Derivative Operator, and set its radius to 1. This will give
us a kernel that is
// 3px x 3px.
typedef itk::ForwardDifferenceOperator<unsigned char, 2> DerivativeOperator;
itk::Size<2> derivative_kernel_radius;
derivative_kernel_radius.Fill( 1 );

DLOG(INFO) << "Creating X Derivative Operator";
// Compute the derivative in the X direction.
DerivativeOperator DerivativeX;
DerivativeX.SetDirection( 0 );
DerivativeX.CreateToRadius( derivative_kernel_radius );

DLOG(INFO) << "Computing X Derivative";
typedef itk::NeighborhoodOperatorImageFilter<ScalarImage, ScalarImage>
NeighborhoodImageFilter;
NeighborhoodImageFilter::Pointer DerivativeXFilter =
NeighborhoodImageFilter::New();
DerivativeXFilter->SetOperator( DerivativeX );
DerivativeXFilter->SetInput( input_depth_map );
DLOG(INFO) << "Primary is set: " << (bool)DerivativeXFilter->HasInput(
"Primary" );
DerivativeXFilter->Update();

#ifndef NDEBUG
DLOG(INFO) << "Saving X Derivative to File";
SaveImage( DerivativeXFilter->GetOutput(), "xDerivative.png" );
#endif


I have done this using the examples on the ITK website. I have also
downloaded the example for NeighborhoodOperatorImageFilter and it functions
properly. Running this code I get the following output:

badrobit at Ubuntu:build {master} $ ./InpaintingDemo
I0712 01:52:24.366832 19445 DepthDerivative.cpp:21] Debugging Enabled, Logs
will also output to Terminal
I0712 01:52:24.366889 19445 DepthDerivative.cpp:27] DephDerivative
Initialized
I0712 01:52:24.366901 19445 Helpers.hpp:62] Starting Image File Read of:
data/test.png
I0712 01:52:24.367377 19445 Helpers.hpp:76] Reading in of Image:
data/test.png is completed
I0712 01:52:24.367399 19445 DepthDerivative.cpp:59] Setting up Forward
Difference Derivative
I0712 01:52:24.367408 19445 DepthDerivative.cpp:66] Creating X Derivative
Operator
I0712 01:52:24.367425 19445 DepthDerivative.cpp:72] Computing X Derivative
I0712 01:52:24.367441 19445 DepthDerivative.cpp:77] Primary is set: 1
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():
 /home/badrobit/InsightToolkit-4.4.2/Modules/Core/Common/src/itkProcessObject.cxx:1380:
itk::ERROR: NeighborhoodOperatorImageFilter(0x26fe4f0): Input Primary is
required but not set.
Aborted (core dumped)

As you can see I am pretty confused because I check before running Update()
if Primary has been set and the function is telling me that it is but as
soon as I run Update() it disappears... This behaviour is exactly the same
in ITK4.5.2 in case you saw the older build number. I am really at a loss
for what to do and I am hoping that the community might be able to help me
out.

Thanks in advance!
Mat Roscoe
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140712/4517ad8f/attachment.html>

From bill.lorensen at gmail.com  Sat Jul 12 09:18:25 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Sat, 12 Jul 2014 09:18:25 -0400
Subject: [ITK-users] itkMeanImageFilter on RGB (how to adjust example
	MedianFilteringOfAnRGBImage?)
In-Reply-To: <CADZJ4hNWVyp-QLcV-JzxHm0acaka8pBoSp+Adr_ZpP5+8k4Z6Q@mail.gmail.com>
References: <53BFD040.8070009@mh-hannover.de>
 <CADZJ4hNWVyp-QLcV-JzxHm0acaka8pBoSp+Adr_ZpP5+8k4Z6Q@mail.gmail.com>
Message-ID: <CADZJ4hN=DDumD9B4-C9C4-2XThj-MXUHMf_AmrqRpZmOqmYuGw@mail.gmail.com>

You are better off using vector pixels versus rgb pixels. No
overriding necessary. You should be able to modify your example by
looking at this one:

On Fri, Jul 11, 2014 at 11:26 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> You need to define a cast operator. SOmething like:
>   operator TComponent()
>   {
>     return this->GetLuminance();
>   }
>
> But I don't think you will get the result you want.
>
> Bill
>
> On Fri, Jul 11, 2014 at 7:53 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>> Dear mailing list members,
>>
>>
>> How would I need to extend/modify the example for
>> MedianFilteringOfAnRGBImage
>>
>> http://itk.org/ITKExamples/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.html
>>
>> to work with itkMeanImageFilter?
>>
>> I modified myRGBPixel like this:
>>
>> namespace itk{
>>   template<typename TComponent>
>>   class myRGBPixel : public RGBPixel<TComponent>{
>>   public:
>>     typedef myRGBPixel     Self;
>>     typedef RGBPixel<TComponent> Superclass;
>>
>>     myRGBPixel():Superclass() {} //avoid candidate expects 1 argument, 0
>> provided
>>     myRGBPixel(int i):Superclass(i) {} //avoid candidate expects 0
>> arguments, 1 provided
>>
>>     using RGBPixel<TComponent>::operator=;
>>
>>     bool operator<=(const Self & r) const{
>>       return (this->GetLuminance() <= r.GetLuminance());
>>     }
>>     bool operator>=(const Self & r) const{
>>       return (this->GetLuminance() >= r.GetLuminance());
>>     }
>>     bool operator<(const Self & r) const{
>>       return (this->GetLuminance() < r.GetLuminance());
>>     }
>>     bool operator>(const Self & r) const{
>>       return (this->GetLuminance() > r.GetLuminance());
>>     }
>>   };
>> }
>>
>>
>> However gcc still yields this error:
>>
>>
>> In file included from
>> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.h:115:0,
>>                  from /net/home/ghky/itk/simple/mean-CPU_02.cxx:8:
>> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx: In instantiation of
>> ?void itk::MeanImageFilter<TInputImage,
>> TOutputImage>::ThreadedGenerateData(const OutputImageRegionType&,
>> itk::ThreadIdType) [with TInputImage = itk::Image<itk::myRGBPixel<unsigned
>> char>, 3u>; TOutputImage = itk::Image<itk::myRGBPixel<unsigned char>, 3u>;
>> itk::MeanImageFilter<TInputImage, TOutputImage>::OutputImageRegionType =
>> itk::ImageRegion<3u>; itk::ThreadIdType = unsigned int]?:
>> /net/home/ghky/itk/simple/mean-CPU_02.cxx:335:5:   required from here
>> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx:81:9: error: invalid
>> static_cast from type
>> ?itk::ConstNeighborhoodIterator<itk::Image<itk::myRGBPixel<unsigned char>,
>> 3u>,
>> itk::ZeroFluxNeumannBoundaryCondition<itk::Image<itk::myRGBPixel<unsigned
>> char>, 3u>, itk::Image<itk::myRGBPixel<unsigned char>, 3u> > >::PixelType
>> {aka itk::myRGBPixel<unsigned char>}? to type
>> ?itk::MeanImageFilter<itk::Image<itk::myRGBPixel<unsigned char>, 3u>,
>> itk::Image<itk::myRGBPixel<unsigned char>, 3u> >::InputRealType {aka
>> double}?
>> make[3]: *** [CMakeFiles/mean-CPU_02.dir/mean-CPU_02.cxx.o] Error 1
>> make[2]: *** [CMakeFiles/mean-CPU_02.dir/all] Error 2
>> make[1]: *** [CMakeFiles/mean-CPU_02.dir/rule] Error 2
>> make: *** [mean-CPU_02] Error 2
>>
>>
>> What am I missing in myRGBPixel?
>>
>> Any help or hints are very much appreciated
>> Roman
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com
-------------- next part --------------
A non-text attachment was scrubbed...
Name: VectorMeanImageFilter.cxx
Type: application/octet-stream
Size: 2098 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140712/71027472/attachment.obj>

From matt.mccormick at kitware.com  Sat Jul 12 13:10:32 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 12 Jul 2014 13:10:32 -0400
Subject: [ITK-users] [ANNOUNCE] ITK 4.6 Release Candidate 3 has been tagged!
Message-ID: <CALzTN-SPv-k6APtSWP1cL0JmU7mp2oW-wbyL5EQVetOkfLWzVQ@mail.gmail.com>

On behalf of the Insight Toolkit community, we are proud to announce
that ITK 4.6.0 release candidate 3 has been tagged and is available
for testing!


To obtain the source code,

  git clone http://itk.org/ITK.git
  cd ITK
  git checkout -q --detach v4.6rc03

For more details, please see the Git documentation [1].


Please test the release candidate and share your experiences on the
mailing list, issue tracker, and Gerrit Code Review. Please help
identify issues submitting an Experimental build to the dashboard [2]
with:

  ctest -M Experimental  -T Configure -T Build -T Test -T Submit

and notifying the mailing list.  Testing your own applications against
the RC is also appreciated.

Those community members wishing to contribute by cleaning up the
dashboard can find a list potential candidates on the issue tracker
[3]. Please do not hesitate to ask about any aspect of the
contribution process.


Congratulations and well done to everyone that has contributed to this
release. Release candidates are tagged every week.  The final release
is scheduled for next week.


[1] http://www.itk.org/Wiki/ITK/Git

[2] http://open.cdash.org/index.php?project=Insight

[3] https://issues.itk.org/jira/issues/?jql=project%20%3D%20ITK%20AND%20fixVersion%20%3D%20%2220140714_ITKv4.6.0_FINAL%22%20AND%20status%20in%20(Open%2C%20%22In%20Progress%22%2C%20Reopened)

New Features
------------------

* CMake improvements
  - Improved Remote Module support
  - Add ITK_FORBID_DOWNLOADS for package maintainers
  - ITK_USE_SYSTEM_EXPAT available

* Filtering Improvements
  - Moved TransformToDisplacementField out of Review
  - An entire noise image generation module
    - http://hdl.handle.net/10380/3158
  - Better pipeline support for ResampleImageFilter
  - Move MagnitudeAndPhaseToComplexImageFilter out of Review
  - Setters for LabelMap overlay filters
  - More consistent filter progress reporting

* ImageIO improvements
  - Register the GE image formats by default
  - More IO modules are built as shared libraries
  - OpenFileForReading/Writing methods in ImageIO
  - Support for system tiff 4.0.0-4.0.2 (e.g. some Ubuntu versions)
  - Mangling to internal OpenJPEG
  - SCIFIO improvements

* Infrastructure improvements
  - MetaDataObject print specialization for common types
  - Improvements to ResourceProbe and RealTimeClock
  - More Solve methods for VNLSparseLUSolverTraits
  - Output stream operator for LightObject exposed
  - FFTW bump to 3.3.3

* New Remote Modules
  - Skull stripper
    - http://hdl.handle.net/10380/3353
  - Wiki examples
  - Sphinx examples
  - Variational registration
    - http://hdl.handle.net/10380/3460
  - AnalyzeObjectMapIO
    - http://hdl.handle.net/1926/593
  - FDFImageIO
  - SplitComponents
    - http://hdl.handle.net/10380/320

* Registrationv4 improvements
  - v4 regular step gradient descent optimizer
  - v4 amoeba optimizer
  - v4 exhaustive optimizer
  - v4 Powell optimizer
  - v4 one-plus-one-evolutionary optimizer
  - v4 LBFGS optimizer improvements
  - Use registration method classes as pipeline filters

* Performance improvements
  - Registrationv4
  - Histogram computation
  - Improved SmartPointer copy
  - CompositeTransform
  - Registration Jacobian re-use

* Wrapping improvements
  - pygccxml 1.0.0
  - .pth symlink usable in a virtualenv
  - Cleaner CMake configuration
  - SWIG and PCRE updated to 3.0.2, 8.34
  - Latest GCCXML, which works with GCC 4.9
  - Sweeping wrapping generation cleanup

* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- some measures put us over 85%!

* *Lots* of important bug fixes

* And more! See details in the log below.

List of changes since v4.6rc02
---------------------------------------

Ali Ghayoor (1):
      ENH: Convert seven ImageRegistration examples to ITKv4

Bradley Lowekamp (2):
      BUG: Remove multiple per-pixel allocations in Mahalanobis Membership
      COMP: Fix unused-local-typedef warnings in the Registration and Numeric

Hans Johnson (1):
      ENH: Prepare for ITKv4 registration Examples

Matthew McCormick (5):
      BUG: Improve module Group membership detection.
      COMP: Fix unused-local-typedef warnings in Group Core.
      BUG: Update TransformReadWrite example.
      COMP: Fix unused-local-typedef warnings in the Filtering Group.
      COMP: Remove unused typedefs.

Nick Tustison (1):
      ENH:  Missed spec for generic computation type.

From medswengineer at gmail.com  Sun Jul 13 09:50:59 2014
From: medswengineer at gmail.com (med aweng)
Date: Sun, 13 Jul 2014 15:50:59 +0200
Subject: [ITK-users] Gray Level Coocurrence Matrix
Message-ID: <CAEMYOQjCae1MmN=QxcQ5P0HumZnD7zn3awg-1EUvmDKWXOCGVQ@mail.gmail.com>

Hello,

I'm new to ITK, and trying to calculate the Gray Level Coocurrence Matrix
(GLCM) features of some image.

I have started as follows:

typedef itk::Image< double, 3 >  MyImageType;

I found that there are two classes to use for my task:

ScalarImageToGreyLevelCooccurrenceMatrixGenerator
<http://www.itk.org/Doxygen320/html/classitk_1_1Statistics_1_1ScalarImageToGreyLevelCooccurrenceMatrixGenerator.html>

GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator
<http://www.itk.org/Doxygen320/html/classitk_1_1Statistics_1_1GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator.html#_details>

Can you just kindly guide me on how to go further with building this
program, just for me to know how the structure of an ITK program should
look like?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140713/a72eb3aa/attachment.html>

From dzenanz at gmail.com  Mon Jul 14 06:29:47 2014
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 14 Jul 2014 12:29:47 +0200
Subject: [ITK-users] Gray Level Coocurrence Matrix
In-Reply-To: <CAEMYOQjCae1MmN=QxcQ5P0HumZnD7zn3awg-1EUvmDKWXOCGVQ@mail.gmail.com>
References: <CAEMYOQjCae1MmN=QxcQ5P0HumZnD7zn3awg-1EUvmDKWXOCGVQ@mail.gmail.com>
Message-ID: <CAPf2UMSwNDg7FCOb_BFt57hcKxJV+Arnoc2B1viY1cQvXaPQtg@mail.gmail.com>

Take a look at this example:
http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures

You might be interested in this code:
https://github.com/blowekamp/itkTextureAnalysis
and this thread:
http://www.itk.org/pipermail/insight-users/2012-February/043764.html


On Sun, Jul 13, 2014 at 3:50 PM, med aweng <medswengineer at gmail.com> wrote:

> Hello,
>
> I'm new to ITK, and trying to calculate the Gray Level Coocurrence Matrix
> (GLCM) features of some image.
>
> I have started as follows:
>
> typedef itk::Image< double, 3 >  MyImageType;
>
> I found that there are two classes to use for my task:
>
> ScalarImageToGreyLevelCooccurrenceMatrixGenerator
> <http://www.itk.org/Doxygen320/html/classitk_1_1Statistics_1_1ScalarImageToGreyLevelCooccurrenceMatrixGenerator.html>
>
> GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator
> <http://www.itk.org/Doxygen320/html/classitk_1_1Statistics_1_1GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator.html#_details>
>
> Can you just kindly guide me on how to go further with building this
> program, just for me to know how the structure of an ITK program should
> look like?
>
> Thanks.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140714/fad24a7e/attachment-0001.html>

From ivans at yahoo.co.jp  Mon Jul 14 06:27:09 2014
From: ivans at yahoo.co.jp (Ivan Setiawan)
Date: Mon, 14 Jul 2014 19:27:09 +0900 (JST)
Subject: [ITK-users] Strange behavior with ResampleImageFilter?
Message-ID: <519113.33257.qm@web101320.mail.kks.yahoo.co.jp>

Dear All,

I have a question regarding a strange behavior of?itk::ResampleImageFilter.
Currently I am using v4.4.0.


I am registering a 3D moving image to a 3D fixed image using BSplineTransform as the transformer.
The registration process seems fine.

However, sometimes, the resampling result (i.e., the final moved image) on the first slice looks identical with the original moving image.
The other slices seems correctly deform and correctly align with the 3D fixed image.

Could you please direct me to the code that should be modified to correct this behavior such that the first slice of the moving image also deforms correctly?


Thank you very much and best regards,
Ivan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140714/c404d4ce/attachment.html>

From mpinkert at wisc.edu  Mon Jul 14 13:58:37 2014
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Mon, 14 Jul 2014 10:58:37 -0700 (PDT)
Subject: [ITK-users]  Largest Connected Region
Message-ID: <1405360717980-7585889.post@n2.nabble.com>

Hi everyone,

I am using the Otsu algorithm as part of a pipeline to segment breast
images, but the results consistently have several holes and isolated regions
of noise, both of which are large problems I am looking to deal with.  I
intend to use morphological operators for the hole problem, but I have not
had luck finding a method to eliminate the isolated regions of noise while
preserving the remainder of the image.  

The breast is a connected region in the results, and the noise is always a
much smaller region.  Is there a filter that could obtain the largest
connected region from from a binary image, so that the breast may be
extracted and the noise removed?

I have looked at some of the various connected region algorithms, but they
require seeds in order to function, and I have not seen one that can
automatically isolate the largest connected region from a binary mask and
make it as an output.

If none of the existing filters work I intend to write a new one to do so,
but I thought it would be best to check first.  

Best regards,
Michael Pinkert



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Largest-Connected-Region-tp7585889.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Mon Jul 14 16:09:15 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 14 Jul 2014 16:09:15 -0400
Subject: [ITK-users] [ITK]  Largest Connected Region
In-Reply-To: <1405360717980-7585889.post@n2.nabble.com>
References: <1405360717980-7585889.post@n2.nabble.com>
Message-ID: <CALzTN-RD_g8kz_uJh6eAJGKT5DwqqR_kuS=u2Vqwjw3Rh_jLZg@mail.gmail.com>

Hi Michael,

This filter [1] can keep the largest object.  Use

  filter->SetAttribute( "PhysicalSize" )

and

  filter->SetNumberOfObject( 1 )

Hope this helps,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryShapeKeepNObjectsImageFilter.html

On Mon, Jul 14, 2014 at 1:58 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:
> Hi everyone,
>
> I am using the Otsu algorithm as part of a pipeline to segment breast
> images, but the results consistently have several holes and isolated regions
> of noise, both of which are large problems I am looking to deal with.  I
> intend to use morphological operators for the hole problem, but I have not
> had luck finding a method to eliminate the isolated regions of noise while
> preserving the remainder of the image.
>
> The breast is a connected region in the results, and the noise is always a
> much smaller region.  Is there a filter that could obtain the largest
> connected region from from a binary image, so that the breast may be
> extracted and the noise removed?
>
> I have looked at some of the various connected region algorithms, but they
> require seeds in order to function, and I have not seen one that can
> automatically isolate the largest connected region from a binary mask and
> make it as an output.
>
> If none of the existing filters work I intend to write a new one to do so,
> but I thought it would be best to check first.
>
> Best regards,
> Michael Pinkert
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Largest-Connected-Region-tp7585889.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

From Roy.Harnish at ucsf.edu  Mon Jul 14 20:19:37 2014
From: Roy.Harnish at ucsf.edu (Harnish, Roy)
Date: Tue, 15 Jul 2014 00:19:37 +0000
Subject: [ITK-users] (no subject)
Message-ID: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>

Hi,

I'm wondering if there is a procedure for adding a dicom dictionary to those that are used by the GDCMImageIO, or a way to parse a private field by furnishing the pertinent info to the right method.  I'm trying to access the field 0119,1030, which is pretty much a 3d version of ImageOrientationPatient.  I have no problem seeing the field in a dcmdump of an image that contains the field, but am having trouble getting my program to handle the field properly.  Here's what a dcmdump of the field looks like:

cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i imageor
(0020,0037) DS [-1\-0\0\-0\-1\0]                        #  16, 6 ImageOrientationPatient
cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i 0119,1030
(0119,1030) DS [-1\-0\0\-0\-1\0\0\0\1]                  #  22, 9 Unknown Tag & Data
cbl-mbp-3369:Release rharnish$

This is a section of code that tires to parse the field:

    std::string tagkey = "0119|1030";
//    std::string tagkey = "0020|0037";
    std::string labelId;
    std::string value;


    if( gdcmImageIO->GetValueFromTag(tagkey, value) )
    {
        std::cout << tagkey << ":  ";
        std::cout << value << std::endl;
    }

Here's the output with     std::string tagkey = "0119|1030";:

0119|1030:  LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==


Here's the output with     std::string tagkey = "0020|0037";

0020|0037:  -1\-0\0\-0\-1\0

Any suggestions would be much appreciated.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140715/24f7e2da/attachment.html>

From mpinkert at wisc.edu  Mon Jul 14 20:46:02 2014
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Mon, 14 Jul 2014 17:46:02 -0700 (PDT)
Subject: [ITK-users] [ITK]  Largest Connected Region
In-Reply-To: <CALzTN-RD_g8kz_uJh6eAJGKT5DwqqR_kuS=u2Vqwjw3Rh_jLZg@mail.gmail.com>
References: <1405360717980-7585889.post@n2.nabble.com>
 <CALzTN-RD_g8kz_uJh6eAJGKT5DwqqR_kuS=u2Vqwjw3Rh_jLZg@mail.gmail.com>
Message-ID: <1405385162973-7585892.post@n2.nabble.com>

Hi Matt,

Thank you very much.  This and another filter that was sent to me have both
been very helpful.  I knew I was probably missing something big.

Best regards,
Michael Pinkert


Matt McCormick-2 wrote
> Hi Michael,
> 
> This filter [1] can keep the largest object.  Use
> 
>   filter->SetAttribute( "PhysicalSize" )
> 
> and
> 
>   filter->SetNumberOfObject( 1 )
> 
> Hope this helps,
> Matt
> 
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1BinaryShapeKeepNObjectsImageFilter.html
> 
> On Mon, Jul 14, 2014 at 1:58 PM, Michael Pinkert &lt;

> mpinkert@

> &gt; wrote:
>> Hi everyone,
>>
>> I am using the Otsu algorithm as part of a pipeline to segment breast
>> images, but the results consistently have several holes and isolated
>> regions
>> of noise, both of which are large problems I am looking to deal with.  I
>> intend to use morphological operators for the hole problem, but I have
>> not
>> had luck finding a method to eliminate the isolated regions of noise
>> while
>> preserving the remainder of the image.
>>
>> The breast is a connected region in the results, and the noise is always
>> a
>> much smaller region.  Is there a filter that could obtain the largest
>> connected region from from a binary image, so that the breast may be
>> extracted and the noise removed?
>>
>> I have looked at some of the various connected region algorithms, but
>> they
>> require seeds in order to function, and I have not seen one that can
>> automatically isolate the largest connected region from a binary mask and
>> make it as an output.
>>
>> If none of the existing filters work I intend to write a new one to do
>> so,
>> but I thought it would be best to check first.
>>
>> Best regards,
>> Michael Pinkert
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Largest-Connected-Region-tp7585889.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> _______________________________________________
>> Community mailing list
>> 

> Community@

>> http://public.kitware.com/mailman/listinfo/community
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users





--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Largest-Connected-Region-tp7585889p7585892.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Mon Jul 14 20:55:01 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 14 Jul 2014 20:55:01 -0400
Subject: [ITK-users] [ITK] How to make ITK-binaries NOT ignore kernel
 out of memory messages?
In-Reply-To: <53A80327.9050701@mh-hannover.de>
References: <53917A66.2060402@mh-hannover.de>
 <CABAUzPrPjJj3h3vtnJs2PBd52PfUxYJXUojyt6V0UUfzUFYhNA@mail.gmail.com>
 <53A80327.9050701@mh-hannover.de>
Message-ID: <CALzTN-QZzjUdYmREq__vdV1diBZbY3gvZ+zEqZwdT7t7KKTk5Q@mail.gmail.com>

Hi Roman,

The CMake configuration variable:

  ITK_COMPUTER_MEMORY_SIZE

is only used to choose which unit tests to run, and has no effect on
your program.


It may be worth a try to run

  export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1

before starting your program on the server to see the effect.  It is
possible that too many threads or being spawned or that the amount of
memory consumed is scaling (poorly) with the number of threads used.

Hope this helps,
Matt

On Mon, Jun 23, 2014 at 6:36 AM, Dr. Roman Grothausmann
<grothausmann.roman at mh-hannover.de> wrote:
> Dear Luis,
>
>
> Many thanks for Your reply. It took me some time to reproduce the problem,
> because Your test program works as expected on our server:
>
> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 1000
> ITK Hello World !
>
> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 10000
> /opt/itk-4.5.1/include/ITK-4.5/itkImportImageContainer.hxx:192:
>
> Failed to allocate memory for image.
>
> One program of mine for which the problem exists is below. The problem
> occurs when BinaryMask3DMeshSource acquires more memory after running for
> some minutes. The very strange thing to me is, that the program is killed by
> the kernel as expected on my desktop PC:
>
> ~/itk/simple/build_itk4_pc3G48243/euler-characteristic_01 13-511_EAA_ot.mha
> 255
> component type is: unsigned_char
> numDimensions: 3
> component size: 1
> pixel type (string): scalar
> pixel type: 1
> _________________________
>
> Executing ImageFileReader  done. Took 2.78 seconds.
> Executing BinaryMask3DMeshSource Killed
>
>
> The header of 13-511_EAA_ot.mha:
>
> ObjectType = Image
> NDims = 3
> BinaryData = True
> BinaryDataByteOrderMSB = False
> CompressedData = True
> CompressedDataSize = 20474538
> TransformMatrix = 1 0 0 0 1 0 0 0 1
> Offset = 0 0 0
> CenterOfRotation = 0 0 0
> AnatomicalOrientation = RAI
> ElementSpacing = 1 1 1
> DimSize = 998 998 1034
> ElementType = MET_UCHAR
> ElementDataFile = LOCAL
>
>
> However on the server it is not terminated when the RAM runs out, instead
> many processes go nuts that had been mostly sleeping and finally the system
> does not respond any more at all and a cold start is necessary. The
> itk-4.5.1 is configured on the server with (see attached
> CMakeCache_itk-4.5.1.txt):
>
> ITK_COMPUTER_MEMORY_SIZE  190
>
> The server has 256GB of RAM an no Swap enabled:
>
> free
>              total       used       free     shared    buffers     cached
> Mem:     264498496    1341020  263157476          0     285760     289120
> -/+ buffers/cache:     766140  263732356
> Swap:            0          0          0
>
>
> Has 12x2 Intel(R) Xeon(R) CPUs:
>
> cat /proc/cpuinfo
> processor       : 0
> vendor_id       : GenuineIntel
> cpu family      : 6
> model           : 45
> model name      : Intel(R) Xeon(R) CPU E5-2630L 0 @ 2.00GHz
> stepping        : 7
> microcode       : 0x710
> cpu MHz         : 1200.000
> cache size      : 15360 KB
> physical id     : 0
> siblings        : 12
> core id         : 0
> cpu cores       : 6
> apicid          : 0
> initial apicid  : 0
> fpu             : yes
> fpu_exception   : yes
> cpuid level     : 13
> wp              : yes
> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
> pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology
> nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2
> ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer
> aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi
> flexpriority ept vpid
> bogomips        : 4000.56
> clflush size    : 64
> cache_alignment : 64
> address sizes   : 46 bits physical, 48 bits virtual
> power management:
> .
> .
> .
>
>
> The server runs a Debian Wheezy (7.2):
> uname -a
> Linux img1-serv 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>
> My desktop PC has the same Debian (also same update state):
> uname -a
> Linux pc3G48243 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>
> free
>              total       used       free     shared    buffers     cached
> Mem:       8180356    1185364    6994992          0      23348     216084
> -/+ buffers/cache:     945932    7234424
> Swap:            0          0          0
>
>
> and 4 AMD FX(tm)-4100 Quad-Core Processors:
>
> cat /proc/cpuinfo
> processor       : 0
> vendor_id       : AuthenticAMD
> cpu family      : 21
> model           : 1
> model name      : AMD FX(tm)-4100 Quad-Core Processor
> stepping        : 2
> microcode       : 0x6000626
> cpu MHz         : 1400.000
> cache size      : 2048 KB
> physical id     : 0
> siblings        : 4
> core id         : 0
> cpu cores       : 2
> apicid          : 16
> initial apicid  : 0
> fpu             : yes
> fpu_exception   : yes
> cpuid level     : 13
> wp              : yes
> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
> cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
> pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc extd_apicid
> aperfmperf pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 popcnt aes xsave
> avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse
> 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 nodeid_msr topoext
> perfctr_core arat cpb hw_pstate npt lbrv svm_lock nrip_save tsc_scale
> vmcb_clean flushbyasid decodeassists pausefilter pfthreshold
> bogomips        : 7233.41
> TLB size        : 1536 4K pages
> clflush size    : 64
> cache_alignment : 64
> address sizes   : 48 bits physical, 48 bits virtual
> power management: ts ttp tm 100mhzsteps hwpstate [9]
>
>
> Knowing now, that itk checks for available RAM, the only sources for this
> problem I can think of would be an odd configuration of ITK itself or its
> use in programs compiled on the server, or some configuration differences in
> the (Debian) system, or some hardware problem.
>
> Do You have any idea what it could be?
> Or do You have any suggestions how I should go on searching for the cause?
>
>
> Any help or hints are very much appriciated.
> Many thanks for Your help again!
>
> Roman
>
>
> _____________________________________________
>
>
>
> ////program to calculate the Euler characteristic of a binary image
> converted to itkQuadEdgeMesh
> ////THEREFORE does NOT take filled regions into account only covering
> surfaces!
> ////if fillings should be accounted use instead a vtk program taking 3D
> cells into account
>
>
>
> #include <itkImageFileReader.h>
> //#include <itkImage.h>
> #include <itkBinaryMask3DMeshSource.h> //itk marching cubes (mc) very slow
> and resource hungry :-(
> #include <itkQuadEdgeMeshTopologyChecker.h>
> #include <itkQuadEdgeMeshBoundaryEdgesMeshFunction.h>
>
>
>
> #include "itkFilterWatcher2.h"
>
>
>
>
> void dispatch_cT(itk::ImageIOBase::IOPixelType,
> itk::ImageIOBase::IOComponentType, size_t, int, char **);
>
> template<typename InputComponentType>
> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t, int, char
> **);
>
> template<typename InputComponentType, typename InputPixelType>
> void dispatch_D(size_t, int, char **);
>
> template<typename InputComponentType, typename InputPixelType, size_t
> Dimension>
> int DoIt(int, char *argv[]);
>
>
>
>
>
> template<typename InputComponentType, typename InputPixelType, size_t
> Dimension>
> int DoIt(int argc, char *argv[]){
>
>   typedef InputPixelType  OutputPixelType;
>
>   typedef itk::Image<InputPixelType, Dimension>  InputImageType;
>   typedef itk::Image<OutputPixelType, Dimension>  OutputImageType;
>
>
>   typedef itk::ImageFileReader<InputImageType> ReaderType;
>   typename ReaderType::Pointer reader = ReaderType::New();
>
>   reader->SetFileName(argv[1]);
>   FilterWatcher watcherI(reader, "reading");
>   watcherI.QuietOn();
>   watcherI.ReportTimeOn();
>   try
>     {
>       reader->Update();
>     }
>   catch (itk::ExceptionObject &ex)
>     {
>       if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>       std::cerr << ex.GetDescription() << std::endl;
>       return EXIT_FAILURE;
>       }
>     }
>
>
>   typedef double        CoordType;
>
>   //typedef itk::Mesh<CoordType> MeshType;
>   typedef itk::QuadEdgeMesh<CoordType, Dimension> InputMeshType;
>
>   const InputPixelType isoValue= static_cast<InputPixelType>(atof(argv[2]));
>
>   typedef itk::BinaryMask3DMeshSource<InputImageType, InputMeshType>
> MeshSourceType;
>   typename MeshSourceType::Pointer meshSource = MeshSourceType::New();
>
>   meshSource->SetInput(reader->GetOutput());
>   meshSource->SetObjectValue(isoValue);
>
>   FilterWatcher watcher(meshSource, "BinaryMask3DMeshSource");
>   watcher.QuietOn();
>   watcher.ReportTimeOn();
>   try
>     {
>       meshSource->Update();
>     }
>   catch (itk::ExceptionObject &ex)
>     {
>       if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>         std::cerr << ex.GetDescription() << std::endl;
>         return EXIT_FAILURE;
>       }
>     }
>
>
>   std::cout << "Nodes = " << meshSource->GetNumberOfNodes() << std::endl;
>   std::cout << "Cells = " << meshSource->GetNumberOfCells() << std::endl;
>
>   typename InputMeshType::Pointer mesh= meshSource->GetOutput();
>
>   //// check if meshSource can be represented as an itkQuadEdgeMesh
>   //// if BinaryMask3DMeshSource caps boundary surfaces this check is not
> necessary!
>
>   typedef itk::QuadEdgeMeshTopologyChecker<InputMeshType> TQEchecker;
>   typename TQEchecker::Pointer QEchecker = TQEchecker::New();
>   QEchecker->SetMesh(mesh);
>   std::cerr << "Executing
> QuadEdgeMeshTopologyChecker->ValidateEulerCharacteristic()";
>   if(!QEchecker->ValidateEulerCharacteristic()){
>     std::cerr << "Not a valid QuadEdgeMesh! Aborting." << std::endl;
>     return EXIT_FAILURE;
>   }
>   std::cerr << " done." << std::endl;
>
>   //// calc Euler characteristics \xi
>   //// For closed smooth manifolds, the Euler characteristic coincides with
> the Euler number:
> http://en.wikipedia.org/wiki/Euler_characteristic#Relations_to_other_invariants
>   //// general formula see:
> http://en.wikipedia.org/wiki/Genus_%28mathematics%29#Orientable_surface
>   ////
>   ////
>   ////
>   //// good QuadEdge explanation:
> http://www.cs.cmu.edu/afs/andrew/scs/cs/15-463/2001/pub/src/a2/quadedge.html
>   /// from itkQuadEdgeMeshTopologyChecker.hxx
>
>   typedef itk::QuadEdgeMeshBoundaryEdgesMeshFunction<InputMeshType>
> BoundaryEdges;
>
>   typename BoundaryEdges::Pointer boundaryEdges = BoundaryEdges::New();
>
>   // Number of USED points
>   typedef typename InputMeshType::PointIdentifier
> PointIdentifier;
>   std::cerr << "ComputeNumberOfPoints";
>   PointIdentifier numPoints = mesh->ComputeNumberOfPoints();
>   std::cerr << " done." << std::endl;
>   // Number of USED edges
>   typedef typename InputMeshType::CellIdentifier
> CellIdentifier;
>   std::cerr << "ComputeNumberOfEdges";
>   CellIdentifier numEdges  = mesh->ComputeNumberOfEdges();
>   std::cerr << " done." << std::endl;
>   // Number of USED faces
>   std::cerr << "ComputeNumberOfFaces";
>   CellIdentifier numFaces  = mesh->ComputeNumberOfFaces();
>   std::cerr << " done." << std::endl;
>   // Number of Boundaries
>   std::cerr << "ComputeNumberOfBoundaryEdges";
>   typename BoundaryEdges::OutputType
>     listOfBoundaries = boundaryEdges->Evaluate((*mesh));
>   std::cerr << " done." << std::endl;
>   CellIdentifier numBounds = listOfBoundaries->size();
>   delete listOfBoundaries;
>
>   /**
>    * Number of points
>    *
>    * There are two methods to get the number of points.
>    * 1. itk::QuadEdgeMesh::ComputeNumberOfPoints()
>    * 2. itk::Mesh::GetNumberOfPoints()
>    *
>    * As an itk::QuadEdgeMesh is an itk::Mesh by inheritance, the user
>    * can use both. 1. will returned the number of points actually
>    * used by at least one edge, while 2. will give you the number
>    * of points in the container. Number of unused points can be found
>    * by making the difference between the two values.
>    */
>   if(mesh->GetNumberOfPoints() != numPoints){
>     std::cerr << "There are isolated vertices! Aborting." << std::endl;
>     return EXIT_FAILURE;
>   }
>
>   // The euler formula states:
>   // numFaces - numEdges + numPoints == 2 - 2 * genus - numBounds == \xi
>   // hence 2 * genus= 2 - numBounds - numFaces + numEdges - numPoints must
> be an oddeven number.
>
>   typedef ::itk::OffsetValueType    OffsetValueType;
>
>   OffsetValueType xi=
>     + OffsetValueType(numFaces)
>     - OffsetValueType(numEdges)
>     + OffsetValueType(numPoints);
>
>   std::cout << "The Euler characteristic Xi is: " << xi << std::endl;
>
>   OffsetValueType twiceGenus=
>     + OffsetValueType(2) - OffsetValueType(numBounds)
>     - xi;
>
>   std::cout << "The genus is: " << twiceGenus/OffsetValueType(2) <<
> std::endl;
>
>   return EXIT_SUCCESS;
>
> }
>
>
> void dispatch_cT(itk::ImageIOBase::IOComponentType componentType,
> itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc,
> char *argv[]){
>
>
> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#a8dc783055a0af6f0a5a26cb080feb178
>   //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00107
>   //IOComponentType: UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT,
> INT, ULONG, LONG, FLOAT, DOUBLE
>
>   switch (componentType){
>   case itk::ImageIOBase::UCHAR:{
>     typedef unsigned char InputComponentType;
>     dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>   }
>     break;
>   case itk::ImageIOBase::CHAR:{
>     typedef char InputComponentType;
>     dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>   }
>     break;
>   case itk::ImageIOBase::USHORT:{
>     typedef unsigned short InputComponentType;
>     dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>   }
>     break;
>   case itk::ImageIOBase::SHORT:{
>     typedef short InputComponentType;
>     dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>   }
>     break;
>   case itk::ImageIOBase::UINT:{
>     typedef unsigned int InputComponentType;
>     dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>   }
>     break;
>   case itk::ImageIOBase::INT:{
>     typedef int InputComponentType;
>     dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>   }
>     break;
>   // case itk::ImageIOBase::ULONG:{
>   //   typedef unsigned long InputComponentType;
>   //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
> argv);
>   // }
>   //   break;
>   // case itk::ImageIOBase::LONG:{
>   //   typedef long InputComponentType;
>   //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
> argv);
>   // }
>   //   break;
>   // case itk::ImageIOBase::FLOAT:{
>   //   typedef float InputComponentType;
>   //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
> argv);
>   // }
>   //   break;
>   // case itk::ImageIOBase::DOUBLE:{
>   //   typedef double InputComponentType;
>   //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
> argv);
>   // }
>   // break;
>   case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
>   default:
>     std::cout << "unknown component type" << std::endl;
>     break;
>   }//switch
> }
>
> template<typename InputComponentType>
> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t
> dimensionType, int argc, char *argv[]){
>
>
> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#abd189f096c2a1b3ea559bc3e4849f658
>     //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00099
>     //IOPixelType:: UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR,
> POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D,
> COMPLEX, FIXEDARRAY, MATRIX
>
>   switch (pixelType){
>   case itk::ImageIOBase::SCALAR:{
>     typedef InputComponentType InputPixelType;
>     //typedef itk::SCALARPixel<InputComponentType> InputPixelType;
>     dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
> argv);
>   }
>     break;
>   // case itk::ImageIOBase::RGB:{
>   //   typedef itk::RGBPixel<InputComponentType> InputPixelType;
>   //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
> argv);
>   // }
>   //   break;
>   // case itk::ImageIOBase::RGBA:{
>   //   typedef itk::RGBAPixel<InputComponentType> InputPixelType;
>   //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
> argv);
>   // }
>   //   break;
>   // case itk::ImageIOBase::VECTOR:{
>   //   //typedef itk::VECTORPixel<InputComponentType> InputPixelType; //does
> not work!
>   //   typedef itk::VariableLengthVector<InputComponentType> InputPixelType;
>   //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
> argv);
>   // }
>   //   break;
>   case itk::ImageIOBase::UNKNOWNPIXELTYPE:
>   default:
>     std::cout << "unknown pixel type" << std::endl;
>     break;
>   }//switch
> }
>
>
> template<typename InputComponentType, typename InputPixelType>
> void dispatch_D(size_t dimensionType, int argc, char *argv[]){
>   switch (dimensionType){
>   // case 1:
>   //   DoIt<InputComponentType, InputPixelType, 1>(argc, argv);
>   //   break;
>   // case 2:
>   //   DoIt<InputComponentType, InputPixelType, 2>(argc, argv);
>   //   break;
>   case 3:
>     DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>     break;
>   case 4:
>     DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>     break;
>   case 5:
>     DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>     break;
>   default:
>     std::cout << "Images of dimension " << dimensionType << " are not
> supported!" << std::endl;
>     break;
>   }
> }
>
>
>
> ////from
> http://itk-users.7.n7.nabble.com/Pad-image-with-0-but-keep-its-type-what-ever-it-is-td27442.html
> //namespace itk{
>   // Description:
>   // Get the PixelType and ComponentType from fileName
>
> void GetImageType (std::string fileName,
>     itk::ImageIOBase::IOPixelType &pixelType,
>     itk::ImageIOBase::IOComponentType &componentType,
>     size_t &dimensionType
>     //ImageIOBase::IODimensionType &dimensionType
>     ){
>     typedef itk::Image<unsigned char, 3> ImageType;
>     itk::ImageFileReader<ImageType>::Pointer imageReader=
> itk::ImageFileReader<ImageType>::New();
>     imageReader->SetFileName(fileName.c_str());
>     imageReader->UpdateOutputInformation();
>
>     pixelType = imageReader->GetImageIO()->GetPixelType();
>     componentType = imageReader->GetImageIO()->GetComponentType();
>     dimensionType= imageReader->GetImageIO()->GetNumberOfDimensions();
>
>     //std::cerr << "Pixel Type is " <<
> imageReader->GetImageIO()->GetComponentTypeAsString(pixelType) << std::endl;
>     std::cerr << "component type is: " <<
> imageReader->GetImageIO()->GetComponentTypeAsString(componentType) <<
> std::endl;
>     std::cerr << "numDimensions: " << dimensionType << std::endl;
>     std::cerr << "component size: " <<
> imageReader->GetImageIO()->GetComponentSize() << std::endl;
>     std::cerr << "pixel type (string): " <<
> imageReader->GetImageIO()->GetPixelTypeAsString(imageReader->GetImageIO()->GetPixelType())
> << std::endl;
>     std::cerr << "pixel type: " << pixelType << std::endl <<
> "_________________________"  << std::endl << std::endl;
>
>
>     }
>
>
>
> int main(int argc, char *argv[]){
>     if ( argc != 3 )
>         {
>         std::cerr << "Missing Parameters: "
>                   << argv[0]
>                   << " Input_Image"
>                   << " isoValue"
>                   << std::endl;
>
>         return EXIT_FAILURE;
>         }
>
>     std::string ifn = argv[1];
>     // std::string ofn = argv[2];
>     // int compress= atoi(argv[3]);
>
>     itk::ImageIOBase::IOPixelType pixelType;
>     typename itk::ImageIOBase::IOComponentType componentType;
>     //itk::ImageIOBase::IOComponentType componentType1;
>     //itk::ImageIOBase::IODimensionType dimensionType1;
>     size_t dimensionType;
>
>
>     try
>         {
>         GetImageType(argv[1], pixelType, componentType, dimensionType);
>
>         dispatch_cT(componentType, pixelType, dimensionType, argc, argv);
>         }//try
>     catch( itk::ExceptionObject &excep)
>         {
>         std::cerr << argv[0] << ": exception caught !" << std::endl;
>         std::cerr << excep << std::endl;
>         return EXIT_FAILURE;
>         }
>
>     return EXIT_SUCCESS;
>
>     }
>
>
>
>
>
>
>
>
>
>
> On 08/06/14 15:51, Luis Ibanez wrote:
>>
>>
>> Roman,
>>
>>
>> Could you please share with the list an example
>> of a program where you are observing this behavior ?
>>
>> In particular, we would like to see if this is occurring with
>> Image filters, or rather with other types of ITK objects.
>>
>>
>>
>> The itk::Image does listen to the (potential) memory allocation messages
>> (that is, the bad_alloc exception).
>>
>>
>>
>> The itk::Image class uses a helper class to store the pixel data.
>>
>>
>>
>> This helper is the:
>>
>> itk::ImportImageContainer
>>
>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.h
>>
>>
>>
>>
>> and its memory allocation is typically done in the AllocateElements()
>> function
>> in line:
>>
>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.hxx#L173
>>
>> the code looks like
>>
>>    TElement *data;
>>
>>    try
>>      {
>>      if ( UseDefaultConstructor )
>>        {
>>        data = new TElement[size](); //POD types initialized to 0, others
>> use
>> default constructor.
>>        }
>>      else
>>        {
>>        data = new TElement[size]; //Faster but uninitialized
>>        }
>>      }
>>    catch ( ... )
>>      {
>>      data = ITK_NULLPTR;
>>      }
>>    if ( !data )
>>      {
>>      // We cannot construct an error string here because we may be out
>>      // of memory.  Do not use the exception macro.
>>      throw MemoryAllocationError(__FILE__, __LINE__,
>>                                  "Failed to allocate memory for image.",
>>                                  ITK_LOCATION);
>>      }
>>    return data;
>>
>>
>>
>> As you can see, the case of exceptions is managed in that function.
>>
>>
>> Here is an example of a test program demonstrating that ITK image
>> will throw exceptions when allocating memory beyond limits.
>>
>>
>> #include "itkImage.h"
>> #include <iostream>
>>
>> int main(int argc, char * argv[] )
>> {
>>    if( argc < 2 )
>>      {
>>      std::cerr << "Missing arguments" << std::endl;
>>      return 1;
>>      }
>>
>>    typedef itk::Image< unsigned short, 3 > ImageType;
>>
>>    ImageType::Pointer image = ImageType::New();
>>
>>    ImageType::RegionType region;
>>    ImageType::SizeType size;
>>
>>    size_t side = atoi( argv[1] );
>>
>>    size[0] = side;
>>    size[1] = side;
>>    size[2] = side;
>>
>>    region.SetSize( size );
>>
>>    image->SetRegions( region );
>>
>>    try
>>      {
>>      image->Allocate();
>>      }
>>    catch( std::exception & excp )
>>      {
>>      std::cerr << excp.what() << std::endl;
>>      return 1;
>>      }
>>
>>    std::cout << "ITK Hello World !" << std::endl;
>>
>>    return 0;
>> }
>>
>>
>> and what happens when executing in an Ubuntu Linux machine with 32GB or
>> RAM
>>
>>
>> $ ./HelloWorld  1000
>> ITK Hello World !
>>
>>
>> $ ./HelloWorld  1000000
>>
>> /home/ibanez/src/ITK/Modules/Core/Common/include/itkImportImageContainer.hxx:199:
>> Failed to allocate memory for image.
>>
>>
>>
>>
>> Please share with the list a minimal example of the problem you are
>> observing,
>> and in this way we will be able to help track the issue.
>>
>>
>>     Thanks
>>
>>
>>         Luis
>>
>>
>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>
> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
>
> Tel. +49 511 532-9574
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Mon Jul 14 21:02:41 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 14 Jul 2014 21:02:41 -0400
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
Message-ID: <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>

Hi Roy,

Does ccalling LoadPrivateTagsOn() [1] or LoadSequencesOn() [2] improve
the result?

Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a26ea3d5e85c0e6a7a614cbfbc05c4478

[2] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a7e81a44773f7daf85c6523866312372e

On Mon, Jul 14, 2014 at 8:19 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi,
>
> I'm wondering if there is a procedure for adding a dicom dictionary to those
> that are used by the GDCMImageIO, or a way to parse a private field by
> furnishing the pertinent info to the right method.  I'm trying to access the
> field 0119,1030, which is pretty much a 3d version of
> ImageOrientationPatient.  I have no problem seeing the field in a dcmdump of
> an image that contains the field, but am having trouble getting my program
> to handle the field properly.  Here's what a dcmdump of the field looks
> like:
>
> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i imageor
> (0020,0037) DS [-1\-0\0\-0\-1\0]                        #  16, 6
> ImageOrientationPatient
> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i 0119,1030
> (0119,1030) DS [-1\-0\0\-0\-1\0\0\0\1]                  #  22, 9 Unknown Tag
> & Data
> cbl-mbp-3369:Release rharnish$
>
> This is a section of code that tires to parse the field:
>
>     std::string tagkey = "0119|1030";
> //    std::string tagkey = "0020|0037";
>     std::string labelId;
>     std::string value;
>
>
>     if( gdcmImageIO->GetValueFromTag(tagkey, value) )
>     {
>         std::cout << tagkey << ":  ";
>         std::cout << value << std::endl;
>     }
>
> Here's the output with     std::string tagkey = "0119|1030";:
>
> 0119|1030:  LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==
>
>
> Here's the output with     std::string tagkey = "0020|0037";
>
> 0020|0037:  -1\-0\0\-0\-1\0
>
> Any suggestions would be much appreciated.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From matt.mccormick at kitware.com  Mon Jul 14 21:18:46 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 14 Jul 2014 21:18:46 -0400
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>
Message-ID: <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>

Hi Roy,

Does calling GetLabelFromTag [1] return true?

Thanks,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#adad2642a7dab4a896a8bf6afea6ff205

On Mon, Jul 14, 2014 at 9:08 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> Thanks for getting back with me so quickly!  I just tried turning both of those on, but I get the same result.
>
> Roy
>
>
> ________________________________________
> From: Matt McCormick [matt.mccormick at kitware.com]
> Sent: Monday, July 14, 2014 6:02 PM
> To: Harnish, Roy
> Cc: insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] (no subject)
>
> Hi Roy,
>
> Does ccalling LoadPrivateTagsOn() [1] or LoadSequencesOn() [2] improve
> the result?
>
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a26ea3d5e85c0e6a7a614cbfbc05c4478
>
> [2] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a7e81a44773f7daf85c6523866312372e
>
> On Mon, Jul 14, 2014 at 8:19 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
>> Hi,
>>
>> I'm wondering if there is a procedure for adding a dicom dictionary to those
>> that are used by the GDCMImageIO, or a way to parse a private field by
>> furnishing the pertinent info to the right method.  I'm trying to access the
>> field 0119,1030, which is pretty much a 3d version of
>> ImageOrientationPatient.  I have no problem seeing the field in a dcmdump of
>> an image that contains the field, but am having trouble getting my program
>> to handle the field properly.  Here's what a dcmdump of the field looks
>> like:
>>
>> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i imageor
>> (0020,0037) DS [-1\-0\0\-0\-1\0]                        #  16, 6
>> ImageOrientationPatient
>> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i 0119,1030
>> (0119,1030) DS [-1\-0\0\-0\-1\0\0\0\1]                  #  22, 9 Unknown Tag
>> & Data
>> cbl-mbp-3369:Release rharnish$
>>
>> This is a section of code that tires to parse the field:
>>
>>     std::string tagkey = "0119|1030";
>> //    std::string tagkey = "0020|0037";
>>     std::string labelId;
>>     std::string value;
>>
>>
>>     if( gdcmImageIO->GetValueFromTag(tagkey, value) )
>>     {
>>         std::cout << tagkey << ":  ";
>>         std::cout << value << std::endl;
>>     }
>>
>> Here's the output with     std::string tagkey = "0119|1030";:
>>
>> 0119|1030:  LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==
>>
>>
>> Here's the output with     std::string tagkey = "0020|0037";
>>
>> 0020|0037:  -1\-0\0\-0\-1\0
>>
>> Any suggestions would be much appreciated.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>

From Roy.Harnish at ucsf.edu  Mon Jul 14 21:27:21 2014
From: Roy.Harnish at ucsf.edu (Harnish, Roy)
Date: Tue, 15 Jul 2014 01:27:21 +0000
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>,
 <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>
Message-ID: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>

Hi Matt,

Here's what I'm running:

    std::string tagkey = "0119|1030";
    std::string labelId;
    std::string value;
    std::cout << "itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): ";
    std::cout << itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ) << std::endl;
    std::cout << "labelId: " << labelId << std::endl;

And here's the output

itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): 0
labelId: 

Roy

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, July 14, 2014 6:18 PM
To: Harnish, Roy; insight-users at itk.org
Subject: Re: [ITK] [ITK-users] (no subject)

Hi Roy,

Does calling GetLabelFromTag [1] return true?

Thanks,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#adad2642a7dab4a896a8bf6afea6ff205

On Mon, Jul 14, 2014 at 9:08 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> Thanks for getting back with me so quickly!  I just tried turning both of those on, but I get the same result.
>
> Roy
>
>
> ________________________________________
> From: Matt McCormick [matt.mccormick at kitware.com]
> Sent: Monday, July 14, 2014 6:02 PM
> To: Harnish, Roy
> Cc: insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] (no subject)
>
> Hi Roy,
>
> Does ccalling LoadPrivateTagsOn() [1] or LoadSequencesOn() [2] improve
> the result?
>
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a26ea3d5e85c0e6a7a614cbfbc05c4478
>
> [2] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a7e81a44773f7daf85c6523866312372e
>
> On Mon, Jul 14, 2014 at 8:19 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
>> Hi,
>>
>> I'm wondering if there is a procedure for adding a dicom dictionary to those
>> that are used by the GDCMImageIO, or a way to parse a private field by
>> furnishing the pertinent info to the right method.  I'm trying to access the
>> field 0119,1030, which is pretty much a 3d version of
>> ImageOrientationPatient.  I have no problem seeing the field in a dcmdump of
>> an image that contains the field, but am having trouble getting my program
>> to handle the field properly.  Here's what a dcmdump of the field looks
>> like:
>>
>> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i imageor
>> (0020,0037) DS [-1\-0\0\-0\-1\0]                        #  16, 6
>> ImageOrientationPatient
>> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i 0119,1030
>> (0119,1030) DS [-1\-0\0\-0\-1\0\0\0\1]                  #  22, 9 Unknown Tag
>> & Data
>> cbl-mbp-3369:Release rharnish$
>>
>> This is a section of code that tires to parse the field:
>>
>>     std::string tagkey = "0119|1030";
>> //    std::string tagkey = "0020|0037";
>>     std::string labelId;
>>     std::string value;
>>
>>
>>     if( gdcmImageIO->GetValueFromTag(tagkey, value) )
>>     {
>>         std::cout << tagkey << ":  ";
>>         std::cout << value << std::endl;
>>     }
>>
>> Here's the output with     std::string tagkey = "0119|1030";:
>>
>> 0119|1030:  LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==
>>
>>
>> Here's the output with     std::string tagkey = "0020|0037";
>>
>> 0020|0037:  -1\-0\0\-0\-1\0
>>
>> Any suggestions would be much appreciated.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>


From Roy.Harnish at ucsf.edu  Mon Jul 14 21:31:22 2014
From: Roy.Harnish at ucsf.edu (Harnish, Roy)
Date: Tue, 15 Jul 2014 01:31:22 +0000
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>,
 <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>,
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>
Message-ID: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6AC@ex04.net.ucsf.edu>

Correction:

Here's what I'm running:

    std::string tagkey = "0119|1030";
    std::string labelId;
    std::string value;
    std::cout << "gdcmImageIO->GetValueFromTag( tagkey, labelId ): ";
    std::cout << gdcmImageIO->GetValueFromTag( tagkey, labelId ) << std::endl;
    std::cout << "labelId: " << labelId << std::endl;

And here's the output:

gdcmImageIO->GetValueFromTag( tagkey, labelId ): 1
labelId: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==


________________________________________
From: Insight-users [insight-users-bounces at itk.org] on behalf of Harnish, Roy [Roy.Harnish at ucsf.edu]
Sent: Monday, July 14, 2014 6:27 PM
To: Matt McCormick
Cc: insight-users at itk.org
Subject: Re: [ITK-users] [ITK]  (no subject)

Hi Matt,

Here's what I'm running:

    std::string tagkey = "0119|1030";
    std::string labelId;
    std::string value;
    std::cout << "itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): ";
    std::cout << itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ) << std::endl;
    std::cout << "labelId: " << labelId << std::endl;

And here's the output

itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): 0
labelId:

Roy

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, July 14, 2014 6:18 PM
To: Harnish, Roy; insight-users at itk.org
Subject: Re: [ITK] [ITK-users] (no subject)

Hi Roy,

Does calling GetLabelFromTag [1] return true?

Thanks,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#adad2642a7dab4a896a8bf6afea6ff205

On Mon, Jul 14, 2014 at 9:08 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> Thanks for getting back with me so quickly!  I just tried turning both of those on, but I get the same result.
>
> Roy
>
>
> ________________________________________
> From: Matt McCormick [matt.mccormick at kitware.com]
> Sent: Monday, July 14, 2014 6:02 PM
> To: Harnish, Roy
> Cc: insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] (no subject)
>
> Hi Roy,
>
> Does ccalling LoadPrivateTagsOn() [1] or LoadSequencesOn() [2] improve
> the result?
>
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a26ea3d5e85c0e6a7a614cbfbc05c4478
>
> [2] http://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html#a7e81a44773f7daf85c6523866312372e
>
> On Mon, Jul 14, 2014 at 8:19 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
>> Hi,
>>
>> I'm wondering if there is a procedure for adding a dicom dictionary to those
>> that are used by the GDCMImageIO, or a way to parse a private field by
>> furnishing the pertinent info to the right method.  I'm trying to access the
>> field 0119,1030, which is pretty much a 3d version of
>> ImageOrientationPatient.  I have no problem seeing the field in a dcmdump of
>> an image that contains the field, but am having trouble getting my program
>> to handle the field properly.  Here's what a dcmdump of the field looks
>> like:
>>
>> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i imageor
>> (0020,0037) DS [-1\-0\0\-0\-1\0]                        #  16, 6
>> ImageOrientationPatient
>> cbl-mbp-3369:Release rharnish$ dcmdump dce.dcm | grep -i 0119,1030
>> (0119,1030) DS [-1\-0\0\-0\-1\0\0\0\1]                  #  22, 9 Unknown Tag
>> & Data
>> cbl-mbp-3369:Release rharnish$
>>
>> This is a section of code that tires to parse the field:
>>
>>     std::string tagkey = "0119|1030";
>> //    std::string tagkey = "0020|0037";
>>     std::string labelId;
>>     std::string value;
>>
>>
>>     if( gdcmImageIO->GetValueFromTag(tagkey, value) )
>>     {
>>         std::cout << tagkey << ":  ";
>>         std::cout << value << std::endl;
>>     }
>>
>> Here's the output with     std::string tagkey = "0119|1030";:
>>
>> 0119|1030:  LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==
>>
>>
>> Here's the output with     std::string tagkey = "0020|0037";
>>
>> 0020|0037:  -1\-0\0\-0\-1\0
>>
>> Any suggestions would be much appreciated.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users


From matt.mccormick at kitware.com  Mon Jul 14 21:39:41 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 14 Jul 2014 21:39:41 -0400
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>
 <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>
Message-ID: <CALzTN-SEWS8Ei6kYK3Hmn-3ZRbAN9Hi6No_DSU=owmaLuxw8Xw@mail.gmail.com>

On Mon, Jul 14, 2014 at 9:27 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> Here's what I'm running:
>
>     std::string tagkey = "0119|1030";
>     std::string labelId;
>     std::string value;
>     std::cout << "itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): ";
>     std::cout << itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ) << std::endl;
>     std::cout << "labelId: " << labelId << std::endl;
>
> And here's the output
>
> itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): 0
> labelId:
>

This means the tag is not found.  For more information, try [1]

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/IO_2DicomImageReadPrintTags_8cxx-example.html#_a2

From Roy.Harnish at ucsf.edu  Mon Jul 14 21:48:48 2014
From: Roy.Harnish at ucsf.edu (Harnish, Roy)
Date: Tue, 15 Jul 2014 01:48:48 +0000
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <CALzTN-SEWS8Ei6kYK3Hmn-3ZRbAN9Hi6No_DSU=owmaLuxw8Xw@mail.gmail.com>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>
 <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>,
 <CALzTN-SEWS8Ei6kYK3Hmn-3ZRbAN9Hi6No_DSU=owmaLuxw8Xw@mail.gmail.com>
Message-ID: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6C9@ex04.net.ucsf.edu>

Hi Matt,

I wasn't calling GetLabelFromTagWith the instance of GDCMImageIO that had been used to read the image.  Here's what I get when I do that:

RUNNING:

    std::string tagkey = "0119|1030";
    std::string labelId;
    std::string value;
    std::cout << "gdcmImageIO->GetValueFromTag( tagkey, labelId ): ";
    std::cout << gdcmImageIO->GetValueFromTag( tagkey, labelId ) << std::endl;
    std::cout << "labelId: " << labelId << std::endl;

OUTPUT:

gdcmImageIO->GetValueFromTag( tagkey, labelId ): 1
labelId: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==

So it looks like there is something returned by get value from tag.

Thanks for taking a look.

Roy

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, July 14, 2014 6:39 PM
To: Harnish, Roy
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] (no subject)

On Mon, Jul 14, 2014 at 9:27 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> Here's what I'm running:
>
>     std::string tagkey = "0119|1030";
>     std::string labelId;
>     std::string value;
>     std::cout << "itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): ";
>     std::cout << itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ) << std::endl;
>     std::cout << "labelId: " << labelId << std::endl;
>
> And here's the output
>
> itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): 0
> labelId:
>

This means the tag is not found.  For more information, try [1]

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/IO_2DicomImageReadPrintTags_8cxx-example.html#_a2


From Roy.Harnish at ucsf.edu  Mon Jul 14 21:54:03 2014
From: Roy.Harnish at ucsf.edu (Harnish, Roy)
Date: Tue, 15 Jul 2014 01:54:03 +0000
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6C9@ex04.net.ucsf.edu>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>
 <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>,
 <CALzTN-SEWS8Ei6kYK3Hmn-3ZRbAN9Hi6No_DSU=owmaLuxw8Xw@mail.gmail.com>,
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6C9@ex04.net.ucsf.edu>
Message-ID: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6E5@ex04.net.ucsf.edu>

One more iteration here with calls to both GetValueFromTag and GetLabelFromTag

CODE:

    std::string tagkey = "0119|1030";
    std::string labelId;
    std::string value;
    
    std::cout << "gdcmImageIO->GetValueFromTag( tagkey, labelId ): ";
    std::cout << gdcmImageIO->GetValueFromTag( tagkey, value ) << std::endl;
    std::cout << "value: " << value << std::endl;
    
    std::cout << "gdcmImageIO->GetLabelFromTag( tagkey, labelId ): ";
    std::cout << gdcmImageIO->GetLabelFromTag( tagkey, labelId ) << std::endl;
    std::cout << "labelId: " << labelId << std::endl;

OUTPUT:

gdcmImageIO->GetValueFromTag( tagkey, labelId ): 1
value: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==
gdcmImageIO->GetLabelFromTag( tagkey, labelId ): 0
labelId: 


________________________________________
From: Harnish, Roy
Sent: Monday, July 14, 2014 6:48 PM
To: Matt McCormick
Cc: insight-users at itk.org
Subject: RE: [ITK] [ITK-users] (no subject)

Hi Matt,

I wasn't calling GetLabelFromTagWith the instance of GDCMImageIO that had been used to read the image.  Here's what I get when I do that:

RUNNING:

    std::string tagkey = "0119|1030";
    std::string labelId;
    std::string value;
    std::cout << "gdcmImageIO->GetValueFromTag( tagkey, labelId ): ";
    std::cout << gdcmImageIO->GetValueFromTag( tagkey, labelId ) << std::endl;
    std::cout << "labelId: " << labelId << std::endl;

OUTPUT:

gdcmImageIO->GetValueFromTag( tagkey, labelId ): 1
labelId: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==

So it looks like there is something returned by get value from tag.

Thanks for taking a look.

Roy

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, July 14, 2014 6:39 PM
To: Harnish, Roy
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] (no subject)

On Mon, Jul 14, 2014 at 9:27 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> Here's what I'm running:
>
>     std::string tagkey = "0119|1030";
>     std::string labelId;
>     std::string value;
>     std::cout << "itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): ";
>     std::cout << itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ) << std::endl;
>     std::cout << "labelId: " << labelId << std::endl;
>
> And here's the output
>
> itk::GDCMImageIO::GetLabelFromTag( tagkey, labelId ): 0
> labelId:
>

This means the tag is not found.  For more information, try [1]

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/IO_2DicomImageReadPrintTags_8cxx-example.html#_a2


From matt.mccormick at kitware.com  Mon Jul 14 22:01:30 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 14 Jul 2014 22:01:30 -0400
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6C9@ex04.net.ucsf.edu>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>
 <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>
 <CALzTN-SEWS8Ei6kYK3Hmn-3ZRbAN9Hi6No_DSU=owmaLuxw8Xw@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6C9@ex04.net.ucsf.edu>
Message-ID: <CALzTN-R8pe_7b_jMYkZNU8sRvQHbWqrqWL8o7x_rnBhMnjAxKg@mail.gmail.com>

On Mon, Jul 14, 2014 at 9:48 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> I wasn't calling GetLabelFromTagWith the instance of GDCMImageIO that had been used to read the image.

Re-using the gdcmImageIO that was used to read the image will ensure
the MetaDataDictionary is populated.  Also, turning on the option to
read private tags before reading the image is a good idea.

HTH,
Matt

From Roy.Harnish at ucsf.edu  Mon Jul 14 22:19:44 2014
From: Roy.Harnish at ucsf.edu (Harnish, Roy)
Date: Tue, 15 Jul 2014 02:19:44 +0000
Subject: [ITK-users] [ITK]  (no subject)
In-Reply-To: <CALzTN-R8pe_7b_jMYkZNU8sRvQHbWqrqWL8o7x_rnBhMnjAxKg@mail.gmail.com>
References: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA663@ex04.net.ucsf.edu>
 <CALzTN-SRzA7oMj9Uf1enGyujw3RwvZfsxyqHa2AAXMfzNtauoQ@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA688@ex04.net.ucsf.edu>
 <CALzTN-RfQuh8hZGrQi8om_WDazP54b_aGMDC2_BQGSDZR70BGA@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA69C@ex04.net.ucsf.edu>
 <CALzTN-SEWS8Ei6kYK3Hmn-3ZRbAN9Hi6No_DSU=owmaLuxw8Xw@mail.gmail.com>
 <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6C9@ex04.net.ucsf.edu>,
 <CALzTN-R8pe_7b_jMYkZNU8sRvQHbWqrqWL8o7x_rnBhMnjAxKg@mail.gmail.com>
Message-ID: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA6FC@ex04.net.ucsf.edu>

Thanks. I'll continue to work with the same gdcmImageIO, and will use the read private tags option as well. In this particular case, I don't think there is a tag for the group and element I am trying to access (0119,1030). If I grep for both 0119 and 1030 in InsightToolkit-4.5.2/Modules/ThirdParty/GDCM/src/gdcm, I don't see anything (other than an entry I tried putting in privatedicts.xml):

cbl-mbp-3369:gdcm rharnish$ pwd
/Users/Shared/OSIAV/ITK/InsightToolkit-4.5.2/Modules/ThirdParty/GDCM/src/gdcm
cbl-mbp-3369:gdcm rharnish$ grep -R 0119 . | grep 1030
./Source/DataDictionary/privatedicts.xml:  <entry owner="RoyHarnish" group="0119" element="1030" vr="DS" vm="9" name="DmiDirectionCosines"/>
cbl-mbp-3369:gdcm rharnish$ 

Roy

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, July 14, 2014 7:01 PM
To: Harnish, Roy
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] (no subject)

On Mon, Jul 14, 2014 at 9:48 PM, Harnish, Roy <Roy.Harnish at ucsf.edu> wrote:
> Hi Matt,
>
> I wasn't calling GetLabelFromTagWith the instance of GDCMImageIO that had been used to read the image.

Re-using the gdcmImageIO that was used to read the image will ensure
the MetaDataDictionary is populated.  Also, turning on the option to
read private tags before reading the image is a good idea.

HTH,
Matt


From iyas.hamdan at gmail.com  Tue Jul 15 05:16:09 2014
From: iyas.hamdan at gmail.com (Iyas Hamdan)
Date: Tue, 15 Jul 2014 11:16:09 +0200
Subject: [ITK-users] 3D registration problem
Message-ID: <CANH4YVhid+KmPy3Dg-EFf9VyOta_EzoD2JL4qKuPS6sh2iszcA@mail.gmail.com>

Hello itk users,

I'm working on 3D image registration, currently I'm trying to register a CT
volume to an MRI volume ( the two volumes have different sizes concerning
the number of slices used to construct the 3D volume).

I'm doing an affine registration using the mutual information as a metric,
and I'm having problems registering those two volumes.

What I thiink the problem is, I have a different field of view between both
volumes, so when I try to register the whole CT volume to the MRI one  the
registration falis. However, when I deleted a dozen of slices from the CT
volume ( so that I had the same field of view in both volumes) it works
just fine and I was able to register the volumes.


And by "the registration failed" I meant it worked with no errors but the
result was really bad! and that the registered volume was nothing like the
fixed one, so if I try to find the difference between each two
corresponding slices for example , they were not aligned at all!

Is that normal that the registration doesnt work when I have a different
field of view in each volume ? or should it deform one volume so that it
corresponds to the other one even if they had two different fields of view
?

Any help would be really appreciated,

Thanks in advance,

Iyas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140715/3dc45fe0/attachment.html>

From iyas.hamdan at gmail.com  Tue Jul 15 05:26:17 2014
From: iyas.hamdan at gmail.com (Iyas Hamdan)
Date: Tue, 15 Jul 2014 11:26:17 +0200
Subject: [ITK-users] 3D registration problem
Message-ID: <CANH4YVgmoJ-qGHD5qphkdEZW3t74d0TzF9coNKREXT3zkEXydg@mail.gmail.com>

Hello itk users,

I'm working on 3D image registration, currently I'm trying to register a CT
volume to an MRI volume ( the two volumes have different sizes concerning
the number of slices used to construct the 3D volume).

I'm doing an affine registration using the mutual information as a metric,
and I'm having problems registering those two volumes.

What I thiink the problem is, I have a different field of view between both
volumes, so when I try to register the whole CT volume to the MRI one  the
registration falis. However, when I deleted a dozen of slices from the CT
volume ( so that I had the same field of view in both volumes) it works
just fine and I was able to register the volumes.


And by "the registration failed" I meant it worked with no errors but the
result was really bad! and that the registered volume was nothing like the
fixed one, so if I try to find the difference between each two
corresponding slices for example , they were not aligned at all!

Is that normal that the registration doesnt work when I have a different
field of view in each volume ? or should it deform one volume so that it
corresponds to the other one even if they had two different fields of view
?

Any help would be really appreciated,

Thanks in advance,

Iyas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140715/78b3e23c/attachment.html>

From grothausmann.roman at mh-hannover.de  Tue Jul 15 06:51:31 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Tue, 15 Jul 2014 12:51:31 +0200
Subject: [ITK-users] itkMeanImageFilter on RGB (how to adjust example
 MedianFilteringOfAnRGBImage?)
In-Reply-To: <CADZJ4hN=DDumD9B4-C9C4-2XThj-MXUHMf_AmrqRpZmOqmYuGw@mail.gmail.com>
References: <53BFD040.8070009@mh-hannover.de>	<CADZJ4hNWVyp-QLcV-JzxHm0acaka8pBoSp+Adr_ZpP5+8k4Z6Q@mail.gmail.com>
 <CADZJ4hN=DDumD9B4-C9C4-2XThj-MXUHMf_AmrqRpZmOqmYuGw@mail.gmail.com>
Message-ID: <53C507B3.7070900@mh-hannover.de>

Many thanks Bill, both hints are very helpful.

On 12/07/14 15:18, Bill Lorensen wrote:
> You are better off using vector pixels versus rgb pixels. No
> overriding necessary. You should be able to modify your example by
> looking at this one:
>
> On Fri, Jul 11, 2014 at 11:26 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> You need to define a cast operator. SOmething like:
>>    operator TComponent()
>>    {
>>      return this->GetLuminance();
>>    }
>>
>> But I don't think you will get the result you want.
>>
>> Bill
>>
>> On Fri, Jul 11, 2014 at 7:53 AM, Dr. Roman Grothausmann
>> <grothausmann.roman at mh-hannover.de> wrote:
>>> Dear mailing list members,
>>>
>>>
>>> How would I need to extend/modify the example for
>>> MedianFilteringOfAnRGBImage
>>>
>>> http://itk.org/ITKExamples/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.html
>>>
>>> to work with itkMeanImageFilter?
>>>
>>> I modified myRGBPixel like this:
>>>
>>> namespace itk{
>>>    template<typename TComponent>
>>>    class myRGBPixel : public RGBPixel<TComponent>{
>>>    public:
>>>      typedef myRGBPixel     Self;
>>>      typedef RGBPixel<TComponent> Superclass;
>>>
>>>      myRGBPixel():Superclass() {} //avoid candidate expects 1 argument, 0
>>> provided
>>>      myRGBPixel(int i):Superclass(i) {} //avoid candidate expects 0
>>> arguments, 1 provided
>>>
>>>      using RGBPixel<TComponent>::operator=;
>>>
>>>      bool operator<=(const Self & r) const{
>>>        return (this->GetLuminance() <= r.GetLuminance());
>>>      }
>>>      bool operator>=(const Self & r) const{
>>>        return (this->GetLuminance() >= r.GetLuminance());
>>>      }
>>>      bool operator<(const Self & r) const{
>>>        return (this->GetLuminance() < r.GetLuminance());
>>>      }
>>>      bool operator>(const Self & r) const{
>>>        return (this->GetLuminance() > r.GetLuminance());
>>>      }
>>>    };
>>> }
>>>
>>>
>>> However gcc still yields this error:
>>>
>>>
>>> In file included from
>>> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.h:115:0,
>>>                   from /net/home/ghky/itk/simple/mean-CPU_02.cxx:8:
>>> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx: In instantiation of
>>> ?void itk::MeanImageFilter<TInputImage,
>>> TOutputImage>::ThreadedGenerateData(const OutputImageRegionType&,
>>> itk::ThreadIdType) [with TInputImage = itk::Image<itk::myRGBPixel<unsigned
>>> char>, 3u>; TOutputImage = itk::Image<itk::myRGBPixel<unsigned char>, 3u>;
>>> itk::MeanImageFilter<TInputImage, TOutputImage>::OutputImageRegionType =
>>> itk::ImageRegion<3u>; itk::ThreadIdType = unsigned int]?:
>>> /net/home/ghky/itk/simple/mean-CPU_02.cxx:335:5:   required from here
>>> /opt/itk-4.5.1/include/ITK-4.5/itkMeanImageFilter.hxx:81:9: error: invalid
>>> static_cast from type
>>> ?itk::ConstNeighborhoodIterator<itk::Image<itk::myRGBPixel<unsigned char>,
>>> 3u>,
>>> itk::ZeroFluxNeumannBoundaryCondition<itk::Image<itk::myRGBPixel<unsigned
>>> char>, 3u>, itk::Image<itk::myRGBPixel<unsigned char>, 3u> > >::PixelType
>>> {aka itk::myRGBPixel<unsigned char>}? to type
>>> ?itk::MeanImageFilter<itk::Image<itk::myRGBPixel<unsigned char>, 3u>,
>>> itk::Image<itk::myRGBPixel<unsigned char>, 3u> >::InputRealType {aka
>>> double}?
>>> make[3]: *** [CMakeFiles/mean-CPU_02.dir/mean-CPU_02.cxx.o] Error 1
>>> make[2]: *** [CMakeFiles/mean-CPU_02.dir/all] Error 2
>>> make[1]: *** [CMakeFiles/mean-CPU_02.dir/rule] Error 2
>>> make: *** [mean-CPU_02] Error 2
>>>
>>>
>>> What am I missing in myRGBPixel?
>>>
>>> Any help or hints are very much appreciated
>>> Roman
>>>
>>> --
>>> Dr. Roman Grothausmann
>>>
>>> Tomographie und Digitale Bildverarbeitung
>>> Tomography and Digital Image Analysis
>>>
>>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>>> Medizinische Hochschule Hannover
>>> Carl-Neuberg-Str. 1
>>> D-30625 Hannover
>>>
>>> Tel. +49 511 532-9574
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

From mpinkert at wisc.edu  Tue Jul 15 12:27:37 2014
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Tue, 15 Jul 2014 09:27:37 -0700 (PDT)
Subject: [ITK-users] Connected Threshold Filter crashes but only for large
 images
Message-ID: <1405441657014-7585907.post@n2.nabble.com>

Hi everyone,

I am working with sets of 3D MRI data from multiple years for my research. 
I am using the connected threshold filter in a pipeline after a binary
thresholding procedure using Otsu segmentation.

The algorithm functions when there are 124 slices in the image, but crashes
with an abort message when there are 248 slices and when there are 156
slices.  

I have tested this with multiple data sets and the pattern holds.  The
strange part is that this still happens even if I resample the number of
slices down to 124, so I really am confused as to what is happening.

Is there any reason why the filter would be crashing for images that are too
large like this, even after being resampled smaller?

Best regards,
Michael Pinkert



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Connected-Threshold-Filter-crashes-but-only-for-large-images-tp7585907.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From Roy.Harnish at ucsf.edu  Tue Jul 15 22:19:03 2014
From: Roy.Harnish at ucsf.edu (Harnish, Roy)
Date: Wed, 16 Jul 2014 02:19:03 +0000
Subject: [ITK-users] [Insight-users] GDCM custom tag dictionary
Message-ID: <F968C6DCE9D2F04CB8519CB3ACF06E9959AFA7A8@ex04.net.ucsf.edu>

Hi,

I'm revisiting the thread below since I'm having trouble getting the DicomImageReadPrintTags.cxx example to use the .dic file I provide. I am trying to correctly interpret the (0119,1030) tag from a dicom file.  The element is very similar to an ImageOrientationPatient, but defines direction cosines for slices in addition to rows and columns. I'm wondering if I should continue trying to specify my own .dic (or is it XML?), of if there is an alternative. Perhaps I could try to parse the output ((0119|1030)  is: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==) as a 9 element DS. Syntax suggestions for that would be much appreciated.

Yours,

Roy


This is a comparison of dcmdumps:

cbl-mbp-3369:data rharnish$ dcmdump dce.dcm | grep 0119,1030
(0119,1030) DS [-1\-0\0\-0\-1\0\0\0\1]                  #  22, 9 Unknown Tag & Data
cbl-mbp-3369:data rharnish$ dcmdump dce.dcm | grep ImageOri
(0020,0037) DS [-1\-0\0\-0\-1\0]                        #  16, 6 ImageOrientationPatient
cbl-mbp-3369:data rharnish$ 


This is the modified version of DicomImageReadPrintTags.cxx I'm using:

#include "itkImageFileReader.h"
#include "itkGDCMImageIO.h"
#include "itkMetaDataObject.h"

#include "gdcmGlobal.h"

int
main (int argc, char* argv[])
{
  if (argc < 2)
    {
      std::cerr << "Usage: " << argv[0] << " DicomFile [user defined dict]" << std::endl;
      return EXIT_FAILURE;
    }

  typedef unsigned short PixelType;
  const unsigned int Dimension = 3;

  typedef itk::Image<PixelType, Dimension> ImageType;

  if (argc == 3)
    {
      // Specify a path where XML dicts can be found (Part 3/4 & 6)
      gdcm::Global::GetInstance ().Prepend (itksys::SystemTools::GetFilenamePath (argv[2]).c_str ());
      // Load them !
      gdcm::Global::GetInstance ().LoadResourcesFiles ();

      std::cout << argv[2] << std::endl;
      std::cout << itksys::SystemTools::GetFilenamePath (argv[2]).c_str () << std::endl;
    }

  typedef itk::ImageFileReader<ImageType> ReaderType;
  ReaderType::Pointer reader = ReaderType::New ();
  typedef itk::GDCMImageIO ImageIOType;
  ImageIOType::Pointer dicomIO = ImageIOType::New ();
  dicomIO->LoadSequencesOn ();
  dicomIO->LoadPrivateTagsOn ();

  reader->SetFileName (argv[1]);
  reader->SetImageIO (dicomIO);

  try
    {
      reader->Update ();
    }
  catch (itk::ExceptionObject &ex)
    {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
    }

  std::cout << "has key: " << dicomIO->GetMetaDataDictionary ().HasKey ("0119|1030") << std::endl;

  typedef itk::MetaDataDictionary DictionaryType;
  const DictionaryType & dictionary = dicomIO->GetMetaDataDictionary ();
  typedef itk::MetaDataObject<std::string> MetaDataStringType;

  DictionaryType::ConstIterator itr = dictionary.Begin ();
  DictionaryType::ConstIterator end = dictionary.End ();

  // try to print value of 0119|1030
  std::string entryId = "0119|1030";
  DictionaryType::ConstIterator tagItr = dictionary.Find (entryId);
  if (tagItr != end)
    {
      MetaDataStringType::ConstPointer entryvalue = dynamic_cast<const MetaDataStringType *> (tagItr->second.GetPointer ());

      if (entryvalue)
	{
	  std::string tagvalue = entryvalue->GetMetaDataObjectValue ();
	  std::cout << "(" << entryId << ") ";
	  std::cout << " is: " << tagvalue.c_str () << std::endl;
	}

    }

  // try to print value of ImageOrientationPatient
  entryId = "0020|0037";
  tagItr = dictionary.Find (entryId);
  if (tagItr != end)
    {
      MetaDataStringType::ConstPointer entryvalue = dynamic_cast<const MetaDataStringType *> (tagItr->second.GetPointer ());

      if (entryvalue)
	{
	  std::string tagvalue = entryvalue->GetMetaDataObjectValue ();
	  std::cout << "(" << entryId << ") ";
	  std::cout << " is: " << tagvalue.c_str () << std::endl;
	}

    }

  return EXIT_SUCCESS;
}


This is the program output:

/Users/rharnish/Projects/itkImageProcessing/io/DicomTags/data/test.dic
/Users/rharnish/Projects/itkImageProcessing/io/DicomTags/data
has key: 1
(0119|1030)  is: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==
(0020|0037)  is: -1\-0\0\-0\-1\0


This is the contents of test.dic:

0119 1030 DS 9 3DDirectionCosines






Angela.Y Wang wrote:
> I am trying to read processed data in dicom file format and would like
> to create a GDCM dictionary for the private tags.  In a previous
> message, it was suggested to create a custom tag dictionary and put it
> in the GDCM search path.  Could somebody please tell me how to go about
> doing this?


Hi Angela,

	I have added an example on how to user dynamically loaded user defined 
DICOM dictionary:

$ cvs ci -m"ENH: Add example on how to use a user defined dict" 

/cvsroot/Insight/Insight/Examples/IO/DicomImageReadPrintTags.cxx,v  <-- 
  DicomImageReadPrintTags.cxx
new revision: 1.16; previous revision: 1.15
/cvsroot/Insight/Insight/Examples/IO/itk.dic,v  <--  itk.dic
initial revision: 1.1


	You should be able to now type in:

$ ./bin/DicomImageReadPrintTags /path/to/012345.002.050 
/path/to/Insight/Examples/IO/itk.dic

First argument is the DICOM file, second (optional) argument is a user 
defined dictionary which should look like:

http://public.kitware.com/cgi-bin/viewcvs.cgi/*checkout*/Examples/IO/itk.dic?rev=1.1&root=Insight

HTH
Mathieu

From grothausmann.roman at mh-hannover.de  Wed Jul 16 09:06:05 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Wed, 16 Jul 2014 15:06:05 +0200
Subject: [ITK-users] [ITK] How to make ITK-binaries NOT ignore kernel
 out of memory messages?
In-Reply-To: <CALzTN-QZzjUdYmREq__vdV1diBZbY3gvZ+zEqZwdT7t7KKTk5Q@mail.gmail.com>
References: <53917A66.2060402@mh-hannover.de>	<CABAUzPrPjJj3h3vtnJs2PBd52PfUxYJXUojyt6V0UUfzUFYhNA@mail.gmail.com>	<53A80327.9050701@mh-hannover.de>
 <CALzTN-QZzjUdYmREq__vdV1diBZbY3gvZ+zEqZwdT7t7KKTk5Q@mail.gmail.com>
Message-ID: <53C678BD.2040908@mh-hannover.de>

Hi Matt,


Many thanks for Your reply. I'll check if ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 
prevents the problems. Although I'd be astonished if it does because 
BinaryMask3DMeshSource seems to use only one core anyway.

Thanks again for Your help
Roman

On 15/07/14 02:55, Matt McCormick wrote:
> Hi Roman,
>
> The CMake configuration variable:
>
>    ITK_COMPUTER_MEMORY_SIZE
>
> is only used to choose which unit tests to run, and has no effect on
> your program.
>
>
> It may be worth a try to run
>
>    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
>
> before starting your program on the server to see the effect.  It is
> possible that too many threads or being spawned or that the amount of
> memory consumed is scaling (poorly) with the number of threads used.
>
> Hope this helps,
> Matt
>
> On Mon, Jun 23, 2014 at 6:36 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>> Dear Luis,
>>
>>
>> Many thanks for Your reply. It took me some time to reproduce the problem,
>> because Your test program works as expected on our server:
>>
>> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 1000
>> ITK Hello World !
>>
>> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 10000
>> /opt/itk-4.5.1/include/ITK-4.5/itkImportImageContainer.hxx:192:
>>
>> Failed to allocate memory for image.
>>
>> One program of mine for which the problem exists is below. The problem
>> occurs when BinaryMask3DMeshSource acquires more memory after running for
>> some minutes. The very strange thing to me is, that the program is killed by
>> the kernel as expected on my desktop PC:
>>
>> ~/itk/simple/build_itk4_pc3G48243/euler-characteristic_01 13-511_EAA_ot.mha
>> 255
>> component type is: unsigned_char
>> numDimensions: 3
>> component size: 1
>> pixel type (string): scalar
>> pixel type: 1
>> _________________________
>>
>> Executing ImageFileReader  done. Took 2.78 seconds.
>> Executing BinaryMask3DMeshSource Killed
>>
>>
>> The header of 13-511_EAA_ot.mha:
>>
>> ObjectType = Image
>> NDims = 3
>> BinaryData = True
>> BinaryDataByteOrderMSB = False
>> CompressedData = True
>> CompressedDataSize = 20474538
>> TransformMatrix = 1 0 0 0 1 0 0 0 1
>> Offset = 0 0 0
>> CenterOfRotation = 0 0 0
>> AnatomicalOrientation = RAI
>> ElementSpacing = 1 1 1
>> DimSize = 998 998 1034
>> ElementType = MET_UCHAR
>> ElementDataFile = LOCAL
>>
>>
>> However on the server it is not terminated when the RAM runs out, instead
>> many processes go nuts that had been mostly sleeping and finally the system
>> does not respond any more at all and a cold start is necessary. The
>> itk-4.5.1 is configured on the server with (see attached
>> CMakeCache_itk-4.5.1.txt):
>>
>> ITK_COMPUTER_MEMORY_SIZE  190
>>
>> The server has 256GB of RAM an no Swap enabled:
>>
>> free
>>               total       used       free     shared    buffers     cached
>> Mem:     264498496    1341020  263157476          0     285760     289120
>> -/+ buffers/cache:     766140  263732356
>> Swap:            0          0          0
>>
>>
>> Has 12x2 Intel(R) Xeon(R) CPUs:
>>
>> cat /proc/cpuinfo
>> processor       : 0
>> vendor_id       : GenuineIntel
>> cpu family      : 6
>> model           : 45
>> model name      : Intel(R) Xeon(R) CPU E5-2630L 0 @ 2.00GHz
>> stepping        : 7
>> microcode       : 0x710
>> cpu MHz         : 1200.000
>> cache size      : 15360 KB
>> physical id     : 0
>> siblings        : 12
>> core id         : 0
>> cpu cores       : 6
>> apicid          : 0
>> initial apicid  : 0
>> fpu             : yes
>> fpu_exception   : yes
>> cpuid level     : 13
>> wp              : yes
>> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
>> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
>> pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology
>> nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2
>> ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer
>> aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi
>> flexpriority ept vpid
>> bogomips        : 4000.56
>> clflush size    : 64
>> cache_alignment : 64
>> address sizes   : 46 bits physical, 48 bits virtual
>> power management:
>> .
>> .
>> .
>>
>>
>> The server runs a Debian Wheezy (7.2):
>> uname -a
>> Linux img1-serv 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>>
>> My desktop PC has the same Debian (also same update state):
>> uname -a
>> Linux pc3G48243 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>>
>> free
>>               total       used       free     shared    buffers     cached
>> Mem:       8180356    1185364    6994992          0      23348     216084
>> -/+ buffers/cache:     945932    7234424
>> Swap:            0          0          0
>>
>>
>> and 4 AMD FX(tm)-4100 Quad-Core Processors:
>>
>> cat /proc/cpuinfo
>> processor       : 0
>> vendor_id       : AuthenticAMD
>> cpu family      : 21
>> model           : 1
>> model name      : AMD FX(tm)-4100 Quad-Core Processor
>> stepping        : 2
>> microcode       : 0x6000626
>> cpu MHz         : 1400.000
>> cache size      : 2048 KB
>> physical id     : 0
>> siblings        : 4
>> core id         : 0
>> cpu cores       : 2
>> apicid          : 16
>> initial apicid  : 0
>> fpu             : yes
>> fpu_exception   : yes
>> cpuid level     : 13
>> wp              : yes
>> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
>> cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
>> pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc extd_apicid
>> aperfmperf pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 popcnt aes xsave
>> avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse
>> 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 nodeid_msr topoext
>> perfctr_core arat cpb hw_pstate npt lbrv svm_lock nrip_save tsc_scale
>> vmcb_clean flushbyasid decodeassists pausefilter pfthreshold
>> bogomips        : 7233.41
>> TLB size        : 1536 4K pages
>> clflush size    : 64
>> cache_alignment : 64
>> address sizes   : 48 bits physical, 48 bits virtual
>> power management: ts ttp tm 100mhzsteps hwpstate [9]
>>
>>
>> Knowing now, that itk checks for available RAM, the only sources for this
>> problem I can think of would be an odd configuration of ITK itself or its
>> use in programs compiled on the server, or some configuration differences in
>> the (Debian) system, or some hardware problem.
>>
>> Do You have any idea what it could be?
>> Or do You have any suggestions how I should go on searching for the cause?
>>
>>
>> Any help or hints are very much appriciated.
>> Many thanks for Your help again!
>>
>> Roman
>>
>>
>> _____________________________________________
>>
>>
>>
>> ////program to calculate the Euler characteristic of a binary image
>> converted to itkQuadEdgeMesh
>> ////THEREFORE does NOT take filled regions into account only covering
>> surfaces!
>> ////if fillings should be accounted use instead a vtk program taking 3D
>> cells into account
>>
>>
>>
>> #include <itkImageFileReader.h>
>> //#include <itkImage.h>
>> #include <itkBinaryMask3DMeshSource.h> //itk marching cubes (mc) very slow
>> and resource hungry :-(
>> #include <itkQuadEdgeMeshTopologyChecker.h>
>> #include <itkQuadEdgeMeshBoundaryEdgesMeshFunction.h>
>>
>>
>>
>> #include "itkFilterWatcher2.h"
>>
>>
>>
>>
>> void dispatch_cT(itk::ImageIOBase::IOPixelType,
>> itk::ImageIOBase::IOComponentType, size_t, int, char **);
>>
>> template<typename InputComponentType>
>> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t, int, char
>> **);
>>
>> template<typename InputComponentType, typename InputPixelType>
>> void dispatch_D(size_t, int, char **);
>>
>> template<typename InputComponentType, typename InputPixelType, size_t
>> Dimension>
>> int DoIt(int, char *argv[]);
>>
>>
>>
>>
>>
>> template<typename InputComponentType, typename InputPixelType, size_t
>> Dimension>
>> int DoIt(int argc, char *argv[]){
>>
>>    typedef InputPixelType  OutputPixelType;
>>
>>    typedef itk::Image<InputPixelType, Dimension>  InputImageType;
>>    typedef itk::Image<OutputPixelType, Dimension>  OutputImageType;
>>
>>
>>    typedef itk::ImageFileReader<InputImageType> ReaderType;
>>    typename ReaderType::Pointer reader = ReaderType::New();
>>
>>    reader->SetFileName(argv[1]);
>>    FilterWatcher watcherI(reader, "reading");
>>    watcherI.QuietOn();
>>    watcherI.ReportTimeOn();
>>    try
>>      {
>>        reader->Update();
>>      }
>>    catch (itk::ExceptionObject &ex)
>>      {
>>        if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>>        std::cerr << ex.GetDescription() << std::endl;
>>        return EXIT_FAILURE;
>>        }
>>      }
>>
>>
>>    typedef double        CoordType;
>>
>>    //typedef itk::Mesh<CoordType> MeshType;
>>    typedef itk::QuadEdgeMesh<CoordType, Dimension> InputMeshType;
>>
>>    const InputPixelType isoValue= static_cast<InputPixelType>(atof(argv[2]));
>>
>>    typedef itk::BinaryMask3DMeshSource<InputImageType, InputMeshType>
>> MeshSourceType;
>>    typename MeshSourceType::Pointer meshSource = MeshSourceType::New();
>>
>>    meshSource->SetInput(reader->GetOutput());
>>    meshSource->SetObjectValue(isoValue);
>>
>>    FilterWatcher watcher(meshSource, "BinaryMask3DMeshSource");
>>    watcher.QuietOn();
>>    watcher.ReportTimeOn();
>>    try
>>      {
>>        meshSource->Update();
>>      }
>>    catch (itk::ExceptionObject &ex)
>>      {
>>        if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>>          std::cerr << ex.GetDescription() << std::endl;
>>          return EXIT_FAILURE;
>>        }
>>      }
>>
>>
>>    std::cout << "Nodes = " << meshSource->GetNumberOfNodes() << std::endl;
>>    std::cout << "Cells = " << meshSource->GetNumberOfCells() << std::endl;
>>
>>    typename InputMeshType::Pointer mesh= meshSource->GetOutput();
>>
>>    //// check if meshSource can be represented as an itkQuadEdgeMesh
>>    //// if BinaryMask3DMeshSource caps boundary surfaces this check is not
>> necessary!
>>
>>    typedef itk::QuadEdgeMeshTopologyChecker<InputMeshType> TQEchecker;
>>    typename TQEchecker::Pointer QEchecker = TQEchecker::New();
>>    QEchecker->SetMesh(mesh);
>>    std::cerr << "Executing
>> QuadEdgeMeshTopologyChecker->ValidateEulerCharacteristic()";
>>    if(!QEchecker->ValidateEulerCharacteristic()){
>>      std::cerr << "Not a valid QuadEdgeMesh! Aborting." << std::endl;
>>      return EXIT_FAILURE;
>>    }
>>    std::cerr << " done." << std::endl;
>>
>>    //// calc Euler characteristics \xi
>>    //// For closed smooth manifolds, the Euler characteristic coincides with
>> the Euler number:
>> http://en.wikipedia.org/wiki/Euler_characteristic#Relations_to_other_invariants
>>    //// general formula see:
>> http://en.wikipedia.org/wiki/Genus_%28mathematics%29#Orientable_surface
>>    ////
>>    ////
>>    ////
>>    //// good QuadEdge explanation:
>> http://www.cs.cmu.edu/afs/andrew/scs/cs/15-463/2001/pub/src/a2/quadedge.html
>>    /// from itkQuadEdgeMeshTopologyChecker.hxx
>>
>>    typedef itk::QuadEdgeMeshBoundaryEdgesMeshFunction<InputMeshType>
>> BoundaryEdges;
>>
>>    typename BoundaryEdges::Pointer boundaryEdges = BoundaryEdges::New();
>>
>>    // Number of USED points
>>    typedef typename InputMeshType::PointIdentifier
>> PointIdentifier;
>>    std::cerr << "ComputeNumberOfPoints";
>>    PointIdentifier numPoints = mesh->ComputeNumberOfPoints();
>>    std::cerr << " done." << std::endl;
>>    // Number of USED edges
>>    typedef typename InputMeshType::CellIdentifier
>> CellIdentifier;
>>    std::cerr << "ComputeNumberOfEdges";
>>    CellIdentifier numEdges  = mesh->ComputeNumberOfEdges();
>>    std::cerr << " done." << std::endl;
>>    // Number of USED faces
>>    std::cerr << "ComputeNumberOfFaces";
>>    CellIdentifier numFaces  = mesh->ComputeNumberOfFaces();
>>    std::cerr << " done." << std::endl;
>>    // Number of Boundaries
>>    std::cerr << "ComputeNumberOfBoundaryEdges";
>>    typename BoundaryEdges::OutputType
>>      listOfBoundaries = boundaryEdges->Evaluate((*mesh));
>>    std::cerr << " done." << std::endl;
>>    CellIdentifier numBounds = listOfBoundaries->size();
>>    delete listOfBoundaries;
>>
>>    /**
>>     * Number of points
>>     *
>>     * There are two methods to get the number of points.
>>     * 1. itk::QuadEdgeMesh::ComputeNumberOfPoints()
>>     * 2. itk::Mesh::GetNumberOfPoints()
>>     *
>>     * As an itk::QuadEdgeMesh is an itk::Mesh by inheritance, the user
>>     * can use both. 1. will returned the number of points actually
>>     * used by at least one edge, while 2. will give you the number
>>     * of points in the container. Number of unused points can be found
>>     * by making the difference between the two values.
>>     */
>>    if(mesh->GetNumberOfPoints() != numPoints){
>>      std::cerr << "There are isolated vertices! Aborting." << std::endl;
>>      return EXIT_FAILURE;
>>    }
>>
>>    // The euler formula states:
>>    // numFaces - numEdges + numPoints == 2 - 2 * genus - numBounds == \xi
>>    // hence 2 * genus= 2 - numBounds - numFaces + numEdges - numPoints must
>> be an oddeven number.
>>
>>    typedef ::itk::OffsetValueType    OffsetValueType;
>>
>>    OffsetValueType xi=
>>      + OffsetValueType(numFaces)
>>      - OffsetValueType(numEdges)
>>      + OffsetValueType(numPoints);
>>
>>    std::cout << "The Euler characteristic Xi is: " << xi << std::endl;
>>
>>    OffsetValueType twiceGenus=
>>      + OffsetValueType(2) - OffsetValueType(numBounds)
>>      - xi;
>>
>>    std::cout << "The genus is: " << twiceGenus/OffsetValueType(2) <<
>> std::endl;
>>
>>    return EXIT_SUCCESS;
>>
>> }
>>
>>
>> void dispatch_cT(itk::ImageIOBase::IOComponentType componentType,
>> itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc,
>> char *argv[]){
>>
>>
>> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#a8dc783055a0af6f0a5a26cb080feb178
>>    //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00107
>>    //IOComponentType: UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT,
>> INT, ULONG, LONG, FLOAT, DOUBLE
>>
>>    switch (componentType){
>>    case itk::ImageIOBase::UCHAR:{
>>      typedef unsigned char InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::CHAR:{
>>      typedef char InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::USHORT:{
>>      typedef unsigned short InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::SHORT:{
>>      typedef short InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::UINT:{
>>      typedef unsigned int InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::INT:{
>>      typedef int InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    // case itk::ImageIOBase::ULONG:{
>>    //   typedef unsigned long InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::LONG:{
>>    //   typedef long InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::FLOAT:{
>>    //   typedef float InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::DOUBLE:{
>>    //   typedef double InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    // break;
>>    case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
>>    default:
>>      std::cout << "unknown component type" << std::endl;
>>      break;
>>    }//switch
>> }
>>
>> template<typename InputComponentType>
>> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t
>> dimensionType, int argc, char *argv[]){
>>
>>
>> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#abd189f096c2a1b3ea559bc3e4849f658
>>      //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00099
>>      //IOPixelType:: UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR,
>> POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D,
>> COMPLEX, FIXEDARRAY, MATRIX
>>
>>    switch (pixelType){
>>    case itk::ImageIOBase::SCALAR:{
>>      typedef InputComponentType InputPixelType;
>>      //typedef itk::SCALARPixel<InputComponentType> InputPixelType;
>>      dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    }
>>      break;
>>    // case itk::ImageIOBase::RGB:{
>>    //   typedef itk::RGBPixel<InputComponentType> InputPixelType;
>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::RGBA:{
>>    //   typedef itk::RGBAPixel<InputComponentType> InputPixelType;
>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::VECTOR:{
>>    //   //typedef itk::VECTORPixel<InputComponentType> InputPixelType; //does
>> not work!
>>    //   typedef itk::VariableLengthVector<InputComponentType> InputPixelType;
>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    case itk::ImageIOBase::UNKNOWNPIXELTYPE:
>>    default:
>>      std::cout << "unknown pixel type" << std::endl;
>>      break;
>>    }//switch
>> }
>>
>>
>> template<typename InputComponentType, typename InputPixelType>
>> void dispatch_D(size_t dimensionType, int argc, char *argv[]){
>>    switch (dimensionType){
>>    // case 1:
>>    //   DoIt<InputComponentType, InputPixelType, 1>(argc, argv);
>>    //   break;
>>    // case 2:
>>    //   DoIt<InputComponentType, InputPixelType, 2>(argc, argv);
>>    //   break;
>>    case 3:
>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>      break;
>>    case 4:
>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>      break;
>>    case 5:
>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>      break;
>>    default:
>>      std::cout << "Images of dimension " << dimensionType << " are not
>> supported!" << std::endl;
>>      break;
>>    }
>> }
>>
>>
>>
>> ////from
>> http://itk-users.7.n7.nabble.com/Pad-image-with-0-but-keep-its-type-what-ever-it-is-td27442.html
>> //namespace itk{
>>    // Description:
>>    // Get the PixelType and ComponentType from fileName
>>
>> void GetImageType (std::string fileName,
>>      itk::ImageIOBase::IOPixelType &pixelType,
>>      itk::ImageIOBase::IOComponentType &componentType,
>>      size_t &dimensionType
>>      //ImageIOBase::IODimensionType &dimensionType
>>      ){
>>      typedef itk::Image<unsigned char, 3> ImageType;
>>      itk::ImageFileReader<ImageType>::Pointer imageReader=
>> itk::ImageFileReader<ImageType>::New();
>>      imageReader->SetFileName(fileName.c_str());
>>      imageReader->UpdateOutputInformation();
>>
>>      pixelType = imageReader->GetImageIO()->GetPixelType();
>>      componentType = imageReader->GetImageIO()->GetComponentType();
>>      dimensionType= imageReader->GetImageIO()->GetNumberOfDimensions();
>>
>>      //std::cerr << "Pixel Type is " <<
>> imageReader->GetImageIO()->GetComponentTypeAsString(pixelType) << std::endl;
>>      std::cerr << "component type is: " <<
>> imageReader->GetImageIO()->GetComponentTypeAsString(componentType) <<
>> std::endl;
>>      std::cerr << "numDimensions: " << dimensionType << std::endl;
>>      std::cerr << "component size: " <<
>> imageReader->GetImageIO()->GetComponentSize() << std::endl;
>>      std::cerr << "pixel type (string): " <<
>> imageReader->GetImageIO()->GetPixelTypeAsString(imageReader->GetImageIO()->GetPixelType())
>> << std::endl;
>>      std::cerr << "pixel type: " << pixelType << std::endl <<
>> "_________________________"  << std::endl << std::endl;
>>
>>
>>      }
>>
>>
>>
>> int main(int argc, char *argv[]){
>>      if ( argc != 3 )
>>          {
>>          std::cerr << "Missing Parameters: "
>>                    << argv[0]
>>                    << " Input_Image"
>>                    << " isoValue"
>>                    << std::endl;
>>
>>          return EXIT_FAILURE;
>>          }
>>
>>      std::string ifn = argv[1];
>>      // std::string ofn = argv[2];
>>      // int compress= atoi(argv[3]);
>>
>>      itk::ImageIOBase::IOPixelType pixelType;
>>      typename itk::ImageIOBase::IOComponentType componentType;
>>      //itk::ImageIOBase::IOComponentType componentType1;
>>      //itk::ImageIOBase::IODimensionType dimensionType1;
>>      size_t dimensionType;
>>
>>
>>      try
>>          {
>>          GetImageType(argv[1], pixelType, componentType, dimensionType);
>>
>>          dispatch_cT(componentType, pixelType, dimensionType, argc, argv);
>>          }//try
>>      catch( itk::ExceptionObject &excep)
>>          {
>>          std::cerr << argv[0] << ": exception caught !" << std::endl;
>>          std::cerr << excep << std::endl;
>>          return EXIT_FAILURE;
>>          }
>>
>>      return EXIT_SUCCESS;
>>
>>      }
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 08/06/14 15:51, Luis Ibanez wrote:
>>>
>>>
>>> Roman,
>>>
>>>
>>> Could you please share with the list an example
>>> of a program where you are observing this behavior ?
>>>
>>> In particular, we would like to see if this is occurring with
>>> Image filters, or rather with other types of ITK objects.
>>>
>>>
>>>
>>> The itk::Image does listen to the (potential) memory allocation messages
>>> (that is, the bad_alloc exception).
>>>
>>>
>>>
>>> The itk::Image class uses a helper class to store the pixel data.
>>>
>>>
>>>
>>> This helper is the:
>>>
>>> itk::ImportImageContainer
>>>
>>>
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.h
>>>
>>>
>>>
>>>
>>> and its memory allocation is typically done in the AllocateElements()
>>> function
>>> in line:
>>>
>>>
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.hxx#L173
>>>
>>> the code looks like
>>>
>>>     TElement *data;
>>>
>>>     try
>>>       {
>>>       if ( UseDefaultConstructor )
>>>         {
>>>         data = new TElement[size](); //POD types initialized to 0, others
>>> use
>>> default constructor.
>>>         }
>>>       else
>>>         {
>>>         data = new TElement[size]; //Faster but uninitialized
>>>         }
>>>       }
>>>     catch ( ... )
>>>       {
>>>       data = ITK_NULLPTR;
>>>       }
>>>     if ( !data )
>>>       {
>>>       // We cannot construct an error string here because we may be out
>>>       // of memory.  Do not use the exception macro.
>>>       throw MemoryAllocationError(__FILE__, __LINE__,
>>>                                   "Failed to allocate memory for image.",
>>>                                   ITK_LOCATION);
>>>       }
>>>     return data;
>>>
>>>
>>>
>>> As you can see, the case of exceptions is managed in that function.
>>>
>>>
>>> Here is an example of a test program demonstrating that ITK image
>>> will throw exceptions when allocating memory beyond limits.
>>>
>>>
>>> #include "itkImage.h"
>>> #include <iostream>
>>>
>>> int main(int argc, char * argv[] )
>>> {
>>>     if( argc < 2 )
>>>       {
>>>       std::cerr << "Missing arguments" << std::endl;
>>>       return 1;
>>>       }
>>>
>>>     typedef itk::Image< unsigned short, 3 > ImageType;
>>>
>>>     ImageType::Pointer image = ImageType::New();
>>>
>>>     ImageType::RegionType region;
>>>     ImageType::SizeType size;
>>>
>>>     size_t side = atoi( argv[1] );
>>>
>>>     size[0] = side;
>>>     size[1] = side;
>>>     size[2] = side;
>>>
>>>     region.SetSize( size );
>>>
>>>     image->SetRegions( region );
>>>
>>>     try
>>>       {
>>>       image->Allocate();
>>>       }
>>>     catch( std::exception & excp )
>>>       {
>>>       std::cerr << excp.what() << std::endl;
>>>       return 1;
>>>       }
>>>
>>>     std::cout << "ITK Hello World !" << std::endl;
>>>
>>>     return 0;
>>> }
>>>
>>>
>>> and what happens when executing in an Ubuntu Linux machine with 32GB or
>>> RAM
>>>
>>>
>>> $ ./HelloWorld  1000
>>> ITK Hello World !
>>>
>>>
>>> $ ./HelloWorld  1000000
>>>
>>> /home/ibanez/src/ITK/Modules/Core/Common/include/itkImportImageContainer.hxx:199:
>>> Failed to allocate memory for image.
>>>
>>>
>>>
>>>
>>> Please share with the list a minimal example of the problem you are
>>> observing,
>>> and in this way we will be able to help track the issue.
>>>
>>>
>>>      Thanks
>>>
>>>
>>>          Luis
>>>
>>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

From blowekamp at mail.nih.gov  Wed Jul 16 09:13:47 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 16 Jul 2014 09:13:47 -0400
Subject: [ITK-users] Connected Threshold Filter crashes but only for
	large images
In-Reply-To: <1405441657014-7585907.post@n2.nabble.com>
References: <1405441657014-7585907.post@n2.nabble.com>
Message-ID: <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>

Hello,

I have had great success running this algorithm on very large data sets. And consider the implementation very robust.

There could be something different about your pipeline, or something unique about your image, or how you compiled it.

First are you running 32 or 64-bits? Perhaps you are running out of memory?

Perhaps there is something odd about your pipeline. If you just do a ImageFileRead->Connected Threshold->ImageFileWrite does it still crash?

If you are familiar with Python, perhaps you could try running this filter with a binary download of SimpleITK? This would check to see if there is something intrinsically wrong with the algorithm?

Just some ideas to help narrow it down...
Brad


On Jul 15, 2014, at 12:27 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:

> Hi everyone,
> 
> I am working with sets of 3D MRI data from multiple years for my research. 
> I am using the connected threshold filter in a pipeline after a binary
> thresholding procedure using Otsu segmentation.
> 
> The algorithm functions when there are 124 slices in the image, but crashes
> with an abort message when there are 248 slices and when there are 156
> slices.  
> 
> I have tested this with multiple data sets and the pattern holds.  The
> strange part is that this still happens even if I resample the number of
> slices down to 124, so I really am confused as to what is happening.
> 
> Is there any reason why the filter would be crashing for images that are too
> large like this, even after being resampled smaller?
> 
> Best regards,
> Michael Pinkert
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Connected-Threshold-Filter-crashes-but-only-for-large-images-tp7585907.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From blowekamp at mail.nih.gov  Wed Jul 16 09:17:59 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 16 Jul 2014 09:17:59 -0400
Subject: [ITK-users] 3D registration problem
In-Reply-To: <CANH4YVgmoJ-qGHD5qphkdEZW3t74d0TzF9coNKREXT3zkEXydg@mail.gmail.com>
References: <CANH4YVgmoJ-qGHD5qphkdEZW3t74d0TzF9coNKREXT3zkEXydg@mail.gmail.com>
Message-ID: <261FEDF7-8004-40D8-A84F-5E489AACD127@mail.nih.gov>

Hello,

This not the expected behavior for a good registration program.

Is your initialization good?

You haven't shared anything about the registration components you are using. Perhaps you scales are way off? How does the convergence look when monitoring the output?

Perhaps you have too many free parameters? Maybe you are trying to optimize an transform with too many parameters when you are not close. Perhaps you need to do a Translation + Rotation transform such as Euler or Versor first?

Hope that helps,
Brad

On Jul 15, 2014, at 5:26 AM, Iyas Hamdan <iyas.hamdan at gmail.com> wrote:

> Hello itk users,
> 
> I'm working on 3D image registration, currently I'm trying to register a CT volume to an MRI volume ( the two volumes have different sizes concerning the number of slices used to construct the 3D volume). 
> 
> I'm doing an affine registration using the mutual information as a metric, and I'm having problems registering those two volumes.
> 
> What I thiink the problem is, I have a different field of view between both volumes, so when I try to register the whole CT volume to the MRI one  the registration falis. However, when I deleted a dozen of slices from the CT volume ( so that I had the same field of view in both volumes) it works just fine and I was able to register the volumes. 
> 
> 
> And by "the registration failed" I meant it worked with no errors but the result was really bad! and that the registered volume was nothing like the fixed one, so if I try to find the difference between each two corresponding slices for example , they were not aligned at all! 
> 
> Is that normal that the registration doesnt work when I have a different field of view in each volume ? or should it deform one volume so that it corresponds to the other one even if they had two different fields of view ? 
> 
> Any help would be really appreciated, 
> 
> Thanks in advance, 
> 
> Iyas
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From iyas.hamdan at gmail.com  Wed Jul 16 09:52:43 2014
From: iyas.hamdan at gmail.com (Iyas Hamdan)
Date: Wed, 16 Jul 2014 15:52:43 +0200
Subject: [ITK-users] 3D registration problem
In-Reply-To: <261FEDF7-8004-40D8-A84F-5E489AACD127@mail.nih.gov>
References: <CANH4YVgmoJ-qGHD5qphkdEZW3t74d0TzF9coNKREXT3zkEXydg@mail.gmail.com>
 <261FEDF7-8004-40D8-A84F-5E489AACD127@mail.nih.gov>
Message-ID: <CANH4YVhZikaA4KtcX-QrjLBtxv78fP66KLgOy+Rq5AiOQS5yBA@mail.gmail.com>

Hello,

Thanks for your reply!

It's true I haven't shared alot of information about the methode I'm using
sorry about that.

My code is based on the example "ImageRegistration20.cxx" with some
modifications;

So I'm basically using a 3D Affine registration with Mattes mutual
information being the metric and the regular step gradient descent as the
optimizer and finally a linear interpolator.

For the initialization, its good and there's no problem here.

But for the result, concerning the registered volume, the scale is good as
well but the problem is that the its not aligned with the fixed volume.

And for the parameters, I have only a few ones for the metric ( number of
histogram bins and spatial samples ) and I dont think they would have that
much of effect on the output, but I tried to change them and I ended up
always with almost the same result.
And for the optimizer, same as before I tried so many values for the
relaxation factor and the max/min step lengths as well.

So the problem is not the scale nor the parameters but the registration
itself; since it can't find, for each slice of the fixed volume, the slice
in the moving volume that corresponds the maximum. So on the output I have
a volume that has the same scale as the fixed one but they are not aligned
and have no mutual information between them I would say. Even though I
tried to change the initialization to prevent the local minimas and I'm
starting now with a good initialization but still the same result.


And what I found wierd is that when I deleted few slices from the end of
the moving volume, the registration worked perfectly and I had good results!



Hope this was clear and these information was enough, and please let me
know if you have any other suggestions or advices.

Thanks in advance,

Iyas


On Wed, Jul 16, 2014 at 3:17 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> This not the expected behavior for a good registration program.
>
> Is your initialization good?
>
> You haven't shared anything about the registration components you are
> using. Perhaps you scales are way off? How does the convergence look when
> monitoring the output?
>
> Perhaps you have too many free parameters? Maybe you are trying to
> optimize an transform with too many parameters when you are not close.
> Perhaps you need to do a Translation + Rotation transform such as Euler or
> Versor first?
>
> Hope that helps,
> Brad
>
> On Jul 15, 2014, at 5:26 AM, Iyas Hamdan <iyas.hamdan at gmail.com> wrote:
>
> > Hello itk users,
> >
> > I'm working on 3D image registration, currently I'm trying to register a
> CT volume to an MRI volume ( the two volumes have different sizes
> concerning the number of slices used to construct the 3D volume).
> >
> > I'm doing an affine registration using the mutual information as a
> metric, and I'm having problems registering those two volumes.
> >
> > What I thiink the problem is, I have a different field of view between
> both volumes, so when I try to register the whole CT volume to the MRI one
>  the registration falis. However, when I deleted a dozen of slices from the
> CT volume ( so that I had the same field of view in both volumes) it works
> just fine and I was able to register the volumes.
> >
> >
> > And by "the registration failed" I meant it worked with no errors but
> the result was really bad! and that the registered volume was nothing like
> the fixed one, so if I try to find the difference between each two
> corresponding slices for example , they were not aligned at all!
> >
> > Is that normal that the registration doesnt work when I have a different
> field of view in each volume ? or should it deform one volume so that it
> corresponds to the other one even if they had two different fields of view ?
> >
> > Any help would be really appreciated,
> >
> > Thanks in advance,
> >
> > Iyas
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140716/4c42a438/attachment.html>

From blowekamp at mail.nih.gov  Wed Jul 16 10:03:38 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 16 Jul 2014 10:03:38 -0400
Subject: [ITK-users] 3D registration problem
In-Reply-To: <CANH4YVhZikaA4KtcX-QrjLBtxv78fP66KLgOy+Rq5AiOQS5yBA@mail.gmail.com>
References: <CANH4YVgmoJ-qGHD5qphkdEZW3t74d0TzF9coNKREXT3zkEXydg@mail.gmail.com>
 <261FEDF7-8004-40D8-A84F-5E489AACD127@mail.nih.gov>
 <CANH4YVhZikaA4KtcX-QrjLBtxv78fP66KLgOy+Rq5AiOQS5yBA@mail.gmail.com>
Message-ID: <B37CC518-A17B-4F66-BF20-65F0E85682B5@mail.nih.gov>

Have you looked at the histograms of the two image with the parameters provided to the metric?

Perhaps this example will be of use:
http://www.itk.org/Doxygen/html/RegistrationITKv3_2ImageRegistrationHistogramPlotter_8cxx-example.html

Brad
On Jul 16, 2014, at 9:52 AM, Iyas Hamdan <iyas.hamdan at gmail.com> wrote:

> Hello, 
> 
> Thanks for your reply! 
> 
> It's true I haven't shared alot of information about the methode I'm using sorry about that.
> 
> My code is based on the example "ImageRegistration20.cxx" with some modifications; 
> 
> So I'm basically using a 3D Affine registration with Mattes mutual information being the metric and the regular step gradient descent as the optimizer and finally a linear interpolator.
> 
> For the initialization, its good and there's no problem here. 
> 
> But for the result, concerning the registered volume, the scale is good as well but the problem is that the its not aligned with the fixed volume. 
> 
> And for the parameters, I have only a few ones for the metric ( number of histogram bins and spatial samples ) and I dont think they would have that much of effect on the output, but I tried to change them and I ended up always with almost the same result. 
> And for the optimizer, same as before I tried so many values for the relaxation factor and the max/min step lengths as well. 
> 
> So the problem is not the scale nor the parameters but the registration itself; since it can't find, for each slice of the fixed volume, the slice in the moving volume that corresponds the maximum. So on the output I have a volume that has the same scale as the fixed one but they are not aligned and have no mutual information between them I would say. Even though I tried to change the initialization to prevent the local minimas and I'm starting now with a good initialization but still the same result. 
> 
> 
> And what I found wierd is that when I deleted few slices from the end of the moving volume, the registration worked perfectly and I had good results!
> 
> 
> 
> Hope this was clear and these information was enough, and please let me know if you have any other suggestions or advices.
> 
> Thanks in advance, 
> 
> Iyas
> 
> 
> On Wed, Jul 16, 2014 at 3:17 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> This not the expected behavior for a good registration program.
> 
> Is your initialization good?
> 
> You haven't shared anything about the registration components you are using. Perhaps you scales are way off? How does the convergence look when monitoring the output?
> 
> Perhaps you have too many free parameters? Maybe you are trying to optimize an transform with too many parameters when you are not close. Perhaps you need to do a Translation + Rotation transform such as Euler or Versor first?
> 
> Hope that helps,
> Brad
> 
> On Jul 15, 2014, at 5:26 AM, Iyas Hamdan <iyas.hamdan at gmail.com> wrote:
> 
> > Hello itk users,
> >
> > I'm working on 3D image registration, currently I'm trying to register a CT volume to an MRI volume ( the two volumes have different sizes concerning the number of slices used to construct the 3D volume).
> >
> > I'm doing an affine registration using the mutual information as a metric, and I'm having problems registering those two volumes.
> >
> > What I thiink the problem is, I have a different field of view between both volumes, so when I try to register the whole CT volume to the MRI one  the registration falis. However, when I deleted a dozen of slices from the CT volume ( so that I had the same field of view in both volumes) it works just fine and I was able to register the volumes.
> >
> >
> > And by "the registration failed" I meant it worked with no errors but the result was really bad! and that the registered volume was nothing like the fixed one, so if I try to find the difference between each two corresponding slices for example , they were not aligned at all!
> >
> > Is that normal that the registration doesnt work when I have a different field of view in each volume ? or should it deform one volume so that it corresponds to the other one even if they had two different fields of view ?
> >
> > Any help would be really appreciated,
> >
> > Thanks in advance,
> >
> > Iyas
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140716/015d3610/attachment-0001.html>

From mpinkert at wisc.edu  Wed Jul 16 13:53:12 2014
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Wed, 16 Jul 2014 10:53:12 -0700 (PDT)
Subject: [ITK-users] Connected Threshold Filter crashes but only for
 large images
In-Reply-To: <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
Message-ID: <1405533192912-7585914.post@n2.nabble.com>

Hi,

I think the problem may be unique to the data set I was working with.  New
scans I acquired from different patients have been working fine, so it looks
like it is something wrong with the images that is the issue.  Thank you for
your help, and I'll keep your advice in mind in case I run into this problem
again.

Best regards,
Michael Pinkert


Bradley Lowekamp wrote
> Hello,
> 
> I have had great success running this algorithm on very large data sets.
> And consider the implementation very robust.
> 
> There could be something different about your pipeline, or something
> unique about your image, or how you compiled it.
> 
> First are you running 32 or 64-bits? Perhaps you are running out of
> memory?
> 
> Perhaps there is something odd about your pipeline. If you just do a
> ImageFileRead->Connected Threshold->ImageFileWrite does it still crash?
> 
> If you are familiar with Python, perhaps you could try running this filter
> with a binary download of SimpleITK? This would check to see if there is
> something intrinsically wrong with the algorithm?
> 
> Just some ideas to help narrow it down...
> Brad
> 
> 
> On Jul 15, 2014, at 12:27 PM, Michael Pinkert &lt;

> mpinkert@

> &gt; wrote:
> 
>> Hi everyone,
>> 
>> I am working with sets of 3D MRI data from multiple years for my
>> research. 
>> I am using the connected threshold filter in a pipeline after a binary
>> thresholding procedure using Otsu segmentation.
>> 
>> The algorithm functions when there are 124 slices in the image, but
>> crashes
>> with an abort message when there are 248 slices and when there are 156
>> slices.  
>> 
>> I have tested this with multiple data sets and the pattern holds.  The
>> strange part is that this still happens even if I resample the number of
>> slices down to 124, so I really am confused as to what is happening.
>> 
>> Is there any reason why the filter would be crashing for images that are
>> too
>> large like this, even after being resampled smaller?
>> 
>> Best regards,
>> Michael Pinkert
>> 
>> 
>> 
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Connected-Threshold-Filter-crashes-but-only-for-large-images-tp7585907.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users





--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Connected-Threshold-Filter-crashes-but-only-for-large-images-tp7585907p7585914.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From marco.ulge at gmail.com  Wed Jul 16 17:34:34 2014
From: marco.ulge at gmail.com (Marco Ulge)
Date: Wed, 16 Jul 2014 14:34:34 -0700 (PDT)
Subject: [ITK-users] [ITK-Users] Help with ITK and CMake
Message-ID: <1405546474692-7585915.post@n2.nabble.com>

Good evening,

I need to create a .dll (and a .so for linux) with ITK code inside. I was
wandering if anyone of you knows how i should write my cmakelists to make
the dll standalone. Actually i got no problem generating the dll file but it
is not standalone and i'm struggling to figure out why.

Any help's appreciated

Regards,

Marco



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Users-Help-with-ITK-and-CMake-tp7585915.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From k09tranhoan at gmail.com  Thu Jul 17 03:36:21 2014
From: k09tranhoan at gmail.com (zoro)
Date: Thu, 17 Jul 2014 00:36:21 -0700 (PDT)
Subject: [ITK-users] L-BFGS optimizer's in versor space
Message-ID: <1405582581330-7585916.post@n2.nabble.com>

Dear all,

I tried to implement L-BFGS optimizer in the versor space and registration
framework with the algorithm as below:

http://en.wikipedia.org/wiki/Limited-memory_BFGS

L-BFGS produced the direction and base on that, I used the line-search to
update parameters ( number of parameters is 6, anyway). But sometimes,
direction goes to irregular places where translation direction is extremely
large.  And the convergence is not good. It does not show the effect of BFGS
but only line-search.

I thought that with constraint of versor space (in unit cube surface), it's
not straight as the algorithm above. For example, in versor space (vec_a -
vec_b) actually equal to composition of  vec_a and Conjugate of vec_b.
Calculating (vec_a - vec_b) in simple way (in the algorithm above) leads to
problem of irregular jumping in parameters space.

Is anyone who deals with L-BFGS in versor space? 
I will appreciate if you give me some advice.

Thank you!
Regards,




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/L-BFGS-optimizer-s-in-versor-space-tp7585916.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From iyas.hamdan at gmail.com  Thu Jul 17 05:16:21 2014
From: iyas.hamdan at gmail.com (Iyas Hamdan)
Date: Thu, 17 Jul 2014 11:16:21 +0200
Subject: [ITK-users] 3D registration problem
In-Reply-To: <B37CC518-A17B-4F66-BF20-65F0E85682B5@mail.nih.gov>
References: <CANH4YVgmoJ-qGHD5qphkdEZW3t74d0TzF9coNKREXT3zkEXydg@mail.gmail.com>
 <261FEDF7-8004-40D8-A84F-5E489AACD127@mail.nih.gov>
 <CANH4YVhZikaA4KtcX-QrjLBtxv78fP66KLgOy+Rq5AiOQS5yBA@mail.gmail.com>
 <B37CC518-A17B-4F66-BF20-65F0E85682B5@mail.nih.gov>
Message-ID: <CANH4YViJN45tupOkR-WTojGaPmyUw0gdhDfbBn=Fw59CvGGTsQ@mail.gmail.com>

Hello,
and thanks again for your reply Brad,

I haven't actually give it a look yet, but I think it won't help in my case
since I'm working with images from different modalities. I mean I know that
the joint histogram should be concentrated in the diagnoal but isn't that
the case only when we're working with images from the same modalities ?

or should it work as well in my case ?

regards,

Iyas



On Wed, Jul 16, 2014 at 4:03 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Have you looked at the histograms of the two image with the parameters
> provided to the metric?
>
> Perhaps this example will be of use:
>
> http://www.itk.org/Doxygen/html/RegistrationITKv3_2ImageRegistrationHistogramPlotter_8cxx-example.html
>
> Brad
>
> On Jul 16, 2014, at 9:52 AM, Iyas Hamdan <iyas.hamdan at gmail.com> wrote:
>
> Hello,
>
> Thanks for your reply!
>
> It's true I haven't shared alot of information about the methode I'm using
> sorry about that.
>
> My code is based on the example "ImageRegistration20.cxx" with some
> modifications;
>
> So I'm basically using a 3D Affine registration with Mattes mutual
> information being the metric and the regular step gradient descent as the
> optimizer and finally a linear interpolator.
>
> For the initialization, its good and there's no problem here.
>
> But for the result, concerning the registered volume, the scale is good as
> well but the problem is that the its not aligned with the fixed volume.
>
> And for the parameters, I have only a few ones for the metric ( number of
> histogram bins and spatial samples ) and I dont think they would have that
> much of effect on the output, but I tried to change them and I ended up
> always with almost the same result.
> And for the optimizer, same as before I tried so many values for the
> relaxation factor and the max/min step lengths as well.
>
> So the problem is not the scale nor the parameters but the registration
> itself; since it can't find, for each slice of the fixed volume, the slice
> in the moving volume that corresponds the maximum. So on the output I have
> a volume that has the same scale as the fixed one but they are not aligned
> and have no mutual information between them I would say. Even though I
> tried to change the initialization to prevent the local minimas and I'm
> starting now with a good initialization but still the same result.
>
>
> And what I found wierd is that when I deleted few slices from the end of
> the moving volume, the registration worked perfectly and I had good results!
>
>
>
> Hope this was clear and these information was enough, and please let me
> know if you have any other suggestions or advices.
>
> Thanks in advance,
>
> Iyas
>
>
> On Wed, Jul 16, 2014 at 3:17 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> Hello,
>>
>> This not the expected behavior for a good registration program.
>>
>> Is your initialization good?
>>
>> You haven't shared anything about the registration components you are
>> using. Perhaps you scales are way off? How does the convergence look when
>> monitoring the output?
>>
>> Perhaps you have too many free parameters? Maybe you are trying to
>> optimize an transform with too many parameters when you are not close.
>> Perhaps you need to do a Translation + Rotation transform such as Euler or
>> Versor first?
>>
>> Hope that helps,
>> Brad
>>
>> On Jul 15, 2014, at 5:26 AM, Iyas Hamdan <iyas.hamdan at gmail.com> wrote:
>>
>> > Hello itk users,
>> >
>> > I'm working on 3D image registration, currently I'm trying to register
>> a CT volume to an MRI volume ( the two volumes have different sizes
>> concerning the number of slices used to construct the 3D volume).
>> >
>> > I'm doing an affine registration using the mutual information as a
>> metric, and I'm having problems registering those two volumes.
>> >
>> > What I thiink the problem is, I have a different field of view between
>> both volumes, so when I try to register the whole CT volume to the MRI one
>>  the registration falis. However, when I deleted a dozen of slices from the
>> CT volume ( so that I had the same field of view in both volumes) it works
>> just fine and I was able to register the volumes.
>> >
>> >
>> > And by "the registration failed" I meant it worked with no errors but
>> the result was really bad! and that the registered volume was nothing like
>> the fixed one, so if I try to find the difference between each two
>> corresponding slices for example , they were not aligned at all!
>> >
>> > Is that normal that the registration doesnt work when I have a
>> different field of view in each volume ? or should it deform one volume so
>> that it corresponds to the other one even if they had two different fields
>> of view ?
>> >
>> > Any help would be really appreciated,
>> >
>> > Thanks in advance,
>> >
>> > Iyas
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/ab10b9d2/attachment.html>

From elena.bresciani87 at gmail.com  Thu Jul 17 08:43:46 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Thu, 17 Jul 2014 14:43:46 +0200
Subject: [ITK-users] Using C++ functions in ITK pipeline
Message-ID: <CACxk=WxTvMLCL3dD91BEgeg46-29MYqONuuQbhLKjgovBxOBRg@mail.gmail.com>

Hello guys,

I'm developing a really complicated pipeline and to avoid repetitions and
unreadeble code I thought of writing the different pieces of code as
functions, each with a single specific purpose.
Since I'm not really a C++ master I started with a very simple pipeline
(reader -> rescale intensity filter -> writer), where the rescale intensity
filter is in a separate function, outside the main().
The code compiles and it even runs but the output is not what it would have
to be.

Can someone help me find where is the error?

Attached you can find my code, a test image and the respective output.

Thanks in advance

Elena
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/43f16c58/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: TEST.jpg
Type: image/jpeg
Size: 3641 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/43f16c58/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: testFunzioni.cxx
Type: text/x-c++src
Size: 1895 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/43f16c58/attachment.cxx>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: TEST_out.jpg
Type: image/jpeg
Size: 17543 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/43f16c58/attachment-0001.jpg>

From nicgallego at gmail.com  Thu Jul 17 09:46:19 2014
From: nicgallego at gmail.com (Nicolas Gallego)
Date: Thu, 17 Jul 2014 15:46:19 +0200
Subject: [ITK-users] Fwd: [ITK]  Using C++ functions in ITK pipeline
In-Reply-To: <CAHFTQh6tTVPC5yJ_AbNtvVJUEUqU3bkBTp+13Mmk-Oxo=hpacg@mail.gmail.com>
References: <CACxk=WxTvMLCL3dD91BEgeg46-29MYqONuuQbhLKjgovBxOBRg@mail.gmail.com>
 <CAHFTQh6tTVPC5yJ_AbNtvVJUEUqU3bkBTp+13Mmk-Oxo=hpacg@mail.gmail.com>
Message-ID: <CAHFTQh4Ao3tHk_T00aSux1dpVRkoM8yJy8PE3PD7svjhJRndxQ@mail.gmail.com>

Hi Elena,
I compiled and tested your example code.
I found that there was a conflict between the return of the function and
the argument (output),
also I think output allocation on the function is not necesary since you
assign it a valid output.
Here a version of your code that worked.


Nicol?s Gallego-Ortiz
Universit? catholique de Louvain, Belgium


2014-07-17 14:43 GMT+02:00 elena bresciani <elena.bresciani87 at gmail.com>:

> Hello guys,
>
> I'm developing a really complicated pipeline and to avoid repetitions and
> unreadeble code I thought of writing the different pieces of code as
> functions, each with a single specific purpose.
> Since I'm not really a C++ master I started with a very simple pipeline
> (reader -> rescale intensity filter -> writer), where the rescale intensity
> filter is in a separate function, outside the main().
> The code compiles and it even runs but the output is not what it would
> have to be.
>
> Can someone help me find where is the error?
>
> Attached you can find my code, a test image and the respective output.
>
> Thanks in advance
>
> Elena
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/1115dd32/attachment.html>
-------------- next part --------------
PROJECT(funzioni)
CMAKE_MINIMUM_REQUIRED(VERSION 2.8)

FIND_PACKAGE(ITK)
IF(ITK_FOUND)
    INCLUDE(${ITK_USE_FILE})
ELSE(ITK_FOUND)
    MESSAGE(FATAL_ERROR
            "ITK not found. Please set ITK_DIR.")
ENDIF(ITK_FOUND)

ADD_EXECUTABLE( testFunzioni testFunzioni.cxx )
TARGET_LINK_LIBRARIES( testFunzioni ${ITK_LIBRARIES} )
-------------- next part --------------
A non-text attachment was scrubbed...
Name: TEST.jpg
Type: image/jpeg
Size: 3641 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/1115dd32/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: myTestOut.jpg
Type: image/jpeg
Size: 2342 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/1115dd32/attachment-0001.jpg>
-------------- next part --------------
#include <iostream>
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"

typedef itk::Image < unsigned char, 2 > ImageType;

// may be a conflict between return value and outImage as argument by reference
//ImageType::Pointer RescaleIntensity (ImageType::Pointer inputImage, ImageType::Pointer outputImage);
ImageType::Pointer RescaleIntensity (ImageType::Pointer inputImage);

int main (int argc, char * argv[])

    {
    typedef itk::ImageFileReader < ImageType > ReaderType;
    ReaderType::Pointer reader = ReaderType::New();
    
    reader -> SetFileName (argv[1]);
    try {
        reader -> Update();
    } catch (itk::ExceptionObject & excp)
    {
            std::cerr << "Problem encountered while reading file: " << std::endl;
            std::cerr << excp << std::endl;
            return EXIT_FAILURE;
    }

    ImageType::Pointer inputImg = reader -> GetOutput();
    
//    ImageType::Pointer outputImage = ImageType::New();
    ImageType::Pointer outputImage = RescaleIntensity( inputImg );
//    RescaleIntensity (inputImg, outputImage);

    typedef itk::ImageFileWriter < ImageType > WriterType;
    WriterType::Pointer writer = WriterType::New();
    
    writer -> SetFileName (argv[2]);
    writer -> SetInput (outputImage);
//    writer->SetInput( rescale->GetOutput() );
    
    try
        {
        writer->Update();
        }
    catch (itk::ExceptionObject & excp)
        {
        std::cerr << "Problem encountered while writing file: " << std::endl;
        std::cerr << excp << std::endl;
        return EXIT_FAILURE;
        }
    
    return EXIT_SUCCESS;
    
    }
    
//ImageType::Pointer RescaleIntensity (ImageType::Pointer inputImage, ImageType::Pointer outputImage)
ImageType::Pointer RescaleIntensity(ImageType::Pointer inputImage)
{
//    std::cout << inputImage << std::endl;
//    outputImage -> SetRegions (inputImage -> GetLargestPossibleRegion());
//    outputImage -> SetSpacing (inputImage ->GetSpacing());
//    outputImage -> Allocate();
    
    typedef itk::RescaleIntensityImageFilter < ImageType, ImageType > RescaleType;
    RescaleType::Pointer rescale = RescaleType::New();
    
    rescale -> SetInput (inputImage);
    rescale -> SetOutputMinimum (0);
    rescale -> SetOutputMaximum (255);
    rescale -> Update();
    return rescale->GetOutput();
//    outputImage = rescale -> GetOutput();
    
//    return outputImage;
}

//////////////
//typedef itk::RescaleIntensityImageFilter < ImageType, ImageType > RescaleType;
//RescaleType::Pointer rescale = RescaleType::New();

//rescale -> SetInput ( reader->GetOutput() );
//rescale -> SetOutputMinimum (0);
//rescale -> SetOutputMaximum (255);

From elena.bresciani87 at gmail.com  Thu Jul 17 09:57:10 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Thu, 17 Jul 2014 15:57:10 +0200
Subject: [ITK-users] Fwd: [ITK] Using C++ functions in ITK pipeline
In-Reply-To: <CAHFTQh4Ao3tHk_T00aSux1dpVRkoM8yJy8PE3PD7svjhJRndxQ@mail.gmail.com>
References: <CACxk=WxTvMLCL3dD91BEgeg46-29MYqONuuQbhLKjgovBxOBRg@mail.gmail.com>
 <CAHFTQh6tTVPC5yJ_AbNtvVJUEUqU3bkBTp+13Mmk-Oxo=hpacg@mail.gmail.com>
 <CAHFTQh4Ao3tHk_T00aSux1dpVRkoM8yJy8PE3PD7svjhJRndxQ@mail.gmail.com>
Message-ID: <CACxk=WxciuHKVvjVwiUHtZJ2HKfbnVtf8YHD2R35ZYZaqiutcA@mail.gmail.com>

Thank you very much Nicolas!

Cheers
Elena


2014-07-17 15:46 GMT+02:00 Nicolas Gallego <nicgallego at gmail.com>:

>
> Hi Elena,
> I compiled and tested your example code.
> I found that there was a conflict between the return of the function and
> the argument (output),
> also I think output allocation on the function is not necesary since you
> assign it a valid output.
> Here a version of your code that worked.
>
>
> Nicol?s Gallego-Ortiz
> Universit? catholique de Louvain, Belgium
>
>
> 2014-07-17 14:43 GMT+02:00 elena bresciani <elena.bresciani87 at gmail.com>:
>
>>  Hello guys,
>>
>> I'm developing a really complicated pipeline and to avoid repetitions and
>> unreadeble code I thought of writing the different pieces of code as
>> functions, each with a single specific purpose.
>> Since I'm not really a C++ master I started with a very simple pipeline
>> (reader -> rescale intensity filter -> writer), where the rescale intensity
>> filter is in a separate function, outside the main().
>> The code compiles and it even runs but the output is not what it would
>> have to be.
>>
>> Can someone help me find where is the error?
>>
>> Attached you can find my code, a test image and the respective output.
>>
>> Thanks in advance
>>
>> Elena
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140717/8d5db2c6/attachment.html>

From jchoate at ononesoftware.com  Fri Jul 18 15:39:54 2014
From: jchoate at ononesoftware.com (Jim Choate)
Date: Fri, 18 Jul 2014 12:39:54 -0700
Subject: [ITK-users] Does ITK 4.6 support C++11 for OSX?
Message-ID: <1258083356-318480384@mail.ononesoftware.com>



Hi, has anyone successfully used ITK 4.6 with a project built in XCode 5 for C++11?




Right now, we're getting 'Undefined symbols for architecture x86_64' for many symbols, such as itk::ProcessObject::MakeOutput when linking.    




The owner of ITK on our team says this is caused by ITK not supporting C++11.?  Is this true?




He rebuilt ITK 4.6 with C++11 flags.




Thank you!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140718/e71189c8/attachment.html>

From sean at rogue-research.com  Fri Jul 18 16:21:12 2014
From: sean at rogue-research.com (Sean McBride)
Date: Fri, 18 Jul 2014 16:21:12 -0400
Subject: [ITK-users] Does ITK 4.6 support C++11 for OSX?
In-Reply-To: <1258083356-318480384@mail.ononesoftware.com>
References: <1258083356-318480384@mail.ononesoftware.com>
Message-ID: <20140718202112.1276685154@mail.rogue-research.com>

On Fri, 18 Jul 2014 12:39:54 -0700, Jim Choate said:

>Hi, has anyone successfully used ITK 4.6 with a project built in XCode 5
>for C++11?
>
>Right now, we're getting 'Undefined symbols for architecture x86_64' for
>many symbols, such as itk::ProcessObject::MakeOutput when linking.    

Are you building both the ITK libraries and your application with the same exact compiler, same STL library, and same C++ variant?  ex: don't build one with gcc, libstdc++, C++03 and the other with clang, libc++, and C++11.  You have to match them up.

Cheers,

-- 
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com 
Mac Software Developer              Montr?al, Qu?bec, Canada



From Jared.Becksfort at STJUDE.ORG  Fri Jul 18 16:27:17 2014
From: Jared.Becksfort at STJUDE.ORG (Becksfort, Jared)
Date: Fri, 18 Jul 2014 15:27:17 -0500
Subject: [ITK-users] Does ITK 4.6 support C++11 for OSX?
In-Reply-To: <1258083356-318480384@mail.ononesoftware.com>
References: <1258083356-318480384@mail.ononesoftware.com>
Message-ID: <8172D639BA76A14AA5C9DE7E13E0CEBE7362BE71CF@10.stjude.org>

I had trouble at one point with a C++11 build.  My problem was that OSX 10.8 did not use the correct standard library by default.  It used (I believe) cstdlib, but libc++ is what is needed.  You can try your luck at using libc++ in the build commands or upgrade to 10.9 if you haven?t already.

I am 99% sure I build ITK version 4.6 on it.  I don?t have that computer handy at the moment so I can?t check.  The computer is a work computer, so I actually just had it re-imaged to 10.9 rather than a straight upgrade.  That could result in some differences potentially.

Good Luck,
Jared

From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Jim Choate
Sent: Friday, July 18, 2014 2:40 PM
To: insight-users at itk.org
Subject: [ITK-users] Does ITK 4.6 support C++11 for OSX?


Hi, has anyone successfully used ITK 4.6 with a project built in XCode 5 for C++11?



Right now, we're getting 'Undefined symbols for architecture x86_64' for many symbols, such as itk::ProcessObject::MakeOutput when linking.



The owner of ITK on our team says this is caused by ITK not supporting C++11.  Is this true?



He rebuilt ITK 4.6 with C++11 flags.



Thank you!

________________________________
Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140718/552070ef/attachment-0001.html>

From dr.tim.allman at gmail.com  Fri Jul 18 18:53:49 2014
From: dr.tim.allman at gmail.com (Tim Allman)
Date: Fri, 18 Jul 2014 18:53:49 -0400
Subject: [ITK-users] Does ITK 4.6 support C++11 for OSX?
In-Reply-To: <8172D639BA76A14AA5C9DE7E13E0CEBE7362BE71CF@10.stjude.org>
References: <1258083356-318480384@mail.ononesoftware.com>
 <8172D639BA76A14AA5C9DE7E13E0CEBE7362BE71CF@10.stjude.org>
Message-ID: <1D8EC044-D594-4A82-B83D-A094BAC13D9A@gmail.com>

I have compiled ITK 4.6 successfully on OSX 10.9. The options I used in CMAKE_CXX_FLAGS are -std=gnu++11 -stdlib=libstdc++.

The important option is -stdlib. The current default for clang++ is libc++ but the default for Xcode 5 is libstdc++ so if you are not careful you will get ITK built with one and your project built with the other. This will give linker errors.

Tim


On Jul 18, 2014, at 16:27 , Becksfort, Jared <Jared.Becksfort at STJUDE.ORG> wrote:

> I had trouble at one point with a C++11 build.  My problem was that OSX 10.8 did not use the correct standard library by default.  It used (I believe) cstdlib, but libc++ is what is needed.  You can try your luck at using libc++ in the build commands or upgrade to 10.9 if you haven?t already.
>  
> I am 99% sure I build ITK version 4.6 on it.  I don?t have that computer handy at the moment so I can?t check.  The computer is a work computer, so I actually just had it re-imaged to 10.9 rather than a straight upgrade.  That could result in some differences potentially.
>  
> Good Luck,
> Jared
>  
> From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Jim Choate
> Sent: Friday, July 18, 2014 2:40 PM
> To: insight-users at itk.org
> Subject: [ITK-users] Does ITK 4.6 support C++11 for OSX?
>  
> Hi, has anyone successfully used ITK 4.6 with a project built in XCode 5 for C++11?
>  
> Right now, we're getting 'Undefined symbols for architecture x86_64' for many symbols, such as itk::ProcessObject::MakeOutput when linking.
>  
> The owner of ITK on our team says this is caused by ITK not supporting C++11.  Is this true?
>  
> He rebuilt ITK 4.6 with C++11 flags.
>  
> Thank you!
> 
> Email Disclaimer: www.stjude.org/emaildisclaimer
> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From medswengineer at gmail.com  Sun Jul 20 06:40:33 2014
From: medswengineer at gmail.com (med aweng)
Date: Sun, 20 Jul 2014 12:40:33 +0200
Subject: [ITK-users] Gray Level Coocurrence Matrix
In-Reply-To: <CAPf2UMSwNDg7FCOb_BFt57hcKxJV+Arnoc2B1viY1cQvXaPQtg@mail.gmail.com>
References: <CAEMYOQjCae1MmN=QxcQ5P0HumZnD7zn3awg-1EUvmDKWXOCGVQ@mail.gmail.com>
 <CAPf2UMSwNDg7FCOb_BFt57hcKxJV+Arnoc2B1viY1cQvXaPQtg@mail.gmail.com>
Message-ID: <CAEMYOQi8oS2HNmc-n1mqHZEqwsA-xR__nOKXjzTaS-p011vfZw@mail.gmail.com>

Thanks a lot Dzenan for your kind reply.


On Mon, Jul 14, 2014 at 12:29 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Take a look at this example:
> http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures
>
> You might be interested in this code:
> https://github.com/blowekamp/itkTextureAnalysis
> and this thread:
> http://www.itk.org/pipermail/insight-users/2012-February/043764.html
>
>
> On Sun, Jul 13, 2014 at 3:50 PM, med aweng <medswengineer at gmail.com>
> wrote:
>
>> Hello,
>>
>> I'm new to ITK, and trying to calculate the Gray Level Coocurrence Matrix
>> (GLCM) features of some image.
>>
>> I have started as follows:
>>
>> typedef itk::Image< double, 3 >  MyImageType;
>>
>> I found that there are two classes to use for my task:
>>
>> ScalarImageToGreyLevelCooccurrenceMatrixGenerator
>> <http://www.itk.org/Doxygen320/html/classitk_1_1Statistics_1_1ScalarImageToGreyLevelCooccurrenceMatrixGenerator.html>
>>
>> GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator
>> <http://www.itk.org/Doxygen320/html/classitk_1_1Statistics_1_1GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator.html#_details>
>>
>> Can you just kindly guide me on how to go further with building this
>> program, just for me to know how the structure of an ITK program should
>> look like?
>>
>> Thanks.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140720/a7740352/attachment.html>

From medswengineer at gmail.com  Sun Jul 20 06:43:27 2014
From: medswengineer at gmail.com (med aweng)
Date: Sun, 20 Jul 2014 12:43:27 +0200
Subject: [ITK-users] Grey Level Run Length Matrix
Message-ID: <CAEMYOQhMkhDCt7BWt9OJYQ_atidk=+P1O+yx=39yYY-yeszTkA@mail.gmail.com>

I'm trying to implement the "Grey Level Run Length Matrix" in ITK. I'm just
having some issues on how to start with that.

I came to the following function:

http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToRunLengthMatrixFilter.html

Would that function be the starting point? Can you just kindly guide me how
to start with that?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140720/4e617bbf/attachment.html>

From medswengineer at gmail.com  Sun Jul 20 09:30:27 2014
From: medswengineer at gmail.com (med aweng)
Date: Sun, 20 Jul 2014 15:30:27 +0200
Subject: [ITK-users] Question about "ScalarImageToRunLengthMatrixFilter"
Message-ID: <CAEMYOQhSEWMWLx-DrO_BuR=NuP84XXcCNNBV6QzcmN-4Oe0Q3w@mail.gmail.com>

Hello,

I have a question about the "ScalarImageToRunLengthMatrixFilter" here:

http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToRunLengthMatrixFilter.html

- What does the "THistogramFrequencyContainer" mean?
- How can I obtain its value?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140720/4d30c90e/attachment.html>

From medswengineer at gmail.com  Mon Jul 21 07:44:12 2014
From: medswengineer at gmail.com (med aweng)
Date: Mon, 21 Jul 2014 13:44:12 +0200
Subject: [ITK-users] (no subject)
Message-ID: <CAEMYOQgZ-QHaE7C=0izB0=zu7uOqPE7ak69xG_Oa8bKLsUUDew@mail.gmail.com>

Hello,

In the following example:
http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures

When it says:

//calculate features for one offset


What does this mean?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140721/5209061f/attachment.html>

From medswengineer at gmail.com  Mon Jul 21 10:53:18 2014
From: medswengineer at gmail.com (med aweng)
Date: Mon, 21 Jul 2014 16:53:18 +0200
Subject: [ITK-users] Offset type
Message-ID: <CAEMYOQhz_iJgGcwM0T4hO9JgNeaWgf-P+h2UpCuab10OUCRFcg@mail.gmail.com>

Hi,

What is meant by the "OffsetType" in this code?

https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/test/itkScalarImageToRunLengthMatrixFilterTest.cxx

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140721/e7264a0e/attachment.html>

From daviddoria at gmail.com  Mon Jul 21 12:44:09 2014
From: daviddoria at gmail.com (David Doria)
Date: Mon, 21 Jul 2014 12:44:09 -0400
Subject: [ITK-users] Offset type
In-Reply-To: <CAEMYOQhz_iJgGcwM0T4hO9JgNeaWgf-P+h2UpCuab10OUCRFcg@mail.gmail.com>
References: <CAEMYOQhz_iJgGcwM0T4hO9JgNeaWgf-P+h2UpCuab10OUCRFcg@mail.gmail.com>
Message-ID: <CABDpjT=YjbKbL6vfQZsiaMQOD5ZhG1xEzqPNg3dKMZX1Ue=3=w@mail.gmail.com>

On Mon, Jul 21, 2014 at 10:53 AM, med aweng <medswengineer at gmail.com> wrote:

> Hi,
>
> What is meant by the "OffsetType" in this code?
>
>
> https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/test/itkScalarImageToRunLengthMatrixFilterTest.cxx
>
> Thanks.
>

OffsetType is an instance of this class:

http://www.itk.org/Doxygen/html/classitk_1_1Offset.html

that is compatible with the ImageType.

David
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140721/4a0e5f3f/attachment.html>

From medswengineer at gmail.com  Mon Jul 21 14:24:07 2014
From: medswengineer at gmail.com (med aweng)
Date: Mon, 21 Jul 2014 20:24:07 +0200
Subject: [ITK-users] Offset directions
Message-ID: <CAEMYOQhWL4BDz0YzCpVbvcKzFw4dhAV0rZyAGSW7yTkVS4rY1w@mail.gmail.com>

Hello,


For the directions (degrees): 0, 45, 90, 135, if I want to apply them on an
image, I knew that for instance here:
https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/test/itkScalarImageToRunLengthMatrixFilterTest.cxx

 {0,-1} is "vertical", and {-1,0} is "horizontal".

Can you kindly just clarify to me how it was known that the first is
vertical and the later is horizontal? And, if we want to represent 35
degrees and 135 degrees, how will this be represented?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140721/4d697898/attachment.html>

From ahmed at mufradat.com  Tue Jul 22 03:37:05 2014
From: ahmed at mufradat.com (ahmed at mufradat.com)
Date: Tue, 22 Jul 2014 09:37:05 +0200
Subject: [ITK-users] Smartpointer as a default parameter for a function
Message-ID: <74500304cea08473af6cfd3b37c686c6@mufradat.com>

Hello All,

Suppose I have class like

class A{
     public:
     A(int a, ImageType::Pointer ptr){
         // whatever!
     }
};

My question is, what's the default value for that ptr? I'd like to be 
able to create an instance of that class using

A myA(5);

so for the definition of the constructor of A:

A(int a, ImageType::Pointer ptr = WHAT?)

Best regards,
Ahmed

From bilgincc at gmail.com  Tue Jul 22 03:58:17 2014
From: bilgincc at gmail.com (Cagatay Bilgin)
Date: Tue, 22 Jul 2014 00:58:17 -0700
Subject: [ITK-users] Motion under Mean Curvature with LevelSetv4 Framework
Message-ID: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>

Dear ITK Community,

I am trying to familiarize myself with the new level set classes. My goal
is to simulate motion under mean curvature using the new design.

I have put together the following, looking at the examples and tests.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872740/ is a great source to
understand the design and tests in source directory are very helpful, thank
you for the resources!

The test scenario I have is a L shaped object. I would expect the object to
become somewhat ellipse and then disappear at the end of the evolution.
However I get the following results attached to the email. I don't quite
follow these results. Am I missing something obvious?

Here is the code and CMakeLists.txt. I ran the program with ./Motion 100 0
0 0.05

#include "itkBinaryImageToLevelSetImageAdaptor.h"
#include "itkImageFileReader.h"
#include "itkLevelSetContainer.h"
#include "itkLevelSetEquationPropagationTerm.h"
#include "itkLevelSetEquationAdvectionTerm2.h"
#include "itkLevelSetEquationContainer.h"
#include "itkLevelSetEquationTermContainer.h"
#include "itkLevelSetEvolution.h"
#include "itkLevelSetEvolutionNumberOfIterationsStoppingCriterion.h"
#include "itkLevelSetDenseImage.h"
#include "itkVTKVisualizeImageLevelSetIsoValues.h"
#include "itkSinRegularizedHeavisideStepFunction.h"
#include "itkLevelSetIterationUpdateCommand.h"
#include "itkLevelSetEquationCurvatureTerm.h"
#include "itkCastImageFilter.h"
#include "itkWhitakerSparseLevelSetImage.h"
#include "itkSpatialObjectToImageFilter.h"
#include "itkEllipseSpatialObject.h"

typedef itk::Image< float, 2 >  FIT;

/*
 * L Shape
 */
void CreateSquareImage(FIT::Pointer image)
{
    FIT::RegionType region;
    FIT::IndexType start;
    start[0] = 0;
    start[1] = 0;

    FIT::SizeType size;
    size[0] = 200;
    size[1] = 300;

    region.SetSize(size);
    region.SetIndex(start);

    image->SetRegions(region);
    image->Allocate();

    // Set pixels in a square to one value
    for(unsigned int r = 20; r < 160; r++)
    {
        for(unsigned int c = 30; c < 100; c++)
        {
            FIT::IndexType pixelIndex;
            pixelIndex[0] = r;
            pixelIndex[1] = c;

            image->SetPixel(pixelIndex, 255);
        }
    }

    for(unsigned int r = 20; r < 80; r++)
    {
        for(unsigned int c = 100; c < 200; c++)
        {
            FIT::IndexType pixelIndex;
            pixelIndex[0] = r;
            pixelIndex[1] = c;

            image->SetPixel(pixelIndex, 255);
        }
    }
}


/*
 */
int main( int argc, char* argv[] )
{
    if( argc != 5)
    {
        std::cerr << "Missing Arguments" << std::endl;
        std::cerr << argv[0] << std::endl;
        std::cerr << "1- Number of Iterations" << std::endl;
        std::cerr << "2- Propagation Term" << std::endl;
        std::cerr << "3- Advection Term" << std::endl;
        std::cerr << "4- Curvature Term" << std::endl;
        return EXIT_FAILURE;
    }

    // Image Dimension
    const unsigned int Dimension = 2;

    typedef unsigned char                            InputPixelType;
    typedef itk::Image< InputPixelType, Dimension >  IIT;
    typedef itk::Image< float, 2 >  FIT;

    FIT::Pointer input = FIT::New();
    CreateSquareImage(input);

    int numberOfIterations = atoi( argv[1]);

    typedef float                                         LevelSetPixelType;
    typedef itk::Image< LevelSetPixelType, Dimension >    LSIT;
    typedef itk::LevelSetDenseImage< LSIT >  LST;
    //typedef itk::WhitakerSparseLevelSetImage< LevelSetPixelType, 2 > LST;

    typedef LST::OutputType                      LevelSetOutputType;
    typedef LST::OutputRealType                  LevelSetRealType;

    // convert a binary mask to a level-set function
    typedef itk::BinaryImageToLevelSetImageAdaptor<FIT, LST >  BI2LST;
    BI2LST::Pointer adaptor = BI2LST::New();
    adaptor->SetInputImage( input );
    adaptor->Initialize();
    LST::Pointer levelSet = adaptor->GetLevelSet();

    // The Heaviside function
    typedef itk::SinRegularizedHeavisideStepFunction< LevelSetRealType,
LevelSetRealType > HeavisideFunctionType;
    HeavisideFunctionType::Pointer heaviside = HeavisideFunctionType::New();
    heaviside->SetEpsilon( 1 );

    // Create the level set container
    typedef itk::LevelSetContainer< itk::IdentifierType, LST > LSContainerT;
    LSContainerT::Pointer levelSetContainer = LSContainerT::New();
    levelSetContainer->SetHeaviside( heaviside );
    levelSetContainer->AddLevelSet( 0, levelSet );

    // Create the terms.
    typedef itk::LevelSetEquationPropagationTerm<FIT, LSContainerT>
 PropagationTermType;
    PropagationTermType::Pointer propagationTerm =
PropagationTermType::New();
    propagationTerm->SetInput(input);
    propagationTerm->SetCoefficient(atof(argv[2]));

    typedef itk::LevelSetEquationAdvectionTerm2<FIT, LSContainerT>
 AdvectionTermType;
    AdvectionTermType::Pointer advectionTerm = AdvectionTermType::New();
    advectionTerm->SetInput(input);
    advectionTerm->SetCoefficient(atof(argv[3]));

    typedef itk::LevelSetEquationCurvatureTerm<FIT, LSContainerT>
 CurvatureTermType;
    CurvatureTermType::Pointer curvatureTerm = CurvatureTermType::New();
    //curvatureTerm->SetInput(input);
    curvatureTerm->SetCoefficient(atof(argv[4]));


    // Create term container (equation rhs)
    typedef itk::LevelSetEquationTermContainer< FIT, LSContainerT >
TermContainerType;
    TermContainerType::Pointer termContainer = TermContainerType::New();
    termContainer->SetLevelSetContainer( levelSetContainer );
    termContainer->SetInput( input );
    //termContainer->AddTerm( 0, propagationTerm );
    //termContainer->AddTerm( 1, advectionTerm );
    termContainer->AddTerm( 0, curvatureTerm );

    // Create equation container
    typedef itk::LevelSetEquationContainer< TermContainerType >
EquationContainerType;
    EquationContainerType::Pointer equationContainer =
EquationContainerType::New();
    equationContainer->SetLevelSetContainer( levelSetContainer );
    equationContainer->AddEquation( 0, termContainer );

    // Create stopping criteria
    typedef itk::LevelSetEvolutionNumberOfIterationsStoppingCriterion<
LSContainerT > StoppingCriterionType;
    StoppingCriterionType::Pointer criterion = StoppingCriterionType::New();
    criterion->SetNumberOfIterations( numberOfIterations );

    // Create the visualizer
    typedef itk::VTKVisualizeImageLevelSetIsoValues< FIT, LST >
VisualizationType;
    VisualizationType::Pointer visualizer = VisualizationType::New();
    visualizer->SetInputImage( input );
    visualizer->SetLevelSet( levelSet );
    visualizer->SetScreenCapture( true );

    // Create evolution class
    typedef itk::LevelSetEvolution< EquationContainerType, LST >
LevelSetEvolutionType;
    LevelSetEvolutionType::Pointer evolution = LevelSetEvolutionType::New();
    evolution->SetEquationContainer( equationContainer );
    evolution->SetStoppingCriterion( criterion );
    evolution->SetLevelSetContainer( levelSetContainer );

    typedef itk::LevelSetIterationUpdateCommand< LevelSetEvolutionType,
VisualizationType > IterationUpdateCommandType;
    IterationUpdateCommandType::Pointer iterationUpdateCommand =
IterationUpdateCommandType::New();
    iterationUpdateCommand->SetFilterToUpdate( visualizer );
    iterationUpdateCommand->SetUpdatePeriod( 1 );

    evolution->AddObserver( itk::IterationEvent(), iterationUpdateCommand );

    evolution->Update();

    return EXIT_SUCCESS;
}



cmake_minimum_required(VERSION 2.8)

project(CurvatureMotion)

find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

find_package(VTK REQUIRED)
include(${VTK_USE_FILE})

add_executable(Motion main.cpp)
target_link_libraries(Motion ${ITK_LIBRARIES}  ${VTK_LIBRARIES})

[image: Inline image 4][image: Inline image 3]
-- 
Cemal Cagatay Bilgin, PhD
Life Sciences Division
Lawrence Berkeley National Lab
MS977, One Cyclotron Road
Berkeley, CA 94720, USA
Email: ccbilgin at lbl.gov
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/87e3963c/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: levelset_000.png
Type: image/png
Size: 2652 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/87e3963c/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: levelset_040.png
Type: image/png
Size: 3421 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/87e3963c/attachment-0001.png>

From marco.ulge at gmail.com  Tue Jul 22 04:39:22 2014
From: marco.ulge at gmail.com (Marco Ulge)
Date: Tue, 22 Jul 2014 01:39:22 -0700 (PDT)
Subject: [ITK-users] Offset directions
In-Reply-To: <CAEMYOQhWL4BDz0YzCpVbvcKzFw4dhAV0rZyAGSW7yTkVS4rY1w@mail.gmail.com>
References: <CAEMYOQhWL4BDz0YzCpVbvcKzFw4dhAV0rZyAGSW7yTkVS4rY1w@mail.gmail.com>
Message-ID: <1406018362419-34277.post@n7.nabble.com>

Offsets are defined in ITK wether you are using them for GLCM or Neighborhood
Iterators for example. I believe you can find a complete list off offset in
the Software Guide in the Neighborhood Iterator section (chapter 11).

Anyway here's the list of offsets (with distance = 1):

0 degree : {1,0}
45 degree: {1, -1}
90 degree: {0,-1}
135 degree: {-1,-1}
180 degree: {-1,0}
225 degree: {-1,1}
270 degree: {0,1}
315 degree: {1,1}

Please notice that there is no offset for 35 degrees, that just doesn't make
sense

Marco




--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Offset-directions-tp34274p34277.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From vincent.ngai at gmail.com  Tue Jul 22 04:49:02 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Tue, 22 Jul 2014 16:49:02 +0800
Subject: [ITK-users] Smartpointer as a default parameter for a function
In-Reply-To: <74500304cea08473af6cfd3b37c686c6@mufradat.com>
References: <74500304cea08473af6cfd3b37c686c6@mufradat.com>
Message-ID: <CAC3nAP03t8kpZc2_0CfO=MSLVG4CCu_jSQmeP8KVRBxdfHcLPg@mail.gmail.com>

Technically it should be A(int a, ImageType::Pointer ptr =
ImageType::Pointer() );

But I"m not sure if parameter defaults are supported on non-POD parameter
types. Why not just overload the ctor and create another
class A
{
 A(int a, ImageType::Pointer ptr);
 A( int a );
};


On Tue, Jul 22, 2014 at 3:37 PM, <ahmed at mufradat.com> wrote:

> Hello All,
>
> Suppose I have class like
>
> class A{
>     public:
>     A(int a, ImageType::Pointer ptr){
>         // whatever!
>     }
> };
>
> My question is, what's the default value for that ptr? I'd like to be able
> to create an instance of that class using
>
> A myA(5);
>
> so for the definition of the constructor of A:
>
> A(int a, ImageType::Pointer ptr = WHAT?)
>
> Best regards,
> Ahmed
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>



-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/1ea1b985/attachment.html>

From medswengineer at gmail.com  Tue Jul 22 06:26:12 2014
From: medswengineer at gmail.com (med aweng)
Date: Tue, 22 Jul 2014 12:26:12 +0200
Subject: [ITK-users] Should we use two braces with the offset?
Message-ID: <CAEMYOQgAEt_c+te+=74ZFwpyov=b_ZEOKUgaf-gHms-mB7Wd=w@mail.gmail.com>

Hi,

As you can see in the following statement:

    InputImageType::OffsetType offset1 = {{0, -1}};

>From here:https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/test/itkScalarImageToRunLengthMatrixFilterTest.cxx

Two braces have been used with the "offset". Should this be done? Why is that?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/fff8b14d/attachment.html>

From medswengineer at gmail.com  Tue Jul 22 06:32:54 2014
From: medswengineer at gmail.com (med aweng)
Date: Tue, 22 Jul 2014 12:32:54 +0200
Subject: [ITK-users] OffsetVectorPointer and OffsetVector
Message-ID: <CAEMYOQjdch7RnP1iR8JtziiEmqfo3wa9yUQL+qTD2FFT0KFupQ@mail.gmail.com>

Hi,

Following the code here:
https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/test/itkScalarImageToRunLengthMatrixFilterTest.cxx

I came to the following statement:

FilterType::OffsetVectorPointer offsetV = FilterType::OffsetVector::New();

- What do "OffsetVectorPointer" and "OffsetVector" mean? Why do we need
them here?

- I tried to find the documentation for them, but couldn't find the
documentation. Do you know a link that refers to those?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/cf3bffcf/attachment.html>

From blowekamp at mail.nih.gov  Tue Jul 22 07:51:22 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 22 Jul 2014 07:51:22 -0400
Subject: [ITK-users] Should we use two braces with the offset?
In-Reply-To: <CAEMYOQgAEt_c+te+=74ZFwpyov=b_ZEOKUgaf-gHms-mB7Wd=w@mail.gmail.com>
References: <CAEMYOQgAEt_c+te+=74ZFwpyov=b_ZEOKUgaf-gHms-mB7Wd=w@mail.gmail.com>
Message-ID: <D1202E25-972C-46B1-8362-A79AF777EC8D@mail.nih.gov>

How this helps:

http://en.cppreference.com/w/cpp/language/aggregate_initialization


On Jul 22, 2014, at 6:26 AM, med aweng <medswengineer at gmail.com> wrote:

> Hi,
> 
> As you can see in the following statement:
> 
>     InputImageType::OffsetType offset1 = {{0, -1}};
> 
> 
> From here:https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/test/itkScalarImageToRunLengthMatrixFilterTest.cxx
> 
> 
> Two braces have been used with the "offset". Should this be done? Why is that?
> 
> Thanks.
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/5ab94d94/attachment.html>

From medswengineer at gmail.com  Tue Jul 22 08:04:48 2014
From: medswengineer at gmail.com (med aweng)
Date: Tue, 22 Jul 2014 14:04:48 +0200
Subject: [ITK-users] Should we use two braces with the offset?
In-Reply-To: <D1202E25-972C-46B1-8362-A79AF777EC8D@mail.nih.gov>
References: <CAEMYOQgAEt_c+te+=74ZFwpyov=b_ZEOKUgaf-gHms-mB7Wd=w@mail.gmail.com>
 <D1202E25-972C-46B1-8362-A79AF777EC8D@mail.nih.gov>
Message-ID: <CAEMYOQjkf2VyZ-VJD7+zPWGpca-_KanRtxKA47MNhZLtW31cUg@mail.gmail.com>

Thanks a lot Bradely...


On Tue, Jul 22, 2014 at 1:51 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> How this helps:
>
> http://en.cppreference.com/w/cpp/language/aggregate_initialization
>
>
> On Jul 22, 2014, at 6:26 AM, med aweng <medswengineer at gmail.com> wrote:
>
> Hi,
>
> As you can see in the following statement:
>
>     InputImageType::OffsetType offset1 = {{0, -1}};
>
> From here:https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/test/itkScalarImageToRunLengthMatrixFilterTest.cxx
>
> Two braces have been used with the "offset". Should this be done? Why is that?
>
> Thanks.
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/eac94478/attachment.html>

From medswengineer at gmail.com  Tue Jul 22 08:05:30 2014
From: medswengineer at gmail.com (med aweng)
Date: Tue, 22 Jul 2014 14:05:30 +0200
Subject: [ITK-users] Offset directions
In-Reply-To: <CAEMYOQjY3EhmLHbk7A+HWsuZcf_VmTDSF=zro5SEb0P+Ta102w@mail.gmail.com>
References: <CAEMYOQhWL4BDz0YzCpVbvcKzFw4dhAV0rZyAGSW7yTkVS4rY1w@mail.gmail.com>
 <1406018362419-34277.post@n7.nabble.com>
 <CAEMYOQiGswnyLU9ouYwfjbRz1aPOO=KzA+Kc+QguWLrgsKs+bg@mail.gmail.com>
 <CA+=+rrB0nDpKGPhkdC3-GnST5ATnPosumYmAhetQcbScWxycZw@mail.gmail.com>
 <CAEMYOQjY3EhmLHbk7A+HWsuZcf_VmTDSF=zro5SEb0P+Ta102w@mail.gmail.com>
Message-ID: <CAEMYOQiGgqopzWpyT-npXJ+n+FY4z_-j-KkPEHz2uhhEucn9kg@mail.gmail.com>

>
> Thanks a lot Marco for your thorough explanation. I know how the degrees
> will look like, but, the main issue was for instance why 45 degrees' offset
> is {1,-1}, and likewise for the other degrees. Is that just a convention?
> Or, there is a way to find that 45 degrees is {1,-1}?
>
> Thanks.
>
>
> On Tue, Jul 22, 2014 at 12:52 PM, Marco Ulgelmo <marco.ulge at gmail.com>
> wrote:
>
>> Let's make an example, let's suppose that you have a 4x4 matrix defined
>> this way:
>>
>> A = [0, 1, 0, 2
>>        0, 2 , 1, 1
>>        3, 1, 0, 0
>>        0, 0, 2, 3]
>>
>> with distance 1 and direction = 45 degrees
>>
>> The GLCM associated to A will be a 4x4 matrix because values in A are
>> from 0 to 3. If A had values ranging from 0 to 7 than the GLCM would have
>> been 8x8. GLCM by definition tells you the grey level occurrences.
>>
>> Now our goal is to understand how we should populate the GLCM matrix.
>> Let's start from GLCM[0][0]. Since as i said before the GLCM tells you the
>> occurrences in gray level, GLCM[0][0] will be the number of occurrences of
>> (0, 0) according to 45 degrees.
>> So you take each pixel in the A matrix which is 0 and count the pairs for
>> each 0 which has a 0 with distance 1 in its 45 degree diagonal. In A we can
>> easily observe the only A[3][1] satisfies this property, in fact we take
>> take pixel, we notice that the pixel according to 45 degree direction will
>> be 0 so we found a pair (0,0) with the required direction.
>>
>> Since there is only 1 occurrence of (0, 0) with direction= 45 degrees,
>> GLCM[0][0] will be 1 (infact 1 is the number of occurrences).
>>
>> In the same way, GLCM[1][0] will look for all the occurrences of pair
>> (1,0) with direction 45 degrees and we can observe that there are no
>> occurrences in A so GLCM[1][0] = 0.
>>
>> GLCM[2][0] = 2 (A[1][1] and A[3][2] satify the direction) and so on.
>>
>> I suggest you taking a look at this example:
>> http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures
>>
>> Beside what this code does (which is not what you are looking for maybe),
>> you can see that it's enough changin the line
>>
>> glcmGenerator->SetOffset(offset);
>>
>>
>> with the offset you want.
>>
>>
>> If you need to compute GLCM for different directions (obtaining a single
>> GLCM as result), you first compute GLCM for each direction and then compute
>> finalGLCM as a mean of the others GLCM
>>
>> Regards,
>>
>> Marco
>>
>>
>> 2014-07-22 12:13 GMT+02:00 med aweng <medswengineer at gmail.com>:
>>
>> Dear Marco,
>>>
>>> Thanks a lot for your reply and very helpful answer. For instance, when
>>> we say that {1,-1} is 45 degrees. How can this be understood geometrically?
>>> In other words, say that I have an image represented as a set of pixels
>>> (squares). How can I derive that {1,-1} for instance mean 45 degrees, and
>>> likewise for the other degrees?
>>>
>>> Thanks.
>>>
>>>
>>> On Tue, Jul 22, 2014 at 10:39 AM, Marco Ulge <marco.ulge at gmail.com>
>>> wrote:
>>>
>>>> Offsets are defined in ITK wether you are using them for GLCM or
>>>> Neighborhood
>>>> Iterators for example. I believe you can find a complete list off
>>>> offset in
>>>> the Software Guide in the Neighborhood Iterator section (chapter 11).
>>>>
>>>> Anyway here's the list of offsets (with distance = 1):
>>>>
>>>> 0 degree : {1,0}
>>>> 45 degree: {1, -1}
>>>> 90 degree: {0,-1}
>>>> 135 degree: {-1,-1}
>>>> 180 degree: {-1,0}
>>>> 225 degree: {-1,1}
>>>> 270 degree: {0,1}
>>>> 315 degree: {1,1}
>>>>
>>>> Please notice that there is no offset for 35 degrees, that just doesn't
>>>> make
>>>> sense
>>>>
>>>> Marco
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://itk-users.7.n7.nabble.com/ITK-users-Offset-directions-tp34274p34277.html
>>>> Sent from the ITK - Users mailing list archive at Nabble.com.
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/e937f9e5/attachment-0001.html>

From blowekamp at mail.nih.gov  Tue Jul 22 08:37:43 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 22 Jul 2014 08:37:43 -0400
Subject: [ITK-users] [ITK] Smartpointer as a default parameter for a
	function
In-Reply-To: <CAC3nAP03t8kpZc2_0CfO=MSLVG4CCu_jSQmeP8KVRBxdfHcLPg@mail.gmail.com>
References: <74500304cea08473af6cfd3b37c686c6@mufradat.com>
 <CAC3nAP03t8kpZc2_0CfO=MSLVG4CCu_jSQmeP8KVRBxdfHcLPg@mail.gmail.com>
Message-ID: <32E9224C-0DE8-41F0-B796-B89BEAA63A63@mail.nih.gov>

Hello,

You can use just about any object type for a default parameter, and pass parameters to the constructor too.

You want to be very careful with constructor with only one parameter especial just an integer. A constructor with just one parameter can be used for implicit conversion. Add the "explicit" keyword before to prevent this:

class A {
  explicit A(int A, PointerType ptr = NULL )
};

And that takes advantage of the implicit conversion with the smart pointer constructor.

Hope that help,
Brad

On Jul 22, 2014, at 4:49 AM, vincent ngai <vincent.ngai at gmail.com> wrote:

> Technically it should be A(int a, ImageType::Pointer ptr = ImageType::Pointer() );
> 
> But I"m not sure if parameter defaults are supported on non-POD parameter types. Why not just overload the ctor and create another 
> class A
> {
>  A(int a, ImageType::Pointer ptr);
>  A( int a );
> };
> 
> 
> On Tue, Jul 22, 2014 at 3:37 PM, <ahmed at mufradat.com> wrote:
> Hello All,
> 
> Suppose I have class like
> 
> class A{
>     public:
>     A(int a, ImageType::Pointer ptr){
>         // whatever!
>     }
> };
> 
> My question is, what's the default value for that ptr? I'd like to be able to create an instance of that class using
> 
> A myA(5);
> 
> so for the definition of the constructor of A:
> 
> A(int a, ImageType::Pointer ptr = WHAT?)
> 
> Best regards,
> Ahmed
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> 
> -- 
> Regards,
> Vincent
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140722/61e17aa7/attachment.html>

From davis.vigneault at gmail.com  Tue Jul 22 17:53:01 2014
From: davis.vigneault at gmail.com (DVigneault)
Date: Tue, 22 Jul 2014 14:53:01 -0700 (PDT)
Subject: [ITK-users] Assigning to VariableSizeMatrix
Message-ID: <1406065981751-34285.post@n7.nabble.com>

All--

I'm getting a segmentation fault upon attempting to assign to an
itk::VariableSizeMatrix.  I tried to find an example of its usage in the
doxygen, wiki, and software manual, but didn't see one.  Here's a minimal
example of my problem:

#include "itkVariableSizeMatrix.h"

int main( int argc, char * argv[] )
{
	
	if( argc != 1 )
    {
        std::cerr << "Usage: " << argv[0] << std::endl;
        return EXIT_FAILURE;
    }
    
    typedef itk::VariableSizeMatrix< double > MatrixType;

	MatrixType matrix;
	matrix(0,0) = 1.0; // Segmentation fault: 11

  return EXIT_SUCCESS;
  
}

Can anyone point out my mistake, or point me toward an example?

Best, and thanks,

--Davis



--
View this message in context: http://itk-users.7.n7.nabble.com/Assigning-to-VariableSizeMatrix-tp34285.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Tue Jul 22 17:58:29 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 22 Jul 2014 17:58:29 -0400
Subject: [ITK-users] Assigning to VariableSizeMatrix
In-Reply-To: <1406065981751-34285.post@n7.nabble.com>
References: <1406065981751-34285.post@n7.nabble.com>
Message-ID: <A8504674-AC27-41AD-9B8F-5982CE889D10@mail.nih.gov>

Where do you set the size of the matrix? Likely this the buffer is initialized to NULL and being dereferenced.

Likely you should do it in the constructor[1] or with the SetSize method[2].

Brad

[1] http://www.itk.org/Doxygen/html/classitk_1_1VariableSizeMatrix.html#a42fd764a36e3a229de900bcec3997de7
[2] http://www.itk.org/Doxygen/html/classitk_1_1VariableSizeMatrix.html#a422d01338a63aa30041b1fc7c7e504a2
On Jul 22, 2014, at 5:53 PM, DVigneault <davis.vigneault at gmail.com> wrote:

> All--
> 
> I'm getting a segmentation fault upon attempting to assign to an
> itk::VariableSizeMatrix.  I tried to find an example of its usage in the
> doxygen, wiki, and software manual, but didn't see one.  Here's a minimal
> example of my problem:
> 
> #include "itkVariableSizeMatrix.h"
> 
> int main( int argc, char * argv[] )
> {
> 	
> 	if( argc != 1 )
>    {
>        std::cerr << "Usage: " << argv[0] << std::endl;
>        return EXIT_FAILURE;
>    }
> 
>    typedef itk::VariableSizeMatrix< double > MatrixType;
> 
> 	MatrixType matrix;
> 	matrix(0,0) = 1.0; // Segmentation fault: 11
> 
>  return EXIT_SUCCESS;
> 
> }
> 
> Can anyone point out my mistake, or point me toward an example?
> 
> Best, and thanks,
> 
> --Davis
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Assigning-to-VariableSizeMatrix-tp34285.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From davis.vigneault at gmail.com  Tue Jul 22 18:29:25 2014
From: davis.vigneault at gmail.com (DVigneault)
Date: Tue, 22 Jul 2014 15:29:25 -0700 (PDT)
Subject: [ITK-users] Assigning to VariableSizeMatrix
In-Reply-To: <A8504674-AC27-41AD-9B8F-5982CE889D10@mail.nih.gov>
References: <1406065981751-34285.post@n7.nabble.com>
 <A8504674-AC27-41AD-9B8F-5982CE889D10@mail.nih.gov>
Message-ID: <1406068165960-34287.post@n7.nabble.com>

Thanks very much, Brad!

I did not set the size--I thought that in a variable matrix the size would
be implied from the index I gave it when assigning to it.

Thanks again,

--Davis



--
View this message in context: http://itk-users.7.n7.nabble.com/Assigning-to-VariableSizeMatrix-tp34285p34287.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From nady.khalily at gmail.com  Wed Jul 23 05:19:58 2014
From: nady.khalily at gmail.com (Nadieh Khalili)
Date: Wed, 23 Jul 2014 11:19:58 +0200
Subject: [ITK-users] 4D Dicom sorting
Message-ID: <CAPs8MRcNWqcX8OLdXXxmvGYO2qqWTJo7RFs3jK3s7RvPRGkOVA@mail.gmail.com>

Hi
I have 4D DCE images and already wrote a code to order and make 3d images
from 4D dicom images, for sorting of images, I used acquisition number from
dicom tags and divide total number of slices to got slice number, but in
two of my data the acquisition number is not true(don't know why). So when
I look at 3D image, it is one and half of normal image. I am thinking to
use slice number tags directly( 0054,0081) but because I have 3d images, my
program just crash during debugging. Do you have any idea how to use that?
any other ideas for achieving slice number are well com.

Cheers,
Nady
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/60f90956/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 06:19:06 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 12:19:06 +0200
Subject: [ITK-users] VectorContainer
Message-ID: <CAEMYOQgT5uGXqNQvcN+CTg3PFd-sZK=rNExQC0b5UAXZGktVnQ@mail.gmail.com>

Hi,

I came about the VectorContainer here:
http://www.itk.org/Doxygen/html/classitk_1_1VectorContainer.html

The description of the class was not clear. Can you kindly clarify what is
the purpose of this class?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/b925ec10/attachment.html>

From elena.bresciani87 at gmail.com  Wed Jul 23 06:20:56 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Wed, 23 Jul 2014 12:20:56 +0200
Subject: [ITK-users] Fwd: ERROR: MeanSquaresImageToImageMetric: Too many
 samples map outside moving image buffer
In-Reply-To: <CACxk=WxkVnWo6sc0J52u-fL2+woxi2z25RW__RWX2Dak4w-0WQ@mail.gmail.com>
References: <CACxk=WxkVnWo6sc0J52u-fL2+woxi2z25RW__RWX2Dak4w-0WQ@mail.gmail.com>
Message-ID: <CACxk=WxAPjyGFTvVDBba2UOW-ccYi8tN63uVmUexpv46p9juKw@mail.gmail.com>

Hello folks,

I have a registration problem for you. I'm using the code in the example
ImageRegistration5.cxx in order to align image of drugs blisters to assess
if they are the same or not.

The code works well even though for certain images couples I get the error
in this message object.
I thought the problem could be the relative difference in images size and
tried to pad the smallest one to have the same size as the biggest: same
error.
After reading comments on the same topic I tried to add to the code the
line

registration -> SetFixedImageRegion (fixedImage -> GetBufferedRegion());

again not solving my problem.
Attached you can find example images: while I can register image "1" on
image "0", if I try to register "2" on "1" I get the ERROR.

Any guess?

Cheers,
Elena



[image: Immagine in linea 3][image: Immagine in linea 2][image: Immagine in
linea 1]
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/910d7547/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2.jpg
Type: image/jpeg
Size: 43787 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/910d7547/attachment-0003.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 0.jpg
Type: image/jpeg
Size: 43096 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/910d7547/attachment-0004.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1.jpg
Type: image/jpeg
Size: 43321 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/910d7547/attachment-0005.jpg>

From medswengineer at gmail.com  Wed Jul 23 06:52:53 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 12:52:53 +0200
Subject: [ITK-users] typename keyword
Message-ID: <CAEMYOQgY3xDBEyp1JpD_-=PXeiWqoNnYnW=0k8orW5F8HHxZ+Q@mail.gmail.com>

Hi,

I know that this question may be a C++ more question, but thought of asking
it here as I couldn't find a clear explanation of the issue.

In the page here:
https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthMatrixFilter.h#L129

I came about this statement:

  typedef typename ImageType::OffsetType OffsetType;

What does "typename" mean here? When do we use it?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/cddab1dc/attachment.html>

From daviddoria at gmail.com  Wed Jul 23 07:04:10 2014
From: daviddoria at gmail.com (David Doria)
Date: Wed, 23 Jul 2014 07:04:10 -0400
Subject: [ITK-users] typename keyword
In-Reply-To: <CAEMYOQgY3xDBEyp1JpD_-=PXeiWqoNnYnW=0k8orW5F8HHxZ+Q@mail.gmail.com>
References: <CAEMYOQgY3xDBEyp1JpD_-=PXeiWqoNnYnW=0k8orW5F8HHxZ+Q@mail.gmail.com>
Message-ID: <CABDpjT=gxnu_TYB9pTijDruvhEQY=ywA5u0RGwkr6HLaojp4aQ@mail.gmail.com>

On Wed, Jul 23, 2014 at 6:52 AM, med aweng <medswengineer at gmail.com> wrote:

> Hi,
>
> I know that this question may be a C++ more question, but thought of
> asking it here as I couldn't find a clear explanation of the issue.
>
> In the page here:
> https://github.com/ComplexSystemsModeling/DCMTK-ITK/blob/master/Modules/Numerics/Statistics/include/itkScalarImageToRunLengthMatrixFilter.h#L129
>
> I came about this statement:
>
>   typedef typename ImageType::OffsetType OffsetType;
>
> What does "typename" mean here? When do we use it?
>
> Thanks.
>
> http://en.wikipedia.org/wiki/Typename
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/843a0f6d/attachment.html>

From blowekamp at mail.nih.gov  Wed Jul 23 07:47:51 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 23 Jul 2014 07:47:51 -0400
Subject: [ITK-users] ERROR: MeanSquaresImageToImageMetric: Too many
	samples map outside moving image buffer
In-Reply-To: <CACxk=WxAPjyGFTvVDBba2UOW-ccYi8tN63uVmUexpv46p9juKw@mail.gmail.com>
References: <CACxk=WxkVnWo6sc0J52u-fL2+woxi2z25RW__RWX2Dak4w-0WQ@mail.gmail.com>
 <CACxk=WxAPjyGFTvVDBba2UOW-ccYi8tN63uVmUexpv46p9juKw@mail.gmail.com>
Message-ID: <D23C5E06-577F-4001-925A-6EC0EB8446B5@mail.nih.gov>

What is the error you are getting?

Brad
On Jul 23, 2014, at 6:20 AM, elena bresciani <elena.bresciani87 at gmail.com> wrote:

> Hello folks,
> 
> I have a registration problem for you. I'm using the code in the example ImageRegistration5.cxx in order to align image of drugs blisters to assess if they are the same or not.
> 
> The code works well even though for certain images couples I get the error in this message object.
> I thought the problem could be the relative difference in images size and tried to pad the smallest one to have the same size as the biggest: same error. 
> After reading comments on the same topic I tried to add to the code the line 
> 
> registration -> SetFixedImageRegion (fixedImage -> GetBufferedRegion());
> 
> again not solving my problem.
> Attached you can find example images: while I can register image "1" on image "0", if I try to register "2" on "1" I get the ERROR.
> 
> Any guess?
> 
> Cheers,
> Elena
> 
> 
> 
> <0.jpg><1.jpg><2.jpg>
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From blowekamp at mail.nih.gov  Wed Jul 23 07:49:48 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 23 Jul 2014 07:49:48 -0400
Subject: [ITK-users] [ITK]  VectorContainer
In-Reply-To: <CAEMYOQgT5uGXqNQvcN+CTg3PFd-sZK=rNExQC0b5UAXZGktVnQ@mail.gmail.com>
References: <CAEMYOQgT5uGXqNQvcN+CTg3PFd-sZK=rNExQC0b5UAXZGktVnQ@mail.gmail.com>
Message-ID: <2064C252-C343-42CF-9D83-26BA8086B044@mail.nih.gov>

Hello,

This class is a wrapper for std::vector in a class derived from itk::Object. This allows the object to be used with ITK smart pointers, and other features in the base class.

Brad

On Jul 23, 2014, at 6:19 AM, med aweng <medswengineer at gmail.com> wrote:

> Hi,
> 
> I came about the VectorContainer here: http://www.itk.org/Doxygen/html/classitk_1_1VectorContainer.html
> 
> The description of the class was not clear. Can you kindly clarify what is the purpose of this class?
> 
> Thanks.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/ec952009/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 07:53:52 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 13:53:52 +0200
Subject: [ITK-users] push_back
Message-ID: <CAEMYOQifG0wiE=PSVUS9ChsydfFVcFc2im_TaC5pWeQmm7aU-Q@mail.gmail.com>

Hello,

What is "push_back" used for in ITK? I tried to find a documentation for
that but wasn't able to.

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/ebd48308/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 07:55:25 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 13:55:25 +0200
Subject: [ITK-users] [ITK]  VectorContainer
In-Reply-To: <2064C252-C343-42CF-9D83-26BA8086B044@mail.nih.gov>
References: <CAEMYOQgT5uGXqNQvcN+CTg3PFd-sZK=rNExQC0b5UAXZGktVnQ@mail.gmail.com>
 <2064C252-C343-42CF-9D83-26BA8086B044@mail.nih.gov>
Message-ID: <CAEMYOQiEJPF3-C1-y8X2otdTU+XNhN=+BEds+mGY4vZ-GW9u2A@mail.gmail.com>

Hello Bradely,

Thanks for your kind reply. So, it is basically a "vector", is that right?
But, made to be used with ITK?

Thanks.


On Wed, Jul 23, 2014 at 1:49 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> This class is a wrapper for std::vector in a class derived from
> itk::Object. This allows the object to be used with ITK smart pointers, and
> other features in the base class.
>
> Brad
>
> On Jul 23, 2014, at 6:19 AM, med aweng <medswengineer at gmail.com> wrote:
>
> Hi,
>
> I came about the VectorContainer here:
> http://www.itk.org/Doxygen/html/classitk_1_1VectorContainer.html
>
> The description of the class was not clear. Can you kindly clarify what is
> the purpose of this class?
>
> Thanks.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/b3b09bee/attachment.html>

From blowekamp at mail.nih.gov  Wed Jul 23 07:59:01 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 23 Jul 2014 07:59:01 -0400
Subject: [ITK-users] push_back
In-Reply-To: <CAEMYOQifG0wiE=PSVUS9ChsydfFVcFc2im_TaC5pWeQmm7aU-Q@mail.gmail.com>
References: <CAEMYOQifG0wiE=PSVUS9ChsydfFVcFc2im_TaC5pWeQmm7aU-Q@mail.gmail.com>
Message-ID: <1D841E04-01AD-41B8-9135-9F0A081F3415@mail.nih.gov>

Hello,

I am unfortunately not sure how to help you again with this question.

Perhaps this would help:
http://www.vtk.org/Wiki/VTK/FAQ#How_should_I_ask_questions_on_the_mailing_lists.3F

Brad

On Jul 23, 2014, at 7:53 AM, med aweng <medswengineer at gmail.com> wrote:

> Hello,
> 
> What is "push_back" used for in ITK? I tried to find a documentation for that but wasn't able to.
> 
> Thanks.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From medswengineer at gmail.com  Wed Jul 23 08:07:24 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 14:07:24 +0200
Subject: [ITK-users] Implementing the Gray Level Run Length algorithm
Message-ID: <CAEMYOQj1FWNat-d_ZALZrB0qqgpcyX2L8HuCFHUJfCJgU8e24g@mail.gmail.com>

Hello,

I have understood how the "Gray Level Run Length" method works, and trying
to implement that in ITK.

I'm kind of new to ITK, and just need some guidance on how to proceed.

This is what I have done so far for instance:

typedef itk::Image<double, 3> InputImageType;
typedef itk::Statistics::ScalarImageToRunLengthMatrixFilter<InputImageType>
FilterType;
typedef VectorContainer<unsigned char, OffsetType> OffsetVector;
typedef typename OffsetVector::Pointer OffsetVectorPointer;
InputImageType::Pointer image = InputImageType::New();
FilterType::Pointer filter = FilterType::New();
filter->SetInput(image);

InputImageType::OffsetType offset1 ={{1,0}};

FilterType::OffsetVectorPointer offsetV = FilterType::OffsetVector::New();
offsetV.push_back(offset1);

filter->SetOffsets(offsetV);

Any guidance or hints on how to proceed on that?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/9db6ff78/attachment.html>

From jhlegarreta at vicomtech.org  Wed Jul 23 08:16:59 2014
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 23 Jul 2014 14:16:59 +0200
Subject: [ITK-users] Implementing the Gray Level Run Length algorithm
In-Reply-To: <CAEMYOQj1FWNat-d_ZALZrB0qqgpcyX2L8HuCFHUJfCJgU8e24g@mail.gmail.com>
References: <CAEMYOQj1FWNat-d_ZALZrB0qqgpcyX2L8HuCFHUJfCJgU8e24g@mail.gmail.com>
Message-ID: <CAAKhGh99Fa0CArbXy5rqfG1nESTUi5y-Z4ZU3xo0MdZFdHMgbQ@mail.gmail.com>

Hi,
I haven't used it personally, but just in case you haven't done it yet,
having a look ar the Insight Journal article [1] that first proposed the
related classes, functions or analysis may be of help.

It includes a paper on the features of the original filters, and the source
code, including a test that shows how to use them.

HTH,
JON HAITZ


[1] http://www.insight-journal.org/browse/publication/231


On 23 July 2014 14:07, med aweng <medswengineer at gmail.com> wrote:

> Hello,
>
> I have understood how the "Gray Level Run Length" method works, and trying
> to implement that in ITK.
>
> I'm kind of new to ITK, and just need some guidance on how to proceed.
>
> This is what I have done so far for instance:
>
> typedef itk::Image<double, 3> InputImageType;
> typedef
> itk::Statistics::ScalarImageToRunLengthMatrixFilter<InputImageType>
> FilterType;
> typedef VectorContainer<unsigned char, OffsetType> OffsetVector;
> typedef typename OffsetVector::Pointer OffsetVectorPointer;
> InputImageType::Pointer image = InputImageType::New();
> FilterType::Pointer filter = FilterType::New();
> filter->SetInput(image);
>
> InputImageType::OffsetType offset1 ={{1,0}};
>
> FilterType::OffsetVectorPointer offsetV = FilterType::OffsetVector::New();
> offsetV.push_back(offset1);
>
> filter->SetOffsets(offsetV);
>
> Any guidance or hints on how to proceed on that?
>
> Thanks.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/edf3c5bb/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 08:19:45 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 14:19:45 +0200
Subject: [ITK-users] Implementing the Gray Level Run Length algorithm
In-Reply-To: <CAAKhGh99Fa0CArbXy5rqfG1nESTUi5y-Z4ZU3xo0MdZFdHMgbQ@mail.gmail.com>
References: <CAEMYOQj1FWNat-d_ZALZrB0qqgpcyX2L8HuCFHUJfCJgU8e24g@mail.gmail.com>
 <CAAKhGh99Fa0CArbXy5rqfG1nESTUi5y-Z4ZU3xo0MdZFdHMgbQ@mail.gmail.com>
Message-ID: <CAEMYOQjbkGGbbkj_KhwAr9Cuo_vn_q+jDmDYgwgukEfjb4BwxQ@mail.gmail.com>

Hi Jon,

Thanks for your kind reply. For the test, would this be the file I should
be looking at?
https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx

Thanks.


On Wed, Jul 23, 2014 at 2:16 PM, Jon Haitz Legarreta <
jhlegarreta at vicomtech.org> wrote:

> Hi,
> I haven't used it personally, but just in case you haven't done it yet,
> having a look ar the Insight Journal article [1] that first proposed the
> related classes, functions or analysis may be of help.
>
> It includes a paper on the features of the original filters, and the
> source code, including a test that shows how to use them.
>
> HTH,
> JON HAITZ
>
>
> [1] http://www.insight-journal.org/browse/publication/231
>
>
> On 23 July 2014 14:07, med aweng <medswengineer at gmail.com> wrote:
>
>> Hello,
>>
>> I have understood how the "Gray Level Run Length" method works, and
>> trying to implement that in ITK.
>>
>> I'm kind of new to ITK, and just need some guidance on how to proceed.
>>
>> This is what I have done so far for instance:
>>
>> typedef itk::Image<double, 3> InputImageType;
>> typedef
>> itk::Statistics::ScalarImageToRunLengthMatrixFilter<InputImageType>
>> FilterType;
>> typedef VectorContainer<unsigned char, OffsetType> OffsetVector;
>> typedef typename OffsetVector::Pointer OffsetVectorPointer;
>> InputImageType::Pointer image = InputImageType::New();
>> FilterType::Pointer filter = FilterType::New();
>> filter->SetInput(image);
>>
>> InputImageType::OffsetType offset1 ={{1,0}};
>>
>> FilterType::OffsetVectorPointer offsetV = FilterType::OffsetVector::New();
>> offsetV.push_back(offset1);
>>
>> filter->SetOffsets(offsetV);
>>
>> Any guidance or hints on how to proceed on that?
>>
>> Thanks.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/4bf5c38f/attachment.html>

From jhlegarreta at vicomtech.org  Wed Jul 23 08:24:46 2014
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 23 Jul 2014 14:24:46 +0200
Subject: [ITK-users] Implementing the Gray Level Run Length algorithm
In-Reply-To: <CAEMYOQjbkGGbbkj_KhwAr9Cuo_vn_q+jDmDYgwgukEfjb4BwxQ@mail.gmail.com>
References: <CAEMYOQj1FWNat-d_ZALZrB0qqgpcyX2L8HuCFHUJfCJgU8e24g@mail.gmail.com>
 <CAAKhGh99Fa0CArbXy5rqfG1nESTUi5y-Z4ZU3xo0MdZFdHMgbQ@mail.gmail.com>
 <CAEMYOQjbkGGbbkj_KhwAr9Cuo_vn_q+jDmDYgwgukEfjb4BwxQ@mail.gmail.com>
Message-ID: <CAAKhGh9FP35sv8t=KNHEBebwBhj3ZciMvk-NocDYqr6vKQcmjA@mail.gmail.com>

Yes.

JON HAITZ


On 23 July 2014 14:19, med aweng <medswengineer at gmail.com> wrote:

> Hi Jon,
>
> Thanks for your kind reply. For the test, would this be the file I should
> be looking at?
> https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx
>
> Thanks.
>
>
> On Wed, Jul 23, 2014 at 2:16 PM, Jon Haitz Legarreta <
> jhlegarreta at vicomtech.org> wrote:
>
>> Hi,
>> I haven't used it personally, but just in case you haven't done it yet,
>> having a look ar the Insight Journal article [1] that first proposed the
>> related classes, functions or analysis may be of help.
>>
>> It includes a paper on the features of the original filters, and the
>> source code, including a test that shows how to use them.
>>
>> HTH,
>> JON HAITZ
>>
>>
>> [1] http://www.insight-journal.org/browse/publication/231
>>
>>
>> On 23 July 2014 14:07, med aweng <medswengineer at gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I have understood how the "Gray Level Run Length" method works, and
>>> trying to implement that in ITK.
>>>
>>> I'm kind of new to ITK, and just need some guidance on how to proceed.
>>>
>>> This is what I have done so far for instance:
>>>
>>> typedef itk::Image<double, 3> InputImageType;
>>> typedef
>>> itk::Statistics::ScalarImageToRunLengthMatrixFilter<InputImageType>
>>> FilterType;
>>> typedef VectorContainer<unsigned char, OffsetType> OffsetVector;
>>> typedef typename OffsetVector::Pointer OffsetVectorPointer;
>>> InputImageType::Pointer image = InputImageType::New();
>>> FilterType::Pointer filter = FilterType::New();
>>> filter->SetInput(image);
>>>
>>> InputImageType::OffsetType offset1 ={{1,0}};
>>>
>>> FilterType::OffsetVectorPointer offsetV =
>>> FilterType::OffsetVector::New();
>>> offsetV.push_back(offset1);
>>>
>>> filter->SetOffsets(offsetV);
>>>
>>> Any guidance or hints on how to proceed on that?
>>>
>>> Thanks.
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/78d1a3d5/attachment.html>

From elena.bresciani87 at gmail.com  Wed Jul 23 08:30:32 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Wed, 23 Jul 2014 14:30:32 +0200
Subject: [ITK-users] ERROR: MeanSquaresImageToImageMetric: Too many
 samples map outside moving image buffer
In-Reply-To: <D23C5E06-577F-4001-925A-6EC0EB8446B5@mail.nih.gov>
References: <CACxk=WxkVnWo6sc0J52u-fL2+woxi2z25RW__RWX2Dak4w-0WQ@mail.gmail.com>
 <CACxk=WxAPjyGFTvVDBba2UOW-ccYi8tN63uVmUexpv46p9juKw@mail.gmail.com>
 <D23C5E06-577F-4001-925A-6EC0EB8446B5@mail.nih.gov>
Message-ID: <CACxk=Wz01mpwuQ0fEneeyERSyn-9icn980gDQJCrmbvd=JG=Zw@mail.gmail.com>

ExceptionObject caught !

itk::ExceptionObject (0x3043350)
Location: "void itk::MeanSquaresImageToImageMetric<TFixedImage,
TMovingImage>::GetValueAndDerivative(const ParametersType&,
itk::MeanSquaresImageToImageMetric<TFixedImage,
TMovingImage>::MeasureType&,
itk::MeanSquaresImageToImageMetric<TFixedImage,
TMovingImage>::DerivativeType&) const [with TFixedImage =
itk::Image<unsigned char, 2u>; TMovingImage = itk::Image<unsigned char,
2u>; itk::MeanSquaresImageToImageMetric<TFixedImage,
TMovingImage>::ParametersType = itk::OptimizerParameters<double>;
itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::MeasureType
= double; itk::MeanSquaresImageToImageMetric<TFixedImage,
TMovingImage>::DerivativeType = itk::Array<double>]"
File: /usr/local/include/ITK-4.5/itkMeanSquaresImageToImageMetric.hxx
Line: 257
Description: itk::ERROR: MeanSquaresImageToImageMetric(0x30384c0): Too many
samples map outside moving image buffer: 4042 / 568832


2014-07-23 13:47 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> What is the error you are getting?
>
> Brad
> On Jul 23, 2014, at 6:20 AM, elena bresciani <elena.bresciani87 at gmail.com>
> wrote:
>
> > Hello folks,
> >
> > I have a registration problem for you. I'm using the code in the example
> ImageRegistration5.cxx in order to align image of drugs blisters to assess
> if they are the same or not.
> >
> > The code works well even though for certain images couples I get the
> error in this message object.
> > I thought the problem could be the relative difference in images size
> and tried to pad the smallest one to have the same size as the biggest:
> same error.
> > After reading comments on the same topic I tried to add to the code the
> line
> >
> > registration -> SetFixedImageRegion (fixedImage -> GetBufferedRegion());
> >
> > again not solving my problem.
> > Attached you can find example images: while I can register image "1" on
> image "0", if I try to register "2" on "1" I get the ERROR.
> >
> > Any guess?
> >
> > Cheers,
> > Elena
> >
> >
> >
> > <0.jpg><1.jpg><2.jpg>
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/c7ee724b/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 08:45:12 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 14:45:12 +0200
Subject: [ITK-users] Implementing the Gray Level Run Length algorithm
In-Reply-To: <CAAKhGh9FP35sv8t=KNHEBebwBhj3ZciMvk-NocDYqr6vKQcmjA@mail.gmail.com>
References: <CAEMYOQj1FWNat-d_ZALZrB0qqgpcyX2L8HuCFHUJfCJgU8e24g@mail.gmail.com>
 <CAAKhGh99Fa0CArbXy5rqfG1nESTUi5y-Z4ZU3xo0MdZFdHMgbQ@mail.gmail.com>
 <CAEMYOQjbkGGbbkj_KhwAr9Cuo_vn_q+jDmDYgwgukEfjb4BwxQ@mail.gmail.com>
 <CAAKhGh9FP35sv8t=KNHEBebwBhj3ZciMvk-NocDYqr6vKQcmjA@mail.gmail.com>
Message-ID: <CAEMYOQhEY9qap+TKee2i8PnHXpGmdrTWesX9EUVEAXbmFW-x3Q@mail.gmail.com>

Thanks a lot Jon for your kind replies.


On Wed, Jul 23, 2014 at 2:24 PM, Jon Haitz Legarreta <
jhlegarreta at vicomtech.org> wrote:

> Yes.
>
> JON HAITZ
>
>
>
> On 23 July 2014 14:19, med aweng <medswengineer at gmail.com> wrote:
>
>> Hi Jon,
>>
>> Thanks for your kind reply. For the test, would this be the file I should
>> be looking at?
>> https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx
>>
>> Thanks.
>>
>>
>> On Wed, Jul 23, 2014 at 2:16 PM, Jon Haitz Legarreta <
>> jhlegarreta at vicomtech.org> wrote:
>>
>>> Hi,
>>> I haven't used it personally, but just in case you haven't done it yet,
>>> having a look ar the Insight Journal article [1] that first proposed the
>>> related classes, functions or analysis may be of help.
>>>
>>> It includes a paper on the features of the original filters, and the
>>> source code, including a test that shows how to use them.
>>>
>>> HTH,
>>> JON HAITZ
>>>
>>>
>>> [1] http://www.insight-journal.org/browse/publication/231
>>>
>>>
>>> On 23 July 2014 14:07, med aweng <medswengineer at gmail.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> I have understood how the "Gray Level Run Length" method works, and
>>>> trying to implement that in ITK.
>>>>
>>>> I'm kind of new to ITK, and just need some guidance on how to proceed.
>>>>
>>>> This is what I have done so far for instance:
>>>>
>>>> typedef itk::Image<double, 3> InputImageType;
>>>> typedef
>>>> itk::Statistics::ScalarImageToRunLengthMatrixFilter<InputImageType>
>>>> FilterType;
>>>> typedef VectorContainer<unsigned char, OffsetType> OffsetVector;
>>>> typedef typename OffsetVector::Pointer OffsetVectorPointer;
>>>> InputImageType::Pointer image = InputImageType::New();
>>>> FilterType::Pointer filter = FilterType::New();
>>>> filter->SetInput(image);
>>>>
>>>> InputImageType::OffsetType offset1 ={{1,0}};
>>>>
>>>> FilterType::OffsetVectorPointer offsetV =
>>>> FilterType::OffsetVector::New();
>>>> offsetV.push_back(offset1);
>>>>
>>>> filter->SetOffsets(offsetV);
>>>>
>>>> Any guidance or hints on how to proceed on that?
>>>>
>>>> Thanks.
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/becc66d5/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 08:47:40 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 14:47:40 +0200
Subject: [ITK-users] < > or " " in #include
Message-ID: <CAEMYOQjhH9qrxcYA635ykRz1vtBAhCdQsbwzrc8m1Z0yigLV2g@mail.gmail.com>

Hello,

Does it matter if I use " " or < > in the following #include?

#include <itkDenseFrequencyContainer.h>

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/a252a1a6/attachment.html>

From blowekamp at mail.nih.gov  Wed Jul 23 08:48:25 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 23 Jul 2014 08:48:25 -0400
Subject: [ITK-users] ERROR: MeanSquaresImageToImageMetric: Too many
	samples map outside moving image buffer
In-Reply-To: <CACxk=Wz01mpwuQ0fEneeyERSyn-9icn980gDQJCrmbvd=JG=Zw@mail.gmail.com>
References: <CACxk=WxkVnWo6sc0J52u-fL2+woxi2z25RW__RWX2Dak4w-0WQ@mail.gmail.com>
 <CACxk=WxAPjyGFTvVDBba2UOW-ccYi8tN63uVmUexpv46p9juKw@mail.gmail.com>
 <D23C5E06-577F-4001-925A-6EC0EB8446B5@mail.nih.gov>
 <CACxk=Wz01mpwuQ0fEneeyERSyn-9icn980gDQJCrmbvd=JG=Zw@mail.gmail.com>
Message-ID: <DEDB389F-D53D-4164-9166-11C0FEC31C7A@mail.nih.gov>

Is this at the first iteration of after a few? Are iterations converging, diverging or erratic?

If it's the first it's an indication that initial transform is poor and they don't overlap much. There for the results of the transform initializer should be evaluated.

If it's after a few iterations, then is the iteration of the metric and optimizer needs to be examine. Is the value of the metric correct and correlated with the correct solution? Is the step size too big? Would smoothing the fixed and moving images smooth optimization? etc?

These registration examples are not designed to be turn key solution, they are a stepping stone to learn about the registration framework, and begin analyzing the behavior of the components so that a solution to your problem can be constructed.

Brad

On Jul 23, 2014, at 8:30 AM, elena bresciani <elena.bresciani87 at gmail.com> wrote:

> ExceptionObject caught !
> 
> itk::ExceptionObject (0x3043350)
> Location: "void itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::GetValueAndDerivative(const ParametersType&, itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::MeasureType&, itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::DerivativeType&) const [with TFixedImage = itk::Image<unsigned char, 2u>; TMovingImage = itk::Image<unsigned char, 2u>; itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::ParametersType = itk::OptimizerParameters<double>; itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::MeasureType = double; itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::DerivativeType = itk::Array<double>]" 
> File: /usr/local/include/ITK-4.5/itkMeanSquaresImageToImageMetric.hxx
> Line: 257
> Description: itk::ERROR: MeanSquaresImageToImageMetric(0x30384c0): Too many samples map outside moving image buffer: 4042 / 568832
> 
> 
> 2014-07-23 13:47 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> What is the error you are getting?
> 
> Brad
> On Jul 23, 2014, at 6:20 AM, elena bresciani <elena.bresciani87 at gmail.com> wrote:
> 
> > Hello folks,
> >
> > I have a registration problem for you. I'm using the code in the example ImageRegistration5.cxx in order to align image of drugs blisters to assess if they are the same or not.
> >
> > The code works well even though for certain images couples I get the error in this message object.
> > I thought the problem could be the relative difference in images size and tried to pad the smallest one to have the same size as the biggest: same error.
> > After reading comments on the same topic I tried to add to the code the line
> >
> > registration -> SetFixedImageRegion (fixedImage -> GetBufferedRegion());
> >
> > again not solving my problem.
> > Attached you can find example images: while I can register image "1" on image "0", if I try to register "2" on "1" I get the ERROR.
> >
> > Any guess?
> >
> > Cheers,
> > Elena
> >
> >
> >
> > <0.jpg><1.jpg><2.jpg>
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/6a2bbdb4/attachment.html>

From elena.bresciani87 at gmail.com  Wed Jul 23 08:52:59 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Wed, 23 Jul 2014 14:52:59 +0200
Subject: [ITK-users] ERROR: MeanSquaresImageToImageMetric: Too many
 samples map outside moving image buffer
In-Reply-To: <DEDB389F-D53D-4164-9166-11C0FEC31C7A@mail.nih.gov>
References: <CACxk=WxkVnWo6sc0J52u-fL2+woxi2z25RW__RWX2Dak4w-0WQ@mail.gmail.com>
 <CACxk=WxAPjyGFTvVDBba2UOW-ccYi8tN63uVmUexpv46p9juKw@mail.gmail.com>
 <D23C5E06-577F-4001-925A-6EC0EB8446B5@mail.nih.gov>
 <CACxk=Wz01mpwuQ0fEneeyERSyn-9icn980gDQJCrmbvd=JG=Zw@mail.gmail.com>
 <DEDB389F-D53D-4164-9166-11C0FEC31C7A@mail.nih.gov>
Message-ID: <CACxk=WzU2Q0EiPKum1Dhr=8x6z04QBwdE0FA1Wf57KHiY8Rwrw@mail.gmail.com>

I get the error immediately after running the script, so I think the
problem is in the transform initialization.
Should I try with itkCenteredTransformInitializer.h
<http://www.itk.org/Doxygen/html/itkCenteredTransformInitializer_8h_source.html>
?


2014-07-23 14:48 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> Is this at the first iteration of after a few? Are iterations converging,
> diverging or erratic?
>
> If it's the first it's an indication that initial transform is poor and
> they don't overlap much. There for the results of the transform initializer
> should be evaluated.
>
> If it's after a few iterations, then is the iteration of the metric and
> optimizer needs to be examine. Is the value of the metric correct and
> correlated with the correct solution? Is the step size too big? Would
> smoothing the fixed and moving images smooth optimization? etc?
>
> These registration examples are not designed to be turn key solution, they
> are a stepping stone to learn about the registration framework, and begin
> analyzing the behavior of the components so that a solution to your problem
> can be constructed.
>
> Brad
>
> On Jul 23, 2014, at 8:30 AM, elena bresciani <elena.bresciani87 at gmail.com>
> wrote:
>
> ExceptionObject caught !
>
> itk::ExceptionObject (0x3043350)
> Location: "void itk::MeanSquaresImageToImageMetric<TFixedImage,
> TMovingImage>::GetValueAndDerivative(const ParametersType&,
> itk::MeanSquaresImageToImageMetric<TFixedImage,
> TMovingImage>::MeasureType&,
> itk::MeanSquaresImageToImageMetric<TFixedImage,
> TMovingImage>::DerivativeType&) const [with TFixedImage =
> itk::Image<unsigned char, 2u>; TMovingImage = itk::Image<unsigned char,
> 2u>; itk::MeanSquaresImageToImageMetric<TFixedImage,
> TMovingImage>::ParametersType = itk::OptimizerParameters<double>;
> itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::MeasureType
> = double; itk::MeanSquaresImageToImageMetric<TFixedImage,
> TMovingImage>::DerivativeType = itk::Array<double>]"
> File: /usr/local/include/ITK-4.5/itkMeanSquaresImageToImageMetric.hxx
> Line: 257
> Description: itk::ERROR: MeanSquaresImageToImageMetric(0x30384c0): Too
> many samples map outside moving image buffer: 4042 / 568832
>
>
> 2014-07-23 13:47 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>
>> What is the error you are getting?
>>
>> Brad
>> On Jul 23, 2014, at 6:20 AM, elena bresciani <elena.bresciani87 at gmail.com>
>> wrote:
>>
>> > Hello folks,
>> >
>> > I have a registration problem for you. I'm using the code in the
>> example ImageRegistration5.cxx in order to align image of drugs blisters to
>> assess if they are the same or not.
>> >
>> > The code works well even though for certain images couples I get the
>> error in this message object.
>> > I thought the problem could be the relative difference in images size
>> and tried to pad the smallest one to have the same size as the biggest:
>> same error.
>> > After reading comments on the same topic I tried to add to the code the
>> line
>> >
>> > registration -> SetFixedImageRegion (fixedImage -> GetBufferedRegion());
>> >
>> > again not solving my problem.
>> > Attached you can find example images: while I can register image "1" on
>> image "0", if I try to register "2" on "1" I get the ERROR.
>> >
>> > Any guess?
>> >
>> > Cheers,
>> > Elena
>> >
>> >
>> >
>> > <0.jpg><1.jpg><2.jpg>
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/6f44c19e/attachment-0001.html>

From medswengineer at gmail.com  Wed Jul 23 09:01:04 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 15:01:04 +0200
Subject: [ITK-users] GetOutput()
Message-ID: <CAEMYOQgnKQmryvGJJ2Gt99-siLkoZrKvmtruMPoRc1yb3UWXGA@mail.gmail.com>

Hello,

Say that I have used the following code portion:

ReaderType::Pointer ImageReader = ReaderType::New();
....
....
filter->SetInput(ImageReader->GetOutput());

What does GetOutput() mean here? I couldn't find a description for this
function.

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/2eff4ec0/attachment.html>

From drescherjm at gmail.com  Wed Jul 23 09:02:51 2014
From: drescherjm at gmail.com (John Drescher)
Date: Wed, 23 Jul 2014 09:02:51 -0400
Subject: [ITK-users] < > or " " in #include
In-Reply-To: <CAEMYOQjhH9qrxcYA635ykRz1vtBAhCdQsbwzrc8m1Z0yigLV2g@mail.gmail.com>
References: <CAEMYOQjhH9qrxcYA635ykRz1vtBAhCdQsbwzrc8m1Z0yigLV2g@mail.gmail.com>
Message-ID: <CAEhu1-7bv7kPJKc6WQFYJhhOnGe7MKhs79SqO6Ma+pMQ7q+Enw@mail.gmail.com>

> Does it matter if I use " " or < > in the following #include?

http://stackoverflow.com/questions/21593/what-is-the-difference-between-include-filename-and-include-filename
John

From medswengineer at gmail.com  Wed Jul 23 09:08:12 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 15:08:12 +0200
Subject: [ITK-users] < > or " " in #include
In-Reply-To: <CAEhu1-7bv7kPJKc6WQFYJhhOnGe7MKhs79SqO6Ma+pMQ7q+Enw@mail.gmail.com>
References: <CAEMYOQjhH9qrxcYA635ykRz1vtBAhCdQsbwzrc8m1Z0yigLV2g@mail.gmail.com>
 <CAEhu1-7bv7kPJKc6WQFYJhhOnGe7MKhs79SqO6Ma+pMQ7q+Enw@mail.gmail.com>
Message-ID: <CAEMYOQhOs3m9YKqf5CYheTWsOXZuK2hcFgFbyo4nFNCkoODweg@mail.gmail.com>

Thanks John...


On Wed, Jul 23, 2014 at 3:02 PM, John Drescher <drescherjm at gmail.com> wrote:

> > Does it matter if I use " " or < > in the following #include?
>
>
> http://stackoverflow.com/questions/21593/what-is-the-difference-between-include-filename-and-include-filename
> John
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/4caa4392/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 09:11:02 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 15:11:02 +0200
Subject: [ITK-users] Questions about some code
Message-ID: <CAEMYOQgtMg9VOrAfMyUNwNGf3RaEg3Oi1jWhtroVGfroJB_Kbg@mail.gmail.com>

Hello,

In the following code:
https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx

I want to ask about this code portion:

RunLengthFilterType::FeatureValueVectorPointer means =
      runLengthFilter->GetFeatureMeans();
    const RunLengthFilterType::FeatureNameVector* names =
      runLengthFilter->GetRequestedFeatures();

    RunLengthFilterType::FeatureValueVector::ConstIterator mIt =
      means->Begin();
    RunLengthFilterType::FeatureNameVector::ConstIterator nIt =
      names->Begin();

What is it trying to find here? I'm actually facing some issues with
reading the documentation, and thus not able to understand what the classes
above mean.

Thanks for your guidance.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/35edc24b/attachment.html>

From chinander at gmail.com  Wed Jul 23 09:11:22 2014
From: chinander at gmail.com (Mike Chinander)
Date: Wed, 23 Jul 2014 08:11:22 -0500
Subject: [ITK-users] GetOutput()
In-Reply-To: <CAEMYOQgnKQmryvGJJ2Gt99-siLkoZrKvmtruMPoRc1yb3UWXGA@mail.gmail.com>
References: <CAEMYOQgnKQmryvGJJ2Gt99-siLkoZrKvmtruMPoRc1yb3UWXGA@mail.gmail.com>
Message-ID: <CAEb_q0dMJH7CbXHxZ_+7VvYJXCXGxi0EUY_tn+OQ+hX5ra-g2A@mail.gmail.com>

The ITK Software Guide covers many of your questions with a lot of
examples. You will save a lot of time by reading it.

http://www.itk.org/ItkSoftwareGuide.pdf


On Wed, Jul 23, 2014 at 8:01 AM, med aweng <medswengineer at gmail.com> wrote:

> Hello,
>
> Say that I have used the following code portion:
>
> ReaderType::Pointer ImageReader = ReaderType::New();
> ....
> ....
> filter->SetInput(ImageReader->GetOutput());
>
> What does GetOutput() mean here? I couldn't find a description for this
> function.
>
> Thanks.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/df395524/attachment.html>

From medswengineer at gmail.com  Wed Jul 23 09:14:30 2014
From: medswengineer at gmail.com (med aweng)
Date: Wed, 23 Jul 2014 15:14:30 +0200
Subject: [ITK-users] GetOutput()
In-Reply-To: <CAEb_q0dMJH7CbXHxZ_+7VvYJXCXGxi0EUY_tn+OQ+hX5ra-g2A@mail.gmail.com>
References: <CAEMYOQgnKQmryvGJJ2Gt99-siLkoZrKvmtruMPoRc1yb3UWXGA@mail.gmail.com>
 <CAEb_q0dMJH7CbXHxZ_+7VvYJXCXGxi0EUY_tn+OQ+hX5ra-g2A@mail.gmail.com>
Message-ID: <CAEMYOQjxq8BiXD5tjFmzk8d_qdUcDV6eR-wm0AQ+3nJXF6G-TA@mail.gmail.com>

Thanks Mike for your reply


On Wed, Jul 23, 2014 at 3:11 PM, Mike Chinander <chinander at gmail.com> wrote:

> The ITK Software Guide covers many of your questions with a lot of
> examples. You will save a lot of time by reading it.
>
> http://www.itk.org/ItkSoftwareGuide.pdf
>
>
> On Wed, Jul 23, 2014 at 8:01 AM, med aweng <medswengineer at gmail.com>
> wrote:
>
>> Hello,
>>
>> Say that I have used the following code portion:
>>
>> ReaderType::Pointer ImageReader = ReaderType::New();
>> ....
>> ....
>> filter->SetInput(ImageReader->GetOutput());
>>
>> What does GetOutput() mean here? I couldn't find a description for this
>> function.
>>
>> Thanks.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/464f48bf/attachment.html>

From davis.vigneault at gmail.com  Wed Jul 23 10:22:29 2014
From: davis.vigneault at gmail.com (DVigneault)
Date: Wed, 23 Jul 2014 07:22:29 -0700 (PDT)
Subject: [ITK-users] Does VUL need to be installed separately from ITK?
Message-ID: <1406125349302-7585971.post@n2.nabble.com>

All--

I noticed that some parts of vxl (such as vnl) are installed with ITK,
whereas others (such as vul) are not.  Is there a ccmake flag I can use when
building ITK that will cause vul to be built along with ITK, or does it need
to be installed separately?  I looked down the list of the flags in the
ccmake command line interface, but nothing jumped out at me.

Best,

--Davis



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Does-VUL-need-to-be-installed-separately-from-ITK-tp7585971.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Wed Jul 23 10:27:59 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 23 Jul 2014 10:27:59 -0400
Subject: [ITK-users] Does VUL need to be installed separately from ITK?
In-Reply-To: <1406125349302-7585971.post@n2.nabble.com>
References: <1406125349302-7585971.post@n2.nabble.com>
Message-ID: <00F63070-7EEF-4963-B32F-D486D7D62E20@mail.nih.gov>

Hello,

You are correct that ITK only has a subset of VXL, mainly VNL, and VCL.

However, ITK does support using a "system" vxl with ITK, with the ITK_USE_SYSTEM_VXL. Which would be the option to enable when you are installing VXL yourself.

Brad

On Jul 23, 2014, at 10:22 AM, DVigneault <davis.vigneault at gmail.com> wrote:

> All--
> 
> I noticed that some parts of vxl (such as vnl) are installed with ITK,
> whereas others (such as vul) are not.  Is there a ccmake flag I can use when
> building ITK that will cause vul to be built along with ITK, or does it need
> to be installed separately?  I looked down the list of the flags in the
> ccmake command line interface, but nothing jumped out at me.
> 
> Best,
> 
> --Davis
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Does-VUL-need-to-be-installed-separately-from-ITK-tp7585971.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From ksatyananda at gmail.com  Wed Jul 23 11:11:16 2014
From: ksatyananda at gmail.com (Satyananda Kashyap)
Date: Wed, 23 Jul 2014 10:11:16 -0500
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
Message-ID: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>

Hello,

I am looking for your expert opinions here. I have a relatively large C++
project I am working on which uses ITK mainly (hence the question here) and
to some extent VTK and OpenCV. I do think that my code is fairly well
written. I was thinking of wrapping my code to python using either SWIG or
boost.python. Here are my questions :


1. I am led to believe that prototyping and code development is much faster
in Python. Given that I have such a big cpp base code is it really worth
the effort to wrap into python and then continue there.

2. From what I have read ITK uses SWIG wrappings for wrapping into Python
while VTK uses the boost.python route. My initial attempts with both have
been relatively unsuccessful. Any opinion on which one is more user
friendly/better when I have to wrap my own custom classes which use a
combination of both ITK and VTK in them.

3. Any suggestion on a road map as to how to proceed. I am not sure at what
base class level I should wrap them and rewrite the dependencies in python.


Thanks,
Regards,
Kashyap
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/de0d3d6a/attachment.html>

From davis.vigneault at gmail.com  Wed Jul 23 11:19:56 2014
From: davis.vigneault at gmail.com (DVigneault)
Date: Wed, 23 Jul 2014 08:19:56 -0700 (PDT)
Subject: [ITK-users] vnl_svd Segfaults on 3xn matrix, but not on nx3?
Message-ID: <1406128796561-7585974.post@n2.nabble.com>

All--

I'm trying to fit a plane through an image (treating indices as x and y and
pixel value as z) by reading an image into a 3xn matrix and computing the
singular value decomposition with vnl.  However, I'm getting a segfault when
I call the SVD function.  I do not get a segfault when I call the SVD on the
transpose of the same matrix.  Could anyone suggest (a) why this is
segfaulting or (b) a better way to fit a plane to an image in ITK?

Below is a minimal example of the problem.  (Apologies for the many
questions--I very much appreciate Brad's and other's help.)

#include "itkImageFileReader.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkVariableSizeMatrix.h"
#include "vnl/vnl_matrix.h"

const unsigned int             Dimension = 2;
typedef double                 WorkPixelType;
typedef itk::Image< WorkPixelType, Dimension >    WorkImageType;
typedef itk::ImageFileReader< WorkImageType > ReaderType;
typedef itk::VariableSizeMatrix< WorkPixelType > MatrixType;
typedef itk::ImageRegionIteratorWithIndex< WorkImageType > ItType;

int main( int argc, char * argv[] )
{

	// Read in file
    ReaderType::Pointer reader = ReaderType::New();
	reader->SetFileName( "../data/input/wrapped_WT_square.png" );
    reader->Update();
    
    WorkImageType::Pointer input = reader->GetOutput();
    
    MatrixType matrix;
    matrix.SetSize(3,
input->GetLargestPossibleRegion().GetSize()[0]*input->GetLargestPossibleRegion().GetSize()[0]);
    
    ItType inputIt( input, input->GetLargestPossibleRegion() );
    inputIt.GoToBegin();
    unsigned int count = 0;
    while(!inputIt.IsAtEnd()) {
    	
    	
    	matrix(0,count) = inputIt.GetIndex()[0];
    	matrix(1,count) = inputIt.GetIndex()[1];
    	matrix(2,count) = inputIt.Get();
    
    	++count;
    	++inputIt;
    	
    }

    vnl_matrix< double > VNLMatrix = matrix.GetVnlMatrix();

    // n x 3 matrix works:
    vnl_svd<double> svdTranspose(VNLMatrix.transpose()); // Segmentation
fault: 11
    std::cout << svdTranspose << std::endl;
    
    // 3 x n matrix segfaults:
    vnl_svd<double> svd(VNLMatrix); // Segmentation fault: 11
    std::cout << svd << std::endl; // Doesn't make it this far

  return EXIT_SUCCESS;
  
}




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/vnl-svd-Segfaults-on-3xn-matrix-but-not-on-nx3-tp7585974.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From norman-k-williams at uiowa.edu  Wed Jul 23 11:23:50 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Wed, 23 Jul 2014 15:23:50 +0000
Subject: [ITK-users] Undefined IOFactoryRegister__Private methods?
Message-ID: <CFF53DB3.9AF1%norman-k-williams@uiowa.edu>

We have a bunch of big Cmake build systems that until very recently (I noticed it yesterday) were working fine. Now we get link errors like this:

  "itk::BMPImageIOFactoryRegister__Private()", referenced from:
      itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in libmaxcurvatureLib.a(maxcurvature.cxx.o)
  "itk::GE4ImageIOFactoryRegister__Private()", referenced from:
      itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in libmaxcurvatureLib.a(maxcurvature.cxx.o)

When I  go looking for these symbols,  I see them where you?d expect them ? libITKBMPIO-4.6.a etc.

The problem seems to be that the IO libraries are being LEFT OUT of the ITK_LIBRARIES Cmake variable.

We use a pretty recent version of ITK:
commit 06d5bfec67805bfadb5dc344b08ab554381592c6
Merge: b960bce c1bcfb7
Author: Matt McCormick <matt.mccormick at kitware.com>
Date:   Tue Jul 15 16:05:22 2014 -0400
o
    Merge topic 'FixThresholdMaxCCWarning'

    c1bcfb73 COMP: Fix implicit conversion warnings



________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/bcc2850a/attachment.html>

From blowekamp at mail.nih.gov  Wed Jul 23 11:28:12 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 23 Jul 2014 11:28:12 -0400
Subject: [ITK-users] [ITK-dev] Undefined IOFactoryRegister__Private
	methods?
In-Reply-To: <CFF53DB3.9AF1%norman-k-williams@uiowa.edu>
References: <CFF53DB3.9AF1%norman-k-williams@uiowa.edu>
Message-ID: <8A284992-A0BD-42FA-A2FA-F9CDCB5C60FC@mail.nih.gov>

How are you "finding" and "using" ITK in the CMake code? Are you using ITK via components?

Brad

On Jul 23, 2014, at 11:23 AM, Williams, Norman K <norman-k-williams at uiowa.edu> wrote:

> We have a bunch of big Cmake build systems that until very recently (I noticed it yesterday) were working fine. Now we get link errors like this:
> 
>   "itk::BMPImageIOFactoryRegister__Private()", referenced from:
>       itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in libmaxcurvatureLib.a(maxcurvature.cxx.o)
>   "itk::GE4ImageIOFactoryRegister__Private()", referenced from:
>       itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in libmaxcurvatureLib.a(maxcurvature.cxx.o)
> 
> When I  go looking for these symbols,  I see them where you?d expect them ? libITKBMPIO-4.6.a etc.
> 
> The problem seems to be that the IO libraries are being LEFT OUT of the ITK_LIBRARIES Cmake variable.
> 
> We use a pretty recent version of ITK:
> commit 06d5bfec67805bfadb5dc344b08ab554381592c6
> Merge: b960bce c1bcfb7
> Author: Matt McCormick <matt.mccormick at kitware.com>
> Date:   Tue Jul 15 16:05:22 2014 -0400
> o
>     Merge topic 'FixThresholdMaxCCWarning'
>     
>     c1bcfb73 COMP: Fix implicit conversion warnings
>  
> 
> 
> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/a2800e1e/attachment.html>

From emilroz at gmail.com  Wed Jul 23 11:44:14 2014
From: emilroz at gmail.com (Emil Rozbicki)
Date: Wed, 23 Jul 2014 16:44:14 +0100
Subject: [ITK-users] Error: no override found for
	'vtkRayCastImageDisplayHelper'
In-Reply-To: <1400765505.497471738@f181.i.mail.ru>
References: <1400765505.497471738@f181.i.mail.ru>
Message-ID: <CAOFELSRVjxqJR7eRhF-=b3LNJWapPz9CnoxPioEs3sLXc+cKHQ@mail.gmail.com>

Hi,

I'm experiencing similar issue although only when using QT and not sure
why. I've compiled the same code with XTools and Qt both compiled using
clang. The executable from Xtools works fine no error, QT one crushes and
says:
"Generic Warning: In
/tmp/vtk-TFA4/Rendering/Volume/vtkRayCastImageDisplayHelper.cxx, line 20
Error: no override found for 'vtkRayCastImageDisplayHelper'."

I've tried QT 5 and 4 in combination with VTK 5 and 6 (6.1 and 6.2) the
same issue persists. I'm on OS X 10.8.5. Any advice how to overcome it
much appreciated.

Cheers,
Emil




On Thu, May 22, 2014 at 2:31 PM, ????? ?????????? <roman_glu at mail.ru> wrote:

>
>
>   Hi all,
>
> i try this example
> https://github.com/Kitware/VTK/blob/master/Examples/VolumeRendering/Cxx/GPURenderDemo.cxx
>
>
> But when i run it, i get this error "no override found for
> 'vtkRayCastImageDisplayHelper".
>
> Thank you for your help
>
> Roman
>
>
> ------------------------------
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/7ddadb87/attachment.html>

From norman-k-williams at uiowa.edu  Wed Jul 23 11:42:33 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Wed, 23 Jul 2014 15:42:33 +0000
Subject: [ITK-users] [ITK-dev] Undefined IOFactoryRegister__Private
	methods?
In-Reply-To: <8A284992-A0BD-42FA-A2FA-F9CDCB5C60FC@mail.nih.gov>
References: <CFF53DB3.9AF1%norman-k-williams@uiowa.edu>
 <8A284992-A0BD-42FA-A2FA-F9CDCB5C60FC@mail.nih.gov>
Message-ID: <CFF540A9.9AF6%norman-k-williams@uiowa.edu>

The ?usual way?

I?m trying to track down where this goes wrong; I wondered if anyone else
had run into this problem. It?s with a package that might need some TLC
with its Cmake build system. http://www.nitrc.org/projects/dtiprocess/

find_package(ITK REQUIRED)
include(${ITK_USE_FILE})


From:  Bradley Lowekamp <blowekamp at mail.nih.gov>
Date:  Wednesday, July 23, 2014 at 10:28 AM
To:  Mushly McMushmaster <norman-k-williams at uiowa.edu>
Cc:  Insight <insight-users at itk.org>, ITK <insight-developers at itk.org>
Subject:  Re: [ITK-dev] Undefined IOFactoryRegister__Private methods?


How are you "finding" and "using" ITK in the CMake code? Are you using ITK
via components?

Brad

On Jul 23, 2014, at 11:23 AM, Williams, Norman K
<norman-k-williams at uiowa.edu> wrote:


We have a bunch of big Cmake build systems that until very recently (I
noticed it yesterday) were working fine. Now we get link errors like this:

  "itk::BMPImageIOFactoryRegister__Private()", referenced from:
      itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in
libmaxcurvatureLib.a(maxcurvature.cxx.o)
  "itk::GE4ImageIOFactoryRegister__Private()", referenced from:
      itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in
libmaxcurvatureLib.a(maxcurvature.cxx.o)


When I  go looking for these symbols,  I see them where you?d expect them
? libITKBMPIO-4.6.a etc.

The problem seems to be that the IO libraries are being LEFT OUT of the
ITK_LIBRARIES Cmake variable.

We use a pretty recent version of ITK:
commit 06d5bfec67805bfadb5dc344b08ab554381592c6
Merge: b960bce c1bcfb7
Author: Matt McCormick <matt.mccormick at kitware.com>
Date:   Tue Jul 15 16:05:22 2014 -0400
o
    Merge topic 'FixThresholdMaxCCWarning'

    c1bcfb73 COMP: Fix implicit conversion warnings



________________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by
the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
confidential and may be legally privileged.  If you are not the intended
recipient, you are hereby notified that any
 retention, dissemination, distribution, or copying of this communication
is strictly prohibited.  Please reply to the sender that you have received
the message in error, then delete it.  Thank you.
________________________________________

_______________________________________________
Powered by www.kitware.com <http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-developers







________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________

From norman-k-williams at uiowa.edu  Wed Jul 23 14:39:18 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Wed, 23 Jul 2014 18:39:18 +0000
Subject: [ITK-users] [ITK-dev] Undefined IOFactoryRegister__Private
	methods?
In-Reply-To: <8A284992-A0BD-42FA-A2FA-F9CDCB5C60FC@mail.nih.gov>
References: <CFF53DB3.9AF1%norman-k-williams@uiowa.edu>
 <8A284992-A0BD-42FA-A2FA-F9CDCB5C60FC@mail.nih.gov>
Message-ID: <CFF56B6C.9B6C%norman-k-williams@uiowa.edu>

This is an issue with recent changes to SlicerExecutionModel, and JC is on the job ;-)

From: Bradley Lowekamp <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>
Date: Wednesday, July 23, 2014 at 10:28 AM
To: Mushly McMushmaster <norman-k-williams at uiowa.edu<mailto:norman-k-williams at uiowa.edu>>
Cc: Insight <insight-users at itk.org<mailto:insight-users at itk.org>>, ITK <insight-developers at itk.org<mailto:insight-developers at itk.org>>
Subject: Re: [ITK-dev] Undefined IOFactoryRegister__Private methods?

How are you "finding" and "using" ITK in the CMake code? Are you using ITK via components?

Brad

On Jul 23, 2014, at 11:23 AM, Williams, Norman K <norman-k-williams at uiowa.edu<mailto:norman-k-williams at uiowa.edu>> wrote:

We have a bunch of big Cmake build systems that until very recently (I noticed it yesterday) were working fine. Now we get link errors like this:

  "itk::BMPImageIOFactoryRegister__Private()", referenced from:
      itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in libmaxcurvatureLib.a(maxcurvature.cxx.o)
  "itk::GE4ImageIOFactoryRegister__Private()", referenced from:
      itk::(anonymous namespace)::ImageIOFactoryRegisterRegisterList in libmaxcurvatureLib.a(maxcurvature.cxx.o)

When I  go looking for these symbols,  I see them where you?d expect them ? libITKBMPIO-4.6.a etc.

The problem seems to be that the IO libraries are being LEFT OUT of the ITK_LIBRARIES Cmake variable.

We use a pretty recent version of ITK:
commit 06d5bfec67805bfadb5dc344b08ab554381592c6
Merge: b960bce c1bcfb7
Author: Matt McCormick <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>>
Date:   Tue Jul 15 16:05:22 2014 -0400
o
    Merge topic 'FixThresholdMaxCCWarning'

    c1bcfb73 COMP: Fix implicit conversion warnings



________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________
_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-developers



________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140723/ef275acf/attachment.html>

From wgt at sjtu.edu.cn  Thu Jul 24 04:41:26 2014
From: wgt at sjtu.edu.cn (guotai)
Date: Thu, 24 Jul 2014 01:41:26 -0700 (PDT)
Subject: [ITK-users] GDCM Update from 2.0.14 to 2.0.15, linker error
In-Reply-To: <1378883369210-32321.post@n7.nabble.com>
References: <E70FE8EA6EBE9241BDB4CA6D8D12E1D801101DC90A70@RZJC1EX.jr1.local>
 <1378883369210-32321.post@n7.nabble.com>
Message-ID: <1406191286576-7585981.post@n2.nabble.com>

Hi, I also have this problem. Have you fixed it ? Could you tell me how did
you fix this problem?
Thanks
Guotai



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/GDCM-Update-from-2-0-14-to-2-0-15-linker-error-tp5432003p7585981.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From michkapopoff at gmail.com  Thu Jul 24 04:54:52 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Thu, 24 Jul 2014 10:54:52 +0200
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
Message-ID: <C0A940AE-05F4-4DA1-9CE8-6D38C9F8B76B@gmail.com>

Hi

I am currently maintaining the Python part of ITK, but I don?t know if I can help you. I just started with this some time ago and can not really compare it to the boost python method as I don?t know it.
There is an old (but outdated) discussion about boost and swig here [1]. But this was written for swig 1.34, and now we already have swig 3.0.2, which brought a lot of improvements.

Swig has been under heavy development lately. What I find nice with Swig is that you get other languages for free, it does not only support python but also Java, Ruby, TCL, ? (you will need to write some code for this support though).
The Swig method is nice once you automatized your process. Depending on the c++ code you wrote, you don?t even need to write interface files for Swig.
For ITK, we have a small pipeline which reads the c++ code with gccxml, and uses a python script [3] (which uses pygccxml) to create interface files from the xml files.

What problems did you encounter when trying the Swig route ? Maybe I can help.

Michka

[1] https://dev.lsstcorp.org/trac/wiki/SwigVsBoostPython
[2] https://github.com/swig/swig
[3] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/SwigInterface/igenerator.py

On 23 juil. 2014, at 17:11, Satyananda Kashyap <ksatyananda at gmail.com> wrote:

> Hello,
> 
> I am looking for your expert opinions here. I have a relatively large C++ project I am working on which uses ITK mainly (hence the question here) and to some extent VTK and OpenCV. I do think that my code is fairly well written. I was thinking of wrapping my code to python using either SWIG or boost.python. Here are my questions : 
> 
> 
> 1. I am led to believe that prototyping and code development is much faster in Python. Given that I have such a big cpp base code is it really worth the effort to wrap into python and then continue there. 
> 
> 2. From what I have read ITK uses SWIG wrappings for wrapping into Python while VTK uses the boost.python route. My initial attempts with both have been relatively unsuccessful. Any opinion on which one is more user friendly/better when I have to wrap my own custom classes which use a combination of both ITK and VTK in them. 
> 
> 3. Any suggestion on a road map as to how to proceed. I am not sure at what base class level I should wrap them and rewrite the dependencies in python.  
> 
> Thanks,
> Regards,
> Kashyap
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From medswengineer at gmail.com  Thu Jul 24 05:40:28 2014
From: medswengineer at gmail.com (med aweng)
Date: Thu, 24 Jul 2014 11:40:28 +0200
Subject: [ITK-users] GetFeatureMeans()
Message-ID: <CAEMYOQhLbNOdY2w1f-WtJ9Yk6yAAV5XZf+W5Hz1Pb=PCjVyc3Q@mail.gmail.com>

Hello,

Does "GetFeatureMeans()" here:
https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx

means that we want to retrieve the "mean" value of the features?

Is there some description for that in the documentation, since I couldn't
find a description for this method.

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/95efe7d1/attachment.html>

From medswengineer at gmail.com  Thu Jul 24 05:43:52 2014
From: medswengineer at gmail.com (med aweng)
Date: Thu, 24 Jul 2014 11:43:52 +0200
Subject: [ITK-users] GetRequestedFeatures()
Message-ID: <CAEMYOQh4yjwJJ=L4+1yMsQEB5ULix2UNAcTZyTj6qGfChbpEeQ@mail.gmail.com>

Hello,

What does the method "GetRequestedFeatures()" mean, here:
https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx

I couldn't find a description for that in the documentation.

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/c7ca2faf/attachment.html>

From medswengineer at gmail.com  Thu Jul 24 05:47:28 2014
From: medswengineer at gmail.com (med aweng)
Date: Thu, 24 Jul 2014 11:47:28 +0200
Subject: [ITK-users] ConstIterator
Message-ID: <CAEMYOQhNWy_3CsTFc+JgkL3ZDmiR74OLD3vsMFWiL+qozoLXHw@mail.gmail.com>

Hello,

What is the purpose of the "ConstIterator". Where can I find its
description?

Thanks.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/099b2d3d/attachment.html>

From marco.ulge at gmail.com  Thu Jul 24 06:07:26 2014
From: marco.ulge at gmail.com (Marco Ulgelmo)
Date: Thu, 24 Jul 2014 12:07:26 +0200
Subject: [ITK-users] ConstIterator
In-Reply-To: <CAEMYOQhNWy_3CsTFc+JgkL3ZDmiR74OLD3vsMFWiL+qozoLXHw@mail.gmail.com>
References: <CAEMYOQhNWy_3CsTFc+JgkL3ZDmiR74OLD3vsMFWiL+qozoLXHw@mail.gmail.com>
Message-ID: <CA+=+rrCzkw2g7XFhQwTeb4uE7h3ppvYUqyrWtfRC_2TL=zE1qQ@mail.gmail.com>

A ConstIterator an iterator which is used to iterate over a constant
container, which means that data in the container can't be modified (unless
you use const_cast). You can find it in the ITK documentation.

Marco


2014-07-24 11:47 GMT+02:00 med aweng <medswengineer at gmail.com>:

> Hello,
>
> What is the purpose of the "ConstIterator". Where can I find its
> description?
>
> Thanks.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/a5990c00/attachment-0001.html>

From marco.ulge at gmail.com  Thu Jul 24 06:08:59 2014
From: marco.ulge at gmail.com (Marco Ulgelmo)
Date: Thu, 24 Jul 2014 12:08:59 +0200
Subject: [ITK-users] GetFeatureMeans()
In-Reply-To: <CAEMYOQhLbNOdY2w1f-WtJ9Yk6yAAV5XZf+W5Hz1Pb=PCjVyc3Q@mail.gmail.com>
References: <CAEMYOQhLbNOdY2w1f-WtJ9Yk6yAAV5XZf+W5Hz1Pb=PCjVyc3Q@mail.gmail.com>
Message-ID: <CA+=+rrBo0swb2AADXu4wNx6yXxDTFUYTyK8LvN3D1py5EK5BOw@mail.gmail.com>

Take a look at:

http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToTextureFeaturesFilter.html

which answers your other question too.

Marco




2014-07-24 11:40 GMT+02:00 med aweng <medswengineer at gmail.com>:

> Hello,
>
> Does "GetFeatureMeans()" here:
> https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx
>
> means that we want to retrieve the "mean" value of the features?
>
> Is there some description for that in the documentation, since I couldn't
> find a description for this method.
>
> Thanks.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/c3e099b7/attachment.html>

From medswengineer at gmail.com  Thu Jul 24 06:09:52 2014
From: medswengineer at gmail.com (med aweng)
Date: Thu, 24 Jul 2014 12:09:52 +0200
Subject: [ITK-users] ConstIterator
In-Reply-To: <CA+=+rrCzkw2g7XFhQwTeb4uE7h3ppvYUqyrWtfRC_2TL=zE1qQ@mail.gmail.com>
References: <CAEMYOQhNWy_3CsTFc+JgkL3ZDmiR74OLD3vsMFWiL+qozoLXHw@mail.gmail.com>
 <CA+=+rrCzkw2g7XFhQwTeb4uE7h3ppvYUqyrWtfRC_2TL=zE1qQ@mail.gmail.com>
Message-ID: <CAEMYOQjp=J3HQKsUAtk7H1xbKHtpgd1GHY9ARW=LHDFn9a6LtA@mail.gmail.com>

Thanks Marco. Is that description in the itk documentation? I really
couldn't find such clear explanation.

Thanks.


On Thu, Jul 24, 2014 at 12:07 PM, Marco Ulgelmo <marco.ulge at gmail.com>
wrote:

> A ConstIterator an iterator which is used to iterate over a constant
> container, which means that data in the container can't be modified (unless
> you use const_cast). You can find it in the ITK documentation.
>
> Marco
>
>
> 2014-07-24 11:47 GMT+02:00 med aweng <medswengineer at gmail.com>:
>
>> Hello,
>>
>> What is the purpose of the "ConstIterator". Where can I find its
>> description?
>>
>> Thanks.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/1081c614/attachment.html>

From medswengineer at gmail.com  Thu Jul 24 06:11:32 2014
From: medswengineer at gmail.com (med aweng)
Date: Thu, 24 Jul 2014 12:11:32 +0200
Subject: [ITK-users] GetFeatureMeans()
In-Reply-To: <CA+=+rrBo0swb2AADXu4wNx6yXxDTFUYTyK8LvN3D1py5EK5BOw@mail.gmail.com>
References: <CAEMYOQhLbNOdY2w1f-WtJ9Yk6yAAV5XZf+W5Hz1Pb=PCjVyc3Q@mail.gmail.com>
 <CA+=+rrBo0swb2AADXu4wNx6yXxDTFUYTyK8LvN3D1py5EK5BOw@mail.gmail.com>
Message-ID: <CAEMYOQgX9UOCRyk1wMtYjMNg733nmV=nNUP=jiMWysOWMDKZCg@mail.gmail.com>

Thanks Marco. Since I'm new to itk, I just noticed the description. I was
able to reach that point (the link you posted), but didn't notice there was
a description for the methods. I can see them now.

Thanks.


On Thu, Jul 24, 2014 at 12:08 PM, Marco Ulgelmo <marco.ulge at gmail.com>
wrote:

> Take a look at:
>
>
> http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToTextureFeaturesFilter.html
>
> which answers your other question too.
>
> Marco
>
>
>
>
> 2014-07-24 11:40 GMT+02:00 med aweng <medswengineer at gmail.com>:
>
>> Hello,
>>
>> Does "GetFeatureMeans()" here:
>> https://github.com/midas-journal/midas-journal-231/blob/master/Source/itkRunLengthFeaturesTest.cxx
>>
>> means that we want to retrieve the "mean" value of the features?
>>
>> Is there some description for that in the documentation, since I couldn't
>> find a description for this method.
>>
>> Thanks.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/39a10867/attachment.html>

From CHernando at telespazio.es  Thu Jul 24 10:25:29 2014
From: CHernando at telespazio.es (Carlos Hernando Ramiro)
Date: Thu, 24 Jul 2014 16:25:29 +0200
Subject: [ITK-users] Use more samples than available in region to compute
 Mattes MI metric
Message-ID: <800D4DFDAF353641B990F5CEB49F05E179B9C9@GORDONS.aurensis.com>

Dear all,

I wanted to compute MattesMutualInformationImageToImageMetric just for a window of my image, so I have set an specific region with SetFixedImageRegion(region).
As I did not know the existence of UseAllPixelsOn(), I initially calculate the size of my window and set the number of samples "manually" with SetNumberOfSpatialSamples() according to that size.
I was calculating the size wrongly and I was giving SetNumberOfSpatialSamples() a number higher than the size of the region. However, after computing the metric and checking the number of pixels used with GetNumberOfPixelsCounted(), it says that it has used all the specified pixels, although they are more than the available in the region. 
When I discovered the error, I thought that although it gave me a number larger than the region it was actually using all the pixels available anyway. However, I did some tests with different numbers of pixels, which were larger than the size of the region and they provide different metric results.
So my question is, is this behaviour normal? If so, where does the metric take the extra pixels from? 

PD. Using UseAllPixelsOn() it seems to work well because at least GetNumberOfPixelsCounted() gives me the number of pixels available in the region, but it would be great if I could somehow confirm it.


Best regards
Carlos

From ksatyananda at gmail.com  Thu Jul 24 11:41:00 2014
From: ksatyananda at gmail.com (Satyananda Kashyap)
Date: Thu, 24 Jul 2014 10:41:00 -0500
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <C0A940AE-05F4-4DA1-9CE8-6D38C9F8B76B@gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <C0A940AE-05F4-4DA1-9CE8-6D38C9F8B76B@gmail.com>
Message-ID: <CADe3NtwUdjgBDQhbX8ky_-Cvqe7YGPAaWxBSvZG4KBfde6WxxQ@mail.gmail.com>

Hi Mickha,

When using SWIG I read that it cannot handle nested classes and that the
interface classes would be needed to expose them separately to python. So I
did actually try to use the interface file pipeline designed for ITK  with
gccxml to see if I could exposes the classes I had written. I am using a
Visual Studio 2010 build. I had two main issues with it :

1. gccxml does not seem to be compatible with versions beyond VS2008. Now I
wasn't sure if redoing my full cpp development in VS2008 would be a good
idea. I could not find a workaround for this (Hence my attempt to try and
use boost.python).

2. Also I needed to modify the interface files so that the other packages
dependencies (i.e. VTK and OpenCV) could also work. I was not sure how to
do that.

Any suggestions on how/where I could start modifying. I like the fact that
I will be able to automate the process and not write any interface files
once I can get it working.

Thanks,
Regards,
Kashyap


On Thu, Jul 24, 2014 at 3:54 AM, Michka Popoff <michkapopoff at gmail.com>
wrote:

> Hi
>
> I am currently maintaining the Python part of ITK, but I don?t know if I
> can help you. I just started with this some time ago and can not really
> compare it to the boost python method as I don?t know it.
> There is an old (but outdated) discussion about boost and swig here [1].
> But this was written for swig 1.34, and now we already have swig 3.0.2,
> which brought a lot of improvements.
>
> Swig has been under heavy development lately. What I find nice with Swig
> is that you get other languages for free, it does not only support python
> but also Java, Ruby, TCL, ? (you will need to write some code for this
> support though).
> The Swig method is nice once you automatized your process. Depending on
> the c++ code you wrote, you don?t even need to write interface files for
> Swig.
> For ITK, we have a small pipeline which reads the c++ code with gccxml,
> and uses a python script [3] (which uses pygccxml) to create interface
> files from the xml files.
>
> What problems did you encounter when trying the Swig route ? Maybe I can
> help.
>
> Michka
>
> [1] https://dev.lsstcorp.org/trac/wiki/SwigVsBoostPython
> [2] https://github.com/swig/swig
> [3]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/SwigInterface/igenerator.py
>
> On 23 juil. 2014, at 17:11, Satyananda Kashyap <ksatyananda at gmail.com>
> wrote:
>
> > Hello,
> >
> > I am looking for your expert opinions here. I have a relatively large
> C++ project I am working on which uses ITK mainly (hence the question here)
> and to some extent VTK and OpenCV. I do think that my code is fairly well
> written. I was thinking of wrapping my code to python using either SWIG or
> boost.python. Here are my questions :
> >
> >
> > 1. I am led to believe that prototyping and code development is much
> faster in Python. Given that I have such a big cpp base code is it really
> worth the effort to wrap into python and then continue there.
> >
> > 2. From what I have read ITK uses SWIG wrappings for wrapping into
> Python while VTK uses the boost.python route. My initial attempts with both
> have been relatively unsuccessful. Any opinion on which one is more user
> friendly/better when I have to wrap my own custom classes which use a
> combination of both ITK and VTK in them.
> >
> > 3. Any suggestion on a road map as to how to proceed. I am not sure at
> what base class level I should wrap them and rewrite the dependencies in
> python.
> >
> > Thanks,
> > Regards,
> > Kashyap
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/c3a3fa6e/attachment.html>

From michkapopoff at gmail.com  Thu Jul 24 13:15:59 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Thu, 24 Jul 2014 19:15:59 +0200
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CADe3NtwUdjgBDQhbX8ky_-Cvqe7YGPAaWxBSvZG4KBfde6WxxQ@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <C0A940AE-05F4-4DA1-9CE8-6D38C9F8B76B@gmail.com>
 <CADe3NtwUdjgBDQhbX8ky_-Cvqe7YGPAaWxBSvZG4KBfde6WxxQ@mail.gmail.com>
Message-ID: <735BADAE-8685-4268-84CE-21BF9A8391B3@gmail.com>

Nested classes are supported by Swig 3.0.0 natively:
http://www.swig.org/Doc3.0/SWIGDocumentation.html#SWIGPlus_nested_classes
I have no clue if we have nested classes in ITK, and how it was wrapped. Maybe I?ll stumble upon this one day.
So I can not really help here but should work.

1. gccxml is limited to VS2008, and we have no replacement for it. This is a known limitation which is also blocking for ITK.

2. For VTK, is this deeply nested in your c++ code ? Maybe you could just rewrite the VTK part using python directly ? This would remove one dependency.
For OpenCV, I don?t know how this could be done. This would need to be researched on google, I found this blog post for example:


Michka



On 24 juil. 2014, at 17:41, Satyananda Kashyap <ksatyananda at gmail.com> wrote:

> Hi Mickha,
> 
> When using SWIG I read that it cannot handle nested classes and that the interface classes would be needed to expose them separately to python. So I did actually try to use the interface file pipeline designed for ITK  with gccxml to see if I could exposes the classes I had written. I am using a Visual Studio 2010 build. I had two main issues with it :
> 
> 1. gccxml does not seem to be compatible with versions beyond VS2008. Now I wasn't sure if redoing my full cpp development in VS2008 would be a good idea. I could not find a workaround for this (Hence my attempt to try and use boost.python). 
> 
> 2. Also I needed to modify the interface files so that the other packages dependencies (i.e. VTK and OpenCV) could also work. I was not sure how to do that. 
> 
> Any suggestions on how/where I could start modifying. I like the fact that I will be able to automate the process and not write any interface files once I can get it working. 
> 
> Thanks,
> Regards,
> Kashyap
> 
> 
> On Thu, Jul 24, 2014 at 3:54 AM, Michka Popoff <michkapopoff at gmail.com> wrote:
> Hi
> 
> I am currently maintaining the Python part of ITK, but I don?t know if I can help you. I just started with this some time ago and can not really compare it to the boost python method as I don?t know it.
> There is an old (but outdated) discussion about boost and swig here [1]. But this was written for swig 1.34, and now we already have swig 3.0.2, which brought a lot of improvements.
> 
> Swig has been under heavy development lately. What I find nice with Swig is that you get other languages for free, it does not only support python but also Java, Ruby, TCL, ? (you will need to write some code for this support though).
> The Swig method is nice once you automatized your process. Depending on the c++ code you wrote, you don?t even need to write interface files for Swig.
> For ITK, we have a small pipeline which reads the c++ code with gccxml, and uses a python script [3] (which uses pygccxml) to create interface files from the xml files.
> 
> What problems did you encounter when trying the Swig route ? Maybe I can help.
> 
> Michka
> 
> [1] https://dev.lsstcorp.org/trac/wiki/SwigVsBoostPython
> [2] https://github.com/swig/swig
> [3] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/SwigInterface/igenerator.py
> 
> On 23 juil. 2014, at 17:11, Satyananda Kashyap <ksatyananda at gmail.com> wrote:
> 
> > Hello,
> >
> > I am looking for your expert opinions here. I have a relatively large C++ project I am working on which uses ITK mainly (hence the question here) and to some extent VTK and OpenCV. I do think that my code is fairly well written. I was thinking of wrapping my code to python using either SWIG or boost.python. Here are my questions :
> >
> >
> > 1. I am led to believe that prototyping and code development is much faster in Python. Given that I have such a big cpp base code is it really worth the effort to wrap into python and then continue there.
> >
> > 2. From what I have read ITK uses SWIG wrappings for wrapping into Python while VTK uses the boost.python route. My initial attempts with both have been relatively unsuccessful. Any opinion on which one is more user friendly/better when I have to wrap my own custom classes which use a combination of both ITK and VTK in them.
> >
> > 3. Any suggestion on a road map as to how to proceed. I am not sure at what base class level I should wrap them and rewrite the dependencies in python.
> >
> > Thanks,
> > Regards,
> > Kashyap
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/0541d0bc/attachment.html>

From ksatyananda at gmail.com  Thu Jul 24 14:47:54 2014
From: ksatyananda at gmail.com (Satyananda Kashyap)
Date: Thu, 24 Jul 2014 13:47:54 -0500
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <735BADAE-8685-4268-84CE-21BF9A8391B3@gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <C0A940AE-05F4-4DA1-9CE8-6D38C9F8B76B@gmail.com>
 <CADe3NtwUdjgBDQhbX8ky_-Cvqe7YGPAaWxBSvZG4KBfde6WxxQ@mail.gmail.com>
 <735BADAE-8685-4268-84CE-21BF9A8391B3@gmail.com>
Message-ID: <CADe3NtxKjYCqvqcEQyqOrDPZjJ65xnDv4hn7NtdGAUZnzsH_Ow@mail.gmail.com>

Thank you for that. VTK is pretty deeply nested in my code. I will have to
write a similar interface file.

Can you suggest a starting point in the ITK interface files I can start
looking at. I want to try and wrap a simple piece of my code modifying them.

Regards,
Kashyap


On Thu, Jul 24, 2014 at 12:15 PM, Michka Popoff <michkapopoff at gmail.com>
wrote:

> Nested classes are supported by Swig 3.0.0 natively:
> http://www.swig.org/Doc3.0/SWIGDocumentation.html#SWIGPlus_nested_classes
> I have no clue if we have nested classes in ITK, and how it was wrapped.
> Maybe I?ll stumble upon this one day.
> So I can not really help here but should work.
>
> 1. gccxml is limited to VS2008, and we have no replacement for it. This is
> a known limitation which is also blocking for ITK.
>
> 2. For VTK, is this deeply nested in your c++ code ? Maybe you could just
> rewrite the VTK part using python directly ? This would remove one
> dependency.
> For OpenCV, I don?t know how this could be done. This would need to be
> researched on google, I found this blog post for example:
>
>
> Michka
>
>
>
> On 24 juil. 2014, at 17:41, Satyananda Kashyap <ksatyananda at gmail.com>
> wrote:
>
> Hi Mickha,
>
> When using SWIG I read that it cannot handle nested classes and that the
> interface classes would be needed to expose them separately to python. So I
> did actually try to use the interface file pipeline designed for ITK  with
> gccxml to see if I could exposes the classes I had written. I am using a
> Visual Studio 2010 build. I had two main issues with it :
>
> 1. gccxml does not seem to be compatible with versions beyond VS2008. Now
> I wasn't sure if redoing my full cpp development in VS2008 would be a good
> idea. I could not find a workaround for this (Hence my attempt to try and
> use boost.python).
>
> 2. Also I needed to modify the interface files so that the other packages
> dependencies (i.e. VTK and OpenCV) could also work. I was not sure how to
> do that.
>
> Any suggestions on how/where I could start modifying. I like the fact that
> I will be able to automate the process and not write any interface files
> once I can get it working.
>
> Thanks,
> Regards,
> Kashyap
>
>
> On Thu, Jul 24, 2014 at 3:54 AM, Michka Popoff <michkapopoff at gmail.com>
> wrote:
>
>> Hi
>>
>> I am currently maintaining the Python part of ITK, but I don?t know if I
>> can help you. I just started with this some time ago and can not really
>> compare it to the boost python method as I don?t know it.
>> There is an old (but outdated) discussion about boost and swig here [1].
>> But this was written for swig 1.34, and now we already have swig 3.0.2,
>> which brought a lot of improvements.
>>
>> Swig has been under heavy development lately. What I find nice with Swig
>> is that you get other languages for free, it does not only support python
>> but also Java, Ruby, TCL, ? (you will need to write some code for this
>> support though).
>> The Swig method is nice once you automatized your process. Depending on
>> the c++ code you wrote, you don?t even need to write interface files for
>> Swig.
>> For ITK, we have a small pipeline which reads the c++ code with gccxml,
>> and uses a python script [3] (which uses pygccxml) to create interface
>> files from the xml files.
>>
>> What problems did you encounter when trying the Swig route ? Maybe I can
>> help.
>>
>> Michka
>>
>> [1] https://dev.lsstcorp.org/trac/wiki/SwigVsBoostPython
>> [2] https://github.com/swig/swig
>> [3]
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/SwigInterface/igenerator.py
>>
>> On 23 juil. 2014, at 17:11, Satyananda Kashyap <ksatyananda at gmail.com>
>> wrote:
>>
>> > Hello,
>> >
>> > I am looking for your expert opinions here. I have a relatively large
>> C++ project I am working on which uses ITK mainly (hence the question here)
>> and to some extent VTK and OpenCV. I do think that my code is fairly well
>> written. I was thinking of wrapping my code to python using either SWIG or
>> boost.python. Here are my questions :
>> >
>> >
>> > 1. I am led to believe that prototyping and code development is much
>> faster in Python. Given that I have such a big cpp base code is it really
>> worth the effort to wrap into python and then continue there.
>> >
>> > 2. From what I have read ITK uses SWIG wrappings for wrapping into
>> Python while VTK uses the boost.python route. My initial attempts with both
>> have been relatively unsuccessful. Any opinion on which one is more user
>> friendly/better when I have to wrap my own custom classes which use a
>> combination of both ITK and VTK in them.
>> >
>> > 3. Any suggestion on a road map as to how to proceed. I am not sure at
>> what base class level I should wrap them and rewrite the dependencies in
>> python.
>> >
>> > Thanks,
>> > Regards,
>> > Kashyap
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/0e8a9492/attachment.html>

From michkapopoff at gmail.com  Thu Jul 24 16:39:35 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Thu, 24 Jul 2014 22:39:35 +0200
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CADe3NtxKjYCqvqcEQyqOrDPZjJ65xnDv4hn7NtdGAUZnzsH_Ow@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <C0A940AE-05F4-4DA1-9CE8-6D38C9F8B76B@gmail.com>
 <CADe3NtwUdjgBDQhbX8ky_-Cvqe7YGPAaWxBSvZG4KBfde6WxxQ@mail.gmail.com>
 <735BADAE-8685-4268-84CE-21BF9A8391B3@gmail.com>
 <CADe3NtxKjYCqvqcEQyqOrDPZjJ65xnDv4hn7NtdGAUZnzsH_Ow@mail.gmail.com>
Message-ID: <CADAB150-DA1A-47BB-B138-BA2F8424BF82@gmail.com>

For VTK, I don?t know what would be the best way to tacle the problem.

For the interface files, the best would be you compile the whole ITK project once to get the .i files.
(You can set the wrapped images dimensions from 2;3 to 2 only, and wrap only the core group, to compile faster).
You can then find the .i files in some folder of the build (I don?t remember in which folder exactly, you will have to search a little bit for them).
You can also look at the base .i file we use, though I will not be able to help you a lot with it, as I did not write it, so it may take some time to decipher:
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/Python/PyBase/pyBase.i

So maybe the starting point would to have a first part of your code compiled with Swig. Build a minimal c++ dummy example to understand how it all works,
And then you?ll need to go step by step. I can not guarantee you will succeed, but I would be definitively interested if it works.
Maybe if you find something out, it would be very nice to have a tutorial on how to do this.

Ho, and I just thought about something else. Once ITK is compiled and installed, you can use it as an external project, even with python:
See one example: https://github.com/InsightSoftwareConsortium/itkPyBuffer
Or this one, at the very end of the page: http://cmake.org/Wiki/index.php?title=ITK/Release_4/Wrapping/BuildProcess&oldid=44313
This is not a tested feature for the moment so you may run into some trouble.

Michka



On 24 juil. 2014, at 20:47, Satyananda Kashyap <ksatyananda at gmail.com> wrote:

> Thank you for that. VTK is pretty deeply nested in my code. I will have to write a similar interface file. 
> 
> Can you suggest a starting point in the ITK interface files I can start looking at. I want to try and wrap a simple piece of my code modifying them.
> 
> Regards,
> Kashyap
> 
> 
> On Thu, Jul 24, 2014 at 12:15 PM, Michka Popoff <michkapopoff at gmail.com> wrote:
> Nested classes are supported by Swig 3.0.0 natively:
> http://www.swig.org/Doc3.0/SWIGDocumentation.html#SWIGPlus_nested_classes
> I have no clue if we have nested classes in ITK, and how it was wrapped. Maybe I?ll stumble upon this one day.
> So I can not really help here but should work.
> 
> 1. gccxml is limited to VS2008, and we have no replacement for it. This is a known limitation which is also blocking for ITK.
> 
> 2. For VTK, is this deeply nested in your c++ code ? Maybe you could just rewrite the VTK part using python directly ? This would remove one dependency.
> For OpenCV, I don?t know how this could be done. This would need to be researched on google, I found this blog post for example:
> 
> 
> Michka
> 
> 
> 
> On 24 juil. 2014, at 17:41, Satyananda Kashyap <ksatyananda at gmail.com> wrote:
> 
>> Hi Mickha,
>> 
>> When using SWIG I read that it cannot handle nested classes and that the interface classes would be needed to expose them separately to python. So I did actually try to use the interface file pipeline designed for ITK  with gccxml to see if I could exposes the classes I had written. I am using a Visual Studio 2010 build. I had two main issues with it :
>> 
>> 1. gccxml does not seem to be compatible with versions beyond VS2008. Now I wasn't sure if redoing my full cpp development in VS2008 would be a good idea. I could not find a workaround for this (Hence my attempt to try and use boost.python). 
>> 
>> 2. Also I needed to modify the interface files so that the other packages dependencies (i.e. VTK and OpenCV) could also work. I was not sure how to do that. 
>> 
>> Any suggestions on how/where I could start modifying. I like the fact that I will be able to automate the process and not write any interface files once I can get it working. 
>> 
>> Thanks,
>> Regards,
>> Kashyap
>> 
>> 
>> On Thu, Jul 24, 2014 at 3:54 AM, Michka Popoff <michkapopoff at gmail.com> wrote:
>> Hi
>> 
>> I am currently maintaining the Python part of ITK, but I don?t know if I can help you. I just started with this some time ago and can not really compare it to the boost python method as I don?t know it.
>> There is an old (but outdated) discussion about boost and swig here [1]. But this was written for swig 1.34, and now we already have swig 3.0.2, which brought a lot of improvements.
>> 
>> Swig has been under heavy development lately. What I find nice with Swig is that you get other languages for free, it does not only support python but also Java, Ruby, TCL, ? (you will need to write some code for this support though).
>> The Swig method is nice once you automatized your process. Depending on the c++ code you wrote, you don?t even need to write interface files for Swig.
>> For ITK, we have a small pipeline which reads the c++ code with gccxml, and uses a python script [3] (which uses pygccxml) to create interface files from the xml files.
>> 
>> What problems did you encounter when trying the Swig route ? Maybe I can help.
>> 
>> Michka
>> 
>> [1] https://dev.lsstcorp.org/trac/wiki/SwigVsBoostPython
>> [2] https://github.com/swig/swig
>> [3] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/SwigInterface/igenerator.py
>> 
>> On 23 juil. 2014, at 17:11, Satyananda Kashyap <ksatyananda at gmail.com> wrote:
>> 
>> > Hello,
>> >
>> > I am looking for your expert opinions here. I have a relatively large C++ project I am working on which uses ITK mainly (hence the question here) and to some extent VTK and OpenCV. I do think that my code is fairly well written. I was thinking of wrapping my code to python using either SWIG or boost.python. Here are my questions :
>> >
>> >
>> > 1. I am led to believe that prototyping and code development is much faster in Python. Given that I have such a big cpp base code is it really worth the effort to wrap into python and then continue there.
>> >
>> > 2. From what I have read ITK uses SWIG wrappings for wrapping into Python while VTK uses the boost.python route. My initial attempts with both have been relatively unsuccessful. Any opinion on which one is more user friendly/better when I have to wrap my own custom classes which use a combination of both ITK and VTK in them.
>> >
>> > 3. Any suggestion on a road map as to how to proceed. I am not sure at what base class level I should wrap them and rewrite the dependencies in python.
>> >
>> > Thanks,
>> > Regards,
>> > Kashyap
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> 
>> 
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/e27e8d21/attachment.html>

From vincent.ngai at gmail.com  Thu Jul 24 23:18:17 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Fri, 25 Jul 2014 11:18:17 +0800
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
Message-ID: <CAC3nAP2kqrxNKOZCSmzH9BXWP9d8b7jjiwo14jpSiDVRBNU2Fw@mail.gmail.com>

I'm no expert, but previously when I worked on projects where we exposed
almost all core functionalities via scripts, it seemed like a good
initially, but what really happened is a shifting of complexities. Rather
than have the complexity on the C++/Compiled codebase side shifted over to
the scripts, in situation where you need to be able to change functionality
without recompiling the source, or even have access to the source, scripts
are the way to go. But shifting complexities to the runtime/script side has
its own issues, I'm happy with the C/C++ toolchain maturity, Visual C++,
GCC, GDB etc, you have very comprehensive debugging and editor facilities
available for C++, but on the script side you have far less tools, and
debugging may be a hassle.

Also for scripts that are scoped by whitespace/tabs and are not strictly
typed, we found that scripts exceeding 1/2 pages in length tend to be less
maintainable, and the chances of nuking a whitespace or overwriting a
variable gets higher.

Just my 2 cents

On Wed, Jul 23, 2014 at 11:11 PM, Satyananda Kashyap <ksatyananda at gmail.com>
wrote:

> Hello,
>
> I am looking for your expert opinions here. I have a relatively large C++
> project I am working on which uses ITK mainly (hence the question here) and
> to some extent VTK and OpenCV. I do think that my code is fairly well
> written. I was thinking of wrapping my code to python using either SWIG or
> boost.python. Here are my questions :
>
>
> 1. I am led to believe that prototyping and code development is much
> faster in Python. Given that I have such a big cpp base code is it really
> worth the effort to wrap into python and then continue there.
>
> 2. From what I have read ITK uses SWIG wrappings for wrapping into Python
> while VTK uses the boost.python route. My initial attempts with both have
> been relatively unsuccessful. Any opinion on which one is more user
> friendly/better when I have to wrap my own custom classes which use a
> combination of both ITK and VTK in them.
>
> 3. Any suggestion on a road map as to how to proceed. I am not sure at
> what base class level I should wrap them and rewrite the dependencies in
> python.
>
> Thanks,
> Regards,
> Kashyap
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>


-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140725/53685588/attachment.html>

From ksatyananda at gmail.com  Fri Jul 25 00:22:36 2014
From: ksatyananda at gmail.com (Satyananda Kashyap)
Date: Thu, 24 Jul 2014 23:22:36 -0500
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CAC3nAP2kqrxNKOZCSmzH9BXWP9d8b7jjiwo14jpSiDVRBNU2Fw@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <CAC3nAP2kqrxNKOZCSmzH9BXWP9d8b7jjiwo14jpSiDVRBNU2Fw@mail.gmail.com>
Message-ID: <CADe3Ntx-9HaS5AmpTMV-H790bgwo9bT4aWHMdOWjSEGeXQN5pQ@mail.gmail.com>

Thanks for your perspective Vincent.

One of my initial questions were about the productivity boost which you get
when using scripting languages. I am reasonably comfortable coding in C++
toolchain. From your experience do you really see a spike in productivity
when you shift over. Is it worth the effort ?

I think I will do some of the core development in C++ and expose them to
Python. I wanted to use the scripting side more for prototyping and testing
purposes.

Regards,
Kashyap


On Thu, Jul 24, 2014 at 10:18 PM, vincent ngai <vincent.ngai at gmail.com>
wrote:

> I'm no expert, but previously when I worked on projects where we exposed
> almost all core functionalities via scripts, it seemed like a good
> initially, but what really happened is a shifting of complexities. Rather
> than have the complexity on the C++/Compiled codebase side shifted over to
> the scripts, in situation where you need to be able to change functionality
> without recompiling the source, or even have access to the source, scripts
> are the way to go. But shifting complexities to the runtime/script side has
> its own issues, I'm happy with the C/C++ toolchain maturity, Visual C++,
> GCC, GDB etc, you have very comprehensive debugging and editor facilities
> available for C++, but on the script side you have far less tools, and
> debugging may be a hassle.
>
> Also for scripts that are scoped by whitespace/tabs and are not strictly
> typed, we found that scripts exceeding 1/2 pages in length tend to be less
> maintainable, and the chances of nuking a whitespace or overwriting a
> variable gets higher.
>
> Just my 2 cents
>
> On Wed, Jul 23, 2014 at 11:11 PM, Satyananda Kashyap <
> ksatyananda at gmail.com> wrote:
>
>> Hello,
>>
>> I am looking for your expert opinions here. I have a relatively large C++
>> project I am working on which uses ITK mainly (hence the question here) and
>> to some extent VTK and OpenCV. I do think that my code is fairly well
>> written. I was thinking of wrapping my code to python using either SWIG or
>> boost.python. Here are my questions :
>>
>>
>> 1. I am led to believe that prototyping and code development is much
>> faster in Python. Given that I have such a big cpp base code is it really
>> worth the effort to wrap into python and then continue there.
>>
>> 2. From what I have read ITK uses SWIG wrappings for wrapping into Python
>> while VTK uses the boost.python route. My initial attempts with both have
>> been relatively unsuccessful. Any opinion on which one is more user
>> friendly/better when I have to wrap my own custom classes which use a
>> combination of both ITK and VTK in them.
>>
>> 3. Any suggestion on a road map as to how to proceed. I am not sure at
>> what base class level I should wrap them and rewrite the dependencies in
>> python.
>>
>> Thanks,
>> Regards,
>> Kashyap
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
> --
> Regards,
> Vincent
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140724/19455182/attachment-0001.html>

From michkapopoff at gmail.com  Fri Jul 25 02:58:50 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Fri, 25 Jul 2014 08:58:50 +0200
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CADe3Ntx-9HaS5AmpTMV-H790bgwo9bT4aWHMdOWjSEGeXQN5pQ@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <CAC3nAP2kqrxNKOZCSmzH9BXWP9d8b7jjiwo14jpSiDVRBNU2Fw@mail.gmail.com>
 <CADe3Ntx-9HaS5AmpTMV-H790bgwo9bT4aWHMdOWjSEGeXQN5pQ@mail.gmail.com>
Message-ID: <8830C7A1-250B-4E85-A718-30E510F34D2F@gmail.com>

Vincent is right in the fact you have less debugging tools (in python for example).
Still, I never needed one for what I was doing, and my app has 50000 pure python lines. You have also very nice tools that integrate to vim, emacs and sublime text that do pep8, pyflakes and pylint checks each time you save the file, so that indentation or syntax errors get statically checked. About strict types, it depends a lot on what type of application you are running, and if this is really critical to you, you should not use python. If you need only integers, floats and strings, you may not need to care. And when code starts to be too long, break it up in classes and methods in different modules, and refactor :)

If your software will be used by beginners, letting them use it with python is very nice, and a lot of softwares are doing it (Paraview for example, but there are many others).
Even for more advanced users, it?s sometimes easier to start off with some python in a software they don?t know.
But I would not say you would get a spike in productivity for advanced users, they already know how to code in c++.
Still, Python is very mature, and as I said, I am running a pure python app to do multiprocessing computing on big files ? and I am happy with it.

The question if it is worth to add python support is a difficult question. It depends how many time and the ressources you have to throw at it :)

On 25 juil. 2014, at 06:22, Satyananda Kashyap <ksatyananda at gmail.com> wrote:

> Thanks for your perspective Vincent. 
> 
> One of my initial questions were about the productivity boost which you get when using scripting languages. I am reasonably comfortable coding in C++ toolchain. From your experience do you really see a spike in productivity when you shift over. Is it worth the effort ?  
> 
> I think I will do some of the core development in C++ and expose them to Python. I wanted to use the scripting side more for prototyping and testing purposes. 
> 
> Regards,
> Kashyap
> 
> 
> On Thu, Jul 24, 2014 at 10:18 PM, vincent ngai <vincent.ngai at gmail.com> wrote:
> I'm no expert, but previously when I worked on projects where we exposed almost all core functionalities via scripts, it seemed like a good initially, but what really happened is a shifting of complexities. Rather than have the complexity on the C++/Compiled codebase side shifted over to the scripts, in situation where you need to be able to change functionality without recompiling the source, or even have access to the source, scripts are the way to go. But shifting complexities to the runtime/script side has its own issues, I'm happy with the C/C++ toolchain maturity, Visual C++, GCC, GDB etc, you have very comprehensive debugging and editor facilities available for C++, but on the script side you have far less tools, and debugging may be a hassle. 
> 
> Also for scripts that are scoped by whitespace/tabs and are not strictly typed, we found that scripts exceeding 1/2 pages in length tend to be less maintainable, and the chances of nuking a whitespace or overwriting a variable gets higher.
> 
> Just my 2 cents
> 
> On Wed, Jul 23, 2014 at 11:11 PM, Satyananda Kashyap <ksatyananda at gmail.com> wrote:
> Hello,
> 
> I am looking for your expert opinions here. I have a relatively large C++ project I am working on which uses ITK mainly (hence the question here) and to some extent VTK and OpenCV. I do think that my code is fairly well written. I was thinking of wrapping my code to python using either SWIG or boost.python. Here are my questions : 
> 
> 
> 1. I am led to believe that prototyping and code development is much faster in Python. Given that I have such a big cpp base code is it really worth the effort to wrap into python and then continue there. 
> 
> 2. From what I have read ITK uses SWIG wrappings for wrapping into Python while VTK uses the boost.python route. My initial attempts with both have been relatively unsuccessful. Any opinion on which one is more user friendly/better when I have to wrap my own custom classes which use a combination of both ITK and VTK in them. 
> 
> 3. Any suggestion on a road map as to how to proceed. I am not sure at what base class level I should wrap them and rewrite the dependencies in python.  
> 
> Thanks,
> Regards,
> Kashyap
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> 
> 
> -- 
> Regards,
> Vincent
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140725/5874b68e/attachment.html>

From vincent.ngai at gmail.com  Fri Jul 25 03:39:10 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Fri, 25 Jul 2014 15:39:10 +0800
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CADe3Ntx-9HaS5AmpTMV-H790bgwo9bT4aWHMdOWjSEGeXQN5pQ@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <CAC3nAP2kqrxNKOZCSmzH9BXWP9d8b7jjiwo14jpSiDVRBNU2Fw@mail.gmail.com>
 <CADe3Ntx-9HaS5AmpTMV-H790bgwo9bT4aWHMdOWjSEGeXQN5pQ@mail.gmail.com>
Message-ID: <CAC3nAP2bmLwAtYz4iFv2H7ZhMoo-kuFkSmWpYwJ=q7ZiJ2Us8Q@mail.gmail.com>

My project was designed as a C++ framework with functionality exposed to
scripts, so it acts like an executable that runs a script that determines
the program behaviour rather than a pure python program. It might be an
important factor whether its a pure python app or an app that runs python.

Honestly I can't tell if relegating some application logic to scripts is
more productive, it works for sure, how productive it is ultimately depends
on how many of our next projects rely on using the existing framework. :)

Sorry I don't have a clear cut answer its a bit early to tell for my
project.


On Fri, Jul 25, 2014 at 12:22 PM, Satyananda Kashyap <ksatyananda at gmail.com>
wrote:

> Thanks for your perspective Vincent.
>
> One of my initial questions were about the productivity boost which you
> get when using scripting languages. I am reasonably comfortable coding in
> C++ toolchain. From your experience do you really see a spike in
> productivity when you shift over. Is it worth the effort ?
>
> I think I will do some of the core development in C++ and expose them to
> Python. I wanted to use the scripting side more for prototyping and testing
> purposes.
>
> Regards,
> Kashyap
>
>
> On Thu, Jul 24, 2014 at 10:18 PM, vincent ngai <vincent.ngai at gmail.com>
> wrote:
>
>> I'm no expert, but previously when I worked on projects where we exposed
>> almost all core functionalities via scripts, it seemed like a good
>> initially, but what really happened is a shifting of complexities. Rather
>> than have the complexity on the C++/Compiled codebase side shifted over to
>> the scripts, in situation where you need to be able to change functionality
>> without recompiling the source, or even have access to the source, scripts
>> are the way to go. But shifting complexities to the runtime/script side has
>> its own issues, I'm happy with the C/C++ toolchain maturity, Visual C++,
>> GCC, GDB etc, you have very comprehensive debugging and editor facilities
>> available for C++, but on the script side you have far less tools, and
>> debugging may be a hassle.
>>
>> Also for scripts that are scoped by whitespace/tabs and are not strictly
>> typed, we found that scripts exceeding 1/2 pages in length tend to be less
>> maintainable, and the chances of nuking a whitespace or overwriting a
>> variable gets higher.
>>
>> Just my 2 cents
>>
>> On Wed, Jul 23, 2014 at 11:11 PM, Satyananda Kashyap <
>> ksatyananda at gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I am looking for your expert opinions here. I have a relatively large
>>> C++ project I am working on which uses ITK mainly (hence the question here)
>>> and to some extent VTK and OpenCV. I do think that my code is fairly well
>>> written. I was thinking of wrapping my code to python using either SWIG or
>>> boost.python. Here are my questions :
>>>
>>>
>>> 1. I am led to believe that prototyping and code development is much
>>> faster in Python. Given that I have such a big cpp base code is it really
>>> worth the effort to wrap into python and then continue there.
>>>
>>> 2. From what I have read ITK uses SWIG wrappings for wrapping into
>>> Python while VTK uses the boost.python route. My initial attempts with both
>>> have been relatively unsuccessful. Any opinion on which one is more user
>>> friendly/better when I have to wrap my own custom classes which use a
>>> combination of both ITK and VTK in them.
>>>
>>> 3. Any suggestion on a road map as to how to proceed. I am not sure at
>>> what base class level I should wrap them and rewrite the dependencies in
>>> python.
>>>
>>> Thanks,
>>> Regards,
>>> Kashyap
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>>
>> --
>> Regards,
>> Vincent
>>
>
>


-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140725/d58a2f8c/attachment.html>

From fdrakopo at gmail.com  Fri Jul 25 15:32:25 2014
From: fdrakopo at gmail.com (Fotis Drakopoulos)
Date: Fri, 25 Jul 2014 15:32:25 -0400
Subject: [ITK-users] Problems with the integration of LASPack package into
	ITK
Message-ID: <CAG6AjRNfc-phtvD0coYnFonXEAKTObtYHAaTmb6-AyNe80MFhA@mail.gmail.com>

Hi ITK developers,

I am working on the integration of the LASPack package (
http://www.netlib.org/linalg/) inside the ITK for solving for solving large
sparse systems of linear equations with iterative methods.
I created a new folder with name laspack under the directory :
Modules/ThirdParty/VNL/src/vxl/v3p/netlib/ with the following CMakeList.txt
:

*PROJECT( laspack )*

*# List sources for each library component.*
*SET(V3P_NETLIB_laspack_SOURCES*
*    eigenval.c*
*    errhandl.c*
*    factor.c*
*    itersolv.c*
*    matrix.c*
*    mlsolv.c*
*    operats.c*
*    precond.c*
*    qmatrix.c*
*    rtc.c*
*    vector.c*
*    eigenval.h*
*    elcmp.h*
*    errhandl.h*
*    factor.h*
*    itersolv.h*
*    lastypes.h*
*    matrix.h*
*    mlsolv.h*
*    operats.h*
*    precond.h*
*    qmatrix.h*
*    rtc.h*
*    vector.h*
*    version.h*
*    copyrght.h*
*    xc/getopts.c*
*    xc/xstring.c*
*    xc/getopts.h*
*    xc/version.h*
*    xc/xstring.h*
*    xc/xtypes.h*
*  )*

*# Create a library .*
*ADD_LIBRARY(itkv3p_laspack ${V3P_NETLIB_laspack_SOURCES})*
*IF(UNIX)*
*  TARGET_LINK_LIBRARIES( itkv3p_laspack m )*
*ENDIF(UNIX)*
*IF(ITK_LIBRARY_PROPERTIES)*
*  SET_TARGET_PROPERTIES(itkv3p_laspack PROPERTIES
${ITK_LIBRARY_PROPERTIES})*
*ENDIF(ITK_LIBRARY_PROPERTIES)*

*IF(NOT VXL_INSTALL_NO_LIBRARIES)*
*  INSTALL(TARGETS itkv3p_laspack*
*    EXPORT ${VXL_INSTALL_EXPORT_NAME}*
*    RUNTIME DESTINATION ${VXL_INSTALL_RUNTIME_DIR} COMPONENT
RuntimeLibraries*
*    LIBRARY DESTINATION ${VXL_INSTALL_LIBRARY_DIR} COMPONENT
RuntimeLibraries*
*    ARCHIVE DESTINATION ${VXL_INSTALL_ARCHIVE_DIR} COMPONENT Development)*
*ENDIF(NOT VXL_INSTALL_NO_LIBRARIES)*
*IF(NOT VXL_INSTALL_NO_DEVELOPMENT)*
*  INSTALL_NOBASE_HEADER_FILES(${VXL_INSTALL_INCLUDE_DIR}
${V3P_NETLIB_laspack_SOURCES})*
*ENDIF(NOT VXL_INSTALL_NO_DEVELOPMENT)*

Also in the CMakeLists.txt located in direcory : Modules/ThirdParty/VNL/src
I added the new *itkv3p_laspack* library as follows:

*add_subdirectory(vxl)*
*foreach(lib itkvcl itkv3p_netlib itkv3p_lsqr itkv3p_laspack itktestlib
itkvnl itkvnl_algo)*
*  itk_module_target(${lib} NO_INSTALL)*
*endforeach()*

When I build ITK I do not get any errors and the *libitkv3p_laspack. a*  is
normally created like all the other ITK libraries.
However when I compile an external project which links to ITK with
TARGET_LINK_LIBRARIES(PROJECT_NAME ${ITK_LIBRARIES}),   I am getting the
following link error:

*/home/fdrakopo/local/bin/ITKDev/release/lib/libitkvnl_algo-4.1.a(vnl_sparse_iterative_solver.cxx.o):
In function
`vnl_sparse_iterative_solver::vnl_sparse_iterative_solver(vnl_sparse_matrix<double>
const&)':*
*vnl_sparse_iterative_solver.cxx:(.text+0x6a): undefined reference to
`Q_SetName(QMatrixType*, char*)'*
*collect2: error: ld returned 1 exit status*
*make[2]: *** [PAPBNRR] Error 1*
*make[1]: *** [CMakeFiles/PAPBNRR.dir/all] Error 2*
*make: *** [all] Error 2*

The vnl_sparse_iterative_solver is a new class I created under :
Modules/ThirdParty/VNL/src/vxl/core/vnl/algo
and encapsulates the implemented calls (functions, etc.) to the LASPack
package (similarly to vnl_sparse_lu class that calls Kenneth's Kundert
SPARSE package).
Also the itkvnl_algo inks to itkv3p_laspack :
*TARGET_LINK_LIBRARIES( itkvnl_algo ${NETLIB_LIBRARIES} itkvnl itkv3p_lsqr
itkv3p_laspack ) *

Any ideas how can I solve the above link error?

Regards,
Fotis Drakopoulos
CRTC lab
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140725/43b46566/attachment.html>

From blowekamp at mail.nih.gov  Fri Jul 25 15:44:51 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 25 Jul 2014 15:44:51 -0400
Subject: [ITK-users] [ITK-dev] Problems with the integration of LASPack
	package into ITK
In-Reply-To: <CAG6AjRNfc-phtvD0coYnFonXEAKTObtYHAaTmb6-AyNe80MFhA@mail.gmail.com>
References: <CAG6AjRNfc-phtvD0coYnFonXEAKTObtYHAaTmb6-AyNe80MFhA@mail.gmail.com>
Message-ID: <BB0E3B5E-49C4-4560-827F-87182513A4A5@mail.nih.gov>

Hello,

I am not certain but I just was looking around at a few things and found some work related to ITKv4 Numerics Refactors[1] here on github that's a bit out dated:
https://github.com/chuckatkins/ITK/commits/numlibs_refactor

Looks like similar work and my first search reveals this may be of use:
https://github.com/chuckatkins/ITK/commit/2c773edc695cbe7b907bebf356ee14e0af66b01a

Brad

[1] http://www.itk.org/Wiki/ITK_Release_4/Refactor_Numerical_Libraries

On Jul 25, 2014, at 3:32 PM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:

> Hi ITK developers,
> 
> I am working on the integration of the LASPack package (http://www.netlib.org/linalg/) inside the ITK for solving for solving large sparse systems of linear equations with iterative methods.
> I created a new folder with name laspack under the directory : Modules/ThirdParty/VNL/src/vxl/v3p/netlib/ with the following CMakeList.txt :
> 
> PROJECT( laspack )
> 
> # List sources for each library component.
> SET(V3P_NETLIB_laspack_SOURCES
>     eigenval.c
>     errhandl.c
>     factor.c
>     itersolv.c
>     matrix.c
>     mlsolv.c
>     operats.c
>     precond.c
>     qmatrix.c
>     rtc.c
>     vector.c
>     eigenval.h
>     elcmp.h
>     errhandl.h
>     factor.h
>     itersolv.h
>     lastypes.h
>     matrix.h
>     mlsolv.h
>     operats.h
>     precond.h
>     qmatrix.h
>     rtc.h
>     vector.h
>     version.h
>     copyrght.h
>     xc/getopts.c
>     xc/xstring.c
>     xc/getopts.h
>     xc/version.h
>     xc/xstring.h
>     xc/xtypes.h
>   )
> 
> # Create a library .
> ADD_LIBRARY(itkv3p_laspack ${V3P_NETLIB_laspack_SOURCES})
> IF(UNIX)
>   TARGET_LINK_LIBRARIES( itkv3p_laspack m )
> ENDIF(UNIX)
> IF(ITK_LIBRARY_PROPERTIES)
>   SET_TARGET_PROPERTIES(itkv3p_laspack PROPERTIES ${ITK_LIBRARY_PROPERTIES})
> ENDIF(ITK_LIBRARY_PROPERTIES)
> 
> IF(NOT VXL_INSTALL_NO_LIBRARIES)
>   INSTALL(TARGETS itkv3p_laspack
>     EXPORT ${VXL_INSTALL_EXPORT_NAME}
>     RUNTIME DESTINATION ${VXL_INSTALL_RUNTIME_DIR} COMPONENT RuntimeLibraries
>     LIBRARY DESTINATION ${VXL_INSTALL_LIBRARY_DIR} COMPONENT RuntimeLibraries
>     ARCHIVE DESTINATION ${VXL_INSTALL_ARCHIVE_DIR} COMPONENT Development)
> ENDIF(NOT VXL_INSTALL_NO_LIBRARIES)
> IF(NOT VXL_INSTALL_NO_DEVELOPMENT)
>   INSTALL_NOBASE_HEADER_FILES(${VXL_INSTALL_INCLUDE_DIR} ${V3P_NETLIB_laspack_SOURCES})
> ENDIF(NOT VXL_INSTALL_NO_DEVELOPMENT)
> 
> Also in the CMakeLists.txt located in direcory : Modules/ThirdParty/VNL/src I added the new itkv3p_laspack library as follows: 
> 
> add_subdirectory(vxl)
> foreach(lib itkvcl itkv3p_netlib itkv3p_lsqr itkv3p_laspack itktestlib itkvnl itkvnl_algo)
>   itk_module_target(${lib} NO_INSTALL)
> endforeach()
> 
> When I build ITK I do not get any errors and the libitkv3p_laspack. a  is normally created like all the other ITK libraries.
> However when I compile an external project which links to ITK with TARGET_LINK_LIBRARIES(PROJECT_NAME ${ITK_LIBRARIES}),   I am getting the following link error:
> 
> /home/fdrakopo/local/bin/ITKDev/release/lib/libitkvnl_algo-4.1.a(vnl_sparse_iterative_solver.cxx.o): In function `vnl_sparse_iterative_solver::vnl_sparse_iterative_solver(vnl_sparse_matrix<double> const&)':
> vnl_sparse_iterative_solver.cxx:(.text+0x6a): undefined reference to `Q_SetName(QMatrixType*, char*)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [PAPBNRR] Error 1
> make[1]: *** [CMakeFiles/PAPBNRR.dir/all] Error 2
> make: *** [all] Error 2
>  
> The vnl_sparse_iterative_solver is a new class I created under : Modules/ThirdParty/VNL/src/vxl/core/vnl/algo 
> and encapsulates the implemented calls (functions, etc.) to the LASPack package (similarly to vnl_sparse_lu class that calls Kenneth's Kundert SPARSE package).
> Also the itkvnl_algo inks to itkv3p_laspack :
> TARGET_LINK_LIBRARIES( itkvnl_algo ${NETLIB_LIBRARIES} itkvnl itkv3p_lsqr itkv3p_laspack ) 
> 
> Any ideas how can I solve the above link error?
> 
> Regards,
> Fotis Drakopoulos
> CRTC lab
> 
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140725/b1b7fad5/attachment.html>

From soccer_zhe at hotmail.com  Sat Jul 26 00:29:44 2014
From: soccer_zhe at hotmail.com (zhe)
Date: Sat, 26 Jul 2014 12:29:44 +0800
Subject: [ITK-users] Building ITK4.5.2 with Python wrapping: A tool returned
 an error code from "Generating ../vcInstall_stamp.c"
Message-ID: <BAY178-W3173F2B872CE3515A14158ECFD0@phx.gbl>




Dear All
I am trying to build ITK with Python wrapping on windows (python 2.7.7 32bit, VS 2008 32bit and Windows 7 64bit). But during the compiling, the VS 2008 reported a error as follow:
 
 
1>1>------ Build started: Project: vcInstallPatch, Configuration: Release Win32 ------
1>1>Generating ../vcInstall_stamp.c
1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc9Include.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc9\Include
1>1>Error running patch.  Output is []
1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc9PlatformSDK.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc9\PlatformSDK
1>1>Error running patch.  Output is []
1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc10Include.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc10\Include
1>1>Error running patch.  Output is []
1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc10PlatformSDK.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc10\PlatformSDK
1>1>Error running patch.  Output is []
1>1>Project : error PRJ0019: A tool returned an error code from "Generating ../vcInstall_stamp.c"
1>1>Build log was saved at "file://d:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\VcInstall\vcInstallPatch.dir\Release\BuildLog.htm"
1>1>vcInstallPatch - 1 error(s), 0 warning(s)
1>========== Build: 0 succeeded, 1 failed, 36 up-to-date, 0 skipped ==========
1>Project : error PRJ0019: A tool returned an error code from "Performing build step for 'GCC_XML'"
1>Build log was saved at "file://d:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\GCC_XML.dir\Release\BuildLog.htm"
1>GCC_XML - 2 error(s), 0 warning(s)
 
How can I solve this problem? 
Thank you very much.
 
Best regards
 
Zhe Luo

 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140726/b76ad531/attachment.html>

From michkapopoff at gmail.com  Sat Jul 26 05:01:18 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Sat, 26 Jul 2014 11:01:18 +0200
Subject: [ITK-users] Building ITK4.5.2 with Python wrapping: A tool
	returned an error code from "Generating ../vcInstall_stamp.c"
In-Reply-To: <BAY178-W3173F2B872CE3515A14158ECFD0@phx.gbl>
References: <BAY178-W3173F2B872CE3515A14158ECFD0@phx.gbl>
Message-ID: <B690D6F4-827C-4BFD-BC17-938E26F3795C@gmail.com>

Hi

I don?t know if it?s a solution, but last time I had trouble with the gccxml part, I had to disable my antivirus (Avast in my case).
It blocks some files to be extracted or to run. You may start with a new build folder and try this.

If it?s still not working, please report back, I will then try to compile it myself, but it should be OK as we have a machine running with this setup on our Dashboard.

Michka

On 26 juil. 2014, at 06:29, zhe <soccer_zhe at hotmail.com> wrote:

> Dear All
> 
> I am trying to build ITK with Python wrapping on windows (python 2.7.7 32bit, VS 2008 32bit and Windows 7 64bit). But during the compiling, the VS 2008 reported a error as follow:
>  
>  
> 1>1>------ Build started: Project: vcInstallPatch, Configuration: Release Win32 ------
> 1>1>Generating ../vcInstall_stamp.c
> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc9Include.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc9\Include
> 1>1>Error running patch.  Output is []
> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc9PlatformSDK.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc9\PlatformSDK
> 1>1>Error running patch.  Output is []
> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc10Include.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc10\Include
> 1>1>Error running patch.  Output is []
> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc10PlatformSDK.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc10\PlatformSDK
> 1>1>Error running patch.  Output is []
> 1>1>Project : error PRJ0019: A tool returned an error code from "Generating ../vcInstall_stamp.c"
> 1>1>Build log was saved at "file://d:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\VcInstall\vcInstallPatch.dir\Release\BuildLog.htm"
> 1>1>vcInstallPatch - 1 error(s), 0 warning(s)
> 1>========== Build: 0 succeeded, 1 failed, 36 up-to-date, 0 skipped ==========
> 1>Project : error PRJ0019: A tool returned an error code from "Performing build step for 'GCC_XML'"
> 1>Build log was saved at "file://d:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\GCC_XML.dir\Release\BuildLog.htm"
> 1>GCC_XML - 2 error(s), 0 warning(s)
>  
> How can I solve this problem? 
> Thank you very much.
>  
> Best regards
>  
> Zhe Luo
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140726/70fd1c14/attachment.html>

From blowekamp at mail.nih.gov  Sat Jul 26 08:46:34 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Sat, 26 Jul 2014 08:46:34 -0400
Subject: [ITK-users] Building ITK4.5.2 with Python wrapping: A tool
 returned an error code from "Generating ../vcInstall_stamp.c"
In-Reply-To: <B690D6F4-827C-4BFD-BC17-938E26F3795C@gmail.com>
References: <BAY178-W3173F2B872CE3515A14158ECFD0@phx.gbl>
 <B690D6F4-827C-4BFD-BC17-938E26F3795C@gmail.com>
Message-ID: <31347E6A-DA8B-479A-8F9D-550CF33AC703@mail.nih.gov>

Hello,

Have you looked into SimpleITK[1]? It provides binary distributions for windows that are readily available, if you are having too much difficulty compiling with the native WrapITK.

[1] http://www.itk.org/Wiki/SimpleITK 

On Jul 26, 2014, at 5:01 AM, Michka Popoff <michkapopoff at gmail.com> wrote:

> Hi
> 
> I don?t know if it?s a solution, but last time I had trouble with the gccxml part, I had to disable my antivirus (Avast in my case).
> It blocks some files to be extracted or to run. You may start with a new build folder and try this.
> 
> If it?s still not working, please report back, I will then try to compile it myself, but it should be OK as we have a machine running with this setup on our Dashboard.
> 
> Michka
> 
> On 26 juil. 2014, at 06:29, zhe <soccer_zhe at hotmail.com> wrote:
> 
>> Dear All
>> 
>> I am trying to build ITK with Python wrapping on windows (python 2.7.7 32bit, VS 2008 32bit and Windows 7 64bit). But during the compiling, the VS 2008 reported a error as follow:
>>  
>>  
>> 1>1>------ Build started: Project: vcInstallPatch, Configuration: Release Win32 ------
>> 1>1>Generating ../vcInstall_stamp.c
>> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc9Include.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc9\Include
>> 1>1>Error running patch.  Output is []
>> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc9PlatformSDK.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc9\PlatformSDK
>> 1>1>Error running patch.  Output is []
>> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc10Include.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc10\Include
>> 1>1>Error running patch.  Output is []
>> 1>1>Executing D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vccat.exe D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vc10PlatformSDK.patch | D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML\GCC_XML\VcInstall\vcpatch.exe -p0 -t -d D:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\Support\Vc10\PlatformSDK
>> 1>1>Error running patch.  Output is []
>> 1>1>Project : error PRJ0019: A tool returned an error code from "Generating ../vcInstall_stamp.c"
>> 1>1>Build log was saved at "file://d:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\gccxml\src\GCC_XML-build\GCC_XML\VcInstall\vcInstallPatch.dir\Release\BuildLog.htm"
>> 1>1>vcInstallPatch - 1 error(s), 0 warning(s)
>> 1>========== Build: 0 succeeded, 1 failed, 36 up-to-date, 0 skipped ==========
>> 1>Project : error PRJ0019: A tool returned an error code from "Performing build step for 'GCC_XML'"
>> 1>Build log was saved at "file://d:\ITK4.5.2\ITK_Build\Wrapping\Generators\GccXML\GCC_XML.dir\Release\BuildLog.htm"
>> 1>GCC_XML - 2 error(s), 0 warning(s)
>>  
>> How can I solve this problem? 
>> Thank you very much.
>>  
>> Best regards
>>  
>> Zhe Luo
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140726/9c82edc4/attachment.html>

From fdrakopo at gmail.com  Sat Jul 26 13:15:02 2014
From: fdrakopo at gmail.com (Fotis Drakopoulos)
Date: Sat, 26 Jul 2014 13:15:02 -0400
Subject: [ITK-users] [ITK-dev] Problems with the integration of LASPack
	package into ITK
In-Reply-To: <BB0E3B5E-49C4-4560-827F-87182513A4A5@mail.nih.gov>
References: <CAG6AjRNfc-phtvD0coYnFonXEAKTObtYHAaTmb6-AyNe80MFhA@mail.gmail.com>
 <BB0E3B5E-49C4-4560-827F-87182513A4A5@mail.nih.gov>
Message-ID: <CAG6AjRNcCeQpR_jwUmBysvnbCxCcpzmxsZ8c6uKYnU1eLs3t-A@mail.gmail.com>

Hi Brad,
I made the appropriate changes to all CMakeLists.txt files according to [1]
but I still get the same error when I link the external project to ITK
libraries.
I also tried NOT to create a separate *libitkv3p_laspack *but to include
laspack into the *itkv3p_netlib*  (like the SPARSE package) and I still get
the same link error.
After spending several days on the LASPack integration I am not sure why I
get this link error...

[1]
https://github.com/chuckatkins/ITK/commit/2c773edc695cbe7b907bebf356ee14e0af66b01a

Best,
Fotis


On Fri, Jul 25, 2014 at 3:44 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> I am not certain but I just was looking around at a few things and found
> some work related to ITKv4 Numerics Refactors[1] here on github that's a
> bit out dated:
> https://github.com/chuckatkins/ITK/commits/numlibs_refactor
>
> Looks like similar work and my first search reveals this may be of use:
>
> https://github.com/chuckatkins/ITK/commit/2c773edc695cbe7b907bebf356ee14e0af66b01a
>
> Brad
>
> [1] http://www.itk.org/Wiki/ITK_Release_4/Refactor_Numerical_Libraries
>
> On Jul 25, 2014, at 3:32 PM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
>
> Hi ITK developers,
>
> I am working on the integration of the LASPack package (
> http://www.netlib.org/linalg/) inside the ITK for solving for solving
> large sparse systems of linear equations with iterative methods.
> I created a new folder with name laspack under the directory :
> Modules/ThirdParty/VNL/src/vxl/v3p/netlib/ with the following CMakeList.txt
> :
>
> *PROJECT( laspack )*
>
>  *# List sources for each library component.*
> *SET(V3P_NETLIB_laspack_SOURCES*
> *    eigenval.c*
> *    errhandl.c*
> *    factor.c*
> *    itersolv.c*
> *    matrix.c*
> *    mlsolv.c*
> *    operats.c*
> *    precond.c*
> *    qmatrix.c*
> *    rtc.c*
> *    vector.c*
> *    eigenval.h*
> *    elcmp.h*
> *    errhandl.h*
> *    factor.h*
> *    itersolv.h*
> *    lastypes.h*
> *    matrix.h*
> *    mlsolv.h*
> *    operats.h*
> *    precond.h*
> *    qmatrix.h*
> *    rtc.h*
> *    vector.h*
> *    version.h*
> *    copyrght.h*
> *    xc/getopts.c*
> *    xc/xstring.c*
> *    xc/getopts.h*
> *    xc/version.h*
> *    xc/xstring.h*
> *    xc/xtypes.h*
> *  )*
>
> *# Create a library .*
> *ADD_LIBRARY(itkv3p_laspack ${V3P_NETLIB_laspack_SOURCES})*
> *IF(UNIX)*
> *  TARGET_LINK_LIBRARIES( itkv3p_laspack m )*
> *ENDIF(UNIX)*
> *IF(ITK_LIBRARY_PROPERTIES)*
> *  SET_TARGET_PROPERTIES(itkv3p_laspack PROPERTIES
> ${ITK_LIBRARY_PROPERTIES})*
> *ENDIF(ITK_LIBRARY_PROPERTIES)*
>
> *IF(NOT VXL_INSTALL_NO_LIBRARIES)*
> *  INSTALL(TARGETS itkv3p_laspack*
> *    EXPORT ${VXL_INSTALL_EXPORT_NAME}*
> *    RUNTIME DESTINATION ${VXL_INSTALL_RUNTIME_DIR} COMPONENT
> RuntimeLibraries*
> *    LIBRARY DESTINATION ${VXL_INSTALL_LIBRARY_DIR} COMPONENT
> RuntimeLibraries*
> *    ARCHIVE DESTINATION ${VXL_INSTALL_ARCHIVE_DIR} COMPONENT Development)*
> *ENDIF(NOT VXL_INSTALL_NO_LIBRARIES)*
> *IF(NOT VXL_INSTALL_NO_DEVELOPMENT)*
> *  INSTALL_NOBASE_HEADER_FILES(${VXL_INSTALL_INCLUDE_DIR}
> ${V3P_NETLIB_laspack_SOURCES})*
> *ENDIF(NOT VXL_INSTALL_NO_DEVELOPMENT)*
>
> Also in the CMakeLists.txt located in direcory :
> Modules/ThirdParty/VNL/src I added the new *itkv3p_laspack* library as
> follows:
>
> *add_subdirectory(vxl)*
> *foreach(lib itkvcl itkv3p_netlib itkv3p_lsqr itkv3p_laspack itktestlib
> itkvnl itkvnl_algo)*
> *  itk_module_target(${lib} NO_INSTALL)*
> *endforeach()*
>
> When I build ITK I do not get any errors and the *libitkv3p_laspack. a*
> is normally created like all the other ITK libraries.
> However when I compile an external project which links to ITK with
> TARGET_LINK_LIBRARIES(PROJECT_NAME ${ITK_LIBRARIES}),   I am getting the
> following link error:
>
> */home/fdrakopo/local/bin/ITKDev/release/lib/libitkvnl_algo-4.1.a(vnl_sparse_iterative_solver.cxx.o):
> In function
> `vnl_sparse_iterative_solver::vnl_sparse_iterative_solver(vnl_sparse_matrix<double>
> const&)':*
> *vnl_sparse_iterative_solver.cxx:(.text+0x6a): undefined reference to
> `Q_SetName(QMatrixType*, char*)'*
> *collect2: error: ld returned 1 exit status*
> *make[2]: *** [PAPBNRR] Error 1*
> *make[1]: *** [CMakeFiles/PAPBNRR.dir/all] Error 2*
> *make: *** [all] Error 2*
>
> The vnl_sparse_iterative_solver is a new class I created under :
> Modules/ThirdParty/VNL/src/vxl/core/vnl/algo
> and encapsulates the implemented calls (functions, etc.) to the LASPack
> package (similarly to vnl_sparse_lu class that calls Kenneth's Kundert
> SPARSE package).
> Also the itkvnl_algo inks to itkv3p_laspack :
> *TARGET_LINK_LIBRARIES( itkvnl_algo ${NETLIB_LIBRARIES} itkvnl itkv3p_lsqr
> itkv3p_laspack ) *
>
> Any ideas how can I solve the above link error?
>
> Regards,
> Fotis Drakopoulos
> CRTC lab
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
>
>  ------------------------------
>
> Spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=02MuHJuoo&m=974aceda4769&t=20140725&c=s>
> Not spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=02MuHJuoo&m=974aceda4769&t=20140725&c=n>
> Forget previous vote
> <https://www.spamtrap.odu.edu/canit/b.php?i=02MuHJuoo&m=974aceda4769&t=20140725&c=f>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140726/383c5ce1/attachment-0001.html>

From grothausmann.roman at mh-hannover.de  Mon Jul 28 10:23:20 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Mon, 28 Jul 2014 16:23:20 +0200
Subject: [ITK-users] Extensions to the MetaImage (MHDs) IO-plugin to support
 compression and MHAs
Message-ID: <53D65CD8.4080305@mh-hannover.de>

Dear mailing list members,


I've extended the MetaImage (used by e.g. ITK/VTK)  IO-plugin from Kang Li 
(http://www.kangli.org/code/MetaImage_Reader_Writer.html) to also support 
compression and local data storage, i.e. MHAs. The MetaImage Reader/Writer from 
(http://ij-plugins.sourceforge.net/plugins/3d-io/) seems not to support this 
either.
Reading and writing in Fiji was tested with MHDs and MHAs created/read by 
ITK-4.5.1. While the plugin handles files bigger than 4GB correctly, (for 
unknown reasons my) ITK seems to have problems with MHDs/MHAs bigger than 4GB 
(in general).
The plugin does not check whether the size of the compressed data is correct, 
ITK however does. If the header lacks an entry of CompressedDataSize, ITK throws 
an error when reading/loading such a file. If the size specified with 
CompressedDataSize is too big, ITK just issues a warning. This was used as a 
workaround because I did not find an easy way in Java to put the correct value 
for CompressedDataSize without using extra temporary files (which might be quite 
big).

Attached are the modified files (java-files, plugins.config and a repacked 
IO_-2.0.0-SNAPSHOT.jar).
A modified HandleExtraFileTypes.java (based on: 
https://github.com/fiji/IO/blob/master/src/main/java/HandleExtraFileTypes.java) 
is also included.
Togehter with the modified Plugin it allows opening MHDs and MHAs directly.


The repacked IO_-2.0.0-SNAPSHOT.jar was generated with:

javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_Reader.java
javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_Writer.java
javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_CWriter.java

javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. HandleExtraFileTypes.java

The compiled Class-files were moved to a subfolder named io/:
ExtendedFileOpener.class  MetaImage_CWriter.class  MetaImage_Writer.class
ExtendedFileSaver.class   MetaImage_Reader.class   ReplacingInputStream.class

And then included/replaced with zip:
zip -r IO_-2.0.0-SNAPSHOT.jar plugins.config HandleExtraFileTypes.class io/

Feel free to add these extensions to the Plugin-Page or the ImageJ/Fiji repository.
Any suggestions concerning improvements are very welcome.


Many thanks for ImageJ/Fiji and the initial Metaimage IO-plugin.
Roman


-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574
-------------- next part --------------
A non-text attachment was scrubbed...
Name: HandleExtraFileTypes.java
Type: text/x-java
Size: 16846 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/d5513378/attachment-0004.java>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: MetaImage_CWriter.java
Type: text/x-java
Size: 11063 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/d5513378/attachment-0005.java>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: MetaImage_Reader.java
Type: text/x-java
Size: 17777 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/d5513378/attachment-0006.java>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: MetaImage_Writer.java
Type: text/x-java
Size: 6219 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/d5513378/attachment-0007.java>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: MetaImageIO.patch
Type: text/x-patch
Size: 17205 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/d5513378/attachment-0002.bin>
-------------- next part --------------
# Author: Roman Grothausmann
File>Save As, "MHD/MHA ...", io.MetaImage_Writer
File>Save As, "MHD/MHA compressed ...", io.MetaImage_CWriter
File>Import, "MHD/MHA...", io.MetaImage_Reader

# Author: Stephan Saalfeld
File>Save As, "DF3 ...", io.Save_DF3
File>Import, "DF3...", io.Open_DF3

# Author: Stephan Preibisch
File>Import, "FIB-SEM ...", io.FIBSEM_Reader

# by Albert Cardona:
File>Import, "MRC Leginon ...", io.Open_MRC_Leginon
File>Import, "PDF ...", io.PDF_Viewer
File>Import, "Extract Images From PDF...", io.Extract_Images_From_PDF
File>Import, "DAT EMMENU ...", io.Open_DAT_EMMENU

# by Greg Jefferis
File>Import, "DM3 Reader...", io.DM3_Reader
File>Import, "TorstenRaw GZ Reader...", io.TorstenRaw_GZ_Reader
File>Import, "Nrrd ...", io.Nrrd_Reader
File>Save As, "Nrrd ... ", io.Nrrd_Writer

# by Johannes Schindelin
File>Import, "ICO...", io.ICO_Reader
File>Save As, "ICO ...", io.ICO_Writer
File>Import, "Icns...", io.Icns_Reader
File>Save As, "Icns ...", io.Icns_Writer
File>Import, "SVG...", io.SVG_Reader
File>Save As, "XPM ...", io.XPM_Writer
File>Import, "LSS16...", io.LSS16_Reader
File>Save As, "LSS16 ...", io.LSS16_Writer

# others:
File>Import, "IPLab Reader...", io.IPLab_Reader
File>Save As, "PDF ... ", io.PDF_Writer
File>Import, "Animated Gif...", io.Animated_Gif_Reader
File>Save As, "Animated Gif ... ", io.Gif_Stack_Writer
File>Save As, "EPS ...", io.Export_EPS
-------------- next part --------------
A non-text attachment was scrubbed...
Name: IO_-2.0.0-SNAPSHOT.jar
Type: application/x-java-archive
Size: 149064 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/d5513378/attachment-0003.bin>

From norman-k-williams at uiowa.edu  Mon Jul 28 13:34:50 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Mon, 28 Jul 2014 17:34:50 +0000
Subject: [ITK-users] Extensions to the MetaImage (MHDs) IO-plugin to
 support compression and MHAs
In-Reply-To: <27272_1406557413_s6SENUxH012254_53D65CD8.4080305@mh-hannover.de>
References: <27272_1406557413_s6SENUxH012254_53D65CD8.4080305@mh-hannover.de>
Message-ID: <CFFBF3B0.9E1B%norman-k-williams@uiowa.edu>

This is a good thing to submit to ITK proper; it would require conversion
to C++, though.

On 7/28/14, 9:23 AM, "Dr. Roman Grothausmann"
<grothausmann.roman at mh-hannover.de> wrote:

>Dear mailing list members,
>
>
>I've extended the MetaImage (used by e.g. ITK/VTK)  IO-plugin from Kang
>Li
>(http://www.kangli.org/code/MetaImage_Reader_Writer.html) to also support
>compression and local data storage, i.e. MHAs. The MetaImage
>Reader/Writer from
>(http://ij-plugins.sourceforge.net/plugins/3d-io/) seems not to support
>this
>either.
>Reading and writing in Fiji was tested with MHDs and MHAs created/read by
>ITK-4.5.1. While the plugin handles files bigger than 4GB correctly, (for
>unknown reasons my) ITK seems to have problems with MHDs/MHAs bigger than
>4GB
>(in general).
>The plugin does not check whether the size of the compressed data is
>correct,
>ITK however does. If the header lacks an entry of CompressedDataSize, ITK
>throws
>an error when reading/loading such a file. If the size specified with
>CompressedDataSize is too big, ITK just issues a warning. This was used
>as a
>workaround because I did not find an easy way in Java to put the correct
>value
>for CompressedDataSize without using extra temporary files (which might
>be quite
>big).
>
>Attached are the modified files (java-files, plugins.config and a
>repacked
>IO_-2.0.0-SNAPSHOT.jar).
>A modified HandleExtraFileTypes.java (based on:
>https://github.com/fiji/IO/blob/master/src/main/java/HandleExtraFileTypes.
>java)
>is also included.
>Togehter with the modified Plugin it allows opening MHDs and MHAs
>directly.
>
>
>The repacked IO_-2.0.0-SNAPSHOT.jar was generated with:
>
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_Reader.java
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_Writer.java
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_CWriter.java
>
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. HandleExtraFileTypes.java
>
>The compiled Class-files were moved to a subfolder named io/:
>ExtendedFileOpener.class  MetaImage_CWriter.class  MetaImage_Writer.class
>ExtendedFileSaver.class   MetaImage_Reader.class
>ReplacingInputStream.class
>
>And then included/replaced with zip:
>zip -r IO_-2.0.0-SNAPSHOT.jar plugins.config HandleExtraFileTypes.class
>io/
>
>Feel free to add these extensions to the Plugin-Page or the ImageJ/Fiji
>repository.
>Any suggestions concerning improvements are very welcome.
>
>
>Many thanks for ImageJ/Fiji and the initial Metaimage IO-plugin.
>Roman
>
>
>--
>Dr. Roman Grothausmann
>
>Tomographie und Digitale Bildverarbeitung
>Tomography and Digital Image Analysis
>
>Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>Medizinische Hochschule Hannover
>Carl-Neuberg-Str. 1
>D-30625 Hannover
>
>Tel. +49 511 532-9574
>
>
>
>======================================================================
>A potentially unsafe attachment has been removed from this email
>message. See http://its.uiowa.edu/support/article/100806 for further
>information.
>
>Removed attachment name(s):
>IO_-2.0.0-SNAPSHOT.jar
>======================================================================
>



________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________

From norman-k-williams at uiowa.edu  Mon Jul 28 17:11:59 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Mon, 28 Jul 2014 21:11:59 +0000
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CAC3nAP2bmLwAtYz4iFv2H7ZhMoo-kuFkSmWpYwJ=q7ZiJ2Us8Q@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <CAC3nAP2kqrxNKOZCSmzH9BXWP9d8b7jjiwo14jpSiDVRBNU2Fw@mail.gmail.com>
 <CADe3Ntx-9HaS5AmpTMV-H790bgwo9bT4aWHMdOWjSEGeXQN5pQ@mail.gmail.com>
 <CAC3nAP2bmLwAtYz4iFv2H7ZhMoo-kuFkSmWpYwJ=q7ZiJ2Us8Q@mail.gmail.com>
Message-ID: <CFFC25D2.9E32%norman-k-williams@uiowa.edu>

The biggest plus in using Python with C++ back end for the compute/graphics intensive stuff is interactive development without a compile/link stage.

There are great python debug tools.  Debugging python in Emacs is easy enough using pdb.  You can set breakpoint in the source code, examine variables, etc.  Debugging python is no more difficult than debugging C++.  There are python IDE that allow source debugging as well.  PyCharm is well regarded.

From: vincent ngai <vincent.ngai at gmail.com<mailto:vincent.ngai at gmail.com>>
Date: Friday, July 25, 2014 at 2:39 AM
To: Satyananda Kashyap <ksatyananda at gmail.com<mailto:ksatyananda at gmail.com>>
Cc: Insight <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: Re: [ITK-users] Suggestions about Python wrapping of cpp project

My project was designed as a C++ framework with functionality exposed to scripts, so it acts like an executable that runs a script that determines the program behaviour rather than a pure python program. It might be an important factor whether its a pure python app or an app that runs python.

Honestly I can't tell if relegating some application logic to scripts is more productive, it works for sure, how productive it is ultimately depends on how many of our next projects rely on using the existing framework. :)

Sorry I don't have a clear cut answer its a bit early to tell for my project.


On Fri, Jul 25, 2014 at 12:22 PM, Satyananda Kashyap <ksatyananda at gmail.com<mailto:ksatyananda at gmail.com>> wrote:
Thanks for your perspective Vincent.

One of my initial questions were about the productivity boost which you get when using scripting languages. I am reasonably comfortable coding in C++ toolchain. From your experience do you really see a spike in productivity when you shift over. Is it worth the effort ?

I think I will do some of the core development in C++ and expose them to Python. I wanted to use the scripting side more for prototyping and testing purposes.

Regards,
Kashyap


On Thu, Jul 24, 2014 at 10:18 PM, vincent ngai <vincent.ngai at gmail.com<mailto:vincent.ngai at gmail.com>> wrote:
I'm no expert, but previously when I worked on projects where we exposed almost all core functionalities via scripts, it seemed like a good initially, but what really happened is a shifting of complexities. Rather than have the complexity on the C++/Compiled codebase side shifted over to the scripts, in situation where you need to be able to change functionality without recompiling the source, or even have access to the source, scripts are the way to go. But shifting complexities to the runtime/script side has its own issues, I'm happy with the C/C++ toolchain maturity, Visual C++, GCC, GDB etc, you have very comprehensive debugging and editor facilities available for C++, but on the script side you have far less tools, and debugging may be a hassle.

Also for scripts that are scoped by whitespace/tabs and are not strictly typed, we found that scripts exceeding 1/2 pages in length tend to be less maintainable, and the chances of nuking a whitespace or overwriting a variable gets higher.

Just my 2 cents

On Wed, Jul 23, 2014 at 11:11 PM, Satyananda Kashyap <ksatyananda at gmail.com<mailto:ksatyananda at gmail.com>> wrote:
Hello,

I am looking for your expert opinions here. I have a relatively large C++ project I am working on which uses ITK mainly (hence the question here) and to some extent VTK and OpenCV. I do think that my code is fairly well written. I was thinking of wrapping my code to python using either SWIG or boost.python. Here are my questions :


1. I am led to believe that prototyping and code development is much faster in Python. Given that I have such a big cpp base code is it really worth the effort to wrap into python and then continue there.

2. From what I have read ITK uses SWIG wrappings for wrapping into Python while VTK uses the boost.python route. My initial attempts with both have been relatively unsuccessful. Any opinion on which one is more user friendly/better when I have to wrap my own custom classes which use a combination of both ITK and VTK in them.

3. Any suggestion on a road map as to how to proceed. I am not sure at what base class level I should wrap them and rewrite the dependencies in python.

Thanks,
Regards,
Kashyap

_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users




--
Regards,
Vincent




--
Regards,
Vincent


________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/64d95136/attachment.html>

From ksatyananda at gmail.com  Mon Jul 28 18:56:38 2014
From: ksatyananda at gmail.com (Satyananda Kashyap)
Date: Mon, 28 Jul 2014 17:56:38 -0500
Subject: [ITK-users] Suggestions about Python wrapping of cpp project
In-Reply-To: <CFFC25D2.9E32%norman-k-williams@uiowa.edu>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
 <CAC3nAP2kqrxNKOZCSmzH9BXWP9d8b7jjiwo14jpSiDVRBNU2Fw@mail.gmail.com>
 <CADe3Ntx-9HaS5AmpTMV-H790bgwo9bT4aWHMdOWjSEGeXQN5pQ@mail.gmail.com>
 <CAC3nAP2bmLwAtYz4iFv2H7ZhMoo-kuFkSmWpYwJ=q7ZiJ2Us8Q@mail.gmail.com>
 <CFFC25D2.9E32%norman-k-williams@uiowa.edu>
Message-ID: <9AD76AB1-2A22-4725-AB39-682D58C0F947@gmail.com>



Regards,
Kashyap


> On Jul 28, 2014, at 4:11 PM, "Williams, Norman K" <norman-k-williams at uiowa.edu> wrote:
> 
> The biggest plus in using Python with C++ back end for the compute/graphics intensive stuff is interactive development without a compile/link stage.
> 
> There are great python debug tools.  Debugging python in Emacs is easy enough using pdb.  You can set breakpoint in the source code, examine variables, etc.  Debugging python is no more difficult than debugging C++.  There are python IDE that allow source debugging as well.  PyCharm is well regarded.
> 
> From: vincent ngai <vincent.ngai at gmail.com>
> Date: Friday, July 25, 2014 at 2:39 AM
> To: Satyananda Kashyap <ksatyananda at gmail.com>
> Cc: Insight <insight-users at itk.org>
> Subject: Re: [ITK-users] Suggestions about Python wrapping of cpp project
> 
> My project was designed as a C++ framework with functionality exposed to scripts, so it acts like an executable that runs a script that determines the program behaviour rather than a pure python program. It might be an important factor whether its a pure python app or an app that runs python. 
> 
> Honestly I can't tell if relegating some application logic to scripts is more productive, it works for sure, how productive it is ultimately depends on how many of our next projects rely on using the existing framework. :)
> 
> Sorry I don't have a clear cut answer its a bit early to tell for my project.
> 
> 
>> On Fri, Jul 25, 2014 at 12:22 PM, Satyananda Kashyap <ksatyananda at gmail.com> wrote:
>> Thanks for your perspective Vincent. 
>> 
>> One of my initial questions were about the productivity boost which you get when using scripting languages. I am reasonably comfortable coding in C++ toolchain. From your experience do you really see a spike in productivity when you shift over. Is it worth the effort ?  
>> 
>> I think I will do some of the core development in C++ and expose them to Python. I wanted to use the scripting side more for prototyping and testing purposes. 
>> 
>> Regards,
>> Kashyap
>> 
>> 
>>> On Thu, Jul 24, 2014 at 10:18 PM, vincent ngai <vincent.ngai at gmail.com> wrote:
>>> I'm no expert, but previously when I worked on projects where we exposed almost all core functionalities via scripts, it seemed like a good initially, but what really happened is a shifting of complexities. Rather than have the complexity on the C++/Compiled codebase side shifted over to the scripts, in situation where you need to be able to change functionality without recompiling the source, or even have access to the source, scripts are the way to go. But shifting complexities to the runtime/script side has its own issues, I'm happy with the C/C++ toolchain maturity, Visual C++, GCC, GDB etc, you have very comprehensive debugging and editor facilities available for C++, but on the script side you have far less tools, and debugging may be a hassle. 
>>> 
>>> Also for scripts that are scoped by whitespace/tabs and are not strictly typed, we found that scripts exceeding 1/2 pages in length tend to be less maintainable, and the chances of nuking a whitespace or overwriting a variable gets higher.
>>> 
>>> Just my 2 cents
>>> 
>>> On Wed, Jul 23, 2014 at 11:11 PM, Satyananda Kashyap <ksatyananda at gmail.com> wrote:
>>>> Hello,
>>>> 
>>>> I am looking for your expert opinions here. I have a relatively large C++ project I am working on which uses ITK mainly (hence the question here) and to some extent VTK and OpenCV. I do think that my code is fairly well written. I was thinking of wrapping my code to python using either SWIG or boost.python. Here are my questions : 
>>>> 
>>>> 
>>>> 1. I am led to believe that prototyping and code development is much faster in Python. Given that I have such a big cpp base code is it really worth the effort to wrap into python and then continue there. 
>>>> 
>>>> 2. From what I have read ITK uses SWIG wrappings for wrapping into Python while VTK uses the boost.python route. My initial attempts with both have been relatively unsuccessful. Any opinion on which one is more user friendly/better when I have to wrap my own custom classes which use a combination of both ITK and VTK in them. 
>>>> 
>>>> 3. Any suggestion on a road map as to how to proceed. I am not sure at what base class level I should wrap them and rewrite the dependencies in python.  
>>>> 
>>>> Thanks,
>>>> Regards,
>>>> Kashyap
>>>> 
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>> 
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>> 
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>> 
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>> 
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>> 
>>> 
>>> 
>>> -- 
>>> Regards,
>>> Vincent
> 
> 
> 
> -- 
> Regards,
> Vincent
> 
> 
> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140728/807c9fc2/attachment.html>

From matt.mccormick at kitware.com  Tue Jul 29 09:52:41 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 29 Jul 2014 09:52:41 -0400
Subject: [ITK-users] [ITK] Suggestions about Python wrapping of cpp
	project
In-Reply-To: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
References: <CADe3NtyXnCk4pw51f+poyFfySbO-X6-s2VC+iH2dGH0TFtv-iw@mail.gmail.com>
Message-ID: <CALzTN-R84sze87PV6yK+STxmQVvaHvF_VP6NqCwM43FjxsZJow@mail.gmail.com>

Hi,

I'm a little late to the party on this thread, but I would recommend
creating the .wrap files for ITK module code.  For code that is not as
highly templated, XDress [1] is another option to keep in mind.

Matt

[1] http://xdress.org/

On Wed, Jul 23, 2014 at 11:11 AM, Satyananda Kashyap
<ksatyananda at gmail.com> wrote:
> Hello,
>
> I am looking for your expert opinions here. I have a relatively large C++
> project I am working on which uses ITK mainly (hence the question here) and
> to some extent VTK and OpenCV. I do think that my code is fairly well
> written. I was thinking of wrapping my code to python using either SWIG or
> boost.python. Here are my questions :
>
>
> 1. I am led to believe that prototyping and code development is much faster
> in Python. Given that I have such a big cpp base code is it really worth the
> effort to wrap into python and then continue there.
>
> 2. From what I have read ITK uses SWIG wrappings for wrapping into Python
> while VTK uses the boost.python route. My initial attempts with both have
> been relatively unsuccessful. Any opinion on which one is more user
> friendly/better when I have to wrap my own custom classes which use a
> combination of both ITK and VTK in them.
>
> 3. Any suggestion on a road map as to how to proceed. I am not sure at what
> base class level I should wrap them and rewrite the dependencies in python.
>
> Thanks,
> Regards,
> Kashyap
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From norman-k-williams at uiowa.edu  Tue Jul 29 12:38:55 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Tue, 29 Jul 2014 16:38:55 +0000
Subject: [ITK-users] ConstIterator
In-Reply-To: <CAEMYOQjp=J3HQKsUAtk7H1xbKHtpgd1GHY9ARW=LHDFn9a6LtA@mail.gmail.com>
References: <CAEMYOQhNWy_3CsTFc+JgkL3ZDmiR74OLD3vsMFWiL+qozoLXHw@mail.gmail.com>
 <CA+=+rrCzkw2g7XFhQwTeb4uE7h3ppvYUqyrWtfRC_2TL=zE1qQ@mail.gmail.com>
 <CAEMYOQjp=J3HQKsUAtk7H1xbKHtpgd1GHY9ARW=LHDFn9a6LtA@mail.gmail.com>
Message-ID: <CFFD33BA.9E9D%norman-k-williams@uiowa.edu>

The documentation for ITK classes is contained in the source code; the web documentation is generated from the source code periodically.

Feel free to sign up to submit changes to ITK ? instructions are here: http://www.itk.org/Wiki/ITK/Git

Documentation fixes and additions are always welcome.

In this case, the meaning of ConstIterator vs Iterator was probably assumed to be obvious, because experienced C++ programmers would be familiar with std::iterator and std::const_iterator.

From: med aweng <medswengineer at gmail.com<mailto:medswengineer at gmail.com>>
Date: Thursday, July 24, 2014 at 5:09 AM
To: Marco Ulgelmo <marco.ulge at gmail.com<mailto:marco.ulge at gmail.com>>
Cc: Insight <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: Re: [ITK-users] ConstIterator

Thanks Marco. Is that description in the itk documentation? I really couldn't find such clear explanation.

Thanks.


On Thu, Jul 24, 2014 at 12:07 PM, Marco Ulgelmo <marco.ulge at gmail.com<mailto:marco.ulge at gmail.com>> wrote:
A ConstIterator an iterator which is used to iterate over a constant container, which means that data in the container can't be modified (unless you use const_cast). You can find it in the ITK documentation.

Marco


2014-07-24 11:47 GMT+02:00 med aweng <medswengineer at gmail.com<mailto:medswengineer at gmail.com>>:
Hello,

What is the purpose of the "ConstIterator". Where can I find its description?

Thanks.

_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users





________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140729/6acbc8c8/attachment.html>

From norman-k-williams at uiowa.edu  Tue Jul 29 12:52:15 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Tue, 29 Jul 2014 16:52:15 +0000
Subject: [ITK-users] Smartpointer as a default parameter for a function
In-Reply-To: <74500304cea08473af6cfd3b37c686c6@mufradat.com>
References: <74500304cea08473af6cfd3b37c686c6@mufradat.com>
Message-ID: <CFFD3936.9ECD%norman-k-williams@uiowa.edu>

You do not need to explicitly initialize <itktype>::Pointer variables.
They have a default constructor that initializes the raw pointer member
m_Pointer to zero.

I would tend to use references to SmartPointers as parameters, because if
you pass a Pointer value, it creates a temporary Pointer on the stack, and
then assigns it to the member variable.  This isn?t a huge overhead but it
does involve semaphore lock/unlock pairs protecting reference count
increment/decrement.
When you pass a Pointer by reference, it ends up doing this.

1. Construct anonymous temp Pointer.
2. assign <temp>.m_Pointer with <parameter>.m_Pointer (I.e. the actual
object pointed to by the smart pointer)
3. lock the object pointed to by <temp>.m_Pointer.
4. Increment the pointed-to object?s reference count.
5. unlock pointed-to object.
6. Inside the method, assign <temp> to local or member variable, repeat
steps 2 through 5.
7. When the function exits, call <temp> destructor
8. lock the pointed-to object
9. decrement reference count
10. unlock pointed-to object

If you pass the smart pointer by reference, you skip creating and
destroying the temp, and only assign to a smart pointer once.

On 7/22/14, 2:37 AM, "ahmed at mufradat.com" <ahmed at mufradat.com> wrote:

>Hello All,
>
>Suppose I have class like
>
>class A{
>     public:
>     A(int a, ImageType::Pointer ptr){
>         // whatever!
>     }
>};
>
>My question is, what's the default value for that ptr? I'd like to be
>able to create an instance of that class using
>
>A myA(5);
>
>so for the definition of the constructor of A:
>
>A(int a, ImageType::Pointer ptr = WHAT?)
>
>Best regards,
>Ahmed
>_____________________________________
>Powered by www.kitware.com
>
>Visit other Kitware open-source projects at
>http://www.kitware.com/opensource/opensource.html
>
>Kitware offers ITK Training Courses, for more information visit:
>http://www.kitware.com/products/protraining.php
>
>Please keep messages on-topic and check the ITK FAQ at:
>http://www.itk.org/Wiki/ITK_FAQ
>
>Follow this link to subscribe/unsubscribe:
>http://public.kitware.com/mailman/listinfo/insight-users



________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________

From fttfzzx227 at 126.com  Tue Jul 29 22:56:51 2014
From: fttfzzx227 at 126.com (=?GBK?B?t+vmw+bD?=)
Date: Wed, 30 Jul 2014 10:56:51 +0800 (CST)
Subject: [ITK-users] how to write grey images into color image using
 itkScalarToRGBColormapImageFilter
Message-ID: <3a761248.dcd8.1478532e5ca.Coremail.fttfzzx227@126.com>

Hi,
    I want to write some jpg (gray level) images into color image to display different intensities, the range of the intensities in the input image is 0~255.And the code I wrote is as below:


typedef itk::Image< OutputPixelType, 2 >  OutputImageType;


 typedef itk::ScalarToRGBColormapImageFilter< jpgScalarImageType, OutputImageType >  RGBFilterType;


  RGBFilterType::Pointer colormapImageFilter = RGBFilterType::New();


  colormapImageFilter->SetColormap( RGBFilterType::Hot );


  colormapImageFilter->SetInput( InputImage );
  try
    {
    colormapImageFilter->Update();
    }
  catch ( itk::ExceptionObject &err )
    {
    std::cerr << err << std::endl;


    //return EXIT_FAILURE;
    }


OutputImageType::Pointer outputImage = colormapImageFilter->GetOutput();


But after I write the outputImage ,it is all black.Did I miss something ,or is there any other solution to write a grey image into a color image?Thank you!


Best regards!


Tina
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140730/01e7a4c3/attachment.html>

From mallikarjun49 at gmail.com  Wed Jul 30 10:18:57 2014
From: mallikarjun49 at gmail.com (Mallikarjun K)
Date: Wed, 30 Jul 2014 19:48:57 +0530
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
Message-ID: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>

Hi All,
I am using itkSmoothingQuadEdgeMeshFilter for Surface Mesh smoothing.This
filter is giving good results what I expected but taking more execution
time.can any one suggest me to reduce the execution time( multi threading
 or any parameters to add/remove )?

Below is the code snippet
///////
typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
qetraits;
typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;

//typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3 > MeshType;

itk::OnesMatrixCoefficients< MeshType > coeff0;

typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
SmoothingQuadEdgeMeshFilter;

    SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
SmoothingQuadEdgeMeshFilter::New();

QEMeshSmoother->SetInput("abc.vtk");
QEMeshSmoother->SetNumberOfIterations(5 );
QEMeshSmoother->SetRelaxationFactor( 0.5 );
QEMeshSmoother->SetDelaunayConforming(true );
QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
QEMeshSmoother->Update();
////

-- 
*Regards:*
Mallik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140730/2159a9a6/attachment.html>

From bill.lorensen at gmail.com  Wed Jul 30 11:59:59 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Wed, 30 Jul 2014 11:59:59 -0400
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
Message-ID: <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>

First, make sure you are building ITK and your app with Release. A
Debug build can be 10-50 times slower.


On Wed, Jul 30, 2014 at 10:18 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> Hi All,
> I am using itkSmoothingQuadEdgeMeshFilter for Surface Mesh smoothing.This
> filter is giving good results what I expected but taking more execution
> time.can any one suggest me to reduce the execution time( multi threading
> or any parameters to add/remove )?
>
> Below is the code snippet
> ///////
> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
> qetraits;
> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>
> //typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3 > MeshType;
>
> itk::OnesMatrixCoefficients< MeshType > coeff0;
>
> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
> SmoothingQuadEdgeMeshFilter;
>
>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
> SmoothingQuadEdgeMeshFilter::New();
>
> QEMeshSmoother->SetInput("abc.vtk");
> QEMeshSmoother->SetNumberOfIterations(5 );
> QEMeshSmoother->SetRelaxationFactor( 0.5 );
> QEMeshSmoother->SetDelaunayConforming(true );
> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
> QEMeshSmoother->Update();
> ////
>
> --
> Regards:
> Mallik
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>



-- 
Unpaid intern in BillsBasement at noware dot com

From blowekamp at mail.nih.gov  Wed Jul 30 11:56:18 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 30 Jul 2014 11:56:18 -0400
Subject: [ITK-users] [ITK] ITK: error: floating-point literal cannot
	appear in a constant-expression
In-Reply-To: <49C3D5F2-E43F-4012-B0E6-51862C4CA841@gmail.com>
References: <2A510655-60E7-466F-BC6B-8D8168BDACCF@gmail.com>
 <88659D55-CC33-4103-8020-FB172FD00270@mail.nih.gov>
 <49C3D5F2-E43F-4012-B0E6-51862C4CA841@gmail.com>
Message-ID: <7CE9E66F-2870-4644-9905-F74CF84C551E@mail.nih.gov>

Nick,

I was a little too specific with the flag to look for in my prior e-mail

The error message you are getting is coming from here[1]. Which used the VECL_STATIC_CONST_INIT_FLOAT_DECL macro defined here[2]. CMake does some try compile to see if this in class declaration of double is supported during your initial configuration when ITK is first built. If it's detected that the compiler supports, then when ever ITK is used this feature is enabled.

Something changed with your compiler, like some addition or removal of flag, which changed the support of the feature.

Hope that helps,
Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h#L387
[2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_config_compiler.h.in#L138-L159

On Jul 30, 2014, at 11:47 AM, Nick Patterson <pattersonnp.work at gmail.com> wrote:

> 
> Dear Brad,
> 
> 	I?m afraid I made no further progress to report on the compilation of my application. It?s very curious. I even tried to roll back to ITK 4.5.2 (rather than the newer 4.6) but I am receiving similar errors. I have no issues with compiling this code on my Macbook? just on my linux box.
> 
> Regards, Nick.
> 
> 
> 
> On 29 Jul 2014, at 22:20, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 
>> Hello,
>> 
>> Is any of your code monkeying around with the "-std=c++11" flags? Did you compile ITK or your application with it?
>> 
>> Brad
>> 
>> On Jul 29, 2014, at 10:59 AM, Nick Patterson <pattersonnp.work at gmail.com> wrote:
>> 
>>> Hi,
>>>  Can I ask if anybody has the following error when compiling code which makes use of ITK? The complilation of ITK was fine, this is an error produced when compiling against ITK in my own application.
>>> 
>>> The error that I am currently getting is:- (Building on Ubuntu Linux). 
>>> 
>>> 
>>> In file included from /usr/local/include/ITK-4.5/vnl/vnl_c_vector.h:26:0,
>>>                from /usr/local/include/ITK-4.5/vnl/vnl_vector.h:22,
>>>                from /usr/local/include/ITK-4.5/vnl/vnl_vector_ref.h:20,
>>>                from /usr/local/include/ITK-4.5/itkVector.h:23,
>>>                from /usr/local/include/ITK-4.5/itkPoint.h:23,
>>>                from /usr/local/include/ITK-4.5/itkContinuousIndex.h:21,
>>>                from /usr/local/include/ITK-4.5/itkImageRegion.h:34,
>>>                from /usr/local/include/ITK-4.5/itkImageIORegion.h:24,
>>>                from /usr/local/include/ITK-4.5/itkImageIOBase.h:26,
>>>                from /usr/local/include/ITK-4.5/itkImageFileReader.h:22,
>>>                from /usr/local/include/ITK-4.5/itkImageSeriesReader.h:26,
>>>                from /home/nppatt/Raydose2/RaydoseNew/src/Simulation/RaydoseNMImageData.cpp:2:
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:387:27: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:387:27: warning: ISO C++ forbids initialization of member constant 'zero' of non-integral type 'const float' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:389:26: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:389:26: warning: ISO C++ forbids initialization of member constant 'one' of non-integral type 'const float' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:391:29: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:391:29: warning: ISO C++ forbids initialization of member constant 'maxval' of non-integral type 'const float' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:410:28: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:410:28: warning: ISO C++ forbids initialization of member constant 'zero' of non-integral type 'const double' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:412:27: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:412:27: warning: ISO C++ forbids initialization of member constant 'one' of non-integral type 'const double' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:414:30: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:414:30: warning: ISO C++ forbids initialization of member constant 'maxval' of non-integral type 'const double' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:433:33: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:433:33: warning: ISO C++ forbids initialization of member constant 'zero' of non-integral type 'const long double' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:435:32: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:435:32: warning: ISO C++ forbids initialization of member constant 'one' of non-integral type 'const long double' [-pedantic]
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:437:35: error: floating-point literal cannot appear in a constant-expression
>>> /usr/local/include/ITK-4.5/vnl/vnl_numeric_traits.h:437:35: warning: ISO C++ forbids initialization of member constant 'maxval' of non-integral type 'const long double' [-pedantic]R
>>> 
>>> 
>>> Regards, Nick
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140730/aad7b7fc/attachment.html>

From matt.mccormick at kitware.com  Wed Jul 30 14:44:08 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 30 Jul 2014 14:44:08 -0400
Subject: [ITK-users] [ANNOUNCE] ITK 4.6.0 has been released!
Message-ID: <CALzTN-T6uCOHxJQy5ZdoVktbONd3AW7X-Ci46rWZ+MPzW+hjFg@mail.gmail.com>

On behalf of the Insight Toolkit community, we are proud to announce
that ITK 4.6.0 has been released!


Links to the Sourceforge.net tarballs can be found on the download page:

 http://www.itk.org/ITK/resources/software.html


Outline
----------

1. Introduction
2. New Documentation
3  New Features
4. ITK Changelog
5. ITK Sphinx Examples Changelog
6. ITK Software Guide Changelog


Introduction
-------------------------

The 4.6 release is a major milestone that marks the hard work of many
outstanding community members.


Among the major contributions in this release are improved Remote
Module support with a number of exciting new Remote Modules.  The
TransformToDisplacementField filter and a entire module of image noise
generation classes were migrated into the default build. A number of
new optimizers were added to the Registrationv4 framework, which also
experienced a number of performance improvements. Performance
improvements were a general theme as was improved code coverage.
Python wrapping underwent a huge cleanup.


Our documentation continues to improve with better examples, Doxygen
documentation, and guidance material.  The Software Guide was split in
anticipation of the release of two new hard copy books.


Thanks to everyone for their hard work!

Enjoy ITK!


New Documentation
-------------------------


Our documentation continues to improve.  Remote modules are now
grouped in the Doxygen Module page [1]. A number of new examples were
added to the Sphinx repository and the Wiki, which can now also be
built as Remote modules. The Software Guide was split into two books
and the ITK configure and build instructions were revised.

[1] http://www.itk.org/Doxygen/html/modules.html


New Features
------------------


* CMake improvements
  - Improved Remote Module support
  - Add ITK_FORBID_DOWNLOADS for package maintainers
  - ITK_USE_SYSTEM_EXPAT available


* Filtering Improvements
  - Moved TransformToDisplacementField out of Review
  - An entire noise image generation module
    - http://hdl.handle.net/10380/3158
  - Better pipeline support for ResampleImageFilter
  - Move MagnitudeAndPhaseToComplexImageFilter out of Review
  - Setters for LabelMap overlay filters
  - More consistent filter progress reporting


* ImageIO improvements
  - Register the GE image formats by default
  - More IO modules are built as shared libraries
  - OpenFileForReading/Writing methods in ImageIO
  - Support for system tiff 4.0.0-4.0.2 (e.g. some Ubuntu versions)
  - Mangling to internal OpenJPEG
  - SCIFIO improvements


* Infrastructure improvements
  - MetaDataObject print specialization for common types
  - Improvements to ResourceProbe and RealTimeClock
  - More Solve methods for VNLSparseLUSolverTraits
  - Output stream operator for LightObject exposed
  - FFTW bump to 3.3.3


* New Remote Modules
  - Skull stripper
    - http://hdl.handle.net/10380/3353
  - Wiki examples
  - Sphinx examples
  - Variational registration
    - http://hdl.handle.net/10380/3460
  - AnalyzeObjectMapIO
    - http://hdl.handle.net/1926/593
  - FDFImageIO
  - SplitComponents
    - http://hdl.handle.net/10380/320


* Registrationv4 improvements
  - v4 regular step gradient descent optimizer
  - v4 amoeba optimizer
  - v4 exhaustive optimizer
  - v4 Powell optimizer
  - v4 one-plus-one-evolutionary optimizer
  - v4 LBFGS optimizer improvements
  - Use registration method classes as pipeline filters


* Performance improvements
  - Registrationv4
  - Histogram computation
  - Improved SmartPointer copy
  - CompositeTransform
  - Registration Jacobian re-use


* Wrapping improvements
  - pygccxml 1.0.0
  - .pth symlink usable in a virtualenv
  - Cleaner CMake configuration
  - SWIG and PCRE updated to 3.0.2, 8.34
  - Latest GCCXML, which works with GCC 4.9
  - Sweeping wrapping generation cleanup

* Many style improvements -- ITK gets more stylish with every release!


* Improved code coverage -- some measures put us over 85%!


* *Lots* of important bug fixes


* And more! See details in the log below.


List of changes since v4.6rc03
--------------------------------------


Arnaud Gelas (1):
     DOC: ThresholdBetween does not exist, it should be ThresholdOutside

Bradley Lowekamp (6):
     BUG: Remove division in inner loop for otsu threshold calculator
     COMP: Fix implicit conversion warnings
     BUG: Print the histogram calculator for auto threshold filter
     BUG: Use tolerant float compare when choosing better otsu threshold
     BUG: Fix out of bounds access for image region size
     BUG: Add export specification to DCMTKFileReader and utilities

Luis Ibanez (1):
     BUG: Increased OtsuThreshold computation precision

Matthew McCormick (13):
     COMP: Remove unused local typedef's.
     COMP: Make Doxygen Modules group definition consistent.
     STYLE: Improve readability and const correctness of ImageIORegion.
     BUG: GDCM does not apply rescale slope / intercept on write.
     COMP: Ignore itkIndex.h -Warray-bounds warnings on GCC 4.9.
     COMP: Remove unused typedefs in ITKReview module.
     COMP: Remove unused FFTW typedef's.
     COMP: Remove unused typedefs from the Examples.
     COMP: Remove unused typedefs in compatibility code.
     BUG: Fix GDCM buffer size when written pixel type is different.
     COMP: Disable array above bounds warnings in FixedArray for GCC 4.9.
     BUG: Increase itkVoronoiPartitioningImageFilterTest1 for 32-bit builds.
     BUG: Set output type to unsigned char when writing uchar in GDCMIO test.

Michka Popoff (3):
     BUG: Fix GeodesicActiveContourImageFilterOutput7.png
     STYLE: Threshold Segmentation LevelSet Image Filter Figure
     ENH: Remove GeodesicActiveContourImageFilter.py example

List of changes since v4.6rc02
---------------------------------------


Ali Ghayoor (1):
          ENH: Convert seven ImageRegistration examples to ITKv4

Bradley Lowekamp (2):
          BUG: Remove multiple per-pixel allocations in Mahalanobis Membership
          COMP: Fix unused-local-typedef warnings in the Registration
and Numeric

Hans Johnson (1):
          ENH: Prepare for ITKv4 registration Examples

Matthew McCormick (5):
          BUG: Improve module Group membership detection.
          COMP: Fix unused-local-typedef warnings in Group Core.
          BUG: Update TransformReadWrite example.
          COMP: Fix unused-local-typedef warnings in the Filtering Group.
          COMP: Remove unused typedefs.

Nick Tustison (1):
          ENH:  Missed spec for generic computation type.


List of changes since v4.6rc01
---------------------------------------


Bradley Lowekamp (3):
     BUG: Do not ENABLED_SHARED for GDCMIO
     DOC: Add break in brief description of Canny edge filter
     BUG: Add additional MetaDataObject explicit instantiation.

Jean-Christophe Fillion-Robin (2):
     COMP: Fix "unused-local-typedefs" warnings
     COMP: Fix "unused-local-typedefs" warning in
LandmarkBasedTransformInitializer

Kent Williams (1):
     COMP: Fix typo in ReflectiveImageRegionConstIterator.

Matthew McCormick (4):
     DOC: CMake warning BRANWEB -> BRAINWEB.
     BUG: Remove -Wno-unused-local-typedefs flag.
     COMP: Fix IOSTL Doxygen group and Windows shared build.
     BUG: Use Remote repository explicitly on git fetch.

Michka Popoff (6):
     COMP: Move itkMatrixCoefficients wrapping to Filtering module
     COMP: Fix wrapping with Core only
     STYLE: Pep8 cleanup for generators
     COMP: Fix default wrapping with all modules
     ENH: Use open() instead of file() for python 3 compatibility
     ENH: Allow to use methods which pass std::string by reference from python

Nick Tustison (1):
     ENH:  Adding generic computation type.


List of changes since v4.5.0
--------------------------------------

Alexander Schmidt-Richberg (1):
      ENH: Added *.remote.cmake for remote module VariationalRegistration


Ali Ghayoor (22):
      ENH: Add a registration test for LBFGS-B optimizer
      ENH: Add versorTransformOptimizerv4 class to ITKv4
      BUG: Fix Coverity defects for LBFGS-B tests
      BUG: avoid division by zero in versorOptimizerv4
      ENH: Add RegularStep gradient optimizer to ITKv4
      DOC: The use of VersorTransformOptimizerv4 is deprecated.
      ENH: [SG]et optimizable params ITKv4 registration
      ENH: remove VersorTransformOptimizerv4 from ITKv4
      ENH: Add AmoebaOptimizerv4 to ITKv4 registration
      ENH: Add ExhaustiveOptimizerv4 to ITKv4 registration
      ENH: Add PowellOptimizerv4 to ITKv4 registration
      BUG: define the GetStopConditionDescription as a public member funciton
      ENH: Add OnePlusOneEvolutionaryOptimizerv4 to ITKv4 registration
      BUG: lbfgsb optimizer could not be used in unbounded mode
      ENH: Add GetCurrentIteration to ExhaustiveOptimizerv4
      ENH: Add currentIteration to the AmoebaOptimizerv4
      PERF: Move the currentIteration to optimizersv4 base class
      ENH: Move the NumberOfIterations to the Optimizersv4 base class
      PERF: Change the parent class of RegularStepGradDescentv4 optimizer
      ENH: Add currentIteration to LBFGSBOptimizerv4
      BUG: Fix memory leak in LBFGSBOptimzierv4
      ENH: Add distance vector to KdTree search API


Bill Lorensen (32):
      BUG: Tiff compression was broken and untested
      ENH: Add SetJPEGQuality method
      COMP: Missing breaks in swithc
      COMP: Uninitialized scalar field
      COMP: Uninitialized scalar field
      COMP: Unused pointer value
      ENH: Add SkullStrip Remote Module
      BUG: Tiff compression was broken and untested
      COMP: Missing breaks in swithc
      ENH: Improved message for missing IO factories
      COMP: Remove vcl_time and vcl_clock
      ENH: Remove vcl_math calls
      COMP: std::abs integral overloads not always provided
      COMP: Array versus singleton access
      COMP: Failed to check dynamic_cast results
      STYLE: Empty lines exceed 3
      COMP: Uninitialized member data
      BUG: Two tests try to write the same file
      ENH: Uninitialized scalar field
      COMP: Constructor initialize list improvement
      COMP: Type warnings in constructors
      BUG: Copy/paste error
      COMP: Arguments of wrong type
      BUG: Buffer not null terminated
      BUG: Dereference after null check
      BUG: Division or modulo by zero
      ENH: Uninitialized scalar field
      BUG: Uninitialized scalar field
      BUG: Not restoring ostream format
      ENH: Add an exception safe state restore class for streams
      BUG: Not restoring ostream format
      ENH: Add WikiExamples as a remote module


Brad King (4):
      COMP: Remove extra calls to cmake_minimum_required
      COMP: Fix cmake_minimum_required call order
      COMP: Set CMake Policies CMP0025 and CMP0042 as necessary
      COMP: Add missing call to cmake_minimum_required


Bradley Lowekamp (91):
      ENH: Removed non-work TCL Examples
      DOC: Add missing const in Doxygen GetConstReferenceMacro
      BUG: Correctly re-throw exception to restore AbortEvent, ProcessAborted
      BUG: Emit StartEvent before a ProgressEvent
      BUG: Do not throw exception in Probes with mis-matched Stop
      BUG: Correctly re-throw exception to restore AbortEvent, ProcessAborted
      BUG: Adding export specification to Exception objects
      COMP: fix unused variable warning in abort test
      BUG: Adding export specification to Exception objects
      COMP: fix failing voronoi segmentation tests
      COMP: Remove explicit typed exception specifications
      ENH: Print Object name for observers of objects
      ENH: Adding progress reporting to some filters
      BUG: fixing grind peak progress to reach 1.0
      COMP: use std::transform with static_cast to avoid conversion warning
      BUG: disable ipa-cp-clone in GDCM
      COMP: fix unused variable warning in abort test
      BUG: Do not throw exception in Probes with mis-matched Stop
      BUG: Address Shared Library issues with SCIFIO
      COMP: fix failing voronoi segmentation tests
      COMP: export required in explicitly defined NumbericTraits consts
      DOC: Make comment the Doxygen brief
      BUG: Adding missing raw data file to MINC test
      BUG: Fix linkage for SmartPointerForwardReference for clang 4
      BUG: Fixing missing char type and doc for Thresholding filters
      BUG: Add support for system libtiff 4.0.0-4.0.2
      BUG: remove second wrapping of BinShrink for scalars
      BUG: Fix LabelStatistics and LabelOverlap to require same image size
      PERF: Remove IncreaseFrequencyOfMeasurement from inner loops
      STYLE: Save deference iterator mapped type to variable
      PERF: switch to scanline and linear iterators
      COMP: Fix checks for system libtiff
      PERF: add namespace swap to SmartPoitners
      PERF: Use stl iterator algorithm in Iterator Partitioner
      BUG: Add mutex lock to MersenneTwister GetInstance
      STYLE: MersenneTwister move methods to cxx, docs
      STYLE: renaming files to standard ITK conventions
      ENH: Improving Noise Simulation Filters
      COMP: Explicitly make constant an unsigned int
      BUG: Fix uninitialized ivar in NoiseBaseImageFilter
      ENH: Make NoiseBaseImageFilter an abstract base class
      COMP: remove extraneous cast to double
      BUG: Same test function in different file causes conflict
      ENH: Explicitly specify internal linkage for internal observer objects
      ENH: Enable observed events to modify observers
      BUG: Catch exception in DeleteEvent
      STYLE: dynamic_cast to pointer does not throw
      COMP: Fix GCC warning about unused typedef in ConceptChecking
      COMP: Adding itkMacro.h for ITK_NULLPTR definition
      ENH: Use DynamicCastInDebugMod for name input macros
      BUG: Add support for signed char output
      BUG: Use NewMacro for Clone with TimeVaryingVElocityFieldTransforms
      ENH: Improve DataObjectDecorator with Modifiable, Graft ReleaseData
      ENH: Improve Resample's use of pipeline inputs
      ENH: Adding output of line and file on test failure
      ENH: Add InitialTransform as pipelined input with inplace option
      ENH: Use Transform base class as default template parameter
      ENH: Use InitialTransform in deformation examples
      COMP: add missing stl algorithm header for std::max
      COMP: add missing stl algorithm header for std::max
      Revert "ENH: Add Remote module group description to Doxygen."
      COMP: Remove incorrect override declaration
      ENH: Encapsulate expat header
      ENH: Make IntialMoving and InitialFixed transforms decorated inputs
      ENH: Update SimpleRegistration test
      BUG: Don't create new Decorator in GenerateData
      BUG: Use referenceImage for output information
      ENH: Adding some ImageIO libraries as shared
      ENH: Use TransformParametersAdaporBase on Transform base class
      ENH: Removing const_casts from ImageRegistrationv4 tests
      BUG: Add AllocateOutputs method to other v4 RegistrationMethods
      ENH: Update v4 registration tests to set initial transform
      BUG: Explicitly instantiate common MetaDataObjects
      BUG: Disable explicit visibility with OSX gcc  and llvm gcc 4.2
      ENH: Register GE Image formats
      COMP: Fix warning for overloading AllocateElements
      COMP: Suppress warning for using extern template instantiation
      PERF: Use shallow swap over deep assignment
      ENH: Use LearingRate member variable for scaling gradient
      ENH: support learning rate estimation for regular step optimizer
      COMP: Add space between string literals
      ENH: remove catch as dynamic_cast of pointers is nothrow
      BUG: Use rounding in TestingStretchIntensity for portability
      BUG: Warn if unsupported ITK_BRAINWEB_DATA_ROOT is being used
      ENH: Use MultiResolutionIteration event for registration
      ENH: Use exception safe copy-and-swap for assignment
      BUG: Use DEPENDS for dependent files
      STYLE: Add itkPrintSelfObjectMacro to improve indenting
      BUG: Print missing member variables
      ENH: Make more IO modules shared.
      COMP: Add missing header for EXIT_FAILURE


Brian Helba (66):
      ENH: Disable tip to enable Uncrustify from SetupForDevelopment
      STYLE: Rename TValueType template parameters to TValue
      COMP: Fix compiler warnings with ITK_USE_SYSTEM_VXL
      BUG: Make all specializations NumericTrails::SetLength re-zero contents
      ENH: 3048, 3224: Refactor *SampleFilters to fix multiple issues
      ENH: Re-enable the array-bounds warnings for GCC 4.7
      DOC: Fix a bug with SquaredEdgeLengthDecimationQuadEdgeMeshFilter
      DOC: Clean up comments in NiftiImageIO, for better Doxygen compatibility
      STYLE: Remove unused typedefs from AlgorithmsPrintTests
      BUG: Fix improper usage of VoronoiSegmentationRGBImageFilter
      ENH: Move OpenFileForReading/Writing from StreamingImageIO to parent class
      ENH: Improve OpenFileForReading/Writing logic and documentation
      BUG: Prevent ObjectFactoryBase from possibly throwing an exception
      STYLE: Make internal-use CMake variables lowercase in KWStyle.cmake
      PERF: Prevent FindKWStyle.cmake from being called multiple times
      BUG: Fix FindKWStyle crash when kwstyle returns empty version info
      BUG: Fix Coverity issue 1081600: Use after free
      BUG: Update SmoothingRecursiveYvvGaussianFilter to fix CMake warnings
      ENH: Update ImageIO classes to use OpenFileForReading/Writing
      COMP: Fix array subscript build warning
      COMP: Except Git's status messages from CTest reporting
      COMP: Suppress Coverity defect when Examples create an ITK object
      BUG: Fix uninitialized variable in GradientRecursiveGaussianImageFilter
      DOC: Fix documentation in VoronoiDiagram2DGenerator
      BUG: Coverity 1081062: Fix big parameter passed by value
      BUG: Update IOSTL to include new bug fixes upstream
      DOC: Improve documentation for StatisticsAlgorithm functions
      BUG: Coverity 1130670: Buffer not null terminated in GE4ImageIO
      BUG: Coverity 1103200: Copy into fixed size buffer in GE5ImageIO
      STYLE: Coverity 1080839: Dead default in switch in
QuadEdgeMeshEulerOperatorJoinVertexTest
      STYLE: Coverity 1080963: Dereference after null check in TreeIteratorBase
      BUG: Coverity 1081009: Missing break in switch in GiftiMeshIO
      BUG: Coverity 1081422: Uninitialized pointer field in
QuadEdgeMeshFrontBaseIterator
      STYLE: Coverity 1081140: Dereference before null check
      BUG: Coverity 1081547: Uninitialized pointer field in
ConnectedRegionsMeshFilter
      STYLE: Coverity 40ee44a9: Self assignment in
VoronoiSegmentationImageFilterTest
      BUG: Coverity 1081129: Dereference before null check in itkIOCommonTest
      COMP: Update libminc from upstream, fixing a compiler warning on OSX
      BUG: Coverity 1081019: Improper use of negative value in StringTools
      COMP: Fix downcast warnings
      BUG: Coverity 1103189: Big parameter passed by value in FindSampleBound
      COMP: Fix implicit conversion warning
      COMP: Fix unused variable warning on Intel compilers
      BUG: Fix uninitialized variable in GradientRecursiveGaussianImageFilter
      BUG: Make all specializations NumericTrails::SetLength re-zero contents
      BUG: Update SmoothingRecursiveYvvGaussianFilter remote module
      BUG: Update SplitComponents remote module
      COMP: Fix implicit conversion warning
      BUG: Update SmoothingRecursiveYvvGaussianFilter remote module
      COMP: Update LesionSizingToolkit remote module from upstream
      STYLE: Coverity 1103618-1103620: Structurally dead code
      STYLE: Coverity 1081585: Structurally dead code
      STYLE: Coverity 1081584: Structurally dead code
      STYLE: Coverity 1081583: Structurally dead code
      STYLE: Coverity 1081580: Structurally dead code
      STYLE: Coverity 1081570-1081578: Structurally dead code
      STYLE: Coverity 1081566-1081568: Structurally dead code
      STYLE: Coverity 1081564: Structurally dead code
      STYLE: Coverity 1080826-1080827: Logically dead code
      STYLE: Coverity 1080862: Logically dead code
      STYLE: Coverity 1081598: Unused pointer value
      BUG: Coverity 1103595: Uninitialized pointer field
      BUG: Coverity 1081508: Uninitialized pointer field
      BUG: Fix uninitialized pointer fields
      BUG: Coverity 1081381: Uninitialized scalar field
      STYLE: Coverity 1103107-1103116: Logically dead code


Constantine Zakkaroff (1):
      DOC: HelloWorld Comments Edit for ITKSoftwareGuide


David Cole (2):
      COMP: Eliminate some level 4 warnings
      BUG: Add missing header files to enable try_run tests to run
without crashing


Dirk Padfield (2):
      DOC: Improved comments and reorganized code for IsolatedConnected
      DOC: Corrected documentation for threshold boundaries.


Eric Greveson (1):
      ENH: Add setters for the overlay functor in labelmap overlay filters.


Fotis Drakopoulos (1):
      ENH: Adding GetFEMFilter method to
PhysicsBasedNonRidgidRegistrationMethod.


GCC-XML Upstream (1):
      pygccxml 1.0.0 (reduced)


Ga?tan Lehmann (1):
      ENH: Importing files from Noise Simulation Article


Gib Bogle (1):
      BUG: Windows BigTIFF errors: stat failure and lack of COMPRESSION_DEFLATE


Google double-conversion Maintainers (1):
      COMP: Google double-conversion (reduced)


Guillaume Pasero (1):
      ENH: Add mangling to internal OpenJpeg


Hans Johnson (40):
      PERF: 15% speed improvement for registration
      PERF: Simplify conditionals in loop
      COMP: Conditional assert check warning unused var.
      COMP: SimpleITK linkage failure
      BUG: Missing Modified() call
      COMP: SimpleITK linkage failure
      BUG: Element numbers 1053, 1052 not hex
      BUG: Remove valgrind reported leak
      BUG: Add missing transform types to factory
      BUG: Missing Modified() call
      PERF: Reviewing code for facilitating compiler optimizations
      COMP: Fix const constructor for const arrays
      ENH: Add LBFGOptimizerv4(for BSPline registration)
      COMP: Test failure from numerical precision
      BUG: Memory leak introduced.
      COMP: Remove deprecated 'register' keyword
      ENH: Ignore autocompletion clang helper files
      ENH: Move to latest remote module tag
      STYLE: Improve testing of member Get/Set functions
      COMP: Update AnalyzeObjectMapIO replacing deprecated
      DOC: Fixed documentation regarding multi-threading
      DOC: Improved Image Representation
      PERF: Minimize redundant function calls
      PERF: Pull loop termination constants out of loop
      ENH: Refactoring the CompositeTransform class
      STYLE: Explicitly declare virtual for derived class member functions
      STYLE: Explicitly recognize virtual functions
      STYLE: Add ITK_NULLPTR supporting c++11 checks
      BUG: Missing parentheses for logic comparison
      STYLE: Explicitly declare virtual (cont. of 1c8609)
      STYLE: Consistency of threadID and threadId
      BUG: FFTConvolutionImageFilter outputs incorrect
      STYLE: GetStopConditionDescription abstract method
      PERF: Re-use jacobian rather than instantiation
      ENH: Improve test in preparation for performance testing
      PERF: Code simplifications for performance testing
      BUG: Missed an API change for Allocate
      STYLE: Remove unnecessary comments.
      BUG: Expose unusable functions
      BUG: Incomplete refactoring of member variable name


Jean-Christophe Fillion-Robin (1):
      COMP: Fix "unused-local-typedefs" warnings


Jens Wetzl (2):
      BUG: Fix race conditions in itkInvertDisplacementFieldImageFilter
      STYLE: Incorporated reviewer suggestions


Jon Haitz Legarreta (8):
      ENH: New test for itkSigmoidTransferFunction.
      COMP: Fix type casting build warning.
      ENH: New test for itkLogSigmoidTransferFunction
      ENH: Added call to Print() method
      STYLE: Changed LogSigmoidTransferFunction template argument names.
      ENH: Added StatisticsRelabelImageFilterTest to testing
      BUG: Fix issues with the BinaryStatisticsOpeningImageFilter test
      COMP: Test for itkCustomColormapFunction


Kent Williams (13):
      ENH: Add remote module for AnalyzeObjectMapIO
      BUG: incorrect loop var increment
      COMP: Update the DoubleConversion library upstream update script.
      ENH: Turn off DCMTK Logger messages by default
      COMP: fixed license test command in UpdateDoubleConversionFromGoogle.sh
      ENH: Add FDFImageIO as a remote module.
      PERF: replace image allocate followed by fillbuffer with allocate(true)
      COMP: Add test to verify Slope/Intercept handling
      BUG: GDCM reporting wrong spacing for some Media Types
      ENH: Add test for itkTestingStretchIntensityImageFilter
      COMP: Fix misplaced closing brace
      ENH: Remove try/catch exception handling around dynamic_catch
      ENH: Disallow vector multiply by itself


Liza Shrestha (1):
      COMP: Added new unit tests for increasing code coverage


Luis Ibanez (11):
      ENH: Add STLMeshIO remote module.
      BUG: Fixed module name IOSTL.
      COMP: Fixing instantiation of templated functions.
      BUG: Fixed Affine test 32bits. Precision checks.
      PERF: Accelerate initialize via selective testing.
      COMP: ShapeUniqueLabelMapFilter test was missing.
      STYLE: Coverity 1103119: Logically dead code
      BUG: itkLoggerThreadWrapper test was disabled.
      BUG: No DiscreteHessianGaussianImageFunctionTest.
      BUG: DiffusionTensorReconstruction lacked Progress
      BUG: TestingExtractSliceImageFilter lacked test.


Luke Bloy (4):
      BUG: Fixes itkBoxSpatialObject part of issue ITK-3153
      BUG: Fixes itkImageMaskSpatialObject part of issue ITK-3153
      BUG: Fixes itkBoxSpatialObject part of issue ITK-3153
      BUG: Fixes itkImageMaskSpatialObject part of issue ITK-3153


Marius Staring (2):
      ENH: add reset function to resource probe
      ENH: adding handle to RealTimeClock


Mark Hiner (1):
      ENH: bump to latest scifio-imageio


Martin Stegh?fer (1):
      BUG: Match behavior of SimpleFastMutexLock on different
platforms (#ITK-3248)


Matthew McCormick (93):
      ENH: Bump CMakeLists.txt to version 4.6.0.
      BUG: Remove unused itkAffineTransformXX.txt content links.
      BUG: Avoid SimpleImageRegistration{Float,Double}Test output clobbering.
      BUG: Prevent MINC transform tests outputs from clobbering.
      BUG: Add random number generator seed for vnl_algo_test_sparse_lm.
      COMP: Update libminc to latest version.
      ENH: Only build tests for modules explicitly enabled.
      BUG: Remove unused forward declarations in RegistrationMethodsv4.
      COMP: Update libminc to latest version.
      ENH: Add REQUIRES_DISPLAY CTest label.
      ENH: Add SplitComponents Remote Module.
      DOC: Suggest MeshFileReader instead VTKPolyDataReader.
      DOC: Add itkSetGetDecoratedInputMacro definition for Doxygen.
      COMP: Bump DCMTK to fix warning.
      BUG: Wrap TransformFileReader, TransformFileWriter.
      BUG: Remove unused itkAffineTransformXX.txt content links.
      COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
      COMP: CommandIterationUpdate has field whose type uses anonymous
namespace.
      COMP: Do not use -fno-ipa-cp-clone with clang.
      ENH: Move TransformToDisplacementFieldSource out of Review.
      ENH: Bump ITK version to 4.5.1.
      COMP: ImageRegistrationHistogramPlotter Clone never referenced.
      ENH: Add the ITK_INSTALL_LIBRARY_DIR to WrapITK.pth.
      ENH: Bump SCIFIO to add wrapping.
      COMP: ImageRegistrationHistogramPlotter unchecked dynamic_cast.
      BUG: Fix Array memory leaks with non-const construction.
      BUG: Prevent ambiguous Array construction methods.
      COMP: HDF5 library version variables contain '@'.
      COMP: Remove add_custom_command(SOURCE...
      COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
      BUG: Wrap TransformFileReader, TransformFileWriter.
      COMP: Add missing itkVerson.h header.
      COMP: LBFGSOptimizerBasev4 explicit Doxygen link request.
      ENH: Bump FFTW to 3.3.3.
      COMP: Duplicated VectorContainer wrapping for real types.
      BUG: Increase tolerance for itkFEMC0TriangularElement-NodalLoads-BCs
      STYLE: Add missing "Test" to GDCM test names and filenames.
      DOC: No ReferenceImage members in TransformToDisplacementFieldSource.
      COMP: Bump LesionSizingToolkit for Doxygen warnings.
      BUG: GDCM Series does not write z-spacing.
      COMP: Remove unreachable return statements.
      ENH: Add ITK_FORBID_DOWNLOADS option. ITK-3239
      COMP: Bump SplitComponents Remote for Doxygen warnings.
      COMP: return will never be executed after exception thrown.
      BUG: Invalid read during ImageIOBase SetDirection.
      COMP: Fix failed itkTIFFImageIOCompressionTest merge.
      ENH: Bump version to 4.5.2.
      COMP: return will never be executed after exception thrown.
      COMP: SigmoidTransferFunction conversion from double.
      BUG: BoxImageFilter GenerateInputRequestRegion public -> protected.
      DOC: KernelImageFilter does not reimplement GenerateInputRequestedRegion.
      STYLE: Remove SigmoidTransferFunction .hxx doxy comments.
      BUG: Clean up Python module2module test.
      BUG: TestingExtractSliceImageFilterTest v3 direction strategy.
      STYLE: Remove duplicated TestingExtractSliceImageFilter doxygen.
      COMP: Use latex formula for HoughTransform doxygen.
      COMP: SigmoidTransferFunction members Alpha, Beta real type.
      STYLE: Fix SigmoidTransformFunction template argument names.
      COMP: BuildHeaderTest.py print_function import.
      BUG: Fix print function errors in pygccxml.
      BUG: Fix print functions in igenerator.py.
      ENH: Add Remote module group description to Doxygen.
      STYLE: Clean up MetaDataObjectBase.
      STYLE: Clean up MetaDataObject.
      ENH: Add unit test for MetaDataObject.
      ENH: Add MetaDataObject Print specialization for common types.
      STYLE: Fix template statements in SigmoidTransformFunction.
      BUG: Remove public MetaDataObject constructors.
      BUG: Add missing private copy constructors to MetaDataObject.
      BUG: Remove FEMRegistrationFilter debug code.
      DOC: Improve documentation and types for SplitRequestedRegion.
      Revert "Revert "ENH: Add Remote module group description to Doxygen.""
      DOC: Remove errant "+" in Remote_documentation.
      ENH: For shared libraries when wrapping.
      ENH: Collect all wrapping configuration checks in one place.
      ENH: Better CMake defaults with wrapping.
      ENH: Replace CSWIG preprocessor definition with ITK_WRAPPING.
      BUG: Remove old itkSampleBuildTest.cmake.in file.
      ENH: Move MagnitudeAndPhaseToComplexImageFilter out of Review.
      COMP: Fix Doxygen warnings in itkMetaDataObject.h.
      BUG: Exclude Remote Modules the default ON Group values.
      COMP: Documentation CMake target must come before add_custom_command.
      BUG: Assign Remote modules to groups more robustly.
      BUG: Remove MagnitudeAndPhaseWriteComplexImageFilter test from
Review Module.
      BUG: Remove old tests from Review for classes that have been removed.
      DOC: Fix Software Guide LaTeX syntax errors in the examples.
      COMP: Define ITKCommon_EXPORT_EXPLICIT for Doxygen.
      COMP: Remove itkImageReadComplexWriteMagnitudeAndPhaseTest.cxx from list.
      BUG: Move MagnitudeAndPhaseToComplexImageFilter to the
ImageIntensity module.
      COMP: StdStreamStateSave Doxygen include.
      ENH: Add Sphinx examples as a Remote Module.
      BUG: Remove ITK_INSTALL_NO_LIBRARIES and ITK_INSTALL_NO_DEVELOPMENT.
      ENH: Make ITK_WRAPPING INTERNAL.


Matthew Woehlke (1):
      COMP: Fix egregious -Wcast-qual warnings


Michka Popoff (53):
      BUG: Fix for the WrapITK.pth destination path
      COMP: Fixes the Python wrapping under OS 10.8.5
      STYLE: Removed itkExtras folder
      BUG: Fix for the WrapITK.pth destination path
      COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
      STYLE: 4 space indentation for python files
      COMP: Fixed itkGradientDescentOptimizerv4 wrapping warnings
      STYLE: Removed deprecated itk functions
      STYLE: Removed unused and misplaced python tests
      STYLE: Removed legacy python importing
      STYLE: Pep8 cleanup for the python files
      STYLE: Remove deprecated python strel function
      COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
      COMP: Fixed itkGradientDescentOptimizerv4 wrapping warnings
      ENH: Use python warnings module for template warnings
      COMP: Duplicated wrapping for double in Array2D
      COMP: Update SWIG to 2.0.12
      COMP: Require at least Python 2.6 for Python wrapping
      ENH: Remove python dl dependency
      ENH: Remove psyco import
      COMP: Update PCRE to 8.34
      ENH: Update Swig to 3.0.0
      STYLE: Remove WrapITK versions
      COMP: Remove cmp0011 in wrapping
      COMP: Remove unused code in ConfigureWrapping.cmake
      COMP: Remove clrLine in itkExtras
      COMP: Fix the python import and progress callbacks
      STYLE: Remove reference to CableSwig
      STYLE: Clean up BinaryThresholdImageFilter (python)
      COMP: Fix the Python ResampleImageFilter test
      ENH: Bump SCIFIO for OS X installation
      ENH: Bump SCIFIO for OS X installation
      COMP: Update PCRE to 8.35
      STYLE: Remove unused compile all code for Python Wrapping
      ENH: Replace python print with print() function
      STYLE: Remove deprecated Python wrapping macros
      COMP: Fix failing header test
      COMP: Fix the writing of .idx files
      COMP: Fix python print import for .pth file creation
      COMP: Fix print import statement in itkExtras.py
      STYLE: Refactor swig call and code cleanup
      COMP: Fix for wrapping warnings (RealTimeClock and SimpleFastMutexLock)
      STYLE: Remove old Python examples
      COMP: Update gccxml
      ENH: Use pygccxml snapshot.
      ENH: Update to swig 3.0.2
      DOC: Update commit instructions for JIRA bugtracker
      ENH: Update GCCXML
      BUG: Fix wrapping with dimension 2 only
      COMP: Temporarily hide pygccxml warnings
      BUG: Do not wrap BinaryMask3DMeshSource when building with 2D only
      COMP: Move itkMatrixCoefficients wrapping to Filtering module
      COMP: Fix wrapping with Core only


Miguel Algaba (1):
      ENH: Added further Solve methods to VNLSparseLUSolverTraits


Nick Tustison (2):
      BUG:  Ignored the case for exceeding iteration limit.
      ENH: Preparing point set metrics for use with registration.


Rashad M (1):
      STYLE: Allow system installed expat library with ITK_USE_SYSTEM_EXPAT=ON


Sean McBride (6):
      BUG: initialize m_SmallBlock ivar in ctor; fixes garbage read
      BUG: changed some variables involved in shifting to unsigned
      COMP: Updated libminc to a78661bb592359ab86f417cc0c298299e593d808
      BUG: initialize m_SmallBlock ivar in ctor; fixes garbage read
      PERF: Mark ImageRegistration8Test with RUNS_LONG
      COMP: workaround clang -Windent warnings by fixing indentation


Sebastian P?lsterl (1):
      BUG: Return null pointer if class label does not exist (#3235)


Taylor Braun-Jones (1):
      ENH: Expose the output stream operator for LightObject


Vladimir Chalupecky (1):
      DOC: Fix description of SpatialObject::GetBoundingBox()


Vladimir S. FONOV (3):
      COMP: Fixed libminc to build on Windows
      COMP: Updated libminc, hopefully reducing number of warnings
      COMP: Improved MINCIOTransform tests


Wei Liu (1):
      BUG: Fixed a bug in ExpectationMaximiationMixtureModelEstimator.


Yves Frederix (1):
      ENH: GeodesicActiveContourShapePrior deals with DerivativeSigma
equal to zero


ITK Sphinx Examples Changelog
-----------------------------------------

Arnaud Gelas (25):
     remove annonying messages about include folders not used with Clang
     ENH: Add one example for LabelMapMakImageFilter
     upgrade breathe to 1.2.0
     add documentation for ITKLabelMap
     ENH: Add one example to convert a triangular mesh to binary image
     ENH: Add example for itk::AccumulateImageFilter
     read an unknown image type
     add example to generate mesh from binary image
     ENH: Add one example for ExpNegativeImageFilter
     add one example for ThresholdImageFilter
     Add one example to translate one itk::Mesh
     add Iterative hole filling example
     wrong directory name
     fix link to c++ code
     link to the wrong folder for canny edge detection example
     Resample scalar image (with identity transform)
     fix command line for cloning in README
     COMP: Fix for failing ApplyAccumulateImageFilter baseline comparison test
     add one example to translate one itk::Image
     add PasteImageFilter example
     fix path in ArchiveBinaryData.py.in
     BUG: error when TEST_IMAGE_PREFIX was used
     fix broken links as detected by linkcheck
     add example for PermuteAxesImageFilter
     Add one example to apply an affine transform given homogeneous matrix

Brian Helba (3):
     ENH: Support ExternalData_OBJECT_STORES being set with a Superbuild
     ENH: Allow ExternalData path to be set by environment on dashboards
     BUG: Set correct URL scheme in dashboard common script

Matt McCormick (21):
     ENH: DilateABinaryImage uses FlatStructuringElement.
     ENH: Add DilateABinaryImage.py.
     ENH: ErodeABinaryImage uses FlatStructuringElement.
     ENH: Add ErodeABinaryImage.py.
     ENH: Use Git email as default when uploading binary data.
     BUG: ITKIOImageBase module directory not included.
     BUG: MaskOneImageGivenLabelMap test name for baseline comparison.
     ENH: Add Register IO Factories example.
     ENH: Add documentation upload to common CDash script.
     ENH: Add ApplyExpNegativeImageFilter.py.
     BUG: Remove non-existent Sphinx example entry.
     DOC: Give an example call to UploadBinaryData.py.
     COMP: Fix Doxygen link to LevelSets visualization classes.
     ENH: Rename module to follow Remote Module convention.
     COMP: QUIET initial find_package( ITK ).
     ENH: Bump ITK Superbuild tag to 4.6.0.
     BUG: Fix ConvertAnITKGrayScaleImageToCVMat compare_to_baseline.
     COMP: Remove breathe link to ConstantPadImageFilter.
     BUG: Fix figure path for Iterative Hole Filling.
     BUG: Evolution.gif needs to be ..only:: html
     COMP: Content not permitted in image:: directive.

Michka Popoff (29):
     ENH: Add examples for grayscale image dilation/erosion
     ENH: Add BinaryThresholdImageFilter example
     COMP: Fix for cmake 3.0 compatibility
     ENH: Clean up ThresholdAnImageUsingOtsu
     ENH: Add missing python documentation call for binarythreshold example
     STYLE: Fix Python subtitles
     ENH: Add CannyEdgeDetectionImageFilter example
     COMP: Add cmake_minimum_required back
     STYLE: Cleanup include( ${ITK_USE_FILE} ) and minor alignements
     COMP: Fix for Canny Edge example
     ENH: Add CastImageFilter.py and code cleanup
     ENH: Add ComputeCurvatureAnisotropicDiffusion example
     ENH: Add GradientAnisotropicDiffusionImageFilter example
     ENH: Add ComputeGradientMagnitudeRecursiveGaussian python example
     ENH: Add CurvatureFlowImageFilter example
     STYLE: Clean up pipeline and uniformize error catching
     ENH: Add mean and median filters
     ENH: Add Laplacian filter example
     ENH: Add an example of image resampling
     COMP: Fix two documentation warnings
     STYLE: Update sys.argv len() checks
     ENH: Add example for Sigmoid computation
     STYLE: Rename python examples to Code.py
     ENH: Fix the git URL
     ENH: Add python code for ThresholdAnImage
     ENH: Add example for SmoothWithRecursiveGaussianImageFilter
     COMP: Fix failing setup of SegmentBloodVessels example
     STYLE: Update title for Apply Affine Transform example
     ENH: Add GeodesicActiveContourLevelSetImageFilter example


ITK Software Guide Changelog
---------------------------------------

Brad King (3):
      SoftwareGuideCover: Port to VTK >= 5
      SoftwareGuideCover: Re-order code to simplify non-interactive run
      SoftwareGuideCover: Adjust colors and camera position for new cover

Bradley Lowekamp (1):
      Fix spelling of Lowekamp

Constantine Zakkaroff (1):
      ENH: Revise Configure and Build Instructions

Hans Johnson (4):
      ENH: Reorder IO and filtering chapters.
      STYLE: Remove end of line spaces.
      COMP: File name change needed
      DOC: Added Direction to the figure

Matt McCormick (39):
      ENH: Improve Hello World directions.
      BUG: Remove extra configuration of SoftwareGuideConfiguration.tex.
      ENH: Update the printed SoftwareGuide authors.
      BUG: Updates to PrintedPreamble.
      BUG: Update the cover sources location.
      STYLE: Update CMake style in SoftwareGuide/Latex/CMakeLists.txt
      ENH: Split into two books.
      BUG: Build resolving citations.
      BUG: Update build process description in SoftwareGuide/README.txt.
      BUG: Remove SoftwareGuide/Latex/00-SoftwareGuide.tex.
      DOC: Move build instructions to top level README.
      ENH: Update funding acknowledgement.
      DOC: Remove minipage about VTK/CMake books.
      STYLE: Improve spacing after preamble year.
      BUG: Update Cover VWSegmentation CMakeLists.txt.
      COMP: Fix compilation of ModerBasedSegmentation.cxx.
      STYLE: Strip trailing whitespace from SoftwareGuide sources.
      COMP: Add -dUseCIEColor when building Printer quality.
      BUG: o -> % in comment.
      ENH: Update the Kitware logo.
      ENH: Update copyright notice.
      STYLE: Place the appendix before \backmatter.
      BUG: Remove commentted content.
      ENH: Matt -> Matthew.
      ENH: Add Ali Ghayoor to contributors.
      ENH: Add contributors for covers.
      BUG: Update participants URL.
      BUG: Move build configuration to PrintedPreamble-Common.
      ENH: Add description for book cover 2.
      BUG: Update index generation.
      BUG: Remove wrapping Tcl entry.
      BUG: Remove old comments.
      ENH: Bump ITK to v4.6.0.
      ENH: Pass PDF_QUALITY_LEVEL in superbuild.
      BUG: Remove unused RunExamples.py imports.
      ENH: Reduce verbosity of RunExamples.py.
      BUG: Do not include RegistrationITKv4 example sources in the build.
      BUG: Fix caption on Confidence Connectened on BrainWeb figures.
      BUG: Bump the ITK superbuild for LaTeX fixes.

From mercikd at thomas.edu  Wed Jul 30 15:25:41 2014
From: mercikd at thomas.edu (Dan Mercik)
Date: Wed, 30 Jul 2014 19:25:41 +0000
Subject: [ITK-users] Adjacent Deblurring Wavelenght fusion?
Message-ID: <a9bc275d472f4a699bef02bffb44cef7@T9.tcnet.thomas.edu>

Hey,

I'm using ITK and wanted to know if there a way I can do Adjacent Deblurring Wavelenght fusion for a stack of images?



Daniel Mercik

Computer Science Major

Thomas College

From oscar.lazzarino at gmail.com  Wed Jul 30 16:23:57 2014
From: oscar.lazzarino at gmail.com (Oscar Lazzarino)
Date: Wed, 30 Jul 2014 22:23:57 +0200
Subject: [ITK-users] Starting with GPU development
Message-ID: <CALXHfx_phrr1rKy8U8LkFjw2LA9OV5ERxKCEyYs3C4ww14r18w@mail.gmail.com>

Hi,

I'd like to experiment a bit with GPU/OpenCL computing, but I'm having some
troubles finding examples and documentation.

The ITK Software Guide mentions "GPU" exactly ZERO times.

I could not find any complete example on the wiki.

The reference documentation is there, but I can't even understand where to
start from.

Let's say I want to put the output on a reader into a GPUImage.

I can't just say MyGPUImageType::Pointer image = reader->getOutput()
because the output of a reader is NOT a GPU image.

How am I supposed to do that? Am I missing something?

Any info (or any pointer to any good info) is REALLY welcome :)

Thanks

Oscar Lazzarino
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140730/df8e257c/attachment.html>

From blowekamp at mail.nih.gov  Wed Jul 30 16:33:47 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 30 Jul 2014 16:33:47 -0400
Subject: [ITK-users] Starting with GPU development
In-Reply-To: <CALXHfx_phrr1rKy8U8LkFjw2LA9OV5ERxKCEyYs3C4ww14r18w@mail.gmail.com>
References: <CALXHfx_phrr1rKy8U8LkFjw2LA9OV5ERxKCEyYs3C4ww14r18w@mail.gmail.com>
Message-ID: <F294CC66-EF9F-4244-A24E-F7736A068997@mail.nih.gov>

The test may be a good starting point for some examples:

$ find  . -name "*GPU*Test.cxx"
./Modules/Core/GPUCommon/test/itkGPUImageTest.cxx
./Modules/Core/GPUCommon/test/itkGPUReductionTest.cxx
./Modules/Registration/GPUPDEDeformable/test/itkGPUDemonsRegistrationFilterTest.cxx
./Modules/Filtering/GPUThresholding/test/itkGPUBinaryThresholdImageFilterTest.cxx
./Modules/Filtering/GPUThresholding/test/itkGPUImageFilterTest.cxx
./Modules/Filtering/GPUImageFilterBase/test/itkGPUNeighborhoodOperatorImageFilterTest.cxx
./Modules/Filtering/GPUAnisotropicSmoothing/test/itkGPUGradientAnisotropicDiffusionImageFilterTest.cxx
./Modules/Filtering/GPUSmoothing/test/itkGPUMeanImageFilterTest.cxx
./Modules/Filtering/GPUSmoothing/test/itkGPUDiscreteGaussianImageFilterTest.cx

Brad

On Jul 30, 2014, at 4:23 PM, Oscar Lazzarino <oscar.lazzarino at gmail.com> wrote:

> Hi,
> 
> I'd like to experiment a bit with GPU/OpenCL computing, but I'm having some troubles finding examples and documentation.
> 
> The ITK Software Guide mentions "GPU" exactly ZERO times.
> 
> I could not find any complete example on the wiki.
> 
> The reference documentation is there, but I can't even understand where to start from.
> 
> Let's say I want to put the output on a reader into a GPUImage.
> 
> I can't just say MyGPUImageType::Pointer image = reader->getOutput() because the output of a reader is NOT a GPU image.
> 
> How am I supposed to do that? Am I missing something?
> 
> Any info (or any pointer to any good info) is REALLY welcome :)
> 
> Thanks
> 
> Oscar Lazzarino
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From mallikarjun49 at gmail.com  Thu Jul 31 01:35:32 2014
From: mallikarjun49 at gmail.com (Mallikarjun K)
Date: Thu, 31 Jul 2014 11:05:32 +0530
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
Message-ID: <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>

Hi Bill,
Thanks for the replay.

Yes,I built both ITK and my app with Release ,I forgot to mention it in the
previous post.Actually the data set is the output of
vtkDiscreteMarchingCubes algorithm(around 5MB) and need to smooth .I saved
this marching cube's output as .vtk file and read it
using itkVTKPolyDataReader and then I am giving this reader's output to
itkSmoothingQuadEdgeMeshFilter's input.

I checked the execution time of each step in the pipeline ,after
SmothingQEMeshFilter has got it's input ,it is taking time to process the
data.

Thank you



On Wed, Jul 30, 2014 at 9:29 PM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:

> First, make sure you are building ITK and your app with Release. A
> Debug build can be 10-50 times slower.
>
>
> On Wed, Jul 30, 2014 at 10:18 AM, Mallikarjun K <mallikarjun49 at gmail.com>
> wrote:
> > Hi All,
> > I am using itkSmoothingQuadEdgeMeshFilter for Surface Mesh smoothing.This
> > filter is giving good results what I expected but taking more execution
> > time.can any one suggest me to reduce the execution time( multi threading
> > or any parameters to add/remove )?
> >
> > Below is the code snippet
> > ///////
> > typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
> > qetraits;
> > typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
> >
> > //typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3 > MeshType;
> >
> > itk::OnesMatrixCoefficients< MeshType > coeff0;
> >
> > typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
> > SmoothingQuadEdgeMeshFilter;
> >
> >     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
> > SmoothingQuadEdgeMeshFilter::New();
> >
> > QEMeshSmoother->SetInput("abc.vtk");
> > QEMeshSmoother->SetNumberOfIterations(5 );
> > QEMeshSmoother->SetRelaxationFactor( 0.5 );
> > QEMeshSmoother->SetDelaunayConforming(true );
> > QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
> > QEMeshSmoother->Update();
> > ////
> >
> > --
> > Regards:
> > Mallik
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>



-- 
*Regards:*
Mallik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140731/3dd9cc6f/attachment.html>

From irina.vidal-migallon at inria.fr  Thu Jul 31 04:29:54 2014
From: irina.vidal-migallon at inria.fr (Irina Vidal Migallon)
Date: Thu, 31 Jul 2014 10:29:54 +0200
Subject: [ITK-users] Starting with GPU development
In-Reply-To: <CALXHfx_phrr1rKy8U8LkFjw2LA9OV5ERxKCEyYs3C4ww14r18w@mail.gmail.com>
References: <CALXHfx_phrr1rKy8U8LkFjw2LA9OV5ERxKCEyYs3C4ww14r18w@mail.gmail.com>
Message-ID: <53D9FE82.1050404@inria.fr>

Hi Oscar,

> Let's say I want to put the output on a reader into a GPUImage.
>
> I can't just say MyGPUImageType::Pointer image = reader->getOutput() 
> because the output of a reader is NOT a GPU image.


If you've defined your reader as a GPUImage reader, as in:

typedef itk::ImageFileReader< itk::GPUImage<MyType, 2> > GPUReaderType;

you can do just that, as you would with any other type of image.


> Any info (or any pointer to any good info) is REALLY welcome :)
>

I found examples and tests in Modules/Filtering/GPU* and/or 
Modules/Core/GPUCommon rather helpful, they will probably get you started.




I.



From bill.lorensen at gmail.com  Thu Jul 31 07:44:39 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Thu, 31 Jul 2014 07:44:39 -0400
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
Message-ID: <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>

If you have it in vtk, I suggest using the vtk pipeline to smooth the data.

On Thu, Jul 31, 2014 at 1:35 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> Hi Bill,
> Thanks for the replay.
>
> Yes,I built both ITK and my app with Release ,I forgot to mention it in the
> previous post.Actually the data set is the output of
> vtkDiscreteMarchingCubes algorithm(around 5MB) and need to smooth .I saved
> this marching cube's output as .vtk file and read it using
> itkVTKPolyDataReader and then I am giving this reader's output to
> itkSmoothingQuadEdgeMeshFilter's input.
>
> I checked the execution time of each step in the pipeline ,after
> SmothingQEMeshFilter has got it's input ,it is taking time to process the
> data.
>
> Thank you
>
>
>
> On Wed, Jul 30, 2014 at 9:29 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> First, make sure you are building ITK and your app with Release. A
>> Debug build can be 10-50 times slower.
>>
>>
>> On Wed, Jul 30, 2014 at 10:18 AM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>> > Hi All,
>> > I am using itkSmoothingQuadEdgeMeshFilter for Surface Mesh
>> > smoothing.This
>> > filter is giving good results what I expected but taking more execution
>> > time.can any one suggest me to reduce the execution time( multi
>> > threading
>> > or any parameters to add/remove )?
>> >
>> > Below is the code snippet
>> > ///////
>> > typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double
>> > >
>> > qetraits;
>> > typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>> >
>> > //typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3 > MeshType;
>> >
>> > itk::OnesMatrixCoefficients< MeshType > coeff0;
>> >
>> > typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>> > SmoothingQuadEdgeMeshFilter;
>> >
>> >     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
>> > SmoothingQuadEdgeMeshFilter::New();
>> >
>> > QEMeshSmoother->SetInput("abc.vtk");
>> > QEMeshSmoother->SetNumberOfIterations(5 );
>> > QEMeshSmoother->SetRelaxationFactor( 0.5 );
>> > QEMeshSmoother->SetDelaunayConforming(true );
>> > QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>> > QEMeshSmoother->Update();
>> > ////
>> >
>> > --
>> > Regards:
>> > Mallik
>> >
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> >
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>
>
>
> --
> Regards:
> Mallik
>



-- 
Unpaid intern in BillsBasement at noware dot com

From elena.bresciani87 at gmail.com  Thu Jul 31 11:22:54 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Thu, 31 Jul 2014 17:22:54 +0200
Subject: [ITK-users] ERROR: MeanSquaresImageToImageMetric: Too many
 samples map outside moving image buffer
In-Reply-To: <CACxk=WzU2Q0EiPKum1Dhr=8x6z04QBwdE0FA1Wf57KHiY8Rwrw@mail.gmail.com>
References: <CACxk=WxkVnWo6sc0J52u-fL2+woxi2z25RW__RWX2Dak4w-0WQ@mail.gmail.com>
 <CACxk=WxAPjyGFTvVDBba2UOW-ccYi8tN63uVmUexpv46p9juKw@mail.gmail.com>
 <D23C5E06-577F-4001-925A-6EC0EB8446B5@mail.nih.gov>
 <CACxk=Wz01mpwuQ0fEneeyERSyn-9icn980gDQJCrmbvd=JG=Zw@mail.gmail.com>
 <DEDB389F-D53D-4164-9166-11C0FEC31C7A@mail.nih.gov>
 <CACxk=WzU2Q0EiPKum1Dhr=8x6z04QBwdE0FA1Wf57KHiY8Rwrw@mail.gmail.com>
Message-ID: <CACxk=WxA_cUNxLx3WVcktm3ZZu=LdS7uXYeHrtF_3KvojoGvDg@mail.gmail.com>

Any hint on how I can resolve my issue?
I'd really appreciate any suggestion?
I should change the metric?
I tried adding a Centered Transform Initializer but whitout success, even
after setting smaller step lenghts I have the same problem.

Cheers Elena


2014-07-23 14:52 GMT+02:00 elena bresciani <elena.bresciani87 at gmail.com>:

> I get the error immediately after running the script, so I think the
> problem is in the transform initialization.
> Should I try with itkCenteredTransformInitializer.h
> <http://www.itk.org/Doxygen/html/itkCenteredTransformInitializer_8h_source.html>
> ?
>
>
> 2014-07-23 14:48 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>
> Is this at the first iteration of after a few? Are iterations converging,
>> diverging or erratic?
>>
>> If it's the first it's an indication that initial transform is poor and
>> they don't overlap much. There for the results of the transform initializer
>> should be evaluated.
>>
>> If it's after a few iterations, then is the iteration of the metric and
>> optimizer needs to be examine. Is the value of the metric correct and
>> correlated with the correct solution? Is the step size too big? Would
>> smoothing the fixed and moving images smooth optimization? etc?
>>
>> These registration examples are not designed to be turn key solution,
>> they are a stepping stone to learn about the registration framework, and
>> begin analyzing the behavior of the components so that a solution to your
>> problem can be constructed.
>>
>> Brad
>>
>> On Jul 23, 2014, at 8:30 AM, elena bresciani <elena.bresciani87 at gmail.com>
>> wrote:
>>
>> ExceptionObject caught !
>>
>> itk::ExceptionObject (0x3043350)
>> Location: "void itk::MeanSquaresImageToImageMetric<TFixedImage,
>> TMovingImage>::GetValueAndDerivative(const ParametersType&,
>> itk::MeanSquaresImageToImageMetric<TFixedImage,
>> TMovingImage>::MeasureType&,
>> itk::MeanSquaresImageToImageMetric<TFixedImage,
>> TMovingImage>::DerivativeType&) const [with TFixedImage =
>> itk::Image<unsigned char, 2u>; TMovingImage = itk::Image<unsigned char,
>> 2u>; itk::MeanSquaresImageToImageMetric<TFixedImage,
>> TMovingImage>::ParametersType = itk::OptimizerParameters<double>;
>> itk::MeanSquaresImageToImageMetric<TFixedImage, TMovingImage>::MeasureType
>> = double; itk::MeanSquaresImageToImageMetric<TFixedImage,
>> TMovingImage>::DerivativeType = itk::Array<double>]"
>> File: /usr/local/include/ITK-4.5/itkMeanSquaresImageToImageMetric.hxx
>> Line: 257
>> Description: itk::ERROR: MeanSquaresImageToImageMetric(0x30384c0): Too
>> many samples map outside moving image buffer: 4042 / 568832
>>
>>
>> 2014-07-23 13:47 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>>
>>> What is the error you are getting?
>>>
>>> Brad
>>> On Jul 23, 2014, at 6:20 AM, elena bresciani <
>>> elena.bresciani87 at gmail.com> wrote:
>>>
>>> > Hello folks,
>>> >
>>> > I have a registration problem for you. I'm using the code in the
>>> example ImageRegistration5.cxx in order to align image of drugs blisters to
>>> assess if they are the same or not.
>>> >
>>> > The code works well even though for certain images couples I get the
>>> error in this message object.
>>> > I thought the problem could be the relative difference in images size
>>> and tried to pad the smallest one to have the same size as the biggest:
>>> same error.
>>> > After reading comments on the same topic I tried to add to the code
>>> the line
>>> >
>>> > registration -> SetFixedImageRegion (fixedImage ->
>>> GetBufferedRegion());
>>> >
>>> > again not solving my problem.
>>> > Attached you can find example images: while I can register image "1"
>>> on image "0", if I try to register "2" on "1" I get the ERROR.
>>> >
>>> > Any guess?
>>> >
>>> > Cheers,
>>> > Elena
>>> >
>>> >
>>> >
>>> > <0.jpg><1.jpg><2.jpg>
>>> >
>>> > _____________________________________
>>> > Powered by www.kitware.com
>>> >
>>> > Visit other Kitware open-source projects at
>>> > http://www.kitware.com/opensource/opensource.html
>>> >
>>> > Kitware offers ITK Training Courses, for more information visit:
>>> > http://www.kitware.com/products/protraining.php
>>> >
>>> > Please keep messages on-topic and check the ITK FAQ at:
>>> > http://www.itk.org/Wiki/ITK_FAQ
>>> >
>>> > Follow this link to subscribe/unsubscribe:
>>> > http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140731/83409eb4/attachment.html>

From oscar.lazzarino at gmail.com  Thu Jul 31 13:58:56 2014
From: oscar.lazzarino at gmail.com (Oscar Lazzarino)
Date: Thu, 31 Jul 2014 19:58:56 +0200
Subject: [ITK-users] Starting with GPU development
In-Reply-To: <53D9FE82.1050404@inria.fr>
References: <CALXHfx_phrr1rKy8U8LkFjw2LA9OV5ERxKCEyYs3C4ww14r18w@mail.gmail.com>
 <53D9FE82.1050404@inria.fr>
Message-ID: <CALXHfx_Eoijg4PGQzpLmdYu5QTK-8_quwYHm3hB0n+j7bQbwpg@mail.gmail.com>

Thank you both, that's a start.

O.


On Thu, Jul 31, 2014 at 10:29 AM, Irina Vidal Migallon <
irina.vidal-migallon at inria.fr> wrote:

> Hi Oscar,
>
>
>  Let's say I want to put the output on a reader into a GPUImage.
>>
>> I can't just say MyGPUImageType::Pointer image = reader->getOutput()
>> because the output of a reader is NOT a GPU image.
>>
>
>
> If you've defined your reader as a GPUImage reader, as in:
>
> typedef itk::ImageFileReader< itk::GPUImage<MyType, 2> > GPUReaderType;
>
> you can do just that, as you would with any other type of image.
>
>
>
>  Any info (or any pointer to any good info) is REALLY welcome :)
>>
>>
> I found examples and tests in Modules/Filtering/GPU* and/or
> Modules/Core/GPUCommon rather helpful, they will probably get you started.
>
>
>
>
> I.
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140731/d0a5289a/attachment.html>

From donelron at web.de  Thu Jul 31 14:58:30 2014
From: donelron at web.de (donelron)
Date: Thu, 31 Jul 2014 11:58:30 -0700 (PDT)
Subject: [ITK-users] Inconsistent results for same histogram on same image
 when PixelType of image is different
Message-ID: <1406833109934-34366.post@n7.nabble.com>

Dear ITK users,

I have the following function that generates two scalar images with a
constant intensity value, then combines them to a vector image and then
calculates a histogram of the vector image:


template<typename TinputImage>
void TestHistogram()
{
	//Create an "empty" image in which all pixels will be 13
	TinputImage::Pointer pImage13pixels=TinputImage::New();
	CreateImage<TinputImage>(pImage13pixels, 50, 50, 13);

	//Create an "empty" image in which all pixels will be 42
	TinputImage::Pointer pImage42pixels=TinputImage::New();
	CreateImage<TinputImage>(pImage42pixels, 50, 50, 42);

	
	typedef itk::JoinImageFilter<TinputImage, TinputImage> JoinImageFilterType;


	JoinImageFilterType::Pointer joinFilter = JoinImageFilterType::New();
	joinFilter->SetInput1(pImage13pixels);
	joinFilter->SetInput2(pImage42pixels);
	joinFilter->Update();



	//Calculation of histogram
	const unsigned int MeasurementVectorSize = 2; // 2 channels, as image is
combination of two images (see above)
	const unsigned int binsPerDimension = 200;

	typedef itk::VectorImage<TinputImage::PixelType, 2>  Vector2DImageType;  
//vector image has the same pixel type as the input image
	//When using the join filter, determine the OutputImageType like this: 
JoinImageFilterType::OutputImageType
	typedef itk::Statistics::ImageToHistogramFilter<
JoinImageFilterType::OutputImageType > ImageToHistogramFilterType;
	


	ImageToHistogramFilterType::HistogramType::MeasurementVectorType
lowerBound(binsPerDimension);
	lowerBound.Fill(0);

	ImageToHistogramFilterType::HistogramType::MeasurementVectorType
upperBound(binsPerDimension);
	upperBound.Fill(binsPerDimension-1);   


	ImageToHistogramFilterType::HistogramType::SizeType
size(MeasurementVectorSize);
	size.Fill(binsPerDimension);

	ImageToHistogramFilterType::Pointer imageToHistogramFilter =
ImageToHistogramFilterType::New();
	imageToHistogramFilter->SetInput( joinFilter->GetOutput() );
	imageToHistogramFilter->SetHistogramBinMinimum( lowerBound );
	imageToHistogramFilter->SetHistogramBinMaximum( upperBound );
	imageToHistogramFilter->SetHistogramSize( size );

	try
	{
		imageToHistogramFilter->Update();
	}
	catch( itk::ExceptionObject & error )
	{
		std::cerr << "Error: " << error << std::endl;
		system("pause");
	}


	ImageToHistogramFilterType::HistogramType* histogram =
imageToHistogramFilter->GetOutput();




	// Walking through all of the histogram bins and getting the corresponding
frequencies
	typedef ImageToHistogramFilterType::HistogramType HistogramType;

	HistogramType::ConstIterator itr = histogram->Begin();
	HistogramType::ConstIterator end = histogram->End();
	typedef HistogramType::AbsoluteFrequencyType AbsoluteFrequencyType;
	TinputImage::PixelType indexElement;
	HistogramType::IndexType index;  //this is an itk::Array of signed long
elements in the current ITK version

	
	while( itr != end )
	{
		const AbsoluteFrequencyType frequency = itr.GetFrequency();		
		if (frequency>0)
		{
			index = histogram->GetIndex(itr.GetInstanceIdentifier());
			std::cout << "index= " << index << ", Frequency:" << frequency <<
std::endl;	
		}

		++itr;
	}
}


--------------------------------------------------------------


void CreateImage is defined as:

template <typename TImage>
void CreateImage(TImage* const image, int width, int height, int intensity)
{
    typename TImage::IndexType corner = {{0,0}};

    unsigned int NumRows = height;
    unsigned int NumCols = width;
    typename TImage::SizeType size = {{NumRows, NumCols}};

    typename TImage::RegionType region(corner, size);

    image->SetRegions(region);
    image->Allocate();

    image->FillBuffer(intensity);
}


----------------------------------------------------------

Then I do some typdefs and call the function twice like::

	typedef itk::Image<unsigned int, 2> UintImageType;
	typedef itk::Image<unsigned char, 2>  UcharImageType;
	TestHistogram<UcharImageType>();
	TestHistogram<UintImageType>();


The resulting output is then:

index= [13, 42], Frequency:2500
index= [199, 199], Frequency:2500



However, if I change the number of histogram bins like this:

const unsigned int binsPerDimension = 300;

then the resulting output is:

index= [13, 42], Frequency:2500
index= [299, 299], Frequency:2500

So, it works only for the unsigned char image, but not for the unsigned int,
which is the one, that I actually need!

It seems that for the unsigned int image that whatever the intensity values
in the image are, they are always rounded up to the upper bound as defined
for the histogram. i also tried to use the itk::ComposeImageFilter instead
of the itk::JoinImageFilter, but that did not help in any way. 
What am I doing wrong? And what do I need to change to calculate a histogram
for an image with unsigned int PixelType???

Thanks in advance!



--
View this message in context: http://itk-users.7.n7.nabble.com/Inconsistent-results-for-same-histogram-on-same-image-when-PixelType-of-image-is-different-tp34366.html
Sent from the ITK - Users mailing list archive at Nabble.com.