From donelron at web.de  Fri Aug  1 04:27:22 2014
From: donelron at web.de (donelron)
Date: Fri, 1 Aug 2014 01:27:22 -0700 (PDT)
Subject: [ITK-users] Inconsistent results for same histogram on same
 image when PixelType of image is different
In-Reply-To: <1406833109934-34366.post@n7.nabble.com>
References: <1406833109934-34366.post@n7.nabble.com>
Message-ID: <1406881642374-34367.post@n7.nabble.com>

Just one short addition / correction to my post:

If I was able to use for example <unsigned short int> that would also be
more than enough. Basically, I just need up to around 1000 different gray
values in the image in which I have to calculate the histogram. So, unsigned
char with 256 different values is obviously not enough...



--
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-tp34366p34367.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From mallikarjun49 at gmail.com  Fri Aug  1 07:06:12 2014
From: mallikarjun49 at gmail.com (Mallikarjun K)
Date: Fri, 1 Aug 2014 16:36:12 +0530
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
Message-ID: <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>

Thanks Bill for your answer.

The reason I am using this pipeline is that SmoothingQEMeshFilter has an
additional parameter for smoothing which is delaunay conforming which helps
to optimize aspect ratio of triangles while smoothing and thus produces
better output.Is there anything similar filter in the vtk pipeline.I used
vtkWindowedSincPolydatafilter which is not giving the output as good as
QEMeshSmoothing filter.

Thanks for your help


On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:

> 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
>



-- 
*Regards:*
Mallik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140801/506fb66a/attachment.html>

From rg.bumpy at gmail.com  Fri Aug  1 09:47:48 2014
From: rg.bumpy at gmail.com (Bumpy RG)
Date: Fri, 1 Aug 2014 15:47:48 +0200
Subject: [ITK-users] Whole body Segmentation-Identification
Message-ID: <CAOoMOMDZL+K7LtHkNYdu7EU-m9JrsS3i_w8gmcp90C6XJBS1cQ@mail.gmail.com>

Dear All,

I have a dicom series having whole body image sequences, starting from head
up to legs.

My aim is to write an algorithm to automatically identify the body parts
(lungs, spines, head etc.) from the dicom sequence.

Although I am very new to the ITK world, I am following these steps in ITK (*I
would appreciate if you comment whether I am following correct idea or not*
):

   1. Read dicom series using 'DicomSeriesReadImageWrite2.cxx ' to create a
   3D volume and save the result in mhd format.
   2. Use 'ImageReadRegionOfInterestWrite.cxx' for separating various parts
   (like left lung, right lung, spines, head etc.) and save them in respective
   3D volumes in mhd format.
   3. Pick the various body parts prepared above, one by one and segment
   them using robust algorithm (say
   ThresholdSegmentationLevelSetImageFilter.cxx).
   4. Use Mathematical Morphology to get better results.
   5. Using the various results from above, form an algorithm for
   identifying the various body parts.

Currently I am stuck in the second step because it is so hard to choose the
co-ordinates for selecting proper region of interest.

For example,  I chose these points for ROI of right lung (I checked the
co-ordinates using 3D slicer visualizer) and it does not give me good
results :
start[0] = 255;
start[1] =165;
start[2] = 0;

*However I do not understand how to choose the points properly in ITK.*


I would be really glad to have your response.

Thanking you in advance.
Kind Regards,
Bumpy.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140801/c80b0e48/attachment.html>

From fttfzzx227 at 126.com  Mon Aug  4 14:02:32 2014
From: fttfzzx227 at 126.com (tina)
Date: Tue, 5 Aug 2014 02:02:32 +0800
Subject: [ITK-users] [Insight-users] Principal Axes pre-registration
Message-ID: <000001cfb00e$448ce9b0$cda6bd10$@126.com>

Hi,

Can anybody tell me about how to implement a principal axes registration use
ITK? I use itkCenteredVersorTransformInitializer.txx to initialize the
VersorRigid3DTransform,but this function didn't implement the rotation,so I
try to compute the angle of rotation from the fixedPrincipalAxes and the
movingPrincipalAxes, is there any way else to get the rotation matrix?
Another problem is does the rotation matrix only specify one axis of the
coordinate? I mean: in order to registrate two
coordinates(x,y,z;x',y',z'),we should implement the VersorRigid3DTransform 3
times?
Any help would be greatly appreciated!
Best regards,
Tina

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140805/03fac645/attachment.html>

From blowekamp at mail.nih.gov  Mon Aug  4 14:12:59 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 4 Aug 2014 14:12:59 -0400
Subject: [ITK-users] [Insight-users] Principal Axes pre-registration
In-Reply-To: <000001cfb00e$448ce9b0$cda6bd10$@126.com>
References: <000001cfb00e$448ce9b0$cda6bd10$@126.com>
Message-ID: <5F66F56B-AB5F-491D-91C4-E60A83770043@mail.nih.gov>

Hello,


I just wrapped this class for SimpleITK. I found it odd that by default the "ComputeRotation" parameter is set to off. With turing this parameter on I got good initialization for some anisotropic blobs. Did you turn this on?

Regarding you other question regarding the VersorTransfrom. The "versor" representation for rotation an represent an arbitrary rotation about the origin. So one is quite sufficient.

Brad



On Aug 4, 2014, at 2:02 PM, tina <fttfzzx227 at 126.com> wrote:

> Hi,
> Can anybody tell me about how to implement a principal axes registration use ITK? I use itkCenteredVersorTransformInitializer.txx to initialize the VersorRigid3DTransform,but this function didn?t implement the rotation,so I try to compute the angle of rotation from the fixedPrincipalAxes and the movingPrincipalAxes, is there any way else to get the rotation matrix?
> Another problem is does the rotation matrix only specify one axis of the coordinate? I mean: in order to registrate two coordinates(x,y,z;x?,y?,z?),we should implement the VersorRigid3DTransform 3 times?
> Any help would be greatly appreciated!
> Best regards,
> Tina
>  
> _____________________________________
> 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/20140804/da722a5c/attachment.html>

From ctrueden at wisc.edu  Mon Aug  4 15:35:38 2014
From: ctrueden at wisc.edu (Curtis Rueden)
Date: Mon, 4 Aug 2014 14:35:38 -0500
Subject: [ITK-users] Extensions to the MetaImage (MHDs) IO-plugin to
 support compression and MHAs
In-Reply-To: <CFFBF3B0.9E1B%norman-k-williams@uiowa.edu>
References: <27272_1406557413_s6SENUxH012254_53D65CD8.4080305@mh-hannover.de>
 <CFFBF3B0.9E1B%norman-k-williams@uiowa.edu>
Message-ID: <CADN69y=DcOC1AmBhFd9sT4nug6gprx7dx1KvvEmCPX=zTSb6Pw@mail.gmail.com>

Hi Roman,

> 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).

Interesting work. If you would like to get it upstream into Fiji, I suggest
filing a Pull Request [1] against the IO repository [2].

Please also be aware that ImageJ is moving away from HandleExtraFileTypes
hacks in favor of a unified Java library for image I/O known as SCIFIO [3].
There is already a SCIFIO/ITK bridge project [4, 5] that allows reading and
writing SCIFIO formats within ITK.

Regards,
Curtis

[1] https://help.github.com/articles/using-pull-requests
[2] https://github.com/fiji/IO
[3] http://imagej.net/SCIFIO
[4] https://github.com/scifio/scifio-imageio
[5] https://github.com/scifio/scifio-itk-bridge


On Mon, Jul 28, 2014 at 12:34 PM, Williams, Norman K <
norman-k-williams at uiowa.edu> wrote:

> 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.
> ________________________________
> _____________________________________
> 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/20140804/5e8214b4/attachment-0001.html>

From vincent.ngai at gmail.com  Tue Aug  5 05:26:31 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Tue, 5 Aug 2014 17:26:31 +0800
Subject: [ITK-users] AffineTransform to 4x4 matrix...again maybe
Message-ID: <CAC3nAP3BMLavy5OK=AT4N70_xM9ss67=--8XDXjsGvUKo=e1MQ@mail.gmail.com>

Hi all, apologies if this has been asked before, I googled the above but
only got 4x4 -> AffineTransform and not the other way around.

I need to get the output of an AffineTransform after registration to my
OpenGL renderer.

>From what I understand, the AffineTransform is composed of a Rotation,
Center of Rotation and Translation.

So would the following sequence of 4x4 transformation be correct?

OGLM = InvCRM * Rot * CRM * TM

where

CRM      = 4x4 identity matrix with indices [ 12, 13, 14] set to XYZ value
of GetCenter()
InvCRM  = Inverse of CRM
Rot        = 4x4 Identity matrix with 3x3 set to the rotation parameters
TM        = 4x4 identity matrix with indicies[ 12, 13, 14 ] set to the
translation parameters

Essentially:

1) translate center to origin
2) perform rotation
3) translate back to where we were
4) slap on translation

I am doing the above, but for some reason the translation does not match
up. The rotation seems fine.
-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140805/88d59bd1/attachment.html>

From DotanG at azimutherapy.com  Tue Aug  5 06:50:10 2014
From: DotanG at azimutherapy.com (Dotan Goberman)
Date: Tue, 5 Aug 2014 12:50:10 +0200
Subject: [ITK-users] ContourExtractor2DImageFilter
Message-ID: <E2E78362585A1F4CA9120D49288A098002F6FB71@rnd1.direxdom.local>

Hello itk users.
I saw the ContourExtractor2DImageFilter in the itkreview module, is
there another filter that get as input Image and  extract the isocontour
as Polyline?
Thanx in advance.
Dotan 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140805/2e9e2148/attachment.html>

From blowekamp at mail.nih.gov  Tue Aug  5 09:12:25 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 5 Aug 2014 09:12:25 -0400
Subject: [ITK-users] AffineTransform to 4x4 matrix...again maybe
In-Reply-To: <CAC3nAP3BMLavy5OK=AT4N70_xM9ss67=--8XDXjsGvUKo=e1MQ@mail.gmail.com>
References: <CAC3nAP3BMLavy5OK=AT4N70_xM9ss67=--8XDXjsGvUKo=e1MQ@mail.gmail.com>
Message-ID: <4D7F2AA9-48DF-4C78-BC5E-B8609CBF45E0@mail.nih.gov>

Hello,

That looks pretty close, but I think CRM[12,13,14] should be -GetCenter(), with the negative there.  Then the TM should be applied last, using your original notation with the previously mentioned correction I'd expect this to be correct:

OGLM = TM * InvCRM * Rot * CRM

Hope that helps,
Brad

[1] http://www.itk.org/Doxygen/html/classitk_1_1MatrixOffsetTransformBase.html

On Aug 5, 2014, at 5:26 AM, vincent ngai <vincent.ngai at gmail.com> wrote:

> Hi all, apologies if this has been asked before, I googled the above but only got 4x4 -> AffineTransform and not the other way around.
> 
> I need to get the output of an AffineTransform after registration to my OpenGL renderer. 
> 
> From what I understand, the AffineTransform is composed of a Rotation, Center of Rotation and Translation.
> 
> So would the following sequence of 4x4 transformation be correct?
> 
> OGLM = InvCRM * Rot * CRM * TM
> 
> where
> 
> CRM      = 4x4 identity matrix with indices [ 12, 13, 14] set to XYZ value of GetCenter()
> InvCRM  = Inverse of CRM
> Rot        = 4x4 Identity matrix with 3x3 set to the rotation parameters
> TM        = 4x4 identity matrix with indicies[ 12, 13, 14 ] set to the translation parameters
> 
> Essentially:
>  
> 1) translate center to origin
> 2) perform rotation
> 3) translate back to where we were
> 4) slap on translation
> 
> I am doing the above, but for some reason the translation does not match up. The rotation seems fine.
> -- 
> 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


From mercikd at thomas.edu  Tue Aug  5 14:34:06 2014
From: mercikd at thomas.edu (Dan Mercik)
Date: Tue, 5 Aug 2014 18:34:06 +0000
Subject: [ITK-users] MultiThreader?
Message-ID: <2ceb68bacb674825b2ca5e795c48800c@T9.tcnet.thomas.edu>

Hey,

        After running my code I caught an exception trying to write deconstructing output. The error occurred

 during single method execute. I also got an error That the DownSampleImageFilter subclass should override this method. I took a snippet of error output I received which is located attached to this email. Do you have any idea on how to solve this issue?

Daniel Mercik

Computer Science Major

Service Desk Technician

Thomas College
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Multithreader.JPG
Type: image/jpeg
Size: 56571 bytes
Desc: Multithreader.JPG
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140805/6de943b8/attachment.jpe>

From matt.mccormick at kitware.com  Tue Aug  5 15:04:45 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 5 Aug 2014 15:04:45 -0400
Subject: [ITK-users] [ITK]  MultiThreader?
In-Reply-To: <2ceb68bacb674825b2ca5e795c48800c@T9.tcnet.thomas.edu>
References: <2ceb68bacb674825b2ca5e795c48800c@T9.tcnet.thomas.edu>
Message-ID: <CALzTN-TY6QC3EgYvyF7TXHA-H2ORrpUcARBDP=Drw_=37ALT+g@mail.gmail.com>

Hi Dan,

Does your DownSampleImageFilter have a ThreadedGenerateData method?
If so, its method may need to be updated to use "ThreadIdType" as
indicated in the error message.

Hope this helps,
Matt

On Tue, Aug 5, 2014 at 2:34 PM, Dan Mercik <mercikd at thomas.edu> wrote:
> Hey,
>
>         After running my code I caught an exception trying to write deconstructing output. The error occurred
>
>  during single method execute. I also got an error That the DownSampleImageFilter subclass should override this method. I took a snippet of error output I received which is located attached to this email. Do you have any idea on how to solve this issue?
>
> Daniel Mercik
>
> Computer Science Major
>
> Service Desk Technician
>
> Thomas College
>
> _____________________________________
> 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 vincent.ngai at gmail.com  Tue Aug  5 22:08:13 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Wed, 6 Aug 2014 10:08:13 +0800
Subject: [ITK-users] AffineTransform to 4x4 matrix...again maybe
In-Reply-To: <4D7F2AA9-48DF-4C78-BC5E-B8609CBF45E0@mail.nih.gov>
References: <CAC3nAP3BMLavy5OK=AT4N70_xM9ss67=--8XDXjsGvUKo=e1MQ@mail.gmail.com>
 <4D7F2AA9-48DF-4C78-BC5E-B8609CBF45E0@mail.nih.gov>
Message-ID: <CAC3nAP35L3LbbtaA4KTQgeGOqrgPk4aETu9HZxhzje6wpdNBJA@mail.gmail.com>

Hi Bradley,

Hmm, GetCenter() negated should be the same as InvCRM. I'll flip the order
of the multiplication and see what happens, it could be the C++ operator*()
order being different from the way its written. Its so annoying to get the
results close but not exact :(

Thanks


On Tue, Aug 5, 2014 at 9:12 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> That looks pretty close, but I think CRM[12,13,14] should be -GetCenter(),
> with the negative there.  Then the TM should be applied last, using your
> original notation with the previously mentioned correction I'd expect this
> to be correct:
>
> OGLM = TM * InvCRM * Rot * CRM
>
> Hope that helps,
> Brad
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1MatrixOffsetTransformBase.html
>
> On Aug 5, 2014, at 5:26 AM, vincent ngai <vincent.ngai at gmail.com> wrote:
>
> > Hi all, apologies if this has been asked before, I googled the above but
> only got 4x4 -> AffineTransform and not the other way around.
> >
> > I need to get the output of an AffineTransform after registration to my
> OpenGL renderer.
> >
> > From what I understand, the AffineTransform is composed of a Rotation,
> Center of Rotation and Translation.
> >
> > So would the following sequence of 4x4 transformation be correct?
> >
> > OGLM = InvCRM * Rot * CRM * TM
> >
> > where
> >
> > CRM      = 4x4 identity matrix with indices [ 12, 13, 14] set to XYZ
> value of GetCenter()
> > InvCRM  = Inverse of CRM
> > Rot        = 4x4 Identity matrix with 3x3 set to the rotation parameters
> > TM        = 4x4 identity matrix with indicies[ 12, 13, 14 ] set to the
> translation parameters
> >
> > Essentially:
> >
> > 1) translate center to origin
> > 2) perform rotation
> > 3) translate back to where we were
> > 4) slap on translation
> >
> > I am doing the above, but for some reason the translation does not match
> up. The rotation seems fine.
> > --
> > 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
>
>


-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140806/c05a9ae2/attachment-0001.html>

From matt.mccormick at kitware.com  Wed Aug  6 00:10:56 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 6 Aug 2014 00:10:56 -0400
Subject: [ITK-users] [ITK]  AffineTransform to 4x4 matrix...again maybe
In-Reply-To: <CAC3nAP35L3LbbtaA4KTQgeGOqrgPk4aETu9HZxhzje6wpdNBJA@mail.gmail.com>
References: <CAC3nAP3BMLavy5OK=AT4N70_xM9ss67=--8XDXjsGvUKo=e1MQ@mail.gmail.com>
 <4D7F2AA9-48DF-4C78-BC5E-B8609CBF45E0@mail.nih.gov>
 <CAC3nAP35L3LbbtaA4KTQgeGOqrgPk4aETu9HZxhzje6wpdNBJA@mail.gmail.com>
Message-ID: <CALzTN-QhQFi6RsAGQuHy_=-4T45tcPWfCA74gPy8s+F++v8iAQ@mail.gmail.com>

Hi Vincent,

The values can also be used directly in the matrix as demonstrated here [1].

HTH,
Matt

[1] https://gist.github.com/thewtex/8712205

On Tue, Aug 5, 2014 at 10:08 PM, vincent ngai <vincent.ngai at gmail.com> wrote:
> Hi Bradley,
>
> Hmm, GetCenter() negated should be the same as InvCRM. I'll flip the order
> of the multiplication and see what happens, it could be the C++ operator*()
> order being different from the way its written. Its so annoying to get the
> results close but not exact :(
>
> Thanks
>
>
> On Tue, Aug 5, 2014 at 9:12 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>>
>> Hello,
>>
>> That looks pretty close, but I think CRM[12,13,14] should be -GetCenter(),
>> with the negative there.  Then the TM should be applied last, using your
>> original notation with the previously mentioned correction I'd expect this
>> to be correct:
>>
>> OGLM = TM * InvCRM * Rot * CRM
>>
>> Hope that helps,
>> Brad
>>
>> [1]
>> http://www.itk.org/Doxygen/html/classitk_1_1MatrixOffsetTransformBase.html
>>
>> On Aug 5, 2014, at 5:26 AM, vincent ngai <vincent.ngai at gmail.com> wrote:
>>
>> > Hi all, apologies if this has been asked before, I googled the above but
>> > only got 4x4 -> AffineTransform and not the other way around.
>> >
>> > I need to get the output of an AffineTransform after registration to my
>> > OpenGL renderer.
>> >
>> > From what I understand, the AffineTransform is composed of a Rotation,
>> > Center of Rotation and Translation.
>> >
>> > So would the following sequence of 4x4 transformation be correct?
>> >
>> > OGLM = InvCRM * Rot * CRM * TM
>> >
>> > where
>> >
>> > CRM      = 4x4 identity matrix with indices [ 12, 13, 14] set to XYZ
>> > value of GetCenter()
>> > InvCRM  = Inverse of CRM
>> > Rot        = 4x4 Identity matrix with 3x3 set to the rotation parameters
>> > TM        = 4x4 identity matrix with indicies[ 12, 13, 14 ] set to the
>> > translation parameters
>> >
>> > Essentially:
>> >
>> > 1) translate center to origin
>> > 2) perform rotation
>> > 3) translate back to where we were
>> > 4) slap on translation
>> >
>> > I am doing the above, but for some reason the translation does not match
>> > up. The rotation seems fine.
>> > --
>> > 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
>>
>
>
>
> --
> 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
>

From vincent.ngai at gmail.com  Wed Aug  6 02:51:28 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Wed, 6 Aug 2014 14:51:28 +0800
Subject: [ITK-users] [ITK]  AffineTransform to 4x4 matrix...again maybe
In-Reply-To: <CALzTN-QhQFi6RsAGQuHy_=-4T45tcPWfCA74gPy8s+F++v8iAQ@mail.gmail.com>
References: <CAC3nAP3BMLavy5OK=AT4N70_xM9ss67=--8XDXjsGvUKo=e1MQ@mail.gmail.com>
 <4D7F2AA9-48DF-4C78-BC5E-B8609CBF45E0@mail.nih.gov>
 <CAC3nAP35L3LbbtaA4KTQgeGOqrgPk4aETu9HZxhzje6wpdNBJA@mail.gmail.com>
 <CALzTN-QhQFi6RsAGQuHy_=-4T45tcPWfCA74gPy8s+F++v8iAQ@mail.gmail.com>
Message-ID: <CAC3nAP2c5wqyRhyHntasUHQ_y3dLQa1tTvVhXeq06ykB+mVJQQ@mail.gmail.com>

Thanks Matt for the link.


On Wed, Aug 6, 2014 at 12:10 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Vincent,
>
> The values can also be used directly in the matrix as demonstrated here
> [1].
>
> HTH,
> Matt
>
> [1] https://gist.github.com/thewtex/8712205
>
> On Tue, Aug 5, 2014 at 10:08 PM, vincent ngai <vincent.ngai at gmail.com>
> wrote:
> > Hi Bradley,
> >
> > Hmm, GetCenter() negated should be the same as InvCRM. I'll flip the
> order
> > of the multiplication and see what happens, it could be the C++
> operator*()
> > order being different from the way its written. Its so annoying to get
> the
> > results close but not exact :(
> >
> > Thanks
> >
> >
> > On Tue, Aug 5, 2014 at 9:12 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
> >
> > wrote:
> >>
> >> Hello,
> >>
> >> That looks pretty close, but I think CRM[12,13,14] should be
> -GetCenter(),
> >> with the negative there.  Then the TM should be applied last, using your
> >> original notation with the previously mentioned correction I'd expect
> this
> >> to be correct:
> >>
> >> OGLM = TM * InvCRM * Rot * CRM
> >>
> >> Hope that helps,
> >> Brad
> >>
> >> [1]
> >>
> http://www.itk.org/Doxygen/html/classitk_1_1MatrixOffsetTransformBase.html
> >>
> >> On Aug 5, 2014, at 5:26 AM, vincent ngai <vincent.ngai at gmail.com>
> wrote:
> >>
> >> > Hi all, apologies if this has been asked before, I googled the above
> but
> >> > only got 4x4 -> AffineTransform and not the other way around.
> >> >
> >> > I need to get the output of an AffineTransform after registration to
> my
> >> > OpenGL renderer.
> >> >
> >> > From what I understand, the AffineTransform is composed of a Rotation,
> >> > Center of Rotation and Translation.
> >> >
> >> > So would the following sequence of 4x4 transformation be correct?
> >> >
> >> > OGLM = InvCRM * Rot * CRM * TM
> >> >
> >> > where
> >> >
> >> > CRM      = 4x4 identity matrix with indices [ 12, 13, 14] set to XYZ
> >> > value of GetCenter()
> >> > InvCRM  = Inverse of CRM
> >> > Rot        = 4x4 Identity matrix with 3x3 set to the rotation
> parameters
> >> > TM        = 4x4 identity matrix with indicies[ 12, 13, 14 ] set to the
> >> > translation parameters
> >> >
> >> > Essentially:
> >> >
> >> > 1) translate center to origin
> >> > 2) perform rotation
> >> > 3) translate back to where we were
> >> > 4) slap on translation
> >> >
> >> > I am doing the above, but for some reason the translation does not
> match
> >> > up. The rotation seems fine.
> >> > --
> >> > 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
> >>
> >
> >
> >
> > --
> > 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
> >
>



-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140806/da588d97/attachment.html>

From mallikarjun49 at gmail.com  Wed Aug  6 04:42:35 2014
From: mallikarjun49 at gmail.com (Mallikarjun K)
Date: Wed, 6 Aug 2014 14:12:35 +0530
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
Message-ID: <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>

Hi All,

Can anyone suggest me if anything wrong I am doing in this below pipeline
,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk
QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in
release mode) at itkVtkPolydataReader .


////

typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
qetraits;

typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;

itk::OnesMatrixCoefficients< MeshType > coeff0;

typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
//typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;

//VTKPolyDataWriterType::Pointer
ItkToVtkWriter=VTKPolyDataWriterType::New();
VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();

VtkToItkReader->SetFileName("abc.vtk");
VtkToItkReader->Update();

typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
SmoothingQuadEdgeMeshFilter;

 SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
SmoothingQuadEdgeMeshFilter::New();

QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
QEMeshSmoother->SetNumberOfIterations(5 );
QEMeshSmoother->SetRelaxationFactor( 0.5 );
QEMeshSmoother->SetDelaunayConforming(true );
QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
QEMeshSmoother->Update();

////


On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com>
wrote:

> Thanks Bill for your answer.
>
> The reason I am using this pipeline is that SmoothingQEMeshFilter has an
> additional parameter for smoothing which is delaunay conforming which helps
> to optimize aspect ratio of triangles while smoothing and thus produces
> better output.Is there anything similar filter in the vtk pipeline.I used
> vtkWindowedSincPolydatafilter which is not giving the output as good as
> QEMeshSmoothing filter.
>
> Thanks for your help
>
>
> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>
>> 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
>>
>
>
>
> --
> *Regards:*
> Mallik
>
>


-- 
*Regards:*
Mallik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140806/c6bf7811/attachment.html>

From joseignacio.prieto at gmail.com  Wed Aug  6 10:11:38 2014
From: joseignacio.prieto at gmail.com (Jose Ignacio Prieto)
Date: Wed, 6 Aug 2014 10:11:38 -0400
Subject: [ITK-users] Distance map to 2D polygon
Message-ID: <CANkppu4+469-TvFhG2g3FZh9DxvF+gYKh5veSS48hD9swTq5xQ@mail.gmail.com>

Hi all,
I need to get a distance (preferably signed) map 2D given a polygon input
as polygonSpatialObject. I think it can be done by using
SpatialObjectToImageFilter and then applying a distance map, but I was
thinking that maybe it is not the optimal way to do it. It is more
important that the result is fast rather than accurate.

Thank you very much for any input.

--
Ignacio Prieto
Research Assistant
Biomedical Imaging Center
Pontificia Universidad Catolica de Chile
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140806/5f9ce2d0/attachment.html>

From arnaudgelas at gmail.com  Thu Aug  7 04:52:53 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 7 Aug 2014 10:52:53 +0200
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
Message-ID: <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>

Hi Malik,

First of all, I would recommend using MeshFileReader instead of VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near future?).

Regarding now the smoothing procedure in itself. This class definitively misses some documentation and I will be adding some in the next few days (mainly extracted from the corresponding insight journal).

At the end of each iteration, when the delaunay conforming flag is turned ON, the conformation is performed. So depending on the mesh configuration, mesh size and number of iterations, it can take ages?
How large is your input mesh (number of points)?

You can also check results, by running first a smoothing without delaunay conforming, then apply a delaunay conforming on the output. Results won't be as nice, but you should get significant speed improvement.
Another possibility is to first do a clean poly data in vtk, with a small threshold to remove small edges in the input meshes (which results in lots of edge flipping after smoothing).

HTH
Arnaud


On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:

> Hi All,
> 
> Can anyone suggest me if anything wrong I am doing in this below pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in release mode) at itkVtkPolydataReader .
> 
> 
> ////
> 
> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;
> 	
> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
> 
> itk::OnesMatrixCoefficients< MeshType > coeff0;
> 
> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
> 
> //VTKPolyDataWriterType::Pointer ItkToVtkWriter=VTKPolyDataWriterType::New();
> VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();
> 
> VtkToItkReader->SetFileName("abc.vtk");
> VtkToItkReader->Update();	
> 
> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
> SmoothingQuadEdgeMeshFilter;
> 
>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =   SmoothingQuadEdgeMeshFilter::New();
> 	
> 
> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
> QEMeshSmoother->SetNumberOfIterations(5 );
> QEMeshSmoother->SetRelaxationFactor( 0.5 );
> QEMeshSmoother->SetDelaunayConforming(true );
> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );	
> 	
> QEMeshSmoother->Update();
> 
> ////
> 
> 
> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> Thanks Bill for your answer.
> 
> The reason I am using this pipeline is that SmoothingQEMeshFilter has an additional parameter for smoothing which is delaunay conforming which helps to optimize aspect ratio of triangles while smoothing and thus produces better output.Is there anything similar filter in the vtk pipeline.I used vtkWindowedSincPolydatafilter which is not giving the output as good as QEMeshSmoothing filter.
> 
> Thanks for your help 
> 
> 
> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> 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
> 
> 
> 
> -- 
> Regards:
> Mallik
> 
> 
> 
> 
> -- 
> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140807/1f21c8dd/attachment.html>

From mallikarjun49 at gmail.com  Thu Aug  7 06:09:50 2014
From: mallikarjun49 at gmail.com (Mallikarjun K)
Date: Thu, 7 Aug 2014 15:39:50 +0530
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
Message-ID: <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>

Hi Arnaud,

Thanks for your reply and valuable suggestions.

Number of points in my input mesh are 78928.In my pipeline I am already
cleaning the polydata using vtkCleanPolyData filter.I will check the speed
improvement and results with delaunay conforming turned OFF.

Thank you


On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi Malik,
>
> First of all, I would recommend using MeshFileReader instead of
> VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near
> future?).
>
> Regarding now the smoothing procedure in itself. This class definitively
> misses some documentation and I will be adding some in the next few days
> (mainly extracted from the corresponding insight journal).
>
> At the end of each iteration, when the delaunay conforming flag is turned
> ON, the conformation is performed. So depending on the mesh configuration,
> mesh size and number of iterations, it can take ages?
> How large is your input mesh (number of points)?
>
> You can also check results, by running first a smoothing without delaunay
> conforming, then apply a delaunay conforming on the output. Results won't
> be as nice, but you should get significant speed improvement.
> Another possibility is to first do a clean poly data in vtk, with a small
> threshold to remove small edges in the input meshes (which results in lots
> of edge flipping after smoothing).
>
> HTH
> Arnaud
>
>
> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com>
> wrote:
>
> Hi All,
>
> Can anyone suggest me if anything wrong I am doing in this below pipeline
> ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk
> QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in
> release mode) at itkVtkPolydataReader .
>
>
> ////
>
> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
> qetraits;
>
> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>
> itk::OnesMatrixCoefficients< MeshType > coeff0;
>
> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>
> //VTKPolyDataWriterType::Pointer
> ItkToVtkWriter=VTKPolyDataWriterType::New();
> VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();
>
> VtkToItkReader->SetFileName("abc.vtk");
> VtkToItkReader->Update();
>
> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
> SmoothingQuadEdgeMeshFilter;
>
>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
> SmoothingQuadEdgeMeshFilter::New();
>
> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
> QEMeshSmoother->SetNumberOfIterations(5 );
> QEMeshSmoother->SetRelaxationFactor( 0.5 );
> QEMeshSmoother->SetDelaunayConforming(true );
> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>  QEMeshSmoother->Update();
>
> ////
>
>
> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com>
> wrote:
>
>> Thanks Bill for your answer.
>>
>> The reason I am using this pipeline is that SmoothingQEMeshFilter has an
>> additional parameter for smoothing which is delaunay conforming which helps
>> to optimize aspect ratio of triangles while smoothing and thus produces
>> better output.Is there anything similar filter in the vtk pipeline.I used
>> vtkWindowedSincPolydatafilter which is not giving the output as good as
>> QEMeshSmoothing filter.
>>
>> Thanks for your help
>>
>>
>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>>
>>> 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
>>>
>>
>>
>>
>> --
>> *Regards:*
>> Mallik
>>
>>
>
>
> --
> *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
>
>
>


-- 
*Regards:*
Mallik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140807/6be9f679/attachment.html>

From mallikarjun49 at gmail.com  Thu Aug  7 09:23:15 2014
From: mallikarjun49 at gmail.com (Mallikarjun K)
Date: Thu, 7 Aug 2014 18:53:15 +0530
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
 <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
Message-ID: <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>

Hi Arnaud,

Kindly have a look in the below code ,the problem  is that even after
QEMeshFilter output is saved as .stl file ,the program is still running for
long time.I have observed in my tests that MeshFileReader seems to be the
culprit. Any suggestions ?

/////
#include<iostream>
#include<string>

#include <vtkPolyDataWriter.h>
#include <vtkPolyDataReader.h>
#include <itkMeshFileWriter.h>
#include <itkMeshFileReader.h>
#include <itkMeshIOFactory.h>
#include <itkMeshIOBase.h>
#include <vtkTriangleFilter.h>
#include <vtkCleanPolyData.h>
#include "itkMesh.h"
#include "itkQuadEdgeMesh.h"
#include "itkQuadEdgeMeshTraits.h"
#include "itkSmoothingQuadEdgeMeshFilter.h"
#include "vtkSTLWriter.h"
#include <vtkSmartPointer.h>

int main()
{
std::string Inputfilename="D:/temp.vtk";   //number of points of this mesh
file is around 78K

typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
qetraits;
typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
 itk::OnesMatrixCoefficients< MeshType > coeff0;
typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType
>SmoothingQuadEdgeMeshFilter;

vtkSmartPointer<vtkPolyDataWriter>
polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
vtkSmartPointer<vtkPolyDataReader>
polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();

    SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
SmoothingQuadEdgeMeshFilter::New();
   /* polyDatareader->SetFileName(Inputfilename.c_str() );
polyDatareader->ReleaseDataFlagOn();
polyDatareader->Update();*/

/*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
    vtkSmartPointer<vtkTriangleFilter>::New();
    triangleFilter->SetInput(polyDatareader->GetOutput());
    triangleFilter->Update();*/

//
/* vtkSmartPointer<vtkCleanPolyData> clean =
vtkSmartPointer<vtkCleanPolyData>::New();
#if (VTK_MAJOR_VERSION < 6)
 clean->SetInput(triangleFilter->GetOutput() );
#else
       clean->SetInputData(triangleFilter->GetOutput() );
#endif
    clean->ConvertPolysToLinesOff();
    clean->ConvertLinesToPointsOff();
    clean->Update();

std::string Inputfilename2="D:/cleaned.vtk";*/

////
/*polyDatawriter->SetInput(clean->GetOutput());
polyDatawriter->SetFileName(Inputfilename2.c_str());
polyDatawriter->ReleaseDataFlagOn();
polyDatawriter->Write(); */

typedef itk::MeshFileReader<MeshType> MeshReaderType;
MeshReaderType::Pointer Meshreader = MeshReaderType::New();
       Meshreader->SetFileName(Inputfilename.c_str( ));
Meshreader->Update();

/*MeshType::Pointer mesh =  Meshreader->GetOutput();
         mesh->DisconnectPipeline();*/

QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
QEMeshSmoother->SetNumberOfIterations(1 );
QEMeshSmoother->SetRelaxationFactor( 0.5 );
QEMeshSmoother->SetDelaunayConforming(true);
QEMeshSmoother->SetCoefficientsMethod( &coeff0 );

QEMeshSmoother->ReleaseDataFlagOn();

QEMeshSmoother->Update();

std::string Outputfilename="D:/tempOut.vtk";

typedef itk::MeshFileWriter<MeshType> MeshWriterType;
MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
       Meshwriter->SetFileName(Outputfilename.c_str( ));
Meshwriter->SetInput(QEMeshSmoother->GetOutput());
       Meshwriter->Update();

polyDatareader->SetFileName(Outputfilename.c_str() );
polyDatareader->ReleaseDataFlagOn();
polyDatareader->Update();

vtkSmartPointer<vtkSTLWriter>
stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
 stlWriter->SetInput( polyDatareader->GetOutput());
stlWriter->SetFileName("D:/QEoutput.stl");
stlWriter->SetFileTypeToASCII();
stlWriter->Write();
 //Here it stops and taking long time

return 0;

}
////



On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com>
wrote:

> Hi Arnaud,
>
> Thanks for your reply and valuable suggestions.
>
> Number of points in my input mesh are 78928.In my pipeline I am already
> cleaning the polydata using vtkCleanPolyData filter.I will check the speed
> improvement and results with delaunay conforming turned OFF.
>
> Thank you
>
>
> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
>
>> Hi Malik,
>>
>> First of all, I would recommend using MeshFileReader instead of
>> VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near
>> future?).
>>
>> Regarding now the smoothing procedure in itself. This class definitively
>> misses some documentation and I will be adding some in the next few days
>> (mainly extracted from the corresponding insight journal).
>>
>> At the end of each iteration, when the delaunay conforming flag is turned
>> ON, the conformation is performed. So depending on the mesh configuration,
>> mesh size and number of iterations, it can take ages?
>> How large is your input mesh (number of points)?
>>
>> You can also check results, by running first a smoothing without delaunay
>> conforming, then apply a delaunay conforming on the output. Results won't
>> be as nice, but you should get significant speed improvement.
>> Another possibility is to first do a clean poly data in vtk, with a small
>> threshold to remove small edges in the input meshes (which results in lots
>> of edge flipping after smoothing).
>>
>> HTH
>> Arnaud
>>
>>
>> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>>
>> Hi All,
>>
>> Can anyone suggest me if anything wrong I am doing in this below pipeline
>> ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk
>> QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in
>> release mode) at itkVtkPolydataReader .
>>
>>
>> ////
>>
>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
>> qetraits;
>>
>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>
>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>>
>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>>
>> //VTKPolyDataWriterType::Pointer
>> ItkToVtkWriter=VTKPolyDataWriterType::New();
>> VTKPolyDataReaderType::Pointer
>> VtkToItkReader=VTKPolyDataReaderType::New();
>>
>> VtkToItkReader->SetFileName("abc.vtk");
>> VtkToItkReader->Update();
>>
>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>> SmoothingQuadEdgeMeshFilter;
>>
>>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
>> SmoothingQuadEdgeMeshFilter::New();
>>
>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>> QEMeshSmoother->SetNumberOfIterations(5 );
>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>> QEMeshSmoother->SetDelaunayConforming(true );
>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>  QEMeshSmoother->Update();
>>
>> ////
>>
>>
>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>>
>>> Thanks Bill for your answer.
>>>
>>> The reason I am using this pipeline is that SmoothingQEMeshFilter has an
>>> additional parameter for smoothing which is delaunay conforming which helps
>>> to optimize aspect ratio of triangles while smoothing and thus produces
>>> better output.Is there anything similar filter in the vtk pipeline.I used
>>> vtkWindowedSincPolydatafilter which is not giving the output as good as
>>> QEMeshSmoothing filter.
>>>
>>> Thanks for your help
>>>
>>>
>>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com>
>>> wrote:
>>>
>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> *Regards:*
>>> Mallik
>>>
>>>
>>
>>
>> --
>> *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
>>
>>
>>
>
>
> --
> *Regards:*
> Mallik
>
>


-- 
*Regards:*
Mallik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140807/4fff8dae/attachment-0001.html>

From arnaudgelas at gmail.com  Thu Aug  7 09:31:03 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 7 Aug 2014 15:31:03 +0200
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
 <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
 <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>
Message-ID: <305E1509-8EF7-4770-9236-3D639B9BF155@gmail.com>

Shouldn't it be D://temp.vtk ? Isn't it missing one '/' ?

Can you send this vtk file?

On Aug 7, 2014, at 3:23 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:

> Hi Arnaud,
> 
> Kindly have a look in the below code ,the problem  is that even after QEMeshFilter output is saved as .stl file ,the program is still running for long time.I have observed in my tests that MeshFileReader seems to be the culprit. Any suggestions ?
> 
> /////
> #include<iostream>
> #include<string>
> 
> #include <vtkPolyDataWriter.h>
> #include <vtkPolyDataReader.h>
> #include <itkMeshFileWriter.h>
> #include <itkMeshFileReader.h>
> #include <itkMeshIOFactory.h>
> #include <itkMeshIOBase.h>
> #include <vtkTriangleFilter.h>
> #include <vtkCleanPolyData.h>
> #include "itkMesh.h"
> #include "itkQuadEdgeMesh.h"
> #include "itkQuadEdgeMeshTraits.h"
> #include "itkSmoothingQuadEdgeMeshFilter.h"
> #include "vtkSTLWriter.h"
> #include <vtkSmartPointer.h>
> 
> int main()
> {
> 	std::string Inputfilename="D:/temp.vtk";   //number of points of this mesh file is around 78K
> 
> 	typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;	
> 	typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
> 	
> 	itk::OnesMatrixCoefficients< MeshType > coeff0;
> 	typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >SmoothingQuadEdgeMeshFilter;
>     
> 	vtkSmartPointer<vtkPolyDataWriter> polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
> 	vtkSmartPointer<vtkPolyDataReader> polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();
>    
>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother = SmoothingQuadEdgeMeshFilter::New();
> 	
>    /* polyDatareader->SetFileName(Inputfilename.c_str() );
> 	polyDatareader->ReleaseDataFlagOn();
> 	polyDatareader->Update();*/
> 
> 	/*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
>     vtkSmartPointer<vtkTriangleFilter>::New();
>     triangleFilter->SetInput(polyDatareader->GetOutput());
>     triangleFilter->Update();*/
>   
> 	//
> 	/* vtkSmartPointer<vtkCleanPolyData> clean = vtkSmartPointer<vtkCleanPolyData>::New();
> 	#if (VTK_MAJOR_VERSION < 6)
> 	 clean->SetInput(triangleFilter->GetOutput() );
> 	#else
>        clean->SetInputData(triangleFilter->GetOutput() );
> 	#endif
> 	
>     clean->ConvertPolysToLinesOff();
>     clean->ConvertLinesToPointsOff();
>     clean->Update();
> 
> 	std::string Inputfilename2="D:/cleaned.vtk";*/
> 
> 	////
> 	/*polyDatawriter->SetInput(clean->GetOutput());	
> 	polyDatawriter->SetFileName(Inputfilename2.c_str());
> 	polyDatawriter->ReleaseDataFlagOn();
> 	polyDatawriter->Write(); */ 
>   
> 	typedef itk::MeshFileReader<MeshType> MeshReaderType;
> 	MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>        Meshreader->SetFileName(Inputfilename.c_str( ));
> 	Meshreader->Update();
> 
> 	/*MeshType::Pointer mesh =  Meshreader->GetOutput();
>          mesh->DisconnectPipeline();*/
> 	
> 
> 	QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
> 	QEMeshSmoother->SetNumberOfIterations(1 );
> 	QEMeshSmoother->SetRelaxationFactor( 0.5 );
> 	QEMeshSmoother->SetDelaunayConforming(true);
> 	QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
> 
> 	QEMeshSmoother->ReleaseDataFlagOn();
> 
> 	QEMeshSmoother->Update();	
>     
> 	std::string Outputfilename="D:/tempOut.vtk";
> 
> 	typedef itk::MeshFileWriter<MeshType> MeshWriterType;
> 	MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>        Meshwriter->SetFileName(Outputfilename.c_str( ));
> 	Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>        Meshwriter->Update();	
> 
> 	polyDatareader->SetFileName(Outputfilename.c_str() );
> 	polyDatareader->ReleaseDataFlagOn();
> 	polyDatareader->Update();
> 
> 	vtkSmartPointer<vtkSTLWriter> stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
> 	
> 	stlWriter->SetInput( polyDatareader->GetOutput());
> 	stlWriter->SetFileName("D:/QEoutput.stl");
> 	stlWriter->SetFileTypeToASCII();
> 	stlWriter->Write();
> 	
> 	//Here it stops and taking long time 
> 
> 	return 0;
> 
> 	
> }
> ////
> 
> 
> 
> On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> Hi Arnaud,
> 
> Thanks for your reply and valuable suggestions.
> 
> Number of points in my input mesh are 78928.In my pipeline I am already cleaning the polydata using vtkCleanPolyData filter.I will check the speed improvement and results with delaunay conforming turned OFF.
> 
> Thank you
> 
> 
> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Hi Malik,
> 
> First of all, I would recommend using MeshFileReader instead of VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near future?).
> 
> Regarding now the smoothing procedure in itself. This class definitively misses some documentation and I will be adding some in the next few days (mainly extracted from the corresponding insight journal).
> 
> At the end of each iteration, when the delaunay conforming flag is turned ON, the conformation is performed. So depending on the mesh configuration, mesh size and number of iterations, it can take ages?
> How large is your input mesh (number of points)?
> 
> You can also check results, by running first a smoothing without delaunay conforming, then apply a delaunay conforming on the output. Results won't be as nice, but you should get significant speed improvement.
> Another possibility is to first do a clean poly data in vtk, with a small threshold to remove small edges in the input meshes (which results in lots of edge flipping after smoothing).
> 
> HTH
> Arnaud
> 
> 
> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> 
>> Hi All,
>> 
>> Can anyone suggest me if anything wrong I am doing in this below pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in release mode) at itkVtkPolydataReader .
>> 
>> 
>> ////
>> 
>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;
>> 	
>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>> 
>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>> 
>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>> 
>> //VTKPolyDataWriterType::Pointer ItkToVtkWriter=VTKPolyDataWriterType::New();
>> VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();
>> 
>> VtkToItkReader->SetFileName("abc.vtk");
>> VtkToItkReader->Update();	
>> 
>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>> SmoothingQuadEdgeMeshFilter;
>> 
>>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =   SmoothingQuadEdgeMeshFilter::New();
>> 	
>> 
>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>> QEMeshSmoother->SetNumberOfIterations(5 );
>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>> QEMeshSmoother->SetDelaunayConforming(true );
>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );	
>> 	
>> QEMeshSmoother->Update();
>> 
>> ////
>> 
>> 
>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>> Thanks Bill for your answer.
>> 
>> The reason I am using this pipeline is that SmoothingQEMeshFilter has an additional parameter for smoothing which is delaunay conforming which helps to optimize aspect ratio of triangles while smoothing and thus produces better output.Is there anything similar filter in the vtk pipeline.I used vtkWindowedSincPolydatafilter which is not giving the output as good as QEMeshSmoothing filter.
>> 
>> Thanks for your help 
>> 
>> 
>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> 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
>> 
>> 
>> 
>> -- 
>> Regards:
>> Mallik
>> 
>> 
>> 
>> 
>> -- 
>> 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
> 
> 
> 
> 
> -- 
> Regards:
> Mallik
> 
> 
> 
> 
> -- 
> Regards:
> Mallik
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140807/2c34f56a/attachment.html>

From arnaudgelas at gmail.com  Thu Aug  7 10:40:20 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 7 Aug 2014 16:40:20 +0200
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6xG6tUTOnkbD3ekPQZ5Pdj-hLWS9r7QGbSNjWxCg5HzJg@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
 <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
 <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>
 <305E1509-8EF7-4770-9236-3D639B9BF155@gmail.com>
 <CADJSx6xG6tUTOnkbD3ekPQZ5Pdj-hLWS9r7QGbSNjWxCg5HzJg@mail.gmail.com>
Message-ID: <D1EA86D9-549D-4245-B667-83A93735C0BC@gmail.com>

It takes 29s on my machine in debug to run 5 iterations with Delaunay conforming set to true

https://gist.github.com/arnaudgelas/0f20ebdaf53956f79997


On Aug 7, 2014, at 3:45 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:

> File path is correct.if it is '\'(backward slash) we have to add "D:\\" .since I used '/' it's not required to add "//".
> 
> please find the attached  .vtk file 
> 
> Thanks
> 
> 
> On Thu, Aug 7, 2014 at 7:01 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Shouldn't it be D://temp.vtk ? Isn't it missing one '/' ?
> 
> Can you send this vtk file?
> 
> 
> On Aug 7, 2014, at 3:23 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> 
>> Hi Arnaud,
>> 
>> Kindly have a look in the below code ,the problem  is that even after QEMeshFilter output is saved as .stl file ,the program is still running for long time.I have observed in my tests that MeshFileReader seems to be the culprit. Any suggestions ?
>> 
>> /////
>> #include<iostream>
>> #include<string>
>> 
>> #include <vtkPolyDataWriter.h>
>> #include <vtkPolyDataReader.h>
>> #include <itkMeshFileWriter.h>
>> #include <itkMeshFileReader.h>
>> #include <itkMeshIOFactory.h>
>> #include <itkMeshIOBase.h>
>> #include <vtkTriangleFilter.h>
>> #include <vtkCleanPolyData.h>
>> #include "itkMesh.h"
>> #include "itkQuadEdgeMesh.h"
>> #include "itkQuadEdgeMeshTraits.h"
>> #include "itkSmoothingQuadEdgeMeshFilter.h"
>> #include "vtkSTLWriter.h"
>> #include <vtkSmartPointer.h>
>> 
>> int main()
>> {
>> 	std::string Inputfilename="D:/temp.vtk";   //number of points of this mesh file is around 78K
>> 
>> 	typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;	
>> 	typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>> 	
>> 	itk::OnesMatrixCoefficients< MeshType > coeff0;
>> 	typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >SmoothingQuadEdgeMeshFilter;
>>     
>> 	vtkSmartPointer<vtkPolyDataWriter> polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
>> 	vtkSmartPointer<vtkPolyDataReader> polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();
>>    
>>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother = SmoothingQuadEdgeMeshFilter::New();
>> 	
>>    /* polyDatareader->SetFileName(Inputfilename.c_str() );
>> 	polyDatareader->ReleaseDataFlagOn();
>> 	polyDatareader->Update();*/
>> 
>> 	/*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
>>     vtkSmartPointer<vtkTriangleFilter>::New();
>>     triangleFilter->SetInput(polyDatareader->GetOutput());
>>     triangleFilter->Update();*/
>>   
>> 	//
>> 	/* vtkSmartPointer<vtkCleanPolyData> clean = vtkSmartPointer<vtkCleanPolyData>::New();
>> 	#if (VTK_MAJOR_VERSION < 6)
>> 	 clean->SetInput(triangleFilter->GetOutput() );
>> 	#else
>>        clean->SetInputData(triangleFilter->GetOutput() );
>> 	#endif
>> 	
>>     clean->ConvertPolysToLinesOff();
>>     clean->ConvertLinesToPointsOff();
>>     clean->Update();
>> 
>> 	std::string Inputfilename2="D:/cleaned.vtk";*/
>> 
>> 	////
>> 	/*polyDatawriter->SetInput(clean->GetOutput());	
>> 	polyDatawriter->SetFileName(Inputfilename2.c_str());
>> 	polyDatawriter->ReleaseDataFlagOn();
>> 	polyDatawriter->Write(); */ 
>>   
>> 	typedef itk::MeshFileReader<MeshType> MeshReaderType;
>> 	MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>>        Meshreader->SetFileName(Inputfilename.c_str( ));
>> 	Meshreader->Update();
>> 
>> 	/*MeshType::Pointer mesh =  Meshreader->GetOutput();
>>          mesh->DisconnectPipeline();*/
>> 	
>> 
>> 	QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
>> 	QEMeshSmoother->SetNumberOfIterations(1 );
>> 	QEMeshSmoother->SetRelaxationFactor( 0.5 );
>> 	QEMeshSmoother->SetDelaunayConforming(true);
>> 	QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>> 
>> 	QEMeshSmoother->ReleaseDataFlagOn();
>> 
>> 	QEMeshSmoother->Update();	
>>     
>> 	std::string Outputfilename="D:/tempOut.vtk";
>> 
>> 	typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>> 	MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>>        Meshwriter->SetFileName(Outputfilename.c_str( ));
>> 	Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>>        Meshwriter->Update();	
>> 
>> 	polyDatareader->SetFileName(Outputfilename.c_str() );
>> 	polyDatareader->ReleaseDataFlagOn();
>> 	polyDatareader->Update();
>> 
>> 	vtkSmartPointer<vtkSTLWriter> stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
>> 	
>> 	stlWriter->SetInput( polyDatareader->GetOutput());
>> 	stlWriter->SetFileName("D:/QEoutput.stl");
>> 	stlWriter->SetFileTypeToASCII();
>> 	stlWriter->Write();
>> 	
>> 	//Here it stops and taking long time 
>> 
>> 	return 0;
>> 
>> 	
>> }
>> ////
>> 
>> 
>> 
>> On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>> Hi Arnaud,
>> 
>> Thanks for your reply and valuable suggestions.
>> 
>> Number of points in my input mesh are 78928.In my pipeline I am already cleaning the polydata using vtkCleanPolyData filter.I will check the speed improvement and results with delaunay conforming turned OFF.
>> 
>> Thank you
>> 
>> 
>> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> Hi Malik,
>> 
>> First of all, I would recommend using MeshFileReader instead of VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near future?).
>> 
>> Regarding now the smoothing procedure in itself. This class definitively misses some documentation and I will be adding some in the next few days (mainly extracted from the corresponding insight journal).
>> 
>> At the end of each iteration, when the delaunay conforming flag is turned ON, the conformation is performed. So depending on the mesh configuration, mesh size and number of iterations, it can take ages?
>> How large is your input mesh (number of points)?
>> 
>> You can also check results, by running first a smoothing without delaunay conforming, then apply a delaunay conforming on the output. Results won't be as nice, but you should get significant speed improvement.
>> Another possibility is to first do a clean poly data in vtk, with a small threshold to remove small edges in the input meshes (which results in lots of edge flipping after smoothing).
>> 
>> HTH
>> Arnaud
>> 
>> 
>> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>> 
>>> Hi All,
>>> 
>>> Can anyone suggest me if anything wrong I am doing in this below pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in release mode) at itkVtkPolydataReader .
>>> 
>>> 
>>> ////
>>> 
>>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;
>>> 	
>>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>> 
>>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>>> 
>>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>>> 
>>> //VTKPolyDataWriterType::Pointer ItkToVtkWriter=VTKPolyDataWriterType::New();
>>> VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();
>>> 
>>> VtkToItkReader->SetFileName("abc.vtk");
>>> VtkToItkReader->Update();	
>>> 
>>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>>> SmoothingQuadEdgeMeshFilter;
>>> 
>>>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =   SmoothingQuadEdgeMeshFilter::New();
>>> 	
>>> 
>>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>>> QEMeshSmoother->SetNumberOfIterations(5 );
>>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>> QEMeshSmoother->SetDelaunayConforming(true );
>>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );	
>>> 	
>>> QEMeshSmoother->Update();
>>> 
>>> ////
>>> 
>>> 
>>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>> Thanks Bill for your answer.
>>> 
>>> The reason I am using this pipeline is that SmoothingQEMeshFilter has an additional parameter for smoothing which is delaunay conforming which helps to optimize aspect ratio of triangles while smoothing and thus produces better output.Is there anything similar filter in the vtk pipeline.I used vtkWindowedSincPolydatafilter which is not giving the output as good as QEMeshSmoothing filter.
>>> 
>>> Thanks for your help 
>>> 
>>> 
>>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> Regards:
>>> Mallik
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> 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
>> 
>> 
>> 
>> 
>> -- 
>> Regards:
>> Mallik
>> 
>> 
>> 
>> 
>> -- 
>> Regards:
>> Mallik
>> 
> 
> 
> 
> 
> -- 
> Regards:
> Mallik
> 
> <temp.vtk>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140807/6ef6c3a8/attachment.html>

From mallikarjun49 at gmail.com  Thu Aug  7 11:20:44 2014
From: mallikarjun49 at gmail.com (Mallikarjun K)
Date: Thu, 7 Aug 2014 20:50:44 +0530
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <D1EA86D9-549D-4245-B667-83A93735C0BC@gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
 <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
 <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>
 <305E1509-8EF7-4770-9236-3D639B9BF155@gmail.com>
 <CADJSx6xG6tUTOnkbD3ekPQZ5Pdj-hLWS9r7QGbSNjWxCg5HzJg@mail.gmail.com>
 <D1EA86D9-549D-4245-B667-83A93735C0BC@gmail.com>
Message-ID: <CADJSx6xABVRSoQRQ98Uoh9+Fraz19BwG3XbqR5JhTCBHcgCr+g@mail.gmail.com>

Hi Arnaud,

Thanks,Can you please tell me your machine confuguration. I am running 4GB
RAM,i3  on windows7.
I have downloaded your project and tried to execute it and it is still the
same problem Which I was facing earlier.Any suggestions .....

thank you


On Thu, Aug 7, 2014 at 8:10 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> It takes 29s on my machine in debug to run 5 iterations with Delaunay
> conforming set to true
>
> https://gist.github.com/arnaudgelas/0f20ebdaf53956f79997
>
>
> On Aug 7, 2014, at 3:45 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>
> File path is correct.if it is '\'(backward slash) we have to add "D:\\"
> .since I used '/' it's not required to add "//".
>
> please find the attached  .vtk file
>
> Thanks
>
>
> On Thu, Aug 7, 2014 at 7:01 PM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
>
>> Shouldn't it be D://temp.vtk ? Isn't it missing one '/' ?
>>
>> Can you send this vtk file?
>>
>>
>> On Aug 7, 2014, at 3:23 PM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>>
>> Hi Arnaud,
>>
>> Kindly have a look in the below code ,the problem  is that even after
>> QEMeshFilter output is saved as .stl file ,the program is still running for
>> long time.I have observed in my tests that MeshFileReader seems to be the
>> culprit. Any suggestions ?
>>
>> /////
>> #include<iostream>
>> #include<string>
>>
>> #include <vtkPolyDataWriter.h>
>> #include <vtkPolyDataReader.h>
>> #include <itkMeshFileWriter.h>
>> #include <itkMeshFileReader.h>
>> #include <itkMeshIOFactory.h>
>> #include <itkMeshIOBase.h>
>> #include <vtkTriangleFilter.h>
>> #include <vtkCleanPolyData.h>
>> #include "itkMesh.h"
>> #include "itkQuadEdgeMesh.h"
>> #include "itkQuadEdgeMeshTraits.h"
>> #include "itkSmoothingQuadEdgeMeshFilter.h"
>> #include "vtkSTLWriter.h"
>> #include <vtkSmartPointer.h>
>>
>> int main()
>> {
>> std::string Inputfilename="D:/temp.vtk";   //number of points of this
>> mesh file is around 78K
>>
>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
>> qetraits;
>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>  itk::OnesMatrixCoefficients< MeshType > coeff0;
>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType
>> >SmoothingQuadEdgeMeshFilter;
>>
>> vtkSmartPointer<vtkPolyDataWriter>
>> polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
>> vtkSmartPointer<vtkPolyDataReader>
>> polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();
>>
>>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
>> SmoothingQuadEdgeMeshFilter::New();
>>    /* polyDatareader->SetFileName(Inputfilename.c_str() );
>>  polyDatareader->ReleaseDataFlagOn();
>> polyDatareader->Update();*/
>>
>> /*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
>>     vtkSmartPointer<vtkTriangleFilter>::New();
>>     triangleFilter->SetInput(polyDatareader->GetOutput());
>>     triangleFilter->Update();*/
>>
>> //
>>  /* vtkSmartPointer<vtkCleanPolyData> clean =
>> vtkSmartPointer<vtkCleanPolyData>::New();
>> #if (VTK_MAJOR_VERSION < 6)
>>  clean->SetInput(triangleFilter->GetOutput() );
>> #else
>>        clean->SetInputData(triangleFilter->GetOutput() );
>>  #endif
>>     clean->ConvertPolysToLinesOff();
>>     clean->ConvertLinesToPointsOff();
>>     clean->Update();
>>
>> std::string Inputfilename2="D:/cleaned.vtk";*/
>>
>> ////
>>  /*polyDatawriter->SetInput(clean->GetOutput());
>> polyDatawriter->SetFileName(Inputfilename2.c_str());
>>  polyDatawriter->ReleaseDataFlagOn();
>> polyDatawriter->Write(); */
>>
>> typedef itk::MeshFileReader<MeshType> MeshReaderType;
>>  MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>>        Meshreader->SetFileName(Inputfilename.c_str( ));
>> Meshreader->Update();
>>
>> /*MeshType::Pointer mesh =  Meshreader->GetOutput();
>>          mesh->DisconnectPipeline();*/
>>
>> QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
>> QEMeshSmoother->SetNumberOfIterations(1 );
>>  QEMeshSmoother->SetRelaxationFactor( 0.5 );
>> QEMeshSmoother->SetDelaunayConforming(true);
>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>
>> QEMeshSmoother->ReleaseDataFlagOn();
>>
>> QEMeshSmoother->Update();
>>
>> std::string Outputfilename="D:/tempOut.vtk";
>>
>> typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>>  MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>>        Meshwriter->SetFileName(Outputfilename.c_str( ));
>> Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>>        Meshwriter->Update();
>>
>> polyDatareader->SetFileName(Outputfilename.c_str() );
>>  polyDatareader->ReleaseDataFlagOn();
>> polyDatareader->Update();
>>
>> vtkSmartPointer<vtkSTLWriter>
>> stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
>>  stlWriter->SetInput( polyDatareader->GetOutput());
>> stlWriter->SetFileName("D:/QEoutput.stl");
>>  stlWriter->SetFileTypeToASCII();
>> stlWriter->Write();
>>  //Here it stops and taking long time
>>
>> return 0;
>>
>>  }
>> ////
>>
>>
>>
>> On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>>
>>> Hi Arnaud,
>>>
>>> Thanks for your reply and valuable suggestions.
>>>
>>> Number of points in my input mesh are 78928.In my pipeline I am already
>>> cleaning the polydata using vtkCleanPolyData filter.I will check the speed
>>> improvement and results with delaunay conforming turned OFF.
>>>
>>> Thank you
>>>
>>>
>>> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com>
>>> wrote:
>>>
>>>> Hi Malik,
>>>>
>>>> First of all, I would recommend using MeshFileReader instead of
>>>> VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near
>>>> future?).
>>>>
>>>> Regarding now the smoothing procedure in itself. This class
>>>> definitively misses some documentation and I will be adding some in the
>>>> next few days (mainly extracted from the corresponding insight journal).
>>>>
>>>> At the end of each iteration, when the delaunay conforming flag is
>>>> turned ON, the conformation is performed. So depending on the mesh
>>>> configuration, mesh size and number of iterations, it can take ages?
>>>> How large is your input mesh (number of points)?
>>>>
>>>> You can also check results, by running first a smoothing without
>>>> delaunay conforming, then apply a delaunay conforming on the output.
>>>> Results won't be as nice, but you should get significant speed improvement.
>>>> Another possibility is to first do a clean poly data in vtk, with a
>>>> small threshold to remove small edges in the input meshes (which results in
>>>> lots of edge flipping after smoothing).
>>>>
>>>> HTH
>>>> Arnaud
>>>>
>>>>
>>>> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com>
>>>> wrote:
>>>>
>>>> Hi All,
>>>>
>>>> Can anyone suggest me if anything wrong I am doing in this below
>>>> pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata
>>>> to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5
>>>> mins in release mode) at itkVtkPolydataReader .
>>>>
>>>>
>>>> ////
>>>>
>>>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double
>>>> > qetraits;
>>>>
>>>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>>>
>>>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>>
>>>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>>>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>>>>
>>>> //VTKPolyDataWriterType::Pointer
>>>> ItkToVtkWriter=VTKPolyDataWriterType::New();
>>>> VTKPolyDataReaderType::Pointer
>>>> VtkToItkReader=VTKPolyDataReaderType::New();
>>>>
>>>> VtkToItkReader->SetFileName("abc.vtk");
>>>> VtkToItkReader->Update();
>>>>
>>>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>>>> SmoothingQuadEdgeMeshFilter;
>>>>
>>>>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
>>>> SmoothingQuadEdgeMeshFilter::New();
>>>>
>>>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>>>> QEMeshSmoother->SetNumberOfIterations(5 );
>>>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>> QEMeshSmoother->SetDelaunayConforming(true );
>>>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>>>  QEMeshSmoother->Update();
>>>>
>>>> ////
>>>>
>>>>
>>>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com>
>>>> wrote:
>>>>
>>>>> Thanks Bill for your answer.
>>>>>
>>>>> The reason I am using this pipeline is that SmoothingQEMeshFilter has
>>>>> an additional parameter for smoothing which is delaunay conforming which
>>>>> helps to optimize aspect ratio of triangles while smoothing and thus
>>>>> produces better output.Is there anything similar filter in the vtk
>>>>> pipeline.I used vtkWindowedSincPolydatafilter which is not giving the
>>>>> output as good as QEMeshSmoothing filter.
>>>>>
>>>>> Thanks for your help
>>>>>
>>>>>
>>>>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <
>>>>> bill.lorensen at gmail.com> wrote:
>>>>>
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *Regards:*
>>>>> Mallik
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> *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
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> *Regards:*
>>> Mallik
>>>
>>>
>>
>>
>> --
>> *Regards:*
>> Mallik
>>
>>
>>
>
>
> --
> *Regards:*
> Mallik
>
>  <temp.vtk>
>
>
>


-- 
*Regards:*
Mallik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140807/ac16c967/attachment-0001.html>

From arnaudgelas at gmail.com  Fri Aug  8 04:44:26 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 8 Aug 2014 10:44:26 +0200
Subject: [ITK-users] Motion under Mean Curvature with LevelSetv4
	Framework
In-Reply-To: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
Message-ID: <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>

Hi Cagatay,

I just came back from vacation... Have you solved this problem?
It would be great if we could make the equivalent code in the old framework
to compare and fix what could be wrong. Have you done something like this?

I'll start looking at it...

Best,
Arnaud


On Tue, Jul 22, 2014 at 9:58 AM, Cagatay Bilgin <bilgincc at gmail.com> wrote:

> 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
>
> _____________________________________
> 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/20140808/d9e4d640/attachment.html>
-------------- 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/20140808/d9e4d640/attachment.png>
-------------- 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/20140808/d9e4d640/attachment-0001.png>

From nicgallego at gmail.com  Fri Aug  8 12:18:53 2014
From: nicgallego at gmail.com (Nicolas Gallego)
Date: Fri, 8 Aug 2014 18:18:53 +0200
Subject: [ITK-users] [ITK]  Whole body Segmentation-Identification
In-Reply-To: <CAOoMOMDZL+K7LtHkNYdu7EU-m9JrsS3i_w8gmcp90C6XJBS1cQ@mail.gmail.com>
References: <CAOoMOMDZL+K7LtHkNYdu7EU-m9JrsS3i_w8gmcp90C6XJBS1cQ@mail.gmail.com>
Message-ID: <CAHFTQh6+=KnY6-=ncOQoMSU=AwAvDh9UpBE4ek=Y1jWMitqLrg@mail.gmail.com>

Hi Bumpy,
It seams that your problem is exploratory and will get benefit of manual
interaction. Have you tried visualizing your images in ITKSnap for example?
There are tools to do manual segmentation there.
Hope that helps

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


2014-08-01 15:47 GMT+02:00 Bumpy RG <rg.bumpy at gmail.com>:

> Dear All,
>
> I have a dicom series having whole body image sequences, starting from
> head up to legs.
>
> My aim is to write an algorithm to automatically identify the body parts
> (lungs, spines, head etc.) from the dicom sequence.
>
> Although I am very new to the ITK world, I am following these steps in ITK
> (*I would appreciate if you comment whether I am following correct idea
> or not*):
>
>    1. Read dicom series using 'DicomSeriesReadImageWrite2.cxx ' to create
>    a 3D volume and save the result in mhd format.
>    2. Use 'ImageReadRegionOfInterestWrite.cxx' for separating various
>    parts (like left lung, right lung, spines, head etc.) and save them in
>    respective 3D volumes in mhd format.
>    3. Pick the various body parts prepared above, one by one and segment
>    them using robust algorithm (say
>    ThresholdSegmentationLevelSetImageFilter.cxx).
>    4. Use Mathematical Morphology to get better results.
>    5. Using the various results from above, form an algorithm for
>    identifying the various body parts.
>
> Currently I am stuck in the second step because it is so hard to choose
> the co-ordinates for selecting proper region of interest.
>
> For example,  I chose these points for ROI of right lung (I checked the
> co-ordinates using 3D slicer visualizer) and it does not give me good
> results :
> start[0] = 255;
> start[1] =165;
> start[2] = 0;
>
> *However I do not understand how to choose the points properly in ITK.*
>
>
> I would be really glad to have your response.
>
> Thanking you in advance.
> Kind Regards,
> Bumpy.
>
> _____________________________________
> 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/20140808/9099f86a/attachment.html>

From matimontg at gmail.com  Sat Aug  9 10:34:08 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 9 Aug 2014 11:34:08 -0300
Subject: [ITK-users] ITK ResampleDicom | Tags
Message-ID: <CAKKNfu+THX_L=FR6apejdEgSpPxFUccXHCJKtMcrvqFcwSSAQQ@mail.gmail.com>

Hi,

I'm using the ResmpleDicom example to convert a serie of images to a new
serie with z spacing=1. Images are CT

Everything works fine except that some Tags on the images are deleted
during the process, I even see the rescale intercept is srt to 0 and the
rescaletype is changed as well. The padding value also changes.

Is there a way to avoid all this? My images WL and WC change once I run the
Resample..

Thanks!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140809/b145aeb7/attachment.html>

From matimontg at gmail.com  Sat Aug  9 10:42:28 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 9 Aug 2014 11:42:28 -0300
Subject: [ITK-users] ITK ResampleDicom | Tags
In-Reply-To: <CAKKNfu+THX_L=FR6apejdEgSpPxFUccXHCJKtMcrvqFcwSSAQQ@mail.gmail.com>
References: <CAKKNfu+THX_L=FR6apejdEgSpPxFUccXHCJKtMcrvqFcwSSAQQ@mail.gmail.com>
Message-ID: <CAKKNfu+gju=qrNtKjsXh4Gwa9BrrhCq06G1WdL-DOGykNtDdYg@mail.gmail.com>

I think the key is in this section of the code:
    CopyDictionary (*inputDict, *dict);

Shouldn't copy the entire tags?


On Sat, Aug 9, 2014 at 11:34 AM, Matias Montroull <matimontg at gmail.com>
wrote:

> Hi,
>
> I'm using the ResmpleDicom example to convert a serie of images to a new
> serie with z spacing=1. Images are CT
>
> Everything works fine except that some Tags on the images are deleted
> during the process, I even see the rescale intercept is srt to 0 and the
> rescaletype is changed as well. The padding value also changes.
>
> Is there a way to avoid all this? My images WL and WC change once I run
> the Resample..
>
> Thanks!
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140809/2d27f13a/attachment.html>

From grothausmann.roman at mh-hannover.de  Mon Aug 11 01:15:45 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Mon, 11 Aug 2014 07:15:45 +0200
Subject: [ITK-users] adding a global hierarchical watershed segmentation
	mode to itksnap
Message-ID: <53E85181.8040607@mh-hannover.de>

Dear mailing list members,


For a long time now I've been searching for a replacement of the old 
SegmentationEditor (part of the InsightApplications) which I could not get to 
work even with older ITK-3.x. Somewhere I was told that it was integrated and 
maintained within itksnap. However the only tool in itksnap based on watershed 
segmentation seems to be the adaptive brush. It is very handy, but 
time-consuming in 3D and only for local segmentations. In contrast the 
SegmentationEditor used a global hierarchical watershed segmentation to pick 
labels from, see e.g. the video linked here:
http://www.insight-journal.org/browse/publication/70
Quite often now I've stumbled over data, that would likely have profited a lot 
of such a tool for segmentation.

If such a tool working with ITK-4.x does not exist any more, I thought of 
implementing it as a global WS segmentation mode in itksnap. That way making the 
tool easier to find, to use and to ensure maintenance (should it be integrated 
into the itksnap code base in the end) and also avoiding recoding a GUI with 
mouse interaction and such.

My current idea is to start, similar to the snake-tool, with pre-filtering like 
smoothing and optional edge-detection.
Then the main edit mode to consist of the usual 4 subwindows showing an overlay 
of the grey-image and the watershed segmentation of the hierarchical WS-filter 
(hWS), side-by-side to another label-dataset (loaded like a tiled overlay) which 
consist of the actually chosen labels from the hWS as the final data (FD).
The interaction I'm considering would be to LMB click on a label in the hWS 
which is then added to the FD as the current fg label, or removed with a RMB. 
The hierachrchy level of the hWS could be controlled by a slider or the mouse 
wheel + Shift in nearly real time if some region demands higher or lower 
detailed segmentation. When the fg label is changed, the segmentation added or 
removed with further mouse interactions would modify the new fg label.
When all is done and the global WS mode is left, the FD label-dataset is added 
to the main segmentation of itksnap.

Would that be possible to implement in itksnap 3.x?
What source files of the itksnap code base should I look at for:
- the pre-filtering mode of the snake (for the smoothing and edge detection)
- the mouse interactions (for e.g. adding the whell + Shift interaction)
- possible examples for the dual layout

Thanks for any comments, help or hints.
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 iyas.hamdan at gmail.com  Mon Aug 11 03:35:25 2014
From: iyas.hamdan at gmail.com (Iyas Hamdan)
Date: Mon, 11 Aug 2014 09:35:25 +0200
Subject: [ITK-users] 3D multimodal registration
Message-ID: <CANH4YVg9opdXVC61qi+-KQYoaPqz5fQXepRejtF5Sm-58=c+Zw@mail.gmail.com>

Hello all,

I?m working on 3D multimodal image registration and I have a problem I've
been struggling with for quite a while.

I have a 3D MRI volume (fixed volume) and a 3D CT volume (moving volume),
but those two volumes have different sizes (different dimensions and
different number of slices).

First of all I have a general question, how does the 3D registration in itk
work basically ? I mean does it take the first slice from the fixed volume
and try to find its correspondence in the moving volume ( by optimizing a
metric ) and then go on to the next slice and so on?
Or does it rather work with the whole volume and not slice by slice ?

Because for me, lets imagine I have 50 MRI slices and 150 CT ones for
example, but the field of view is different between both volumes. I mean
the first MRI slice corresponds ( visually ) to the 50th CT slice for
example so the first 49 CT slices don?t exist in the MRI volume.
 So when I apply my registration method ( affine transformation with the
mutual information as the metric ) the registration fails to give a good
result. It show no errors but the result volume is not well aligned with
the fixed one. Although the transformation ( from the outside let?s say )
is correct, meaning the result volume has the same size as the fixed one
and both volumes are on top of each other perfectly but the slices don?t
look alike at all when I try to show both volumes on top of each other.
Knowing that my initialization is good, and I tuned the parameters of the
optimizer ( regular step gradient descent) and always ended up with almost
the same result.
So is that a normal behavior of itk to fail when the field of view is
different ?

Because I tried to cut off the first 49 CT slices, and created a new volume
with the rest of the slices ( so that I had the same field of view with the
MRI volume ), and when I applied the registration between this new volume
and the MRI one, the registration worked perfectly and I had a very good
result.


So what?s wrong here ? and if the field of view is the problem how can I
fix that automatically ? because I can delete the extra slices from one
volume manually, but what I'm looking for is an automatic approach and I
couldn?t think of one.


Any hint would be really appreciated,
Thanks in advance,

Best regards,

Iyas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140811/6d73f6be/attachment.html>

From mercikd at thomas.edu  Mon Aug 11 10:37:37 2014
From: mercikd at thomas.edu (Dan Mercik)
Date: Mon, 11 Aug 2014 14:37:37 +0000
Subject: [ITK-users] Image Diffusion
Message-ID: <ae9da80669e64e9996df290cc4d9c686@T9.tcnet.thomas.edu>

Good Morning,



                I'm doing a project that involves the fusion of multiple images. However, at the end of the fusion process I need to be able to diffuse the fuse imaged back to it's original stack images.   I wanted to know if there an algorithm I can use to defuse my fused image?  Any thoughts are more than welcome and I would be highly appreciative for your input.

Daniel Mercik

Computer Science Major

Service Desk Technician

Thomas College

From lasso at queensu.ca  Mon Aug 11 10:20:58 2014
From: lasso at queensu.ca (Andras Lasso)
Date: Mon, 11 Aug 2014 14:20:58 +0000
Subject: [ITK-users] [ITK] adding a global hierarchical
	watershed	segmentation	mode to itksnap
In-Reply-To: <53E85181.8040607@mh-hannover.de>
References: <53E85181.8040607@mh-hannover.de>
Message-ID: <0f32755d9980441ca0162728b088f00b@queensu.ca>

Have you tried segmentation tools in 3D Slicer? There is a multi-label watershed segmentation tool that works in 3d (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Editor#WatershedFromMarkers), there are also a number of other generic semi-automatic segmentation tools (such as GrowCut) and a few fully-automatic specialized tools (for brain, airways, etc). Download the nightly build and also checkout the Segmentation category in the Extension Manager.

Andras

From: Dr. Roman Grothausmann<mailto:grothausmann.roman at mh-hannover.de>
Sent: ?Monday?, ?August? ?11?, ?2014 ?1?:?15? ?AM
To: itksnap-users at googlegroups.com<mailto:itksnap-users at googlegroups.com>
Cc: ITK Mailing List<mailto:insight-users at itk.org>

Dear mailing list members,


For a long time now I've been searching for a replacement of the old
SegmentationEditor (part of the InsightApplications) which I could not get to
work even with older ITK-3.x. Somewhere I was told that it was integrated and
maintained within itksnap. However the only tool in itksnap based on watershed
segmentation seems to be the adaptive brush. It is very handy, but
time-consuming in 3D and only for local segmentations. In contrast the
SegmentationEditor used a global hierarchical watershed segmentation to pick
labels from, see e.g. the video linked here:
http://www.insight-journal.org/browse/publication/70
Quite often now I've stumbled over data, that would likely have profited a lot
of such a tool for segmentation.

If such a tool working with ITK-4.x does not exist any more, I thought of
implementing it as a global WS segmentation mode in itksnap. That way making the
tool easier to find, to use and to ensure maintenance (should it be integrated
into the itksnap code base in the end) and also avoiding recoding a GUI with
mouse interaction and such.

My current idea is to start, similar to the snake-tool, with pre-filtering like
smoothing and optional edge-detection.
Then the main edit mode to consist of the usual 4 subwindows showing an overlay
of the grey-image and the watershed segmentation of the hierarchical WS-filter
(hWS), side-by-side to another label-dataset (loaded like a tiled overlay) which
consist of the actually chosen labels from the hWS as the final data (FD).
The interaction I'm considering would be to LMB click on a label in the hWS
which is then added to the FD as the current fg label, or removed with a RMB.
The hierachrchy level of the hWS could be controlled by a slider or the mouse
wheel + Shift in nearly real time if some region demands higher or lower
detailed segmentation. When the fg label is changed, the segmentation added or
removed with further mouse interactions would modify the new fg label.
When all is done and the global WS mode is left, the FD label-dataset is added
to the main segmentation of itksnap.

Would that be possible to implement in itksnap 3.x?
What source files of the itksnap code base should I look at for:
- the pre-filtering mode of the snake (for the smoothing and edge detection)
- the mouse interactions (for e.g. adding the whell + Shift interaction)
- possible examples for the dual layout

Thanks for any comments, help or hints.
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
_______________________________________________
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/20140811/86c01350/attachment.html>

From gass at vision.ee.ethz.ch  Mon Aug 11 12:18:03 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Mon, 11 Aug 2014 18:18:03 +0200
Subject: [ITK-users] Anti-alias filter
Message-ID: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>

Dear all,

I'm having problems using the anti-alias filter, which I want to use in
order to smooth a binary segmentation volume. I'm using essentially the
example code from the repository, which for my input file seems to start
oscillating after 2 iterations, leading to weird 'pointy' artifacts on the
surface as can be seen from the attached screenshot (AA filter output is on
the left, input on the right).

Is there any parameter to set/implement which could improve the behavior of
this filter? I'm assuming that my input is reasonable, or is this something
the filter is expected to have problems with? It is notable that such
errors seem to mainly appear in 'flat' regions of the volume, and are not
apparent in the curved shaft of the bone.

Any help, or pointers to further resources are appreciated,
thanks,
Tobias
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140811/3052cfb6/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: AAFIlter.jpg
Type: image/jpeg
Size: 205294 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140811/3052cfb6/attachment-0001.jpg>

From bill.lorensen at gmail.com  Mon Aug 11 13:39:44 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 11 Aug 2014 13:39:44 -0400
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
Message-ID: <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>

Can you post your code. The results do not look correct.


On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <gass at vision.ee.ethz.ch> wrote:
> Dear all,
>
> I'm having problems using the anti-alias filter, which I want to use in
> order to smooth a binary segmentation volume. I'm using essentially the
> example code from the repository, which for my input file seems to start
> oscillating after 2 iterations, leading to weird 'pointy' artifacts on the
> surface as can be seen from the attached screenshot (AA filter output is on
> the left, input on the right).
>
> Is there any parameter to set/implement which could improve the behavior of
> this filter? I'm assuming that my input is reasonable, or is this something
> the filter is expected to have problems with? It is notable that such errors
> seem to mainly appear in 'flat' regions of the volume, and are not apparent
> in the curved shaft of the bone.
>
> Any help, or pointers to further resources are appreciated,
> thanks,
> Tobias
>
> _____________________________________
> 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 gass at vision.ee.ethz.ch  Mon Aug 11 14:47:49 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Mon, 11 Aug 2014 20:47:49 +0200
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
Message-ID: <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>

> Can you post your code. The results do not look correct.


Sure. The {write,read}Image functions are just convenient wrappers for the
respective ITK tools.


#include <stdio.h>

#include <iostream>

#include "argstream.h"

#include "ImageUtils.h"

#include "itkAntiAliasBinaryImageFilter.h"

using namespace std;

using namespace itk;




int main(int argc, char ** argv)

{


 feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);

    typedef  short PixelType;

    typedef double OutputPixelType;

    const unsigned int D=3;

    typedef Image<PixelType,D> ImageType;



    typedef ImageType::Pointer ImagePointerType;



    typedef Image<OutputPixelType,D> OutputImageType;

    typedef OutputImageType::Pointer OutputImagePointerType;



    argstream * as=new argstream(argc,argv);

    string inFile, outFile;

    double thresh=0.0;

    (*as) >> parameter ("in", inFile, " filename...", true);

    (*as) >> parameter ("out", outFile, " filename...", true);


    (*as) >> help();

    as->defaultErrorHandling();


    ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);


    typedef itk::AntiAliasBinaryImageFilter <ImageType, OutputImageType>

        AntiAliasBinaryImageFilterType;



    AntiAliasBinaryImageFilterType::Pointer antiAliasFilter

        = AntiAliasBinaryImageFilterType::New ();

    antiAliasFilter->SetInput(img);

    antiAliasFilter->SetNumberOfIterations(5);

    antiAliasFilter->SetMaximumRMSError(0.02);


    antiAliasFilter->Update();


  // For increased code coverage.  Does nothing.

  antiAliasFilter->GetMaximumRMSError();




  antiAliasFilter->Update();


  std::cout << "Maximum RMS change value threshold was: 0.02 " << std::endl;

  std::cout << "Last RMS change value was: " <<
antiAliasFilter->GetRMSChange() << std::endl;


  std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;


  std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
antiAliasFilter->GetUpperBinaryValue()<<std::endl;


    OutputImagePointerType out=antiAliasFilter->GetOutput();


    ImageUtils<OutputImageType>::writeImage(outFile,out);


 return 1;

}

I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
maxRMSError (0.02 0.07 0.08 0.8), and the best visual results are achieved
after one iteration where RMSE changes by about 0.08. This increases for
all following iterations, which have an RMSE-change of about 0.25 for all
number of  iterations tested. All this is using ITK 4.5 pulled from the GIT
repository a while ago, running on an intel i7 on Debian.

Thanks a lot!
Tobias


>
> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <gass at vision.ee.ethz.ch>
> wrote:
> > Dear all,
> >
> > I'm having problems using the anti-alias filter, which I want to use in
> > order to smooth a binary segmentation volume. I'm using essentially the
> > example code from the repository, which for my input file seems to start
> > oscillating after 2 iterations, leading to weird 'pointy' artifacts on
> the
> > surface as can be seen from the attached screenshot (AA filter output is
> on
> > the left, input on the right).
> >
> > Is there any parameter to set/implement which could improve the behavior
> of
> > this filter? I'm assuming that my input is reasonable, or is this
> something
> > the filter is expected to have problems with? It is notable that such
> errors
> > seem to mainly appear in 'flat' regions of the volume, and are not
> apparent
> > in the curved shaft of the bone.
> >
> > Any help, or pointers to further resources are appreciated,
> > thanks,
> > Tobias
> >
> > _____________________________________
> > 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140811/52da4a1c/attachment.html>

From bill.lorensen at gmail.com  Mon Aug 11 15:22:09 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 11 Aug 2014 15:22:09 -0400
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
Message-ID: <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>

If you change
 typedef  short PixelType;
to
 typedef  double PixelType;

do the results change.


On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <gass at vision.ee.ethz.ch> wrote:
>
>> Can you post your code. The results do not look correct.
>
>
> Sure. The {write,read}Image functions are just convenient wrappers for the
> respective ITK tools.
>
>
> #include <stdio.h>
>
> #include <iostream>
>
> #include "argstream.h"
>
> #include "ImageUtils.h"
>
> #include "itkAntiAliasBinaryImageFilter.h"
>
> using namespace std;
>
> using namespace itk;
>
>
>
>
> int main(int argc, char ** argv)
>
> {
>
>
> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>
>     typedef  short PixelType;
>
>     typedef double OutputPixelType;
>
>     const unsigned int D=3;
>
>     typedef Image<PixelType,D> ImageType;
>
>
>
>     typedef ImageType::Pointer ImagePointerType;
>
>
>
>     typedef Image<OutputPixelType,D> OutputImageType;
>
>     typedef OutputImageType::Pointer OutputImagePointerType;
>
>
>
>     argstream * as=new argstream(argc,argv);
>
>     string inFile, outFile;
>
>     double thresh=0.0;
>
>     (*as) >> parameter ("in", inFile, " filename...", true);
>
>     (*as) >> parameter ("out", outFile, " filename...", true);
>
>
>     (*as) >> help();
>
>     as->defaultErrorHandling();
>
>
>     ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);
>
>
>     typedef itk::AntiAliasBinaryImageFilter <ImageType, OutputImageType>
>
>         AntiAliasBinaryImageFilterType;
>
>
>
>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>
>         = AntiAliasBinaryImageFilterType::New ();
>
>     antiAliasFilter->SetInput(img);
>
>     antiAliasFilter->SetNumberOfIterations(5);
>
>     antiAliasFilter->SetMaximumRMSError(0.02);
>
>
>     antiAliasFilter->Update();
>
>
>   // For increased code coverage.  Does nothing.
>
>   antiAliasFilter->GetMaximumRMSError();
>
>
>
>
>   antiAliasFilter->Update();
>
>
>   std::cout << "Maximum RMS change value threshold was: 0.02 " << std::endl;
>
>   std::cout << "Last RMS change value was: " <<
> antiAliasFilter->GetRMSChange() << std::endl;
>
>
>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>
>
>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>
>
>     OutputImagePointerType out=antiAliasFilter->GetOutput();
>
>
>     ImageUtils<OutputImageType>::writeImage(outFile,out);
>
>
> return 1;
>
> }
>
>
> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and maxRMSError
> (0.02 0.07 0.08 0.8), and the best visual results are achieved after one
> iteration where RMSE changes by about 0.08. This increases for all following
> iterations, which have an RMSE-change of about 0.25 for all number of
> iterations tested. All this is using ITK 4.5 pulled from the GIT repository
> a while ago, running on an intel i7 on Debian.
>
> Thanks a lot!
> Tobias
>
>>
>>
>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>> wrote:
>> > Dear all,
>> >
>> > I'm having problems using the anti-alias filter, which I want to use in
>> > order to smooth a binary segmentation volume. I'm using essentially the
>> > example code from the repository, which for my input file seems to start
>> > oscillating after 2 iterations, leading to weird 'pointy' artifacts on
>> > the
>> > surface as can be seen from the attached screenshot (AA filter output is
>> > on
>> > the left, input on the right).
>> >
>> > Is there any parameter to set/implement which could improve the behavior
>> > of
>> > this filter? I'm assuming that my input is reasonable, or is this
>> > something
>> > the filter is expected to have problems with? It is notable that such
>> > errors
>> > seem to mainly appear in 'flat' regions of the volume, and are not
>> > apparent
>> > in the curved shaft of the bone.
>> >
>> > Any help, or pointers to further resources are appreciated,
>> > thanks,
>> > Tobias
>> >
>> > _____________________________________
>> > 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

From bill.lorensen at gmail.com  Mon Aug 11 15:22:44 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 11 Aug 2014 15:22:44 -0400
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
Message-ID: <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>

How are you extracting the final isosurface?

On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> If you change
>  typedef  short PixelType;
> to
>  typedef  double PixelType;
>
> do the results change.
>
>
> On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <gass at vision.ee.ethz.ch> wrote:
>>
>>> Can you post your code. The results do not look correct.
>>
>>
>> Sure. The {write,read}Image functions are just convenient wrappers for the
>> respective ITK tools.
>>
>>
>> #include <stdio.h>
>>
>> #include <iostream>
>>
>> #include "argstream.h"
>>
>> #include "ImageUtils.h"
>>
>> #include "itkAntiAliasBinaryImageFilter.h"
>>
>> using namespace std;
>>
>> using namespace itk;
>>
>>
>>
>>
>> int main(int argc, char ** argv)
>>
>> {
>>
>>
>> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>>
>>     typedef  short PixelType;
>>
>>     typedef double OutputPixelType;
>>
>>     const unsigned int D=3;
>>
>>     typedef Image<PixelType,D> ImageType;
>>
>>
>>
>>     typedef ImageType::Pointer ImagePointerType;
>>
>>
>>
>>     typedef Image<OutputPixelType,D> OutputImageType;
>>
>>     typedef OutputImageType::Pointer OutputImagePointerType;
>>
>>
>>
>>     argstream * as=new argstream(argc,argv);
>>
>>     string inFile, outFile;
>>
>>     double thresh=0.0;
>>
>>     (*as) >> parameter ("in", inFile, " filename...", true);
>>
>>     (*as) >> parameter ("out", outFile, " filename...", true);
>>
>>
>>     (*as) >> help();
>>
>>     as->defaultErrorHandling();
>>
>>
>>     ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);
>>
>>
>>     typedef itk::AntiAliasBinaryImageFilter <ImageType, OutputImageType>
>>
>>         AntiAliasBinaryImageFilterType;
>>
>>
>>
>>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>>
>>         = AntiAliasBinaryImageFilterType::New ();
>>
>>     antiAliasFilter->SetInput(img);
>>
>>     antiAliasFilter->SetNumberOfIterations(5);
>>
>>     antiAliasFilter->SetMaximumRMSError(0.02);
>>
>>
>>     antiAliasFilter->Update();
>>
>>
>>   // For increased code coverage.  Does nothing.
>>
>>   antiAliasFilter->GetMaximumRMSError();
>>
>>
>>
>>
>>   antiAliasFilter->Update();
>>
>>
>>   std::cout << "Maximum RMS change value threshold was: 0.02 " << std::endl;
>>
>>   std::cout << "Last RMS change value was: " <<
>> antiAliasFilter->GetRMSChange() << std::endl;
>>
>>
>>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>>
>>
>>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
>> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>>
>>
>>     OutputImagePointerType out=antiAliasFilter->GetOutput();
>>
>>
>>     ImageUtils<OutputImageType>::writeImage(outFile,out);
>>
>>
>> return 1;
>>
>> }
>>
>>
>> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and maxRMSError
>> (0.02 0.07 0.08 0.8), and the best visual results are achieved after one
>> iteration where RMSE changes by about 0.08. This increases for all following
>> iterations, which have an RMSE-change of about 0.25 for all number of
>> iterations tested. All this is using ITK 4.5 pulled from the GIT repository
>> a while ago, running on an intel i7 on Debian.
>>
>> Thanks a lot!
>> Tobias
>>
>>>
>>>
>>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>>> wrote:
>>> > Dear all,
>>> >
>>> > I'm having problems using the anti-alias filter, which I want to use in
>>> > order to smooth a binary segmentation volume. I'm using essentially the
>>> > example code from the repository, which for my input file seems to start
>>> > oscillating after 2 iterations, leading to weird 'pointy' artifacts on
>>> > the
>>> > surface as can be seen from the attached screenshot (AA filter output is
>>> > on
>>> > the left, input on the right).
>>> >
>>> > Is there any parameter to set/implement which could improve the behavior
>>> > of
>>> > this filter? I'm assuming that my input is reasonable, or is this
>>> > something
>>> > the filter is expected to have problems with? It is notable that such
>>> > errors
>>> > seem to mainly appear in 'flat' regions of the volume, and are not
>>> > apparent
>>> > in the curved shaft of the bone.
>>> >
>>> > Any help, or pointers to further resources are appreciated,
>>> > thanks,
>>> > Tobias
>>> >
>>> > _____________________________________
>>> > 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



-- 
Unpaid intern in BillsBasement at noware dot com

From gass at vision.ee.ethz.ch  Mon Aug 11 15:38:45 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Mon, 11 Aug 2014 21:38:45 +0200
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
Message-ID: <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>

I will try that tomorrow morning (living in GMT+1). I used paraview to
extract the isosurface, but also looked at the output of the AA-filter
directly (which looked fuzzy). I can also post an image of that tomorrow.

Thanks for your help!
Tobias


2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:

> How are you extracting the final isosurface?
>
> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> > If you change
> >  typedef  short PixelType;
> > to
> >  typedef  double PixelType;
> >
> > do the results change.
> >
> >
> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <gass at vision.ee.ethz.ch>
> wrote:
> >>
> >>> Can you post your code. The results do not look correct.
> >>
> >>
> >> Sure. The {write,read}Image functions are just convenient wrappers for
> the
> >> respective ITK tools.
> >>
> >>
> >> #include <stdio.h>
> >>
> >> #include <iostream>
> >>
> >> #include "argstream.h"
> >>
> >> #include "ImageUtils.h"
> >>
> >> #include "itkAntiAliasBinaryImageFilter.h"
> >>
> >> using namespace std;
> >>
> >> using namespace itk;
> >>
> >>
> >>
> >>
> >> int main(int argc, char ** argv)
> >>
> >> {
> >>
> >>
> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
> >>
> >>     typedef  short PixelType;
> >>
> >>     typedef double OutputPixelType;
> >>
> >>     const unsigned int D=3;
> >>
> >>     typedef Image<PixelType,D> ImageType;
> >>
> >>
> >>
> >>     typedef ImageType::Pointer ImagePointerType;
> >>
> >>
> >>
> >>     typedef Image<OutputPixelType,D> OutputImageType;
> >>
> >>     typedef OutputImageType::Pointer OutputImagePointerType;
> >>
> >>
> >>
> >>     argstream * as=new argstream(argc,argv);
> >>
> >>     string inFile, outFile;
> >>
> >>     double thresh=0.0;
> >>
> >>     (*as) >> parameter ("in", inFile, " filename...", true);
> >>
> >>     (*as) >> parameter ("out", outFile, " filename...", true);
> >>
> >>
> >>     (*as) >> help();
> >>
> >>     as->defaultErrorHandling();
> >>
> >>
> >>     ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);
> >>
> >>
> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType, OutputImageType>
> >>
> >>         AntiAliasBinaryImageFilterType;
> >>
> >>
> >>
> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
> >>
> >>         = AntiAliasBinaryImageFilterType::New ();
> >>
> >>     antiAliasFilter->SetInput(img);
> >>
> >>     antiAliasFilter->SetNumberOfIterations(5);
> >>
> >>     antiAliasFilter->SetMaximumRMSError(0.02);
> >>
> >>
> >>     antiAliasFilter->Update();
> >>
> >>
> >>   // For increased code coverage.  Does nothing.
> >>
> >>   antiAliasFilter->GetMaximumRMSError();
> >>
> >>
> >>
> >>
> >>   antiAliasFilter->Update();
> >>
> >>
> >>   std::cout << "Maximum RMS change value threshold was: 0.02 " <<
> std::endl;
> >>
> >>   std::cout << "Last RMS change value was: " <<
> >> antiAliasFilter->GetRMSChange() << std::endl;
> >>
> >>
> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
> >>
> >>
> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
> >>
> >>
> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
> >>
> >>
> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
> >>
> >>
> >> return 1;
> >>
> >> }
> >>
> >>
> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
> maxRMSError
> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved after one
> >> iteration where RMSE changes by about 0.08. This increases for all
> following
> >> iterations, which have an RMSE-change of about 0.25 for all number of
> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
> repository
> >> a while ago, running on an intel i7 on Debian.
> >>
> >> Thanks a lot!
> >> Tobias
> >>
> >>>
> >>>
> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <gass at vision.ee.ethz.ch>
> >>> wrote:
> >>> > Dear all,
> >>> >
> >>> > I'm having problems using the anti-alias filter, which I want to use
> in
> >>> > order to smooth a binary segmentation volume. I'm using essentially
> the
> >>> > example code from the repository, which for my input file seems to
> start
> >>> > oscillating after 2 iterations, leading to weird 'pointy' artifacts
> on
> >>> > the
> >>> > surface as can be seen from the attached screenshot (AA filter
> output is
> >>> > on
> >>> > the left, input on the right).
> >>> >
> >>> > Is there any parameter to set/implement which could improve the
> behavior
> >>> > of
> >>> > this filter? I'm assuming that my input is reasonable, or is this
> >>> > something
> >>> > the filter is expected to have problems with? It is notable that such
> >>> > errors
> >>> > seem to mainly appear in 'flat' regions of the volume, and are not
> >>> > apparent
> >>> > in the curved shaft of the bone.
> >>> >
> >>> > Any help, or pointers to further resources are appreciated,
> >>> > thanks,
> >>> > Tobias
> >>> >
> >>> > _____________________________________
> >>> > 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
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140811/89706249/attachment.html>

From bill.lorensen at gmail.com  Mon Aug 11 16:17:10 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 11 Aug 2014 16:17:10 -0400
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
 <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
Message-ID: <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>

Paraview should do the right thing.

On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch> wrote:
> I will try that tomorrow morning (living in GMT+1). I used paraview to
> extract the isosurface, but also looked at the output of the AA-filter
> directly (which looked fuzzy). I can also post an image of that tomorrow.
>
> Thanks for your help!
> Tobias
>
>
> 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>
>> How are you extracting the final isosurface?
>>
>> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>> > If you change
>> >  typedef  short PixelType;
>> > to
>> >  typedef  double PixelType;
>> >
>> > do the results change.
>> >
>> >
>> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>> > wrote:
>> >>
>> >>> Can you post your code. The results do not look correct.
>> >>
>> >>
>> >> Sure. The {write,read}Image functions are just convenient wrappers for
>> >> the
>> >> respective ITK tools.
>> >>
>> >>
>> >> #include <stdio.h>
>> >>
>> >> #include <iostream>
>> >>
>> >> #include "argstream.h"
>> >>
>> >> #include "ImageUtils.h"
>> >>
>> >> #include "itkAntiAliasBinaryImageFilter.h"
>> >>
>> >> using namespace std;
>> >>
>> >> using namespace itk;
>> >>
>> >>
>> >>
>> >>
>> >> int main(int argc, char ** argv)
>> >>
>> >> {
>> >>
>> >>
>> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>> >>
>> >>     typedef  short PixelType;
>> >>
>> >>     typedef double OutputPixelType;
>> >>
>> >>     const unsigned int D=3;
>> >>
>> >>     typedef Image<PixelType,D> ImageType;
>> >>
>> >>
>> >>
>> >>     typedef ImageType::Pointer ImagePointerType;
>> >>
>> >>
>> >>
>> >>     typedef Image<OutputPixelType,D> OutputImageType;
>> >>
>> >>     typedef OutputImageType::Pointer OutputImagePointerType;
>> >>
>> >>
>> >>
>> >>     argstream * as=new argstream(argc,argv);
>> >>
>> >>     string inFile, outFile;
>> >>
>> >>     double thresh=0.0;
>> >>
>> >>     (*as) >> parameter ("in", inFile, " filename...", true);
>> >>
>> >>     (*as) >> parameter ("out", outFile, " filename...", true);
>> >>
>> >>
>> >>     (*as) >> help();
>> >>
>> >>     as->defaultErrorHandling();
>> >>
>> >>
>> >>     ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);
>> >>
>> >>
>> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType,
>> >> OutputImageType>
>> >>
>> >>         AntiAliasBinaryImageFilterType;
>> >>
>> >>
>> >>
>> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>> >>
>> >>         = AntiAliasBinaryImageFilterType::New ();
>> >>
>> >>     antiAliasFilter->SetInput(img);
>> >>
>> >>     antiAliasFilter->SetNumberOfIterations(5);
>> >>
>> >>     antiAliasFilter->SetMaximumRMSError(0.02);
>> >>
>> >>
>> >>     antiAliasFilter->Update();
>> >>
>> >>
>> >>   // For increased code coverage.  Does nothing.
>> >>
>> >>   antiAliasFilter->GetMaximumRMSError();
>> >>
>> >>
>> >>
>> >>
>> >>   antiAliasFilter->Update();
>> >>
>> >>
>> >>   std::cout << "Maximum RMS change value threshold was: 0.02 " <<
>> >> std::endl;
>> >>
>> >>   std::cout << "Last RMS change value was: " <<
>> >> antiAliasFilter->GetRMSChange() << std::endl;
>> >>
>> >>
>> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>> >>
>> >>
>> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
>> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>> >>
>> >>
>> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
>> >>
>> >>
>> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
>> >>
>> >>
>> >> return 1;
>> >>
>> >> }
>> >>
>> >>
>> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
>> >> maxRMSError
>> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved after
>> >> one
>> >> iteration where RMSE changes by about 0.08. This increases for all
>> >> following
>> >> iterations, which have an RMSE-change of about 0.25 for all number of
>> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
>> >> repository
>> >> a while ago, running on an intel i7 on Debian.
>> >>
>> >> Thanks a lot!
>> >> Tobias
>> >>
>> >>>
>> >>>
>> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>> >>> wrote:
>> >>> > Dear all,
>> >>> >
>> >>> > I'm having problems using the anti-alias filter, which I want to use
>> >>> > in
>> >>> > order to smooth a binary segmentation volume. I'm using essentially
>> >>> > the
>> >>> > example code from the repository, which for my input file seems to
>> >>> > start
>> >>> > oscillating after 2 iterations, leading to weird 'pointy' artifacts
>> >>> > on
>> >>> > the
>> >>> > surface as can be seen from the attached screenshot (AA filter
>> >>> > output is
>> >>> > on
>> >>> > the left, input on the right).
>> >>> >
>> >>> > Is there any parameter to set/implement which could improve the
>> >>> > behavior
>> >>> > of
>> >>> > this filter? I'm assuming that my input is reasonable, or is this
>> >>> > something
>> >>> > the filter is expected to have problems with? It is notable that
>> >>> > such
>> >>> > errors
>> >>> > seem to mainly appear in 'flat' regions of the volume, and are not
>> >>> > apparent
>> >>> > in the curved shaft of the bone.
>> >>> >
>> >>> > Any help, or pointers to further resources are appreciated,
>> >>> > thanks,
>> >>> > Tobias
>> >>> >
>> >>> > _____________________________________
>> >>> > 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
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>



-- 
Unpaid intern in BillsBasement at noware dot com

From grothausmann.roman at mh-hannover.de  Tue Aug 12 04:14:37 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Tue, 12 Aug 2014 10:14:37 +0200
Subject: [ITK-users] [ITK] adding a global hierarchical watershed
 segmentation mode to itksnap
In-Reply-To: <0f32755d9980441ca0162728b088f00b@queensu.ca>
References: <53E85181.8040607@mh-hannover.de>
 <0f32755d9980441ca0162728b088f00b@queensu.ca>
Message-ID: <53E9CCED.1000604@mh-hannover.de>

Hi Andras,


Many thanks for Your hints. We'll test them on our data. However, our data is 
not as standardized in quality as CT or MRT data and from our experience many of 
the "magic" segmentations demonstrated on CT or MRT data does not work on our data.
However, of all the segmentation modules I could find in Slicer or elsewhere 
none was based on a hierarchical watershed algorithm like the SegmentationEditor 
of the InsightApplications. Is there any other that I've missed?
Concerning my idea to implement this if no tool currently already exists:
Would such an extension be of more use in Slicer or itksnap?
For which of the both would it likely be easier to integrate the extension?

Best wishes
Roman

On 11/08/14 16:20, Andras Lasso wrote:
> Have you tried segmentation tools in 3D Slicer? There is a multi-label watershed
> segmentation tool that works in 3d
> (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Editor#WatershedFromMarkers),
> there are also a number of other generic semi-automatic segmentation tools (such
> as GrowCut) and a few fully-automatic specialized tools (for brain,
> airways, etc). Download the nightly build and also checkout the Segmentation
> category in the Extension Manager.
>
> Andras
>
> *From:* Dr. Roman Grothausmann <mailto:grothausmann.roman at mh-hannover.de>
> *Sent:* ?Monday?, ?August? ?11?, ?2014 ?1?:?15? ?AM
> *To:* itksnap-users at googlegroups.com <mailto:itksnap-users at googlegroups.com>
> *Cc:* ITK Mailing List <mailto:insight-users at itk.org>
>
> Dear mailing list members,
>
>
> For a long time now I've been searching for a replacement of the old
> SegmentationEditor (part of the InsightApplications) which I could not get to
> work even with older ITK-3.x. Somewhere I was told that it was integrated and
> maintained within itksnap. However the only tool in itksnap based on watershed
> segmentation seems to be the adaptive brush. It is very handy, but
> time-consuming in 3D and only for local segmentations. In contrast the
> SegmentationEditor used a global hierarchical watershed segmentation to pick
> labels from, see e.g. the video linked here:
> http://www.insight-journal.org/browse/publication/70
> Quite often now I've stumbled over data, that would likely have profited a lot
> of such a tool for segmentation.
>
> If such a tool working with ITK-4.x does not exist any more, I thought of
> implementing it as a global WS segmentation mode in itksnap. That way making the
> tool easier to find, to use and to ensure maintenance (should it be integrated
> into the itksnap code base in the end) and also avoiding recoding a GUI with
> mouse interaction and such.
>
> My current idea is to start, similar to the snake-tool, with pre-filtering like
> smoothing and optional edge-detection.
> Then the main edit mode to consist of the usual 4 subwindows showing an overlay
> of the grey-image and the watershed segmentation of the hierarchical WS-filter
> (hWS), side-by-side to another label-dataset (loaded like a tiled overlay) which
> consist of the actually chosen labels from the hWS as the final data (FD).
> The interaction I'm considering would be to LMB click on a label in the hWS
> which is then added to the FD as the current fg label, or removed with a RMB.
> The hierachrchy level of the hWS could be controlled by a slider or the mouse
> wheel + Shift in nearly real time if some region demands higher or lower
> detailed segmentation. When the fg label is changed, the segmentation added or
> removed with further mouse interactions would modify the new fg label.
> When all is done and the global WS mode is left, the FD label-dataset is added
> to the main segmentation of itksnap.
>
> Would that be possible to implement in itksnap 3.x?
> What source files of the itksnap code base should I look at for:
> - the pre-filtering mode of the snake (for the smoothing and edge detection)
> - the mouse interactions (for e.g. adding the whell + Shift interaction)
> - possible examples for the dual layout
>
> Thanks for any comments, help or hints.
> 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
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

-- 
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 gass at vision.ee.ethz.ch  Tue Aug 12 04:44:22 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Tue, 12 Aug 2014 10:44:22 +0200
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
 <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
 <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>
Message-ID: <CAKy7kk0H+V8nT+pQHEjjppCqCUA7me-Wwf45zUNQm03UJ0p3YA@mail.gmail.com>

Hi,

changing the PixelType did not yield any change. However, I did some
further tests which seem to point at image spacing or total size to be the
culprit. My original image is fairly high-res, with 0.25mm in-plane
resolution and 0.75mm slice thickness and 512x512x409 voxel size. I tried
resampling the image to different isotropic resolutions (0.25, 0.3, 0.34,
0.35, 0.4, 0.5, 0.75, 1)mm isotropic spacing. For all spacings down to
0.35mm, the AA filter converged nicely and the output looks as I'd expect
it. Lower than 0.35mm spacing, and it fails in the way I described (from
this spacing on the #vox is equal or greater than the #voxels in my
original image).

Any idea what might cause this, or what to further investigate?

Thanks,
Tobias


2014-08-11 22:17 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:

> Paraview should do the right thing.
>
> On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch>
> wrote:
> > I will try that tomorrow morning (living in GMT+1). I used paraview to
> > extract the isosurface, but also looked at the output of the AA-filter
> > directly (which looked fuzzy). I can also post an image of that tomorrow.
> >
> > Thanks for your help!
> > Tobias
> >
> >
> > 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
> >
> >> How are you extracting the final isosurface?
> >>
> >> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen <bill.lorensen at gmail.com
> >
> >> wrote:
> >> > If you change
> >> >  typedef  short PixelType;
> >> > to
> >> >  typedef  double PixelType;
> >> >
> >> > do the results change.
> >> >
> >> >
> >> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <gass at vision.ee.ethz.ch>
> >> > wrote:
> >> >>
> >> >>> Can you post your code. The results do not look correct.
> >> >>
> >> >>
> >> >> Sure. The {write,read}Image functions are just convenient wrappers
> for
> >> >> the
> >> >> respective ITK tools.
> >> >>
> >> >>
> >> >> #include <stdio.h>
> >> >>
> >> >> #include <iostream>
> >> >>
> >> >> #include "argstream.h"
> >> >>
> >> >> #include "ImageUtils.h"
> >> >>
> >> >> #include "itkAntiAliasBinaryImageFilter.h"
> >> >>
> >> >> using namespace std;
> >> >>
> >> >> using namespace itk;
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> int main(int argc, char ** argv)
> >> >>
> >> >> {
> >> >>
> >> >>
> >> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
> >> >>
> >> >>     typedef  short PixelType;
> >> >>
> >> >>     typedef double OutputPixelType;
> >> >>
> >> >>     const unsigned int D=3;
> >> >>
> >> >>     typedef Image<PixelType,D> ImageType;
> >> >>
> >> >>
> >> >>
> >> >>     typedef ImageType::Pointer ImagePointerType;
> >> >>
> >> >>
> >> >>
> >> >>     typedef Image<OutputPixelType,D> OutputImageType;
> >> >>
> >> >>     typedef OutputImageType::Pointer OutputImagePointerType;
> >> >>
> >> >>
> >> >>
> >> >>     argstream * as=new argstream(argc,argv);
> >> >>
> >> >>     string inFile, outFile;
> >> >>
> >> >>     double thresh=0.0;
> >> >>
> >> >>     (*as) >> parameter ("in", inFile, " filename...", true);
> >> >>
> >> >>     (*as) >> parameter ("out", outFile, " filename...", true);
> >> >>
> >> >>
> >> >>     (*as) >> help();
> >> >>
> >> >>     as->defaultErrorHandling();
> >> >>
> >> >>
> >> >>     ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);
> >> >>
> >> >>
> >> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType,
> >> >> OutputImageType>
> >> >>
> >> >>         AntiAliasBinaryImageFilterType;
> >> >>
> >> >>
> >> >>
> >> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
> >> >>
> >> >>         = AntiAliasBinaryImageFilterType::New ();
> >> >>
> >> >>     antiAliasFilter->SetInput(img);
> >> >>
> >> >>     antiAliasFilter->SetNumberOfIterations(5);
> >> >>
> >> >>     antiAliasFilter->SetMaximumRMSError(0.02);
> >> >>
> >> >>
> >> >>     antiAliasFilter->Update();
> >> >>
> >> >>
> >> >>   // For increased code coverage.  Does nothing.
> >> >>
> >> >>   antiAliasFilter->GetMaximumRMSError();
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>   antiAliasFilter->Update();
> >> >>
> >> >>
> >> >>   std::cout << "Maximum RMS change value threshold was: 0.02 " <<
> >> >> std::endl;
> >> >>
> >> >>   std::cout << "Last RMS change value was: " <<
> >> >> antiAliasFilter->GetRMSChange() << std::endl;
> >> >>
> >> >>
> >> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
> >> >>
> >> >>
> >> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
> >> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
> >> >>
> >> >>
> >> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
> >> >>
> >> >>
> >> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
> >> >>
> >> >>
> >> >> return 1;
> >> >>
> >> >> }
> >> >>
> >> >>
> >> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
> >> >> maxRMSError
> >> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved after
> >> >> one
> >> >> iteration where RMSE changes by about 0.08. This increases for all
> >> >> following
> >> >> iterations, which have an RMSE-change of about 0.25 for all number of
> >> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
> >> >> repository
> >> >> a while ago, running on an intel i7 on Debian.
> >> >>
> >> >> Thanks a lot!
> >> >> Tobias
> >> >>
> >> >>>
> >> >>>
> >> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <
> gass at vision.ee.ethz.ch>
> >> >>> wrote:
> >> >>> > Dear all,
> >> >>> >
> >> >>> > I'm having problems using the anti-alias filter, which I want to
> use
> >> >>> > in
> >> >>> > order to smooth a binary segmentation volume. I'm using
> essentially
> >> >>> > the
> >> >>> > example code from the repository, which for my input file seems to
> >> >>> > start
> >> >>> > oscillating after 2 iterations, leading to weird 'pointy'
> artifacts
> >> >>> > on
> >> >>> > the
> >> >>> > surface as can be seen from the attached screenshot (AA filter
> >> >>> > output is
> >> >>> > on
> >> >>> > the left, input on the right).
> >> >>> >
> >> >>> > Is there any parameter to set/implement which could improve the
> >> >>> > behavior
> >> >>> > of
> >> >>> > this filter? I'm assuming that my input is reasonable, or is this
> >> >>> > something
> >> >>> > the filter is expected to have problems with? It is notable that
> >> >>> > such
> >> >>> > errors
> >> >>> > seem to mainly appear in 'flat' regions of the volume, and are not
> >> >>> > apparent
> >> >>> > in the curved shaft of the bone.
> >> >>> >
> >> >>> > Any help, or pointers to further resources are appreciated,
> >> >>> > thanks,
> >> >>> > Tobias
> >> >>> >
> >> >>> > _____________________________________
> >> >>> > 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
> >>
> >>
> >>
> >> --
> >> Unpaid intern in BillsBasement at noware dot com
> >
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot 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/20140812/de98ddee/attachment.html>

From gass at vision.ee.ethz.ch  Tue Aug 12 08:33:14 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Tue, 12 Aug 2014 14:33:14 +0200
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CAKy7kk0H+V8nT+pQHEjjppCqCUA7me-Wwf45zUNQm03UJ0p3YA@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
 <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
 <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>
 <CAKy7kk0H+V8nT+pQHEjjppCqCUA7me-Wwf45zUNQm03UJ0p3YA@mail.gmail.com>
Message-ID: <CAKy7kk08y3ctkz-B8MavCVceRD+Fjq_QH5=9bWHJ8d8BdKz7fA@mail.gmail.com>

Update: meanwhile I also tried cropping the image to investigate the impact
of the overall size (#voxels) of the image. It appears to not have an
effect, the same artifacts occur when processing a significantly smaller
region (1/2 size).


2014-08-12 10:44 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:

> Hi,
>
> changing the PixelType did not yield any change. However, I did some
> further tests which seem to point at image spacing or total size to be the
> culprit. My original image is fairly high-res, with 0.25mm in-plane
> resolution and 0.75mm slice thickness and 512x512x409 voxel size. I tried
> resampling the image to different isotropic resolutions (0.25, 0.3, 0.34,
> 0.35, 0.4, 0.5, 0.75, 1)mm isotropic spacing. For all spacings down to
> 0.35mm, the AA filter converged nicely and the output looks as I'd expect
> it. Lower than 0.35mm spacing, and it fails in the way I described (from
> this spacing on the #vox is equal or greater than the #voxels in my
> original image).
>
> Any idea what might cause this, or what to further investigate?
>
> Thanks,
> Tobias
>
>
> 2014-08-11 22:17 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>
> Paraview should do the right thing.
>>
>> On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>> wrote:
>> > I will try that tomorrow morning (living in GMT+1). I used paraview to
>> > extract the isosurface, but also looked at the output of the AA-filter
>> > directly (which looked fuzzy). I can also post an image of that
>> tomorrow.
>> >
>> > Thanks for your help!
>> > Tobias
>> >
>> >
>> > 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>> >
>> >> How are you extracting the final isosurface?
>> >>
>> >> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen <
>> bill.lorensen at gmail.com>
>> >> wrote:
>> >> > If you change
>> >> >  typedef  short PixelType;
>> >> > to
>> >> >  typedef  double PixelType;
>> >> >
>> >> > do the results change.
>> >> >
>> >> >
>> >> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <gass at vision.ee.ethz.ch
>> >
>> >> > wrote:
>> >> >>
>> >> >>> Can you post your code. The results do not look correct.
>> >> >>
>> >> >>
>> >> >> Sure. The {write,read}Image functions are just convenient wrappers
>> for
>> >> >> the
>> >> >> respective ITK tools.
>> >> >>
>> >> >>
>> >> >> #include <stdio.h>
>> >> >>
>> >> >> #include <iostream>
>> >> >>
>> >> >> #include "argstream.h"
>> >> >>
>> >> >> #include "ImageUtils.h"
>> >> >>
>> >> >> #include "itkAntiAliasBinaryImageFilter.h"
>> >> >>
>> >> >> using namespace std;
>> >> >>
>> >> >> using namespace itk;
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> int main(int argc, char ** argv)
>> >> >>
>> >> >> {
>> >> >>
>> >> >>
>> >> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>> >> >>
>> >> >>     typedef  short PixelType;
>> >> >>
>> >> >>     typedef double OutputPixelType;
>> >> >>
>> >> >>     const unsigned int D=3;
>> >> >>
>> >> >>     typedef Image<PixelType,D> ImageType;
>> >> >>
>> >> >>
>> >> >>
>> >> >>     typedef ImageType::Pointer ImagePointerType;
>> >> >>
>> >> >>
>> >> >>
>> >> >>     typedef Image<OutputPixelType,D> OutputImageType;
>> >> >>
>> >> >>     typedef OutputImageType::Pointer OutputImagePointerType;
>> >> >>
>> >> >>
>> >> >>
>> >> >>     argstream * as=new argstream(argc,argv);
>> >> >>
>> >> >>     string inFile, outFile;
>> >> >>
>> >> >>     double thresh=0.0;
>> >> >>
>> >> >>     (*as) >> parameter ("in", inFile, " filename...", true);
>> >> >>
>> >> >>     (*as) >> parameter ("out", outFile, " filename...", true);
>> >> >>
>> >> >>
>> >> >>     (*as) >> help();
>> >> >>
>> >> >>     as->defaultErrorHandling();
>> >> >>
>> >> >>
>> >> >>     ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);
>> >> >>
>> >> >>
>> >> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType,
>> >> >> OutputImageType>
>> >> >>
>> >> >>         AntiAliasBinaryImageFilterType;
>> >> >>
>> >> >>
>> >> >>
>> >> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>> >> >>
>> >> >>         = AntiAliasBinaryImageFilterType::New ();
>> >> >>
>> >> >>     antiAliasFilter->SetInput(img);
>> >> >>
>> >> >>     antiAliasFilter->SetNumberOfIterations(5);
>> >> >>
>> >> >>     antiAliasFilter->SetMaximumRMSError(0.02);
>> >> >>
>> >> >>
>> >> >>     antiAliasFilter->Update();
>> >> >>
>> >> >>
>> >> >>   // For increased code coverage.  Does nothing.
>> >> >>
>> >> >>   antiAliasFilter->GetMaximumRMSError();
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>   antiAliasFilter->Update();
>> >> >>
>> >> >>
>> >> >>   std::cout << "Maximum RMS change value threshold was: 0.02 " <<
>> >> >> std::endl;
>> >> >>
>> >> >>   std::cout << "Last RMS change value was: " <<
>> >> >> antiAliasFilter->GetRMSChange() << std::endl;
>> >> >>
>> >> >>
>> >> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>> >> >>
>> >> >>
>> >> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
>> >> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>> >> >>
>> >> >>
>> >> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
>> >> >>
>> >> >>
>> >> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
>> >> >>
>> >> >>
>> >> >> return 1;
>> >> >>
>> >> >> }
>> >> >>
>> >> >>
>> >> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
>> >> >> maxRMSError
>> >> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved after
>> >> >> one
>> >> >> iteration where RMSE changes by about 0.08. This increases for all
>> >> >> following
>> >> >> iterations, which have an RMSE-change of about 0.25 for all number
>> of
>> >> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
>> >> >> repository
>> >> >> a while ago, running on an intel i7 on Debian.
>> >> >>
>> >> >> Thanks a lot!
>> >> >> Tobias
>> >> >>
>> >> >>>
>> >> >>>
>> >> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <
>> gass at vision.ee.ethz.ch>
>> >> >>> wrote:
>> >> >>> > Dear all,
>> >> >>> >
>> >> >>> > I'm having problems using the anti-alias filter, which I want to
>> use
>> >> >>> > in
>> >> >>> > order to smooth a binary segmentation volume. I'm using
>> essentially
>> >> >>> > the
>> >> >>> > example code from the repository, which for my input file seems
>> to
>> >> >>> > start
>> >> >>> > oscillating after 2 iterations, leading to weird 'pointy'
>> artifacts
>> >> >>> > on
>> >> >>> > the
>> >> >>> > surface as can be seen from the attached screenshot (AA filter
>> >> >>> > output is
>> >> >>> > on
>> >> >>> > the left, input on the right).
>> >> >>> >
>> >> >>> > Is there any parameter to set/implement which could improve the
>> >> >>> > behavior
>> >> >>> > of
>> >> >>> > this filter? I'm assuming that my input is reasonable, or is this
>> >> >>> > something
>> >> >>> > the filter is expected to have problems with? It is notable that
>> >> >>> > such
>> >> >>> > errors
>> >> >>> > seem to mainly appear in 'flat' regions of the volume, and are
>> not
>> >> >>> > apparent
>> >> >>> > in the curved shaft of the bone.
>> >> >>> >
>> >> >>> > Any help, or pointers to further resources are appreciated,
>> >> >>> > thanks,
>> >> >>> > Tobias
>> >> >>> >
>> >> >>> > _____________________________________
>> >> >>> > 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
>> >>
>> >>
>> >>
>> >> --
>> >> Unpaid intern in BillsBasement at noware dot com
>> >
>> >
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot 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/20140812/d14cff9c/attachment-0001.html>

From lasso at queensu.ca  Tue Aug 12 08:42:31 2014
From: lasso at queensu.ca (Andras Lasso)
Date: Tue, 12 Aug 2014 12:42:31 +0000
Subject: [ITK-users] [ITK] adding a global hierarchical watershed
 segmentation mode to itksnap
In-Reply-To: <53E9CCED.1000604@mh-hannover.de>
References: <53E85181.8040607@mh-hannover.de>
 <0f32755d9980441ca0162728b088f00b@queensu.ca>
 <53E9CCED.1000604@mh-hannover.de>
Message-ID: <B6FC5543F5C41E479B8B89158B0C58FFDF4FDE@MP-DUP-MBX-02.AD.QUEENSU.CA>

Hi Roman,

Try GrowCut segmentation. You paint a few strokes inside and outside your target(s) on one or a few slices and you may get a nice sementation. Using the FastGrowCut version you can edit/refine your inputs and as it is GPU-accelerated, it's fast (initial segmentation may take 20-30 seconds on a high-resolution volume but then the updates take just a few seconds).

I've just used ITKSnap a couple of times, so I don't know it much. Slicer is a large, more comprehensive application framework, with a large user and developer community. You can add new segmentation methods to Slicer by writing a Python script that can use VTK, ITK, numpy, etc. No developer tools are needed, no need to compile anything, just download Slicer and you are ready to go. Of course you can also develop in C++, if you prefer; and if you download Eclipse then you can do step-by-step debugging of your Python module in Slicer, etc. You can share your module with others by uploading it to the extension manager (Slicer app store). More info: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers.

Andras

-----Original Message-----
From: Dr. Roman Grothausmann [mailto:grothausmann.roman at mh-hannover.de] 
Sent: Tuesday, August 12, 2014 4:15 AM
To: Andras Lasso
Cc: itksnap-users at googlegroups.com; ITK Mailing List
Subject: Re: [ITK] [ITK-users] adding a global hierarchical watershed segmentation mode to itksnap

Hi Andras,


Many thanks for Your hints. We'll test them on our data. However, our data is not as standardized in quality as CT or MRT data and from our experience many of the "magic" segmentations demonstrated on CT or MRT data does not work on our data.
However, of all the segmentation modules I could find in Slicer or elsewhere none was based on a hierarchical watershed algorithm like the SegmentationEditor of the InsightApplications. Is there any other that I've missed?
Concerning my idea to implement this if no tool currently already exists:
Would such an extension be of more use in Slicer or itksnap?
For which of the both would it likely be easier to integrate the extension?

Best wishes
Roman

On 11/08/14 16:20, Andras Lasso wrote:
> Have you tried segmentation tools in 3D Slicer? There is a multi-label 
> watershed segmentation tool that works in 3d 
> (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modu
> les/Editor#WatershedFromMarkers), there are also a number of other 
> generic semi-automatic segmentation tools (such as GrowCut) and a few 
> fully-automatic specialized tools (for brain, airways, etc). Download 
> the nightly build and also checkout the Segmentation category in the 
> Extension Manager.
>
> Andras
>
> *From:* Dr. Roman Grothausmann 
> <mailto:grothausmann.roman at mh-hannover.de>
> *Sent:* ?Monday?, ?August? ?11?, ?2014 ?1?:?15? ?AM
> *To:* itksnap-users at googlegroups.com 
> <mailto:itksnap-users at googlegroups.com>
> *Cc:* ITK Mailing List <mailto:insight-users at itk.org>
>
> Dear mailing list members,
>
>
> For a long time now I've been searching for a replacement of the old 
> SegmentationEditor (part of the InsightApplications) which I could not 
> get to work even with older ITK-3.x. Somewhere I was told that it was 
> integrated and maintained within itksnap. However the only tool in 
> itksnap based on watershed segmentation seems to be the adaptive 
> brush. It is very handy, but time-consuming in 3D and only for local 
> segmentations. In contrast the SegmentationEditor used a global 
> hierarchical watershed segmentation to pick labels from, see e.g. the video linked here:
> http://www.insight-journal.org/browse/publication/70
> Quite often now I've stumbled over data, that would likely have 
> profited a lot of such a tool for segmentation.
>
> If such a tool working with ITK-4.x does not exist any more, I thought 
> of implementing it as a global WS segmentation mode in itksnap. That 
> way making the tool easier to find, to use and to ensure maintenance 
> (should it be integrated into the itksnap code base in the end) and 
> also avoiding recoding a GUI with mouse interaction and such.
>
> My current idea is to start, similar to the snake-tool, with 
> pre-filtering like smoothing and optional edge-detection.
> Then the main edit mode to consist of the usual 4 subwindows showing 
> an overlay of the grey-image and the watershed segmentation of the 
> hierarchical WS-filter (hWS), side-by-side to another label-dataset 
> (loaded like a tiled overlay) which consist of the actually chosen labels from the hWS as the final data (FD).
> The interaction I'm considering would be to LMB click on a label in 
> the hWS which is then added to the FD as the current fg label, or removed with a RMB.
> The hierachrchy level of the hWS could be controlled by a slider or 
> the mouse wheel + Shift in nearly real time if some region demands 
> higher or lower detailed segmentation. When the fg label is changed, 
> the segmentation added or removed with further mouse interactions would modify the new fg label.
> When all is done and the global WS mode is left, the FD label-dataset 
> is added to the main segmentation of itksnap.
>
> Would that be possible to implement in itksnap 3.x?
> What source files of the itksnap code base should I look at for:
> - the pre-filtering mode of the snake (for the smoothing and edge 
> detection)
> - the mouse interactions (for e.g. adding the whell + Shift 
> interaction)
> - possible examples for the dual layout
>
> Thanks for any comments, help or hints.
> 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
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

--
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 gass at vision.ee.ethz.ch  Tue Aug 12 08:47:00 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Tue, 12 Aug 2014 14:47:00 +0200
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CAKy7kk08y3ctkz-B8MavCVceRD+Fjq_QH5=9bWHJ8d8BdKz7fA@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
 <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
 <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>
 <CAKy7kk0H+V8nT+pQHEjjppCqCUA7me-Wwf45zUNQm03UJ0p3YA@mail.gmail.com>
 <CAKy7kk08y3ctkz-B8MavCVceRD+Fjq_QH5=9bWHJ8d8BdKz7fA@mail.gmail.com>
Message-ID: <CAKy7kk1CL=7K6uLi_E++MR4SuozSFQjkS-WijsoN2QKB_7bCqQ@mail.gmail.com>

Further update: when manually increasing the spacing of the input image
(without resampling, thus not changing the size), the filter works well.
This probably indicates numerical instability depending on image spacing
somewhere in the code, which would probably be great if it could be fixed.

Best,
Tobias


2014-08-12 14:33 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:

> Update: meanwhile I also tried cropping the image to investigate the
> impact of the overall size (#voxels) of the image. It appears to not have
> an effect, the same artifacts occur when processing a significantly smaller
> region (1/2 size).
>
>
> 2014-08-12 10:44 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
>
> Hi,
>>
>> changing the PixelType did not yield any change. However, I did some
>> further tests which seem to point at image spacing or total size to be the
>> culprit. My original image is fairly high-res, with 0.25mm in-plane
>> resolution and 0.75mm slice thickness and 512x512x409 voxel size. I tried
>> resampling the image to different isotropic resolutions (0.25, 0.3, 0.34,
>> 0.35, 0.4, 0.5, 0.75, 1)mm isotropic spacing. For all spacings down to
>> 0.35mm, the AA filter converged nicely and the output looks as I'd expect
>> it. Lower than 0.35mm spacing, and it fails in the way I described (from
>> this spacing on the #vox is equal or greater than the #voxels in my
>> original image).
>>
>> Any idea what might cause this, or what to further investigate?
>>
>> Thanks,
>> Tobias
>>
>>
>> 2014-08-11 22:17 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>>
>> Paraview should do the right thing.
>>>
>>> On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>>> wrote:
>>> > I will try that tomorrow morning (living in GMT+1). I used paraview to
>>> > extract the isosurface, but also looked at the output of the AA-filter
>>> > directly (which looked fuzzy). I can also post an image of that
>>> tomorrow.
>>> >
>>> > Thanks for your help!
>>> > Tobias
>>> >
>>> >
>>> > 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>>> >
>>> >> How are you extracting the final isosurface?
>>> >>
>>> >> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen <
>>> bill.lorensen at gmail.com>
>>> >> wrote:
>>> >> > If you change
>>> >> >  typedef  short PixelType;
>>> >> > to
>>> >> >  typedef  double PixelType;
>>> >> >
>>> >> > do the results change.
>>> >> >
>>> >> >
>>> >> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <
>>> gass at vision.ee.ethz.ch>
>>> >> > wrote:
>>> >> >>
>>> >> >>> Can you post your code. The results do not look correct.
>>> >> >>
>>> >> >>
>>> >> >> Sure. The {write,read}Image functions are just convenient wrappers
>>> for
>>> >> >> the
>>> >> >> respective ITK tools.
>>> >> >>
>>> >> >>
>>> >> >> #include <stdio.h>
>>> >> >>
>>> >> >> #include <iostream>
>>> >> >>
>>> >> >> #include "argstream.h"
>>> >> >>
>>> >> >> #include "ImageUtils.h"
>>> >> >>
>>> >> >> #include "itkAntiAliasBinaryImageFilter.h"
>>> >> >>
>>> >> >> using namespace std;
>>> >> >>
>>> >> >> using namespace itk;
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> int main(int argc, char ** argv)
>>> >> >>
>>> >> >> {
>>> >> >>
>>> >> >>
>>> >> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>>> >> >>
>>> >> >>     typedef  short PixelType;
>>> >> >>
>>> >> >>     typedef double OutputPixelType;
>>> >> >>
>>> >> >>     const unsigned int D=3;
>>> >> >>
>>> >> >>     typedef Image<PixelType,D> ImageType;
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>     typedef ImageType::Pointer ImagePointerType;
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>     typedef Image<OutputPixelType,D> OutputImageType;
>>> >> >>
>>> >> >>     typedef OutputImageType::Pointer OutputImagePointerType;
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>     argstream * as=new argstream(argc,argv);
>>> >> >>
>>> >> >>     string inFile, outFile;
>>> >> >>
>>> >> >>     double thresh=0.0;
>>> >> >>
>>> >> >>     (*as) >> parameter ("in", inFile, " filename...", true);
>>> >> >>
>>> >> >>     (*as) >> parameter ("out", outFile, " filename...", true);
>>> >> >>
>>> >> >>
>>> >> >>     (*as) >> help();
>>> >> >>
>>> >> >>     as->defaultErrorHandling();
>>> >> >>
>>> >> >>
>>> >> >>     ImagePointerType img =
>>> ImageUtils<ImageType>::readImage(inFile);
>>> >> >>
>>> >> >>
>>> >> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType,
>>> >> >> OutputImageType>
>>> >> >>
>>> >> >>         AntiAliasBinaryImageFilterType;
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>>> >> >>
>>> >> >>         = AntiAliasBinaryImageFilterType::New ();
>>> >> >>
>>> >> >>     antiAliasFilter->SetInput(img);
>>> >> >>
>>> >> >>     antiAliasFilter->SetNumberOfIterations(5);
>>> >> >>
>>> >> >>     antiAliasFilter->SetMaximumRMSError(0.02);
>>> >> >>
>>> >> >>
>>> >> >>     antiAliasFilter->Update();
>>> >> >>
>>> >> >>
>>> >> >>   // For increased code coverage.  Does nothing.
>>> >> >>
>>> >> >>   antiAliasFilter->GetMaximumRMSError();
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>   antiAliasFilter->Update();
>>> >> >>
>>> >> >>
>>> >> >>   std::cout << "Maximum RMS change value threshold was: 0.02 " <<
>>> >> >> std::endl;
>>> >> >>
>>> >> >>   std::cout << "Last RMS change value was: " <<
>>> >> >> antiAliasFilter->GetRMSChange() << std::endl;
>>> >> >>
>>> >> >>
>>> >> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>>> >> >>
>>> >> >>
>>> >> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
>>> >> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>>> >> >>
>>> >> >>
>>> >> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
>>> >> >>
>>> >> >>
>>> >> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
>>> >> >>
>>> >> >>
>>> >> >> return 1;
>>> >> >>
>>> >> >> }
>>> >> >>
>>> >> >>
>>> >> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
>>> >> >> maxRMSError
>>> >> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved
>>> after
>>> >> >> one
>>> >> >> iteration where RMSE changes by about 0.08. This increases for all
>>> >> >> following
>>> >> >> iterations, which have an RMSE-change of about 0.25 for all number
>>> of
>>> >> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
>>> >> >> repository
>>> >> >> a while ago, running on an intel i7 on Debian.
>>> >> >>
>>> >> >> Thanks a lot!
>>> >> >> Tobias
>>> >> >>
>>> >> >>>
>>> >> >>>
>>> >> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <
>>> gass at vision.ee.ethz.ch>
>>> >> >>> wrote:
>>> >> >>> > Dear all,
>>> >> >>> >
>>> >> >>> > I'm having problems using the anti-alias filter, which I want
>>> to use
>>> >> >>> > in
>>> >> >>> > order to smooth a binary segmentation volume. I'm using
>>> essentially
>>> >> >>> > the
>>> >> >>> > example code from the repository, which for my input file seems
>>> to
>>> >> >>> > start
>>> >> >>> > oscillating after 2 iterations, leading to weird 'pointy'
>>> artifacts
>>> >> >>> > on
>>> >> >>> > the
>>> >> >>> > surface as can be seen from the attached screenshot (AA filter
>>> >> >>> > output is
>>> >> >>> > on
>>> >> >>> > the left, input on the right).
>>> >> >>> >
>>> >> >>> > Is there any parameter to set/implement which could improve the
>>> >> >>> > behavior
>>> >> >>> > of
>>> >> >>> > this filter? I'm assuming that my input is reasonable, or is
>>> this
>>> >> >>> > something
>>> >> >>> > the filter is expected to have problems with? It is notable that
>>> >> >>> > such
>>> >> >>> > errors
>>> >> >>> > seem to mainly appear in 'flat' regions of the volume, and are
>>> not
>>> >> >>> > apparent
>>> >> >>> > in the curved shaft of the bone.
>>> >> >>> >
>>> >> >>> > Any help, or pointers to further resources are appreciated,
>>> >> >>> > thanks,
>>> >> >>> > Tobias
>>> >> >>> >
>>> >> >>> > _____________________________________
>>> >> >>> > 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
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Unpaid intern in BillsBasement at noware dot com
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> Unpaid intern in BillsBasement at noware dot 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/20140812/efed2c9c/attachment.html>

From bill.lorensen at gmail.com  Tue Aug 12 09:06:22 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 12 Aug 2014 09:06:22 -0400
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CAKy7kk1CL=7K6uLi_E++MR4SuozSFQjkS-WijsoN2QKB_7bCqQ@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
 <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
 <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>
 <CAKy7kk0H+V8nT+pQHEjjppCqCUA7me-Wwf45zUNQm03UJ0p3YA@mail.gmail.com>
 <CAKy7kk08y3ctkz-B8MavCVceRD+Fjq_QH5=9bWHJ8d8BdKz7fA@mail.gmail.com>
 <CAKy7kk1CL=7K6uLi_E++MR4SuozSFQjkS-WijsoN2QKB_7bCqQ@mail.gmail.com>
Message-ID: <CADZJ4hNnSoHa2BuW_gqiydYKHwhXo8T7j2W07Vy6kLDJ5pEUCg@mail.gmail.com>

Have you tried:
UseImageSpacingOn();


On Tue, Aug 12, 2014 at 8:47 AM, Tobias Gass <gass at vision.ee.ethz.ch> wrote:
> Further update: when manually increasing the spacing of the input image
> (without resampling, thus not changing the size), the filter works well.
> This probably indicates numerical instability depending on image spacing
> somewhere in the code, which would probably be great if it could be fixed.
>
> Best,
> Tobias
>
>
> 2014-08-12 14:33 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
>
>> Update: meanwhile I also tried cropping the image to investigate the
>> impact of the overall size (#voxels) of the image. It appears to not have an
>> effect, the same artifacts occur when processing a significantly smaller
>> region (1/2 size).
>>
>>
>> 2014-08-12 10:44 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
>>
>>> Hi,
>>>
>>> changing the PixelType did not yield any change. However, I did some
>>> further tests which seem to point at image spacing or total size to be the
>>> culprit. My original image is fairly high-res, with 0.25mm in-plane
>>> resolution and 0.75mm slice thickness and 512x512x409 voxel size. I tried
>>> resampling the image to different isotropic resolutions (0.25, 0.3, 0.34,
>>> 0.35, 0.4, 0.5, 0.75, 1)mm isotropic spacing. For all spacings down to
>>> 0.35mm, the AA filter converged nicely and the output looks as I'd expect
>>> it. Lower than 0.35mm spacing, and it fails in the way I described (from
>>> this spacing on the #vox is equal or greater than the #voxels in my original
>>> image).
>>>
>>> Any idea what might cause this, or what to further investigate?
>>>
>>> Thanks,
>>> Tobias
>>>
>>>
>>> 2014-08-11 22:17 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>>>
>>>> Paraview should do the right thing.
>>>>
>>>> On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>>>> wrote:
>>>> > I will try that tomorrow morning (living in GMT+1). I used paraview to
>>>> > extract the isosurface, but also looked at the output of the AA-filter
>>>> > directly (which looked fuzzy). I can also post an image of that
>>>> > tomorrow.
>>>> >
>>>> > Thanks for your help!
>>>> > Tobias
>>>> >
>>>> >
>>>> > 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>>>> >
>>>> >> How are you extracting the final isosurface?
>>>> >>
>>>> >> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen
>>>> >> <bill.lorensen at gmail.com>
>>>> >> wrote:
>>>> >> > If you change
>>>> >> >  typedef  short PixelType;
>>>> >> > to
>>>> >> >  typedef  double PixelType;
>>>> >> >
>>>> >> > do the results change.
>>>> >> >
>>>> >> >
>>>> >> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass
>>>> >> > <gass at vision.ee.ethz.ch>
>>>> >> > wrote:
>>>> >> >>
>>>> >> >>> Can you post your code. The results do not look correct.
>>>> >> >>
>>>> >> >>
>>>> >> >> Sure. The {write,read}Image functions are just convenient wrappers
>>>> >> >> for
>>>> >> >> the
>>>> >> >> respective ITK tools.
>>>> >> >>
>>>> >> >>
>>>> >> >> #include <stdio.h>
>>>> >> >>
>>>> >> >> #include <iostream>
>>>> >> >>
>>>> >> >> #include "argstream.h"
>>>> >> >>
>>>> >> >> #include "ImageUtils.h"
>>>> >> >>
>>>> >> >> #include "itkAntiAliasBinaryImageFilter.h"
>>>> >> >>
>>>> >> >> using namespace std;
>>>> >> >>
>>>> >> >> using namespace itk;
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >> int main(int argc, char ** argv)
>>>> >> >>
>>>> >> >> {
>>>> >> >>
>>>> >> >>
>>>> >> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>>>> >> >>
>>>> >> >>     typedef  short PixelType;
>>>> >> >>
>>>> >> >>     typedef double OutputPixelType;
>>>> >> >>
>>>> >> >>     const unsigned int D=3;
>>>> >> >>
>>>> >> >>     typedef Image<PixelType,D> ImageType;
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>     typedef ImageType::Pointer ImagePointerType;
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>     typedef Image<OutputPixelType,D> OutputImageType;
>>>> >> >>
>>>> >> >>     typedef OutputImageType::Pointer OutputImagePointerType;
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>     argstream * as=new argstream(argc,argv);
>>>> >> >>
>>>> >> >>     string inFile, outFile;
>>>> >> >>
>>>> >> >>     double thresh=0.0;
>>>> >> >>
>>>> >> >>     (*as) >> parameter ("in", inFile, " filename...", true);
>>>> >> >>
>>>> >> >>     (*as) >> parameter ("out", outFile, " filename...", true);
>>>> >> >>
>>>> >> >>
>>>> >> >>     (*as) >> help();
>>>> >> >>
>>>> >> >>     as->defaultErrorHandling();
>>>> >> >>
>>>> >> >>
>>>> >> >>     ImagePointerType img =
>>>> >> >> ImageUtils<ImageType>::readImage(inFile);
>>>> >> >>
>>>> >> >>
>>>> >> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType,
>>>> >> >> OutputImageType>
>>>> >> >>
>>>> >> >>         AntiAliasBinaryImageFilterType;
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>>>> >> >>
>>>> >> >>         = AntiAliasBinaryImageFilterType::New ();
>>>> >> >>
>>>> >> >>     antiAliasFilter->SetInput(img);
>>>> >> >>
>>>> >> >>     antiAliasFilter->SetNumberOfIterations(5);
>>>> >> >>
>>>> >> >>     antiAliasFilter->SetMaximumRMSError(0.02);
>>>> >> >>
>>>> >> >>
>>>> >> >>     antiAliasFilter->Update();
>>>> >> >>
>>>> >> >>
>>>> >> >>   // For increased code coverage.  Does nothing.
>>>> >> >>
>>>> >> >>   antiAliasFilter->GetMaximumRMSError();
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >>   antiAliasFilter->Update();
>>>> >> >>
>>>> >> >>
>>>> >> >>   std::cout << "Maximum RMS change value threshold was: 0.02 " <<
>>>> >> >> std::endl;
>>>> >> >>
>>>> >> >>   std::cout << "Last RMS change value was: " <<
>>>> >> >> antiAliasFilter->GetRMSChange() << std::endl;
>>>> >> >>
>>>> >> >>
>>>> >> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>>>> >> >>
>>>> >> >>
>>>> >> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
>>>> >> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>>>> >> >>
>>>> >> >>
>>>> >> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
>>>> >> >>
>>>> >> >>
>>>> >> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
>>>> >> >>
>>>> >> >>
>>>> >> >> return 1;
>>>> >> >>
>>>> >> >> }
>>>> >> >>
>>>> >> >>
>>>> >> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
>>>> >> >> maxRMSError
>>>> >> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved
>>>> >> >> after
>>>> >> >> one
>>>> >> >> iteration where RMSE changes by about 0.08. This increases for all
>>>> >> >> following
>>>> >> >> iterations, which have an RMSE-change of about 0.25 for all number
>>>> >> >> of
>>>> >> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
>>>> >> >> repository
>>>> >> >> a while ago, running on an intel i7 on Debian.
>>>> >> >>
>>>> >> >> Thanks a lot!
>>>> >> >> Tobias
>>>> >> >>
>>>> >> >>>
>>>> >> >>>
>>>> >> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass
>>>> >> >>> <gass at vision.ee.ethz.ch>
>>>> >> >>> wrote:
>>>> >> >>> > Dear all,
>>>> >> >>> >
>>>> >> >>> > I'm having problems using the anti-alias filter, which I want
>>>> >> >>> > to use
>>>> >> >>> > in
>>>> >> >>> > order to smooth a binary segmentation volume. I'm using
>>>> >> >>> > essentially
>>>> >> >>> > the
>>>> >> >>> > example code from the repository, which for my input file seems
>>>> >> >>> > to
>>>> >> >>> > start
>>>> >> >>> > oscillating after 2 iterations, leading to weird 'pointy'
>>>> >> >>> > artifacts
>>>> >> >>> > on
>>>> >> >>> > the
>>>> >> >>> > surface as can be seen from the attached screenshot (AA filter
>>>> >> >>> > output is
>>>> >> >>> > on
>>>> >> >>> > the left, input on the right).
>>>> >> >>> >
>>>> >> >>> > Is there any parameter to set/implement which could improve the
>>>> >> >>> > behavior
>>>> >> >>> > of
>>>> >> >>> > this filter? I'm assuming that my input is reasonable, or is
>>>> >> >>> > this
>>>> >> >>> > something
>>>> >> >>> > the filter is expected to have problems with? It is notable
>>>> >> >>> > that
>>>> >> >>> > such
>>>> >> >>> > errors
>>>> >> >>> > seem to mainly appear in 'flat' regions of the volume, and are
>>>> >> >>> > not
>>>> >> >>> > apparent
>>>> >> >>> > in the curved shaft of the bone.
>>>> >> >>> >
>>>> >> >>> > Any help, or pointers to further resources are appreciated,
>>>> >> >>> > thanks,
>>>> >> >>> > Tobias
>>>> >> >>> >
>>>> >> >>> > _____________________________________
>>>> >> >>> > 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
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >> Unpaid intern in BillsBasement at noware dot com
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Unpaid intern in BillsBasement at noware dot 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
>>>
>>>
>>
>



-- 
Unpaid intern in BillsBasement at noware dot com

From gass at vision.ee.ethz.ch  Tue Aug 12 10:10:34 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Tue, 12 Aug 2014 16:10:34 +0200
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CADZJ4hNnSoHa2BuW_gqiydYKHwhXo8T7j2W07Vy6kLDJ5pEUCg@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
 <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
 <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>
 <CAKy7kk0H+V8nT+pQHEjjppCqCUA7me-Wwf45zUNQm03UJ0p3YA@mail.gmail.com>
 <CAKy7kk08y3ctkz-B8MavCVceRD+Fjq_QH5=9bWHJ8d8BdKz7fA@mail.gmail.com>
 <CAKy7kk1CL=7K6uLi_E++MR4SuozSFQjkS-WijsoN2QKB_7bCqQ@mail.gmail.com>
 <CADZJ4hNnSoHa2BuW_gqiydYKHwhXo8T7j2W07Vy6kLDJ5pEUCg@mail.gmail.com>
Message-ID: <CAKy7kk2MWfxuHiY82xV_3Dmp5oGjwWpvd7ckJws5CJyaMP7Q6g@mail.gmail.com>

Yes, this does result in the same problems as before.


2014-08-12 15:06 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:

> Have you tried:
> UseImageSpacingOn();
>
>
> On Tue, Aug 12, 2014 at 8:47 AM, Tobias Gass <gass at vision.ee.ethz.ch>
> wrote:
> > Further update: when manually increasing the spacing of the input image
> > (without resampling, thus not changing the size), the filter works well.
> > This probably indicates numerical instability depending on image spacing
> > somewhere in the code, which would probably be great if it could be
> fixed.
> >
> > Best,
> > Tobias
> >
> >
> > 2014-08-12 14:33 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
> >
> >> Update: meanwhile I also tried cropping the image to investigate the
> >> impact of the overall size (#voxels) of the image. It appears to not
> have an
> >> effect, the same artifacts occur when processing a significantly smaller
> >> region (1/2 size).
> >>
> >>
> >> 2014-08-12 10:44 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
> >>
> >>> Hi,
> >>>
> >>> changing the PixelType did not yield any change. However, I did some
> >>> further tests which seem to point at image spacing or total size to be
> the
> >>> culprit. My original image is fairly high-res, with 0.25mm in-plane
> >>> resolution and 0.75mm slice thickness and 512x512x409 voxel size. I
> tried
> >>> resampling the image to different isotropic resolutions (0.25, 0.3,
> 0.34,
> >>> 0.35, 0.4, 0.5, 0.75, 1)mm isotropic spacing. For all spacings down to
> >>> 0.35mm, the AA filter converged nicely and the output looks as I'd
> expect
> >>> it. Lower than 0.35mm spacing, and it fails in the way I described
> (from
> >>> this spacing on the #vox is equal or greater than the #voxels in my
> original
> >>> image).
> >>>
> >>> Any idea what might cause this, or what to further investigate?
> >>>
> >>> Thanks,
> >>> Tobias
> >>>
> >>>
> >>> 2014-08-11 22:17 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
> >>>
> >>>> Paraview should do the right thing.
> >>>>
> >>>> On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch>
> >>>> wrote:
> >>>> > I will try that tomorrow morning (living in GMT+1). I used paraview
> to
> >>>> > extract the isosurface, but also looked at the output of the
> AA-filter
> >>>> > directly (which looked fuzzy). I can also post an image of that
> >>>> > tomorrow.
> >>>> >
> >>>> > Thanks for your help!
> >>>> > Tobias
> >>>> >
> >>>> >
> >>>> > 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
> >>>> >
> >>>> >> How are you extracting the final isosurface?
> >>>> >>
> >>>> >> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen
> >>>> >> <bill.lorensen at gmail.com>
> >>>> >> wrote:
> >>>> >> > If you change
> >>>> >> >  typedef  short PixelType;
> >>>> >> > to
> >>>> >> >  typedef  double PixelType;
> >>>> >> >
> >>>> >> > do the results change.
> >>>> >> >
> >>>> >> >
> >>>> >> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass
> >>>> >> > <gass at vision.ee.ethz.ch>
> >>>> >> > wrote:
> >>>> >> >>
> >>>> >> >>> Can you post your code. The results do not look correct.
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> Sure. The {write,read}Image functions are just convenient
> wrappers
> >>>> >> >> for
> >>>> >> >> the
> >>>> >> >> respective ITK tools.
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> #include <stdio.h>
> >>>> >> >>
> >>>> >> >> #include <iostream>
> >>>> >> >>
> >>>> >> >> #include "argstream.h"
> >>>> >> >>
> >>>> >> >> #include "ImageUtils.h"
> >>>> >> >>
> >>>> >> >> #include "itkAntiAliasBinaryImageFilter.h"
> >>>> >> >>
> >>>> >> >> using namespace std;
> >>>> >> >>
> >>>> >> >> using namespace itk;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> int main(int argc, char ** argv)
> >>>> >> >>
> >>>> >> >> {
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
> >>>> >> >>
> >>>> >> >>     typedef  short PixelType;
> >>>> >> >>
> >>>> >> >>     typedef double OutputPixelType;
> >>>> >> >>
> >>>> >> >>     const unsigned int D=3;
> >>>> >> >>
> >>>> >> >>     typedef Image<PixelType,D> ImageType;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     typedef ImageType::Pointer ImagePointerType;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     typedef Image<OutputPixelType,D> OutputImageType;
> >>>> >> >>
> >>>> >> >>     typedef OutputImageType::Pointer OutputImagePointerType;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     argstream * as=new argstream(argc,argv);
> >>>> >> >>
> >>>> >> >>     string inFile, outFile;
> >>>> >> >>
> >>>> >> >>     double thresh=0.0;
> >>>> >> >>
> >>>> >> >>     (*as) >> parameter ("in", inFile, " filename...", true);
> >>>> >> >>
> >>>> >> >>     (*as) >> parameter ("out", outFile, " filename...", true);
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     (*as) >> help();
> >>>> >> >>
> >>>> >> >>     as->defaultErrorHandling();
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     ImagePointerType img =
> >>>> >> >> ImageUtils<ImageType>::readImage(inFile);
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType,
> >>>> >> >> OutputImageType>
> >>>> >> >>
> >>>> >> >>         AntiAliasBinaryImageFilterType;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
> >>>> >> >>
> >>>> >> >>         = AntiAliasBinaryImageFilterType::New ();
> >>>> >> >>
> >>>> >> >>     antiAliasFilter->SetInput(img);
> >>>> >> >>
> >>>> >> >>     antiAliasFilter->SetNumberOfIterations(5);
> >>>> >> >>
> >>>> >> >>     antiAliasFilter->SetMaximumRMSError(0.02);
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     antiAliasFilter->Update();
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>   // For increased code coverage.  Does nothing.
> >>>> >> >>
> >>>> >> >>   antiAliasFilter->GetMaximumRMSError();
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>   antiAliasFilter->Update();
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>   std::cout << "Maximum RMS change value threshold was: 0.02 "
> <<
> >>>> >> >> std::endl;
> >>>> >> >>
> >>>> >> >>   std::cout << "Last RMS change value was: " <<
> >>>> >> >> antiAliasFilter->GetRMSChange() << std::endl;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
> >>>> >> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> return 1;
> >>>> >> >>
> >>>> >> >> }
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
> >>>> >> >> maxRMSError
> >>>> >> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved
> >>>> >> >> after
> >>>> >> >> one
> >>>> >> >> iteration where RMSE changes by about 0.08. This increases for
> all
> >>>> >> >> following
> >>>> >> >> iterations, which have an RMSE-change of about 0.25 for all
> number
> >>>> >> >> of
> >>>> >> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
> >>>> >> >> repository
> >>>> >> >> a while ago, running on an intel i7 on Debian.
> >>>> >> >>
> >>>> >> >> Thanks a lot!
> >>>> >> >> Tobias
> >>>> >> >>
> >>>> >> >>>
> >>>> >> >>>
> >>>> >> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass
> >>>> >> >>> <gass at vision.ee.ethz.ch>
> >>>> >> >>> wrote:
> >>>> >> >>> > Dear all,
> >>>> >> >>> >
> >>>> >> >>> > I'm having problems using the anti-alias filter, which I want
> >>>> >> >>> > to use
> >>>> >> >>> > in
> >>>> >> >>> > order to smooth a binary segmentation volume. I'm using
> >>>> >> >>> > essentially
> >>>> >> >>> > the
> >>>> >> >>> > example code from the repository, which for my input file
> seems
> >>>> >> >>> > to
> >>>> >> >>> > start
> >>>> >> >>> > oscillating after 2 iterations, leading to weird 'pointy'
> >>>> >> >>> > artifacts
> >>>> >> >>> > on
> >>>> >> >>> > the
> >>>> >> >>> > surface as can be seen from the attached screenshot (AA
> filter
> >>>> >> >>> > output is
> >>>> >> >>> > on
> >>>> >> >>> > the left, input on the right).
> >>>> >> >>> >
> >>>> >> >>> > Is there any parameter to set/implement which could improve
> the
> >>>> >> >>> > behavior
> >>>> >> >>> > of
> >>>> >> >>> > this filter? I'm assuming that my input is reasonable, or is
> >>>> >> >>> > this
> >>>> >> >>> > something
> >>>> >> >>> > the filter is expected to have problems with? It is notable
> >>>> >> >>> > that
> >>>> >> >>> > such
> >>>> >> >>> > errors
> >>>> >> >>> > seem to mainly appear in 'flat' regions of the volume, and
> are
> >>>> >> >>> > not
> >>>> >> >>> > apparent
> >>>> >> >>> > in the curved shaft of the bone.
> >>>> >> >>> >
> >>>> >> >>> > Any help, or pointers to further resources are appreciated,
> >>>> >> >>> > thanks,
> >>>> >> >>> > Tobias
> >>>> >> >>> >
> >>>> >> >>> > _____________________________________
> >>>> >> >>> > 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
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >> --
> >>>> >> Unpaid intern in BillsBasement at noware dot com
> >>>> >
> >>>> >
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Unpaid intern in BillsBasement at noware dot 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
> >>>
> >>>
> >>
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140812/9091ed93/attachment.html>

From mercikd at thomas.edu  Tue Aug 12 19:06:35 2014
From: mercikd at thomas.edu (Dan Mercik)
Date: Tue, 12 Aug 2014 23:06:35 +0000
Subject: [ITK-users] TileImageFilter SideBySide
Message-ID: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>

Good Afternoon,



                    I want to know if it's possible to have more than two image be side by side vertically? If so what would I have to change in the algorithm, would I have to make a loop for the amount of input images? Any help would be greatly appreciative.



Daniel Mercik

Computer Science Major

Service Desk Technician

Thomas College

From michkapopoff at gmail.com  Wed Aug 13 02:32:21 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Wed, 13 Aug 2014 08:32:21 +0200
Subject: [ITK-users] TileImageFilter SideBySide
In-Reply-To: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>
References: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>
Message-ID: <F5E240B8-8207-40A1-A754-219F86CEA066@gmail.com>

Hi

Moving this mail to the new community mailing list

For your problem, you should use the setLayout method [1]

For 4 images, that would be:

itk::FixedArray< unsigned int, 2 > layout;
 
layout[0] = 4;
layout[1] = 0;

Michka

[1] http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_SideBySide

On 13 ao?t 2014, at 01:06, Dan Mercik <mercikd at thomas.edu> wrote:

> Good Afternoon,
> 
> 
> 
>                    I want to know if it's possible to have more than two image be side by side vertically? If so what would I have to change in the algorithm, would I have to make a loop for the amount of input images? Any help would be greatly appreciative.
> 
> 
> 
> Daniel Mercik
> 
> Computer Science Major
> 
> Service Desk Technician
> 
> Thomas College
> _____________________________________
> 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/20140813/812cc5f6/attachment.html>

From sebastian.ordas at gmail.com  Wed Aug 13 13:50:24 2014
From: sebastian.ordas at gmail.com (Sebastian Ordas)
Date: Wed, 13 Aug 2014 14:50:24 -0300
Subject: [ITK-users] FDA agile practices guidance
Message-ID: <53EBA560.208@gmail.com>

Hello friends,

Sorry if it is not the right place for asking this question, but does 
anyone know about resources about FDA guidances for implementing agile 
practices in the development of medical device software? In concrete, 
the document AAMI TIR45:2012 is the one I am seeking online.

thank you,
sebastian

From Jared.Becksfort at STJUDE.ORG  Wed Aug 13 13:57:54 2014
From: Jared.Becksfort at STJUDE.ORG (Becksfort, Jared)
Date: Wed, 13 Aug 2014 12:57:54 -0500
Subject: [ITK-users] Rotation or registration by plane
Message-ID: <D0111152.394A%jared.becksfort@stjude.org>

Hello,

Sorry if this is a dumb question (I feel like it may be).

I have a plane in an MRI.  I would like to either:

 *   Change the coordinate system to refer to this plane (transform coordinates by plane)
 *   Transform the image so that this plane is in the center (transform image by plane)

Is there a registration algorithm that allows this?

Thanks,
Jared

________________________________
Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer


From grothausmann.roman at mh-hannover.de  Thu Aug 14 06:42:10 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Thu, 14 Aug 2014 12:42:10 +0200
Subject: [ITK-users] [ITK] adding a global hierarchical watershed
 segmentation mode to itksnap
In-Reply-To: <CAPR4OGOdH3-OjhhkT-5y9y77_eX-dVxLZd39vek-57bcuNm8vw@mail.gmail.com>
References: <53E85181.8040607@mh-hannover.de>
 <0f32755d9980441ca0162728b088f00b@queensu.ca>
 <53E9CCED.1000604@mh-hannover.de>
 <CAPR4OGOdH3-OjhhkT-5y9y77_eX-dVxLZd39vek-57bcuNm8vw@mail.gmail.com>
Message-ID: <53EC9282.3090904@mh-hannover.de>

Hi Paul,


Many thanks for Your reply. The main problem that I often face with samples from 
material science is, that around 1000 labels are needed per tomogram, e.g. 
individual particles, regions, domains. So setting markers by hand is already 
very timeconsuming. Expanding each of these one after another is way to 
cumbersum. I'm not sure if I have tried clustering. At least it was not 
available as preprocessing mode (possibly because I only have a greyscale 
tomogram) as described in the ReleaseNotes (is there any other new docu?). I did 
not try supervised classification because dev32 does not run on our system and 
the self-compiled binary crashes at start up with a segmentation fault (see below).
Anyway it seems not possible to have the snake-tool make multiple labels compete 
against each other, as e.g. in a global watershed approach.
I'd be very happy if there was already a tool in order to achieve what I need 
but it seems there isn't, so I guess I've to start creating my own.

With Andras hint about using Slicer, I'm now wondering whether I should 
implement it for itksnap or slicer. None of both seem to have a tool to 
join/remove labels from a base map to a result map by just LMB/RMB clicking, 
which I would find very helpful.
Adding a hierarchical watershed to generate the base map and using the mouse 
wheel to change the level/granularity on the fly would then just be an extension.
A tile view (e.g. both maps side by side) for all three axes as in itksnap would 
be handy for this join/remove tool. Does Slicer offer something like that as well?
Is it possible to get also the overlay id together with the click position? That 
would even allow to choose an already existing label in the result map for 
modification by just a click.

Any further recommendations for the start are very welcome.
Thanks,
Roman

______________________

LD_LIBRARY_PATH=/opt/itk-4.5.1/lib/:/opt/qt-5.3.1/5.3/gcc_64/lib/ vglrun 
./ITK-SNAP
QXcbConnection: Failed to initialize XRandr
Qt: XKEYBOARD extension not present on the X server.
*************************************
ITK-SNAP: Segmentation fault
BACKTRACE:
./ITK-SNAP(_Z24SegmentationFaultHandleri+0x133)[0x7af9c3]
/lib/x86_64-linux-gnu/libc.so.6(+0x324f0)[0x7f6e977224f0]
/lib/x86_64-linux-gnu/libc.so.6(+0x11aedf)[0x7f6e9780aedf]
/opt/qt-5.3.1/5.3/gcc_64/lib/libQt5Core.so.5(_ZN16QCoreApplication9argumentsEv+0x8c)[0x7f6ea8dbf6bc]
/opt/qt-5.3.1/5.3/gcc_64/plugins/platforms/libqxcb.so(+0x4b213)[0x7f6e907df213]
/opt/qt-5.3.1/5.3/gcc_64/plugins/platforms/libqxcb.so(+0x4b5f9)[0x7f6e907df5f9]
/opt/qt-5.3.1/5.3/gcc_64/plugins/platforms/libqxcb.so(+0x58127)[0x7f6e907ec127]
/opt/qt-5.3.1/5.3/gcc_64/plugins/platforms/libqxcb.so(+0x4b009)[0x7f6e907df009]
/opt/qt-5.3.1/5.3/gcc_64/lib/libQt5Gui.so.5(_ZN7QWindow6createEv+0x33)[0x7f6ea9e89e03]
/opt/qt-5.3.1/5.3/gcc_64/lib/libQt5OpenGL.so.5(_ZN10QGLContext13chooseContextEPKS_+0x121)[0x7f6eaad4bf51]
/opt/qt-5.3.1/5.3/gcc_64/lib/libQt5OpenGL.so.5(_ZN10QGLContext6createEPKS_+0x39)[0x7f6eaad23609]
/opt/qt-5.3.1/5.3/gcc_64/lib/libQt5OpenGL.so.5(_ZN9QGLWidget10setContextEP10QGLContextPKS0_b+0xa7)[0x7f6eaad4b8b7]
/opt/qt-5.3.1/5.3/gcc_64/lib/libQt5OpenGL.so.5(_ZN16QGLWidgetPrivate11initContextEP10QGLContextPK9QGLWidget+0x7a)[0x7f6eaad28c2a]
/opt/qt-5.3.1/5.3/gcc_64/lib/libQt5OpenGL.so.5(_ZN9QGLWidgetC2EP7QWidgetPKS_6QFlagsIN2Qt10WindowTypeEE+0x111)[0x7f6eaad29031]
./ITK-SNAP(_ZN19QtAbstractOpenGLBoxC1EP7QWidget+0xd)[0x849e3d]
./ITK-SNAP(_ZN16GenericSliceViewC2EP7QWidget+0x10)[0x848310]
./ITK-SNAP(_ZN17Ui_SliceViewPanel7setupUiEP7QWidget+0x235f)[0x840fbf]
./ITK-SNAP(_ZN14SliceViewPanelC1EP7QWidget+0x53)[0x839fc3]
./ITK-SNAP(_ZN18Ui_MainImageWindow7setupUiEP11QMainWindow+0x336b)[0x7d77bb]
./ITK-SNAP(_ZN15MainImageWindowC2EP7QWidget+0x64)[0x7c47b4]
./ITK-SNAP(main+0x1b3)[0x7aa8c3]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x7f6e9770eead]
./ITK-SNAP[0x7af6f9]
*************************************



On 13/08/14 22:15, Paul Yushkevich wrote:
> Hi Roman,
>
> I am not sure, have you experimented with some of the newer segmentation modes
> in ITK-SNAP (clustering, available in the 3.0 release, and supervised
> classification, available in the dev32 branch). These still operate using active
> contours, but can generate per-label probability maps that could then be easily
> converted into multilabel segmentations. I guess my main question is whether
> heirarchical watershed segmentation offers advantages over these modes, and if
> so, whether it may possibly be integrated as another segmentation mode in the
> snake pipeline...
>
> Paul.
>
>
> On Tue, Aug 12, 2014 at 4:14 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de <mailto:grothausmann.roman at mh-hannover.de>>
> wrote:
>
>     Hi Andras,
>
>
>     Many thanks for Your hints. We'll test them on our data. However, our data
>     is not as standardized in quality as CT or MRT data and from our experience
>     many of the "magic" segmentations demonstrated on CT or MRT data does not
>     work on our data.
>     However, of all the segmentation modules I could find in Slicer or elsewhere
>     none was based on a hierarchical watershed algorithm like the
>     SegmentationEditor of the InsightApplications. Is there any other that I've
>     missed?
>     Concerning my idea to implement this if no tool currently already exists:
>     Would such an extension be of more use in Slicer or itksnap?
>     For which of the both would it likely be easier to integrate the extension?
>
>     Best wishes
>     Roman
>
>     On 11/08/14 16:20, Andras Lasso wrote:
>
>         Have you tried segmentation tools in 3D Slicer? There is a multi-label
>         watershed
>         segmentation tool that works in 3d
>         (http://www.slicer.org/__slicerWiki/index.php/__Documentation/Nightly/Modules/__Editor#WatershedFromMarkers
>         <http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Editor#WatershedFromMarkers>),
>         there are also a number of other generic semi-automatic segmentation
>         tools (such
>         as GrowCut) and a few fully-automatic specialized tools (for brain,
>         airways, etc). Download the nightly build and also checkout the Segmentation
>         category in the Extension Manager.
>
>         Andras
>
>         *From:* Dr. Roman Grothausmann
>         <mailto:grothausmann.roman at mh-__hannover.de
>         <mailto:grothausmann.roman at mh-hannover.de>>
>         *Sent:* Monday, August 11, 2014 1:15 AM
>         *To:* itksnap-users at googlegroups.com
>         <mailto:itksnap-users at googlegroups.com>
>         <mailto:itksnap-users at __googlegroups.com
>         <mailto:itksnap-users at googlegroups.com>>
>         *Cc:* ITK Mailing List <mailto:insight-users at itk.org
>         <mailto:insight-users at itk.org>>
>
>
>         Dear mailing list members,
>
>
>         For a long time now I've been searching for a replacement of the old
>         SegmentationEditor (part of the InsightApplications) which I could not
>         get to
>         work even with older ITK-3.x. Somewhere I was told that it was
>         integrated and
>         maintained within itksnap. However the only tool in itksnap based on
>         watershed
>         segmentation seems to be the adaptive brush. It is very handy, but
>         time-consuming in 3D and only for local segmentations. In contrast the
>         SegmentationEditor used a global hierarchical watershed segmentation to pick
>         labels from, see e.g. the video linked here:
>         http://www.insight-journal.__org/browse/publication/70
>         <http://www.insight-journal.org/browse/publication/70>
>         Quite often now I've stumbled over data, that would likely have profited
>         a lot
>         of such a tool for segmentation.
>
>         If such a tool working with ITK-4.x does not exist any more, I thought of
>         implementing it as a global WS segmentation mode in itksnap. That way
>         making the
>         tool easier to find, to use and to ensure maintenance (should it be
>         integrated
>         into the itksnap code base in the end) and also avoiding recoding a GUI with
>         mouse interaction and such.
>
>         My current idea is to start, similar to the snake-tool, with
>         pre-filtering like
>         smoothing and optional edge-detection.
>         Then the main edit mode to consist of the usual 4 subwindows showing an
>         overlay
>         of the grey-image and the watershed segmentation of the hierarchical
>         WS-filter
>         (hWS), side-by-side to another label-dataset (loaded like a tiled
>         overlay) which
>         consist of the actually chosen labels from the hWS as the final data (FD).
>         The interaction I'm considering would be to LMB click on a label in the hWS
>         which is then added to the FD as the current fg label, or removed with a
>         RMB.
>         The hierachrchy level of the hWS could be controlled by a slider or the
>         mouse
>         wheel + Shift in nearly real time if some region demands higher or lower
>         detailed segmentation. When the fg label is changed, the segmentation
>         added or
>         removed with further mouse interactions would modify the new fg label.
>         When all is done and the global WS mode is left, the FD label-dataset is
>         added
>         to the main segmentation of itksnap.
>
>         Would that be possible to implement in itksnap 3.x?
>         What source files of the itksnap code base should I look at for:
>         - the pre-filtering mode of the snake (for the smoothing and edge detection)
>         - the mouse interactions (for e.g. adding the whell + Shift interaction)
>         - possible examples for the dual layout
>
>         Thanks for any comments, help or hints.
>         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 <tel:%2B49%20511%20532-9574>
>         _______________________________________
>         Powered by www.kitware.com <http://www.kitware.com>
>
>         Visit other Kitware open-source projects at
>         http://www.kitware.com/__opensource/opensource.html
>         <http://www.kitware.com/opensource/opensource.html>
>
>         Kitware offers ITK Training Courses, for more information visit:
>         http://www.kitware.com/__products/protraining.php
>         <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 <http://www.itk.org/Wiki/ITK_FAQ>
>
>         Follow this link to subscribe/unsubscribe:
>         http://public.kitware.com/__mailman/listinfo/insight-users
>         <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
>         <http://public.kitware.com/mailman/listinfo/community>
>
>
>     --
>     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 <tel:%2B49%20511%20532-9574>
>
>     --
>     You received this message because you are subscribed to the Google Groups
>     "itksnap-users" group.
>     To unsubscribe from this group and stop receiving emails from it, send an
>     email to itksnap-users+unsubscribe at __googlegroups.com
>     <mailto:itksnap-users%2Bunsubscribe at googlegroups.com>.
>     To post to this group, send email to itksnap-users at googlegroups.com
>     <mailto:itksnap-users at googlegroups.com>__.
>     Visit this group at http://groups.google.com/__group/itksnap-users
>     <http://groups.google.com/group/itksnap-users>.
>     For more options, visit https://groups.google.com/d/__optout
>     <https://groups.google.com/d/optout>.
>
>
>
>
> --
> Paul A. Yushkevich, Ph.D.
> Associate Professor
> Penn Image Computing and Science Laboratory
> Department of Radiology
> University of Pennsylvania
>
> --
> You received this message because you are subscribed to the Google Groups
> "itksnap-users" group.
> To unsubscribe from this group and stop receiving emails from it, send an email
> to itksnap-users+unsubscribe at googlegroups.com
> <mailto:itksnap-users+unsubscribe at googlegroups.com>.
> To post to this group, send email to itksnap-users at googlegroups.com
> <mailto:itksnap-users at googlegroups.com>.
> Visit this group at http://groups.google.com/group/itksnap-users.
> For more options, visit https://groups.google.com/d/optout.

-- 
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 gass at vision.ee.ethz.ch  Thu Aug 14 07:32:06 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Thu, 14 Aug 2014 13:32:06 +0200
Subject: [ITK-users] Anti-alias filter
In-Reply-To: <CAKy7kk2MWfxuHiY82xV_3Dmp5oGjwWpvd7ckJws5CJyaMP7Q6g@mail.gmail.com>
References: <CAKy7kk2_EOFb+PoSJaTgiSxs2mrYnOdnxoUrNKhZU+0WuEgL3w@mail.gmail.com>
 <CADZJ4hPt1T65ALOQa7cmmgd7Qcu+ZZtnA4G9OZVPQAOZog0VDw@mail.gmail.com>
 <CAKy7kk18ywvGWLxt6y7Sq9Qm6HDBPK2Upg4h7OVjjdG+KWuekg@mail.gmail.com>
 <CADZJ4hOkaQsnp1ZAw2YpUJ-jGRYTJ5VckCN_U_krbhvg5F2Wew@mail.gmail.com>
 <CADZJ4hOSigJ5R3=EO+AHf1JELjb9XKOchPFrTT2ksQunmBCpVw@mail.gmail.com>
 <CAKy7kk2m7me0aQ8c4CdantQV=ASUR8xucPFV7sZbF95DpMhNuw@mail.gmail.com>
 <CADZJ4hMdz+H23OBxHmp8Y=Y=0mbeDreTZhHYNrbzvHDDLLohbw@mail.gmail.com>
 <CAKy7kk0H+V8nT+pQHEjjppCqCUA7me-Wwf45zUNQm03UJ0p3YA@mail.gmail.com>
 <CAKy7kk08y3ctkz-B8MavCVceRD+Fjq_QH5=9bWHJ8d8BdKz7fA@mail.gmail.com>
 <CAKy7kk1CL=7K6uLi_E++MR4SuozSFQjkS-WijsoN2QKB_7bCqQ@mail.gmail.com>
 <CADZJ4hNnSoHa2BuW_gqiydYKHwhXo8T7j2W07Vy6kLDJ5pEUCg@mail.gmail.com>
 <CAKy7kk2MWfxuHiY82xV_3Dmp5oGjwWpvd7ckJws5CJyaMP7Q6g@mail.gmail.com>
Message-ID: <CAKy7kk0GD1dZwkvZaP5-Ngg-MHLfOGdDHOp-SUAUQ4kV4MaJKA@mail.gmail.com>

Dear all,

any further ideas on this one?

Thanks,
Tobias


2014-08-12 16:10 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:

> Yes, this does result in the same problems as before.
>
>
> 2014-08-12 15:06 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>
> Have you tried:
>> UseImageSpacingOn();
>>
>>
>> On Tue, Aug 12, 2014 at 8:47 AM, Tobias Gass <gass at vision.ee.ethz.ch>
>> wrote:
>> > Further update: when manually increasing the spacing of the input image
>> > (without resampling, thus not changing the size), the filter works well.
>> > This probably indicates numerical instability depending on image spacing
>> > somewhere in the code, which would probably be great if it could be
>> fixed.
>> >
>> > Best,
>> > Tobias
>> >
>> >
>> > 2014-08-12 14:33 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
>> >
>> >> Update: meanwhile I also tried cropping the image to investigate the
>> >> impact of the overall size (#voxels) of the image. It appears to not
>> have an
>> >> effect, the same artifacts occur when processing a significantly
>> smaller
>> >> region (1/2 size).
>> >>
>> >>
>> >> 2014-08-12 10:44 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
>> >>
>> >>> Hi,
>> >>>
>> >>> changing the PixelType did not yield any change. However, I did some
>> >>> further tests which seem to point at image spacing or total size to
>> be the
>> >>> culprit. My original image is fairly high-res, with 0.25mm in-plane
>> >>> resolution and 0.75mm slice thickness and 512x512x409 voxel size. I
>> tried
>> >>> resampling the image to different isotropic resolutions (0.25, 0.3,
>> 0.34,
>> >>> 0.35, 0.4, 0.5, 0.75, 1)mm isotropic spacing. For all spacings down to
>> >>> 0.35mm, the AA filter converged nicely and the output looks as I'd
>> expect
>> >>> it. Lower than 0.35mm spacing, and it fails in the way I described
>> (from
>> >>> this spacing on the #vox is equal or greater than the #voxels in my
>> original
>> >>> image).
>> >>>
>> >>> Any idea what might cause this, or what to further investigate?
>> >>>
>> >>> Thanks,
>> >>> Tobias
>> >>>
>> >>>
>> >>> 2014-08-11 22:17 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>> >>>
>> >>>> Paraview should do the right thing.
>> >>>>
>> >>>> On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch
>> >
>> >>>> wrote:
>> >>>> > I will try that tomorrow morning (living in GMT+1). I used
>> paraview to
>> >>>> > extract the isosurface, but also looked at the output of the
>> AA-filter
>> >>>> > directly (which looked fuzzy). I can also post an image of that
>> >>>> > tomorrow.
>> >>>> >
>> >>>> > Thanks for your help!
>> >>>> > Tobias
>> >>>> >
>> >>>> >
>> >>>> > 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com
>> >:
>> >>>> >
>> >>>> >> How are you extracting the final isosurface?
>> >>>> >>
>> >>>> >> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen
>> >>>> >> <bill.lorensen at gmail.com>
>> >>>> >> wrote:
>> >>>> >> > If you change
>> >>>> >> >  typedef  short PixelType;
>> >>>> >> > to
>> >>>> >> >  typedef  double PixelType;
>> >>>> >> >
>> >>>> >> > do the results change.
>> >>>> >> >
>> >>>> >> >
>> >>>> >> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass
>> >>>> >> > <gass at vision.ee.ethz.ch>
>> >>>> >> > wrote:
>> >>>> >> >>
>> >>>> >> >>> Can you post your code. The results do not look correct.
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >> Sure. The {write,read}Image functions are just convenient
>> wrappers
>> >>>> >> >> for
>> >>>> >> >> the
>> >>>> >> >> respective ITK tools.
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >> #include <stdio.h>
>> >>>> >> >>
>> >>>> >> >> #include <iostream>
>> >>>> >> >>
>> >>>> >> >> #include "argstream.h"
>> >>>> >> >>
>> >>>> >> >> #include "ImageUtils.h"
>> >>>> >> >>
>> >>>> >> >> #include "itkAntiAliasBinaryImageFilter.h"
>> >>>> >> >>
>> >>>> >> >> using namespace std;
>> >>>> >> >>
>> >>>> >> >> using namespace itk;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >> int main(int argc, char ** argv)
>> >>>> >> >>
>> >>>> >> >> {
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>> >>>> >> >>
>> >>>> >> >>     typedef  short PixelType;
>> >>>> >> >>
>> >>>> >> >>     typedef double OutputPixelType;
>> >>>> >> >>
>> >>>> >> >>     const unsigned int D=3;
>> >>>> >> >>
>> >>>> >> >>     typedef Image<PixelType,D> ImageType;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     typedef ImageType::Pointer ImagePointerType;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     typedef Image<OutputPixelType,D> OutputImageType;
>> >>>> >> >>
>> >>>> >> >>     typedef OutputImageType::Pointer OutputImagePointerType;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     argstream * as=new argstream(argc,argv);
>> >>>> >> >>
>> >>>> >> >>     string inFile, outFile;
>> >>>> >> >>
>> >>>> >> >>     double thresh=0.0;
>> >>>> >> >>
>> >>>> >> >>     (*as) >> parameter ("in", inFile, " filename...", true);
>> >>>> >> >>
>> >>>> >> >>     (*as) >> parameter ("out", outFile, " filename...", true);
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     (*as) >> help();
>> >>>> >> >>
>> >>>> >> >>     as->defaultErrorHandling();
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     ImagePointerType img =
>> >>>> >> >> ImageUtils<ImageType>::readImage(inFile);
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     typedef itk::AntiAliasBinaryImageFilter <ImageType,
>> >>>> >> >> OutputImageType>
>> >>>> >> >>
>> >>>> >> >>         AntiAliasBinaryImageFilterType;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>> >>>> >> >>
>> >>>> >> >>         = AntiAliasBinaryImageFilterType::New ();
>> >>>> >> >>
>> >>>> >> >>     antiAliasFilter->SetInput(img);
>> >>>> >> >>
>> >>>> >> >>     antiAliasFilter->SetNumberOfIterations(5);
>> >>>> >> >>
>> >>>> >> >>     antiAliasFilter->SetMaximumRMSError(0.02);
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     antiAliasFilter->Update();
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>   // For increased code coverage.  Does nothing.
>> >>>> >> >>
>> >>>> >> >>   antiAliasFilter->GetMaximumRMSError();
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>   antiAliasFilter->Update();
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>   std::cout << "Maximum RMS change value threshold was: 0.02 "
>> <<
>> >>>> >> >> std::endl;
>> >>>> >> >>
>> >>>> >> >>   std::cout << "Last RMS change value was: " <<
>> >>>> >> >> antiAliasFilter->GetRMSChange() << std::endl;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>   std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>   std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
>> >>>> >> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     OutputImagePointerType out=antiAliasFilter->GetOutput();
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >>     ImageUtils<OutputImageType>::writeImage(outFile,out);
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >> return 1;
>> >>>> >> >>
>> >>>> >> >> }
>> >>>> >> >>
>> >>>> >> >>
>> >>>> >> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000)
>> and
>> >>>> >> >> maxRMSError
>> >>>> >> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved
>> >>>> >> >> after
>> >>>> >> >> one
>> >>>> >> >> iteration where RMSE changes by about 0.08. This increases for
>> all
>> >>>> >> >> following
>> >>>> >> >> iterations, which have an RMSE-change of about 0.25 for all
>> number
>> >>>> >> >> of
>> >>>> >> >> iterations tested. All this is using ITK 4.5 pulled from the
>> GIT
>> >>>> >> >> repository
>> >>>> >> >> a while ago, running on an intel i7 on Debian.
>> >>>> >> >>
>> >>>> >> >> Thanks a lot!
>> >>>> >> >> Tobias
>> >>>> >> >>
>> >>>> >> >>>
>> >>>> >> >>>
>> >>>> >> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass
>> >>>> >> >>> <gass at vision.ee.ethz.ch>
>> >>>> >> >>> wrote:
>> >>>> >> >>> > Dear all,
>> >>>> >> >>> >
>> >>>> >> >>> > I'm having problems using the anti-alias filter, which I
>> want
>> >>>> >> >>> > to use
>> >>>> >> >>> > in
>> >>>> >> >>> > order to smooth a binary segmentation volume. I'm using
>> >>>> >> >>> > essentially
>> >>>> >> >>> > the
>> >>>> >> >>> > example code from the repository, which for my input file
>> seems
>> >>>> >> >>> > to
>> >>>> >> >>> > start
>> >>>> >> >>> > oscillating after 2 iterations, leading to weird 'pointy'
>> >>>> >> >>> > artifacts
>> >>>> >> >>> > on
>> >>>> >> >>> > the
>> >>>> >> >>> > surface as can be seen from the attached screenshot (AA
>> filter
>> >>>> >> >>> > output is
>> >>>> >> >>> > on
>> >>>> >> >>> > the left, input on the right).
>> >>>> >> >>> >
>> >>>> >> >>> > Is there any parameter to set/implement which could improve
>> the
>> >>>> >> >>> > behavior
>> >>>> >> >>> > of
>> >>>> >> >>> > this filter? I'm assuming that my input is reasonable, or is
>> >>>> >> >>> > this
>> >>>> >> >>> > something
>> >>>> >> >>> > the filter is expected to have problems with? It is notable
>> >>>> >> >>> > that
>> >>>> >> >>> > such
>> >>>> >> >>> > errors
>> >>>> >> >>> > seem to mainly appear in 'flat' regions of the volume, and
>> are
>> >>>> >> >>> > not
>> >>>> >> >>> > apparent
>> >>>> >> >>> > in the curved shaft of the bone.
>> >>>> >> >>> >
>> >>>> >> >>> > Any help, or pointers to further resources are appreciated,
>> >>>> >> >>> > thanks,
>> >>>> >> >>> > Tobias
>> >>>> >> >>> >
>> >>>> >> >>> > _____________________________________
>> >>>> >> >>> > 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
>> >>>> >>
>> >>>> >>
>> >>>> >>
>> >>>> >> --
>> >>>> >> Unpaid intern in BillsBasement at noware dot com
>> >>>> >
>> >>>> >
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>> Unpaid intern in BillsBasement at noware dot 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
>> >>>
>> >>>
>> >>
>> >
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140814/2e223049/attachment.html>

From grothausmann.roman at mh-hannover.de  Fri Aug 15 08:44:40 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Fri, 15 Aug 2014 14:44:40 +0200
Subject: [ITK-users] [Insight-users] enhancing plate like structures (by
 modifying itkHessianSmoothed3DToVesselnessMeasureImageFilter)
In-Reply-To: <22EC75E8215562428ACADFA35877A25A02F9FE@JANEWAY.ts.odu.edu>
References: <22EC75E8215562428ACADFA35877A25A02F9FE@JANEWAY.ts.odu.edu>
Message-ID: <53EE00B8.3030605@mh-hannover.de>

Dear Michel, dear Luca,


Coming back to Hessian-based measures of Yours, which I've tried out two years ago:
Is my understanding correct that the response function V of [Desc?teaux et. 
al.MICCAI 2006] and [Luca ITK-Journal 2007] differ for N=3 and M=2?

i.e. for N=3, M=2:
Rblob = vnl_math_abs( l3 + l3 - l2 - l1 ) / l3 in itkDescoteauxSheetnessImageFilter
corresponding to Ra (NOT Rb) in itkHessianToObjectnessMeasureImageFilter, which 
is undefined for N=3, M=2.

Rsheet = l2 / l3 in itkDescoteauxSheetnessImageFilter
corresponds to Rb in itkHessianToObjectnessMeasureImageFilter, both equal for 
N=3, M=2.


When has each definition its optimal use?

Additionally, In Desc?teaux2006 a zero level-set segmentation approach is 
described based on a vector field constructed from initial ellipsoids positioned 
at high sheetness measures.
Are there ITK-Filters to achieve that same approach or something similar? Which 
would I need?

Many thanks again for Your replies and help.
Roman

On 05/09/12 17:10, Audette, Michel A. wrote:
> Do a google on sheetness. Maxime Desc?teaux and I had modified this type of
> operator a few years back to improve the detection of curviplanar bones (MICCAI
> paper, republished in J. Computer Assisted Surgery), which was a tweak of his
> and Frangi's work on vesselness operators.
>
> Michel
>
> Michel Audette, Ph.D.
> Assistant Professor,
> Department of Modeling, Simulation and Visualization Engineering,
> Old Dominion University,
> Norfolk, VA.
> ________________________________________
> From: insight-users-bounces at itk.org [insight-users-bounces at itk.org] on behalf of
> Ho Cheung [hocheung20 at gmail.com]
> Sent: Wednesday, September 05, 2012 8:41 AM
> To: Dr. Roman Grothausmann
> Cc: insight-users at itk.org; vmtk-users at lists.sourceforge.net; Luca Antiga
> Subject: Re: [Insight-users] enhancing plate like structures (by modifying
> itkHessianSmoothed3DToVesselnessMeasureImageFilter)
>
> Hi Dr. Grothausmann,
>
> The measure in ITK appears to be based on Sato
> (http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/yoshi/node3.html#SECTION00021000000000000000)
> and I don't see an easy way to modify it so that it detects plate like
> structures instead of line like structures.
>
> If speed is not a major concern for you, may I suggest you implement a similar
> measure? Frangi's original vesselness enhancement formula
> (http://www.dtic.upf.edu/~afrangi/articles/miccai1998.pdf) can be easily
> modified for what you need and is based on Eigenvalues like Sato.
>
> According to equations 10, 11, 12, 13 in Frangi's paper and my interpretation of
> what the measures do, what you need is high Ra, Rb, and S values, so the formula
> becomes:
>
> V = [1 - exp(-Ra^2/2a^2)][1 - exp(-Rb^2/2b^2)][1 - exp(-S^2/2c62)]
>
> Hope, this helps,
>
> Ho Cheung
> Research Assistant
> Bio-Image Analytics Laboratory - University of Houston
> (832) 215-6347
>
>
>
> On Sep 5, 2012, at 3:36 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>
>  > Dear mailing list members, dear Luca,
>  >
>  >
>  > Recently I was trying to enhance vascular structures from airways with the
> vessel enhancement filters from ITK (objectness and vessel enhancement). The
> problem is that these vessels are not filled in the tomograms our imaging
> technique yields. Only the airway walls are imaged, which corresponds to an
> uneven 2D surface. Since it is only a 3D not an ND problem, I tried to modify
> itkHessianSmoothed3DToVesselnessMeasureImageFilter to enhance not vessels (1D)
> structures but plates/walls. Therefore I exchanged lambda 1 and 3 in the
> weighting function. Sadly, I could not get the filter  to enhance the airway walls.
>  > Have I missed anything or would enhancing plateness this way only work for
> not-curved planes?
>  >
>  >
>  > Here the important part of the diff of my changes:
>  >
>  > diff -au
> itk/IJ-Vessel_Enhancement_Diffusion.1/itkHessianSmoothed3DToVesselnessMeasureImageFilter.txx
> itk/plateness3D_01/itkHessianSmoothed3DToPlatenessMeasureImageFilter.txx
>  >
>  >
>  >
>  > +      ////swap Lambda1 and Lambda3 to enhance "plateness"
>  > +      double swap_tmp= Lambda1;
>  > +      Lambda3= Lambda1;
>  > +      Lambda1= swap_tmp;
>  > +      ///swapping done
>  > +
>  >       double Lambda1Abs = vnl_math_abs( Lambda1 );
>  >       double Lambda2Abs = vnl_math_abs( Lambda2 );
>  >       double Lambda3Abs = vnl_math_abs( Lambda3 );
>  > @@ -162,14 +168,13 @@
>  >       double vesMeasure_3  =
>  >          ( 1 - vcl_exp( -1.0 * (( vnl_math_sqr( S )) / ( 2.0 * ( GammaSqr)))));
>  >
>  > -      double vesMeasure_4  =
>  > -         vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C )) /
>  > -                                   ( Lambda2Abs * (Lambda3Sqr)));
>  > +      double vesMeasure_4  = 1; ////plateness for now not smoothed
>  > +      //double vesMeasure_4  = vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C ))
> / ( Lambda2Abs * (Lambda3Sqr))); ////check if this makes sense for plateness
>  >
>  >
>  > Many thanks for any help or hints.
>  > 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
>  > 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://www.itk.org/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://www.itk.org/mailman/listinfo/insight-users
>
>
> --
> BEGIN-ANTISPAM-VOTING-LINKS
> ------------------------------------------------------
>
> Teach CanIt if this mail (ID 699566122) is spam:
> Spam: https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=s
> Not spam:
> https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=n
> Forget vote:
> https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=f
> ------------------------------------------------------
> END-ANTISPAM-VOTING-LINKS
>

-- 
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 hms96 at scarletmail.rutgers.edu  Mon Aug 18 10:01:22 2014
From: hms96 at scarletmail.rutgers.edu (Harsh Shah)
Date: Mon, 18 Aug 2014 10:01:22 -0400
Subject: [ITK-users] Question About Buffers
Message-ID: <CABoxBg_wgLVNNNWFFZCB9hA9qWRhEaCzv7_Cn=3Tm3_eSX=xBQ@mail.gmail.com>

Hello,

I wanted to know if itk had any resources that would allow me to set the
value of an itk::Image m_buffer to a buffer I read in from my camera. If
you could point me in the direction of a good example, I would appreciate
it.

Thank You
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140818/64bfd93a/attachment.html>

From grothausmann.roman at mh-hannover.de  Mon Aug 18 10:03:25 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Mon, 18 Aug 2014 16:03:25 +0200
Subject: [ITK-users] difference between trees constructed in
 itkWatershedImageFilter and itkComponentTree
Message-ID: <53F207AD.3030503@mh-hannover.de>

Dear mailing list members,


Wherein lies the difference in the tree constructed in itkWatershedImageFilter 
and itkComponentTree contributed by Ga?tan Lehmann in 
http://www.insight-journal.org/browse/publication/210?

In the article about the itkComponentTree 
(http://www.insight-journal.org/browse/publication/210) it says there is a 
contribution for the binary case in ITK. Which is it? 
ConnectedComponentImageFilter?
Further in the text single template attribute are mentioned. Would these have to 
be computed separately with e.g. itkLabelImageToShapeLabelMapFilter?

Thanks for any answers and explanations
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 mercikd at thomas.edu  Mon Aug 18 10:05:49 2014
From: mercikd at thomas.edu (Dan Mercik)
Date: Mon, 18 Aug 2014 14:05:49 +0000
Subject: [ITK-users] TileImageFilter SideBySide
In-Reply-To: <F5E240B8-8207-40A1-A754-219F86CEA066@gmail.com>
References: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>,
 <F5E240B8-8207-40A1-A754-219F86CEA066@gmail.com>
Message-ID: <cfd1031b0bb6496787228becf7a4dd4d@T9.tcnet.thomas.edu>

Good Morning,



                        The demonstration you showed me works great, however if I wanted to do 20 images that would take  some time. So, I tried doing a for loop which didn't work exactly how I wanted it to work. I would like the program to take any amount of images and output them side by side , any ideas? The attachment shows the for loop I used similar to TileImageFilter CreateVolume example however when I use it for some odd reason only one image is being display side by side multiple times.



Daniel Mercik

Computer Science Major

Service Desk Technician

Thomas College

________________________________
From: Michka Popoff <michkapopoff at gmail.com>
Sent: Wednesday, August 13, 2014 2:32 AM
To: Dan Mercik
Cc: ITK Mailing List; community at itk.org
Subject: Re: [ITK-users] TileImageFilter SideBySide

Hi


Moving this mail to the new community mailing list


For your problem, you should use the setLayout method [1]


For 4 images, that would be:



itk::FixedArray< unsigned int, 2 > layout;

layout[0] = 4;
layout[1] = 0;


Michka


[1] http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_SideBySide

On 13 ao?t 2014, at 01:06, Dan Mercik <mercikd at thomas.edu<mailto:mercikd at thomas.edu>> wrote:

Good Afternoon,



                   I want to know if it's possible to have more than two image be side by side vertically? If so what would I have to change in the algorithm, would I have to make a loop for the amount of input images? Any help would be greatly appreciative.



Daniel Mercik

Computer Science Major

Service Desk Technician

Thomas College
_____________________________________
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

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: TileImageFilter_SideBySide.cxx
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140818/d458eeb4/attachment-0001.ksh>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Tilesidebyside.JPG
Type: image/jpeg
Size: 59821 bytes
Desc: Tilesidebyside.JPG
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140818/d458eeb4/attachment-0001.jpe>

From michkapopoff at gmail.com  Mon Aug 18 11:01:57 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Mon, 18 Aug 2014 17:01:57 +0200
Subject: [ITK-users] TileImageFilter SideBySide
In-Reply-To: <cfd1031b0bb6496787228becf7a4dd4d@T9.tcnet.thomas.edu>
References: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>,
 <F5E240B8-8207-40A1-A754-219F86CEA066@gmail.com>
 <cfd1031b0bb6496787228becf7a4dd4d@T9.tcnet.thomas.edu>
Message-ID: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>

Hi

Going the way described in the CreateVolume example is the way to go.

Why did you uncomment the DisconnectPipeline() call and Update() call in the for loop ? They need to stay there, else you will always use the last image.
That?s why you see the same image, the single update call will be triggered at the end of the script and read only one image.

You don?t need to call tileFilter->Update(), you can remove this line. The writer->Update() will take care of the pipeline update.
As a bonus, you may wrap your writer->Update() call, to fetch errors at the end of the pipeline:

  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & error )
    {
    std::cerr << "Error: " << error << std::endl;
    return EXIT_FAILURE;
    }

I made a little Python prototype, the syntax is a little bit different than in C++ but it gives you the main idea.

Michka



On 18 ao?t 2014, at 16:05, Dan Mercik <mercikd at thomas.edu> wrote:

> Good Morning,
> 
> 
> 
>                        The demonstration you showed me works great, however if I wanted to do 20 images that would take  some time. So, I tried doing a for loop which didn't work exactly how I wanted it to work. I would like the program to take any amount of images and output them side by side , any ideas? The attachment shows the for loop I used similar to TileImageFilter CreateVolume example however when I use it for some odd reason only one image is being display side by side multiple times.
> 
> 
> 
> Daniel Mercik
> 
> Computer Science Major
> 
> Service Desk Technician
> 
> Thomas College
> 
> ________________________________
> From: Michka Popoff <michkapopoff at gmail.com>
> Sent: Wednesday, August 13, 2014 2:32 AM
> To: Dan Mercik
> Cc: ITK Mailing List; community at itk.org
> Subject: Re: [ITK-users] TileImageFilter SideBySide
> 
> Hi
> 
> 
> Moving this mail to the new community mailing list
> 
> 
> For your problem, you should use the setLayout method [1]
> 
> 
> For 4 images, that would be:
> 
> 
> 
> itk::FixedArray< unsigned int, 2 > layout;
> 
> layout[0] = 4;
> layout[1] = 0;
> 
> 
> Michka
> 
> 
> [1] http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_SideBySide
> 
> On 13 ao?t 2014, at 01:06, Dan Mercik <mercikd at thomas.edu<mailto:mercikd at thomas.edu>> wrote:
> 
> Good Afternoon,
> 
> 
> 
>                   I want to know if it's possible to have more than two image be side by side vertically? If so what would I have to change in the algorithm, would I have to make a loop for the amount of input images? Any help would be greatly appreciative.
> 
> 
> 
> Daniel Mercik
> 
> Computer Science Major
> 
> Service Desk Technician
> 
> Thomas College
> _____________________________________
> 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
> 
> <TileImageFilter_SideBySide.cxx><Tilesidebyside.JPG>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140818/79c44d27/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: tiling.py
Type: text/x-python-script
Size: 881 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140818/79c44d27/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140818/79c44d27/attachment-0001.html>

From jan.bergmeier at imes.uni-hannover.de  Mon Aug 18 11:20:48 2014
From: jan.bergmeier at imes.uni-hannover.de (jan)
Date: Mon, 18 Aug 2014 08:20:48 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
	transformation
Message-ID: <1408375248616-7586081.post@n2.nabble.com>

Hello,

I want to perform a registration between two images without any
transformation or optimization. I like to use the
itk::MutualInformationImageToImageMetric. As I understand the itk metric,
you have to use a transformation, an optimizer, an interpolator and so on.

I want to compare one image to a set of images with mutual information as
metric.

So basically, I like to use the   GetValue()   method, without giving any
parameters to it. Is there a way to do that, or another way to get just one
mutual information value between two images?

Thanks in advance,

Jan



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From anton.delehony at gmail.com  Mon Aug 18 22:37:22 2014
From: anton.delehony at gmail.com (Anton Delehony)
Date: Mon, 18 Aug 2014 22:37:22 -0400
Subject: [ITK-users] Deformation Field Modulation
Message-ID: <CAB8ojqRnQqpdgx8OpoMQwB+bkU8WPZuLWMfwt1r05WFiy9fApg@mail.gmail.com>

Hello,

I have a general image processing question that I hope I can get some
guidance from more experienced researchers.

My data is composed of two 3d MRI volumes taken at end-inhale and
end-exhale. I do non-rigid registration (demons) to estimate the overall
transformation field between the two volumes. Then, I also have dynamic 2D
slices that are taken continuously throughout the breathing cycle. I would
like to "modulate" the overall field measured from registration by the
measured 2D planes.  Any suggestions?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140818/744ae11a/attachment.html>

From matt.mccormick at kitware.com  Tue Aug 19 00:31:19 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 19 Aug 2014 00:31:19 -0400
Subject: [ITK-users] Question About Buffers
In-Reply-To: <CABoxBg_wgLVNNNWFFZCB9hA9qWRhEaCzv7_Cn=3Tm3_eSX=xBQ@mail.gmail.com>
References: <CABoxBg_wgLVNNNWFFZCB9hA9qWRhEaCzv7_Cn=3Tm3_eSX=xBQ@mail.gmail.com>
Message-ID: <CALzTN-TEDQ5RNL1b6-WJ_8Q-RBkn0Ain6HYdn1Buj0HTFpU9MQ@mail.gmail.com>

Hi Harsh,

Yes, you can use ImportImageFilter [1] as in this example [2].

Hope this helps,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html

[2] http://www.itk.org/Doxygen/html/DataRepresentation_2Image_2Image5_8cxx-example.html#_a1

On Mon, Aug 18, 2014 at 10:01 AM, Harsh Shah
<hms96 at scarletmail.rutgers.edu> wrote:
> Hello,
>
> I wanted to know if itk had any resources that would allow me to set the
> value of an itk::Image m_buffer to a buffer I read in from my camera. If
> you could point me in the direction of a good example, I would appreciate
> 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://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 grothausmann.roman at mh-hannover.de  Wed Aug 20 03:37:40 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Wed, 20 Aug 2014 09:37:40 +0200
Subject: [ITK-users] TileImageFilter SideBySide
In-Reply-To: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
References: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>,
 <F5E240B8-8207-40A1-A754-219F86CEA066@gmail.com>
 <cfd1031b0bb6496787228becf7a4dd4d@T9.tcnet.thomas.edu>
 <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
Message-ID: <53F45044.8010702@mh-hannover.de>

Hi


As this is a nice case of a question I have always had: In the case of the c++ 
example 
(http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_CreateVolume)

InputImageType::Pointer inputImageTile;

   for (int i = 1; i < argc - 1; i++)
     {
     reader->SetFileName( argv[i] );
     reader->UpdateLargestPossibleRegion();
     inputImageTile = reader->GetOutput();
     inputImageTile->DisconnectPipeline();
     tiler->SetInput( inputImageNumber++, inputImageTile );
     }

When the reader output is assigned to inputImageTile, I thought this is only a 
pointer assignment and not a full copy of the image. However, I wonder, what 
makes sure the address space in the memory is not used (partially) again for the 
next image read? Is there a full copy created "behind the scene" at any point in 
the code? Or does the reader remember the address space of former images read 
even though DisconnectPipeline was called?

Thanks for any explanations
Roman

On 18/08/14 17:01, Michka Popoff wrote:
> Hi
>
> Going the way described in the CreateVolume example is the way to go.
>
> Why did you uncomment the DisconnectPipeline() call and Update() call in the for
> loop ? They need to stay there, else you will always use the last image.
> That?s why you see the same image, the single update call will be triggered at
> the end of the script and read only one image.
>
> You don?t need to call tileFilter->Update(), you can remove this line. The
> writer->Update() will take care of the pipeline update.
> As a bonus, you may wrap your writer->Update() call, to fetch errors at the end
> of the pipeline:
>
>    try
>      {
>      writer->Update();
>      }
>    catch( itk::ExceptionObject & error )
>      {
>      std::cerr << "Error: " << error << std::endl;
>      return EXIT_FAILURE;
>      }
>
> I made a little Python prototype, the syntax is a little bit different than in
> C++ but it gives you the main idea.
>
> Michka
>
>
>
>
> On 18 ao?t 2014, at 16:05, Dan Mercik <mercikd at thomas.edu
> <mailto:mercikd at thomas.edu>> wrote:
>
>> Good Morning,
>>
>>
>>
>>                        The demonstration you showed me works great, however if
>> I wanted to do 20 images that would take  some time. So, I tried doing a for
>> loop which didn't work exactly how I wanted it to work. I would like the
>> program to take any amount of images and output them side by side , any ideas?
>> The attachment shows the for loop I used similar to TileImageFilter
>> CreateVolume example however when I use it for some odd reason only one image
>> is being display side by side multiple times.
>>
>>
>>
>> Daniel Mercik
>>
>> Computer Science Major
>>
>> Service Desk Technician
>>
>> Thomas College
>>
>> ________________________________
>> From: Michka Popoff <michkapopoff at gmail.com <mailto:michkapopoff at gmail.com>>
>> Sent: Wednesday, August 13, 2014 2:32 AM
>> To: Dan Mercik
>> Cc: ITK Mailing List;community at itk.org <mailto:community at itk.org>
>> Subject: Re: [ITK-users] TileImageFilter SideBySide
>>
>> Hi
>>
>>
>> Moving this mail to the new community mailing list
>>
>>
>> For your problem, you should use the setLayout method [1]
>>
>>
>> For 4 images, that would be:
>>
>>
>>
>> itk::FixedArray< unsigned int, 2 > layout;
>>
>> layout[0] = 4;
>> layout[1] = 0;
>>
>>
>> Michka
>>
>>
>> [1]
>> http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_SideBySide
>>
>> On 13 ao?t 2014, at 01:06, Dan Mercik <mercikd at thomas.edu
>> <mailto:mercikd at thomas.edu><mailto:mercikd at thomas.edu>> wrote:
>>
>> Good Afternoon,
>>
>>
>>
>>                   I want to know if it's possible to have more than two image
>> be side by side vertically? If so what would I have to change in the
>> algorithm, would I have to make a loop for the amount of input images? Any
>> help would be greatly appreciative.
>>
>>
>>
>> Daniel Mercik
>>
>> Computer Science Major
>>
>> Service Desk Technician
>>
>> Thomas College
>> _____________________________________
>> Powered bywww.kitware.com <http://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
>>
>> <TileImageFilter_SideBySide.cxx><Tilesidebyside.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
>

-- 
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 millerjv at gmail.com  Wed Aug 20 07:16:59 2014
From: millerjv at gmail.com (Jim Miller)
Date: Wed, 20 Aug 2014 07:16:59 -0400
Subject: [ITK-users] TileImageFilter SideBySide
In-Reply-To: <53F45044.8010702@mh-hannover.de>
References: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>
 <F5E240B8-8207-40A1-A754-219F86CEA066@gmail.com>
 <cfd1031b0bb6496787228becf7a4dd4d@T9.tcnet.thomas.edu>
 <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
 <53F45044.8010702@mh-hannover.de>
Message-ID: <2D7CC2D6-CD96-4778-8DFA-86382739FA01@gmail.com>

Once DisconnectPipeline is called the Image object is completely disassociated with the source filter (in this case a reader). The source filter then constructs a new a Image object to serve as its output. For instance, if you call GetOutput() after calling DisconnectPipeline, you will get a different Image object than one retrieved before DisconnectPipeline is called. 

The pixel buffer is managed by the Image object, not the source/filter/reader. So after a call to DisconnectPipeline(), the reader has a new Image object as it its output and that new Image object has a distinct pixel buffer. Initially this pixel buffer is not even allocated. The act of reading the next image causes the reader to request the Image object to allocate the pixel buffer to an appropriate size. 

If DisconnectPipeline() was not called and the reader was asked to read another image of the same size or smaller, its output Image object would already have an allocated pixel buffer. The reader would still ask the Image object to allocate a pixel buffer of the appropriate size. But in this case, the Image object would recognize that it already has a block of memory of sufficient size and not do another allocation. 

Jim

> On Aug 20, 2014, at 3:37 AM, "Dr. Roman Grothausmann" <grothausmann.roman at mh-hannover.de> wrote:
> 
> Hi
> 
> 
> As this is a nice case of a question I have always had: In the case of the c++ example (http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_CreateVolume)
> 
> InputImageType::Pointer inputImageTile;
> 
>  for (int i = 1; i < argc - 1; i++)
>    {
>    reader->SetFileName( argv[i] );
>    reader->UpdateLargestPossibleRegion();
>    inputImageTile = reader->GetOutput();
>    inputImageTile->DisconnectPipeline();
>    tiler->SetInput( inputImageNumber++, inputImageTile );
>    }
> 
> When the reader output is assigned to inputImageTile, I thought this is only a pointer assignment and not a full copy of the image. However, I wonder, what makes sure the address space in the memory is not used (partially) again for the next image read? Is there a full copy created "behind the scene" at any point in the code? Or does the reader remember the address space of former images read even though DisconnectPipeline was called?
> 
> Thanks for any explanations
> Roman
> 
>> On 18/08/14 17:01, Michka Popoff wrote:
>> Hi
>> 
>> Going the way described in the CreateVolume example is the way to go.
>> 
>> Why did you uncomment the DisconnectPipeline() call and Update() call in the for
>> loop ? They need to stay there, else you will always use the last image.
>> That?s why you see the same image, the single update call will be triggered at
>> the end of the script and read only one image.
>> 
>> You don?t need to call tileFilter->Update(), you can remove this line. The
>> writer->Update() will take care of the pipeline update.
>> As a bonus, you may wrap your writer->Update() call, to fetch errors at the end
>> of the pipeline:
>> 
>>   try
>>     {
>>     writer->Update();
>>     }
>>   catch( itk::ExceptionObject & error )
>>     {
>>     std::cerr << "Error: " << error << std::endl;
>>     return EXIT_FAILURE;
>>     }
>> 
>> I made a little Python prototype, the syntax is a little bit different than in
>> C++ but it gives you the main idea.
>> 
>> Michka
>> 
>> 
>> 
>> 
>> On 18 ao?t 2014, at 16:05, Dan Mercik <mercikd at thomas.edu
>> <mailto:mercikd at thomas.edu>> wrote:
>> 
>>> Good Morning,
>>> 
>>> 
>>> 
>>>                       The demonstration you showed me works great, however if
>>> I wanted to do 20 images that would take  some time. So, I tried doing a for
>>> loop which didn't work exactly how I wanted it to work. I would like the
>>> program to take any amount of images and output them side by side , any ideas?
>>> The attachment shows the for loop I used similar to TileImageFilter
>>> CreateVolume example however when I use it for some odd reason only one image
>>> is being display side by side multiple times.
>>> 
>>> 
>>> 
>>> Daniel Mercik
>>> 
>>> Computer Science Major
>>> 
>>> Service Desk Technician
>>> 
>>> Thomas College
>>> 
>>> ________________________________
>>> From: Michka Popoff <michkapopoff at gmail.com <mailto:michkapopoff at gmail.com>>
>>> Sent: Wednesday, August 13, 2014 2:32 AM
>>> To: Dan Mercik
>>> Cc: ITK Mailing List;community at itk.org <mailto:community at itk.org>
>>> Subject: Re: [ITK-users] TileImageFilter SideBySide
>>> 
>>> Hi
>>> 
>>> 
>>> Moving this mail to the new community mailing list
>>> 
>>> 
>>> For your problem, you should use the setLayout method [1]
>>> 
>>> 
>>> For 4 images, that would be:
>>> 
>>> 
>>> 
>>> itk::FixedArray< unsigned int, 2 > layout;
>>> 
>>> layout[0] = 4;
>>> layout[1] = 0;
>>> 
>>> 
>>> Michka
>>> 
>>> 
>>> [1]
>>> http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_SideBySide
>>> 
>>> On 13 ao?t 2014, at 01:06, Dan Mercik <mercikd at thomas.edu
>>> <mailto:mercikd at thomas.edu><mailto:mercikd at thomas.edu>> wrote:
>>> 
>>> Good Afternoon,
>>> 
>>> 
>>> 
>>>                  I want to know if it's possible to have more than two image
>>> be side by side vertically? If so what would I have to change in the
>>> algorithm, would I have to make a loop for the amount of input images? Any
>>> help would be greatly appreciative.
>>> 
>>> 
>>> 
>>> Daniel Mercik
>>> 
>>> Computer Science Major
>>> 
>>> Service Desk Technician
>>> 
>>> Thomas College
>>> _____________________________________
>>> Powered bywww.kitware.com <http://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
>>> 
>>> <TileImageFilter_SideBySide.cxx><Tilesidebyside.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
> 
> -- 
> 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 grothausmann.roman at mh-hannover.de  Wed Aug 20 07:59:40 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Wed, 20 Aug 2014 13:59:40 +0200
Subject: [ITK-users] TileImageFilter SideBySide
In-Reply-To: <2D7CC2D6-CD96-4778-8DFA-86382739FA01@gmail.com>
References: <ca3b046f9c3649f397d95a0fa95067ba@T9.tcnet.thomas.edu>
 <F5E240B8-8207-40A1-A754-219F86CEA066@gmail.com>
 <cfd1031b0bb6496787228becf7a4dd4d@T9.tcnet.thomas.edu>
 <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
 <53F45044.8010702@mh-hannover.de>
 <2D7CC2D6-CD96-4778-8DFA-86382739FA01@gmail.com>
Message-ID: <53F48DAC.5040005@mh-hannover.de>

Thanks Jim for the great explanation, I understand now.
So in simple CLI programs where an ITK pipeline is only updated once by the 
final writer: In order to limit maximum memory used during execution, would it 
be best to always store the output of a filter in the pipeline in an image 
object and then call DisconnectPipeline (and setting ReleaseDataFlagOn for the 
filter)?

Many thanks again for the answer.
Roman

On 20/08/14 13:16, Jim Miller wrote:
> Once DisconnectPipeline is called the Image object is completely
> disassociated with the source filter (in this case a reader). The source
> filter then constructs a new a Image object to serve as its output. For
> instance, if you call GetOutput() after calling DisconnectPipeline, you will
> get a different Image object than one retrieved before DisconnectPipeline is
> called.
>
> The pixel buffer is managed by the Image object, not the
> source/filter/reader. So after a call to DisconnectPipeline(), the reader has
> a new Image object as it its output and that new Image object has a distinct
> pixel buffer. Initially this pixel buffer is not even allocated. The act of
> reading the next image causes the reader to request the Image object to
> allocate the pixel buffer to an appropriate size.
>
> If DisconnectPipeline() was not called and the reader was asked to read
> another image of the same size or smaller, its output Image object would
> already have an allocated pixel buffer. The reader would still ask the Image
> object to allocate a pixel buffer of the appropriate size. But in this case,
> the Image object would recognize that it already has a block of memory of
> sufficient size and not do another allocation.
>
> Jim
>
>> On Aug 20, 2014, at 3:37 AM, "Dr. Roman Grothausmann"
>> <grothausmann.roman at mh-hannover.de> wrote:
>>
>> Hi
>>
>>
>> As this is a nice case of a question I have always had: In the case of the
>> c++ example
>> (http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_CreateVolume)
>>
>>
>>
InputImageType::Pointer inputImageTile;
>>
>> for (int i = 1; i < argc - 1; i++) { reader->SetFileName( argv[i] );
>> reader->UpdateLargestPossibleRegion(); inputImageTile =
>> reader->GetOutput(); inputImageTile->DisconnectPipeline(); tiler->SetInput(
>> inputImageNumber++, inputImageTile ); }
>>
>> When the reader output is assigned to inputImageTile, I thought this is
>> only a pointer assignment and not a full copy of the image. However, I
>> wonder, what makes sure the address space in the memory is not used
>> (partially) again for the next image read? Is there a full copy created
>> "behind the scene" at any point in the code? Or does the reader remember
>> the address space of former images read even though DisconnectPipeline was
>> called?
>>
>> Thanks for any explanations Roman
>>
>>> On 18/08/14 17:01, Michka Popoff wrote: Hi
>>>
>>> Going the way described in the CreateVolume example is the way to go.
>>>
>>> Why did you uncomment the DisconnectPipeline() call and Update() call in
>>> the for loop ? They need to stay there, else you will always use the last
>>> image. That?s why you see the same image, the single update call will be
>>> triggered at the end of the script and read only one image.
>>>
>>> You don?t need to call tileFilter->Update(), you can remove this line.
>>> The writer->Update() will take care of the pipeline update. As a bonus,
>>> you may wrap your writer->Update() call, to fetch errors at the end of
>>> the pipeline:
>>>
>>> try { writer->Update(); } catch( itk::ExceptionObject & error ) {
>>> std::cerr << "Error: " << error << std::endl; return EXIT_FAILURE; }
>>>
>>> I made a little Python prototype, the syntax is a little bit different
>>> than in C++ but it gives you the main idea.
>>>
>>> Michka
>>>
>>>
>>>
>>>
>>> On 18 ao?t 2014, at 16:05, Dan Mercik <mercikd at thomas.edu
>>> <mailto:mercikd at thomas.edu>> wrote:
>>>
>>>> Good Morning,
>>>>
>>>>
>>>>
>>>> The demonstration you showed me works great, however if I wanted to do
>>>> 20 images that would take  some time. So, I tried doing a for loop
>>>> which didn't work exactly how I wanted it to work. I would like the
>>>> program to take any amount of images and output them side by side , any
>>>> ideas? The attachment shows the for loop I used similar to
>>>> TileImageFilter CreateVolume example however when I use it for some odd
>>>> reason only one image is being display side by side multiple times.
>>>>
>>>>
>>>>
>>>> Daniel Mercik
>>>>
>>>> Computer Science Major
>>>>
>>>> Service Desk Technician
>>>>
>>>> Thomas College
>>>>
>>>> ________________________________ From: Michka Popoff
>>>> <michkapopoff at gmail.com <mailto:michkapopoff at gmail.com>> Sent:
>>>> Wednesday, August 13, 2014 2:32 AM To: Dan Mercik Cc: ITK Mailing
>>>> List;community at itk.org <mailto:community at itk.org> Subject: Re:
>>>> [ITK-users] TileImageFilter SideBySide
>>>>
>>>> Hi
>>>>
>>>>
>>>> Moving this mail to the new community mailing list
>>>>
>>>>
>>>> For your problem, you should use the setLayout method [1]
>>>>
>>>>
>>>> For 4 images, that would be:
>>>>
>>>>
>>>>
>>>> itk::FixedArray< unsigned int, 2 > layout;
>>>>
>>>> layout[0] = 4; layout[1] = 0;
>>>>
>>>>
>>>> Michka
>>>>
>>>>
>>>> [1]
>>>> http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_SideBySide
>>>>
>>>>
>>>>
On 13 ao?t 2014, at 01:06, Dan Mercik <mercikd at thomas.edu
>>>> <mailto:mercikd at thomas.edu><mailto:mercikd at thomas.edu>> wrote:
>>>>
>>>> Good Afternoon,
>>>>
>>>>
>>>>
>>>> I want to know if it's possible to have more than two image be side by
>>>> side vertically? If so what would I have to change in the algorithm,
>>>> would I have to make a loop for the amount of input images? Any help
>>>> would be greatly appreciative.
>>>>
>>>>
>>>>
>>>> Daniel Mercik
>>>>
>>>> Computer Science Major
>>>>
>>>> Service Desk Technician
>>>>
>>>> Thomas College _____________________________________ Powered
>>>> bywww.kitware.com <http://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
>>>>
>>>> <TileImageFilter_SideBySide.cxx><Tilesidebyside.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
>>
>> -- 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 arnaudgelas at gmail.com  Wed Aug 20 10:03:32 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 20 Aug 2014 16:03:32 +0200
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6xABVRSoQRQ98Uoh9+Fraz19BwG3XbqR5JhTCBHcgCr+g@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
 <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
 <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>
 <305E1509-8EF7-4770-9236-3D639B9BF155@gmail.com>
 <CADJSx6xG6tUTOnkbD3ekPQZ5Pdj-hLWS9r7QGbSNjWxCg5HzJg@mail.gmail.com>
 <D1EA86D9-549D-4245-B667-83A93735C0BC@gmail.com>
 <CADJSx6xABVRSoQRQ98Uoh9+Fraz19BwG3XbqR5JhTCBHcgCr+g@mail.gmail.com>
Message-ID: <8E777677-5A6C-47A1-9ED6-030C85AB48B5@gmail.com>

Hi,

I have just submitted this patch for the documentation, can you please review it?

	http://review.source.kitware.com/#/c/16755/

I was running this code on Mac i5 with 4GB RAM, with both ITK and this program compiled in Debug?

Best,
Arnaud

On Aug 7, 2014, at 5:20 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:

> Hi Arnaud,
> 
> Thanks,Can you please tell me your machine confuguration. I am running 4GB RAM,i3  on windows7.
> I have downloaded your project and tried to execute it and it is still the same problem Which I was facing earlier.Any suggestions .....
> 
> thank you 
> 
> 
> On Thu, Aug 7, 2014 at 8:10 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> It takes 29s on my machine in debug to run 5 iterations with Delaunay conforming set to true
> 
> https://gist.github.com/arnaudgelas/0f20ebdaf53956f79997
> 
> 
> On Aug 7, 2014, at 3:45 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> 
>> File path is correct.if it is '\'(backward slash) we have to add "D:\\" .since I used '/' it's not required to add "//".
>> 
>> please find the attached  .vtk file 
>> 
>> Thanks
>> 
>> 
>> On Thu, Aug 7, 2014 at 7:01 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> Shouldn't it be D://temp.vtk ? Isn't it missing one '/' ?
>> 
>> Can you send this vtk file?
>> 
>> 
>> On Aug 7, 2014, at 3:23 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>> 
>>> Hi Arnaud,
>>> 
>>> Kindly have a look in the below code ,the problem  is that even after QEMeshFilter output is saved as .stl file ,the program is still running for long time.I have observed in my tests that MeshFileReader seems to be the culprit. Any suggestions ?
>>> 
>>> /////
>>> #include<iostream>
>>> #include<string>
>>> 
>>> #include <vtkPolyDataWriter.h>
>>> #include <vtkPolyDataReader.h>
>>> #include <itkMeshFileWriter.h>
>>> #include <itkMeshFileReader.h>
>>> #include <itkMeshIOFactory.h>
>>> #include <itkMeshIOBase.h>
>>> #include <vtkTriangleFilter.h>
>>> #include <vtkCleanPolyData.h>
>>> #include "itkMesh.h"
>>> #include "itkQuadEdgeMesh.h"
>>> #include "itkQuadEdgeMeshTraits.h"
>>> #include "itkSmoothingQuadEdgeMeshFilter.h"
>>> #include "vtkSTLWriter.h"
>>> #include <vtkSmartPointer.h>
>>> 
>>> int main()
>>> {
>>> 	std::string Inputfilename="D:/temp.vtk";   //number of points of this mesh file is around 78K
>>> 
>>> 	typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;	
>>> 	typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>> 	
>>> 	itk::OnesMatrixCoefficients< MeshType > coeff0;
>>> 	typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >SmoothingQuadEdgeMeshFilter;
>>>     
>>> 	vtkSmartPointer<vtkPolyDataWriter> polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
>>> 	vtkSmartPointer<vtkPolyDataReader> polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();
>>>    
>>>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother = SmoothingQuadEdgeMeshFilter::New();
>>> 	
>>>    /* polyDatareader->SetFileName(Inputfilename.c_str() );
>>> 	polyDatareader->ReleaseDataFlagOn();
>>> 	polyDatareader->Update();*/
>>> 
>>> 	/*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
>>>     vtkSmartPointer<vtkTriangleFilter>::New();
>>>     triangleFilter->SetInput(polyDatareader->GetOutput());
>>>     triangleFilter->Update();*/
>>>   
>>> 	//
>>> 	/* vtkSmartPointer<vtkCleanPolyData> clean = vtkSmartPointer<vtkCleanPolyData>::New();
>>> 	#if (VTK_MAJOR_VERSION < 6)
>>> 	 clean->SetInput(triangleFilter->GetOutput() );
>>> 	#else
>>>        clean->SetInputData(triangleFilter->GetOutput() );
>>> 	#endif
>>> 	
>>>     clean->ConvertPolysToLinesOff();
>>>     clean->ConvertLinesToPointsOff();
>>>     clean->Update();
>>> 
>>> 	std::string Inputfilename2="D:/cleaned.vtk";*/
>>> 
>>> 	////
>>> 	/*polyDatawriter->SetInput(clean->GetOutput());	
>>> 	polyDatawriter->SetFileName(Inputfilename2.c_str());
>>> 	polyDatawriter->ReleaseDataFlagOn();
>>> 	polyDatawriter->Write(); */ 
>>>   
>>> 	typedef itk::MeshFileReader<MeshType> MeshReaderType;
>>> 	MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>>>        Meshreader->SetFileName(Inputfilename.c_str( ));
>>> 	Meshreader->Update();
>>> 
>>> 	/*MeshType::Pointer mesh =  Meshreader->GetOutput();
>>>          mesh->DisconnectPipeline();*/
>>> 	
>>> 
>>> 	QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
>>> 	QEMeshSmoother->SetNumberOfIterations(1 );
>>> 	QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>> 	QEMeshSmoother->SetDelaunayConforming(true);
>>> 	QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>> 
>>> 	QEMeshSmoother->ReleaseDataFlagOn();
>>> 
>>> 	QEMeshSmoother->Update();	
>>>     
>>> 	std::string Outputfilename="D:/tempOut.vtk";
>>> 
>>> 	typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>>> 	MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>>>        Meshwriter->SetFileName(Outputfilename.c_str( ));
>>> 	Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>>>        Meshwriter->Update();	
>>> 
>>> 	polyDatareader->SetFileName(Outputfilename.c_str() );
>>> 	polyDatareader->ReleaseDataFlagOn();
>>> 	polyDatareader->Update();
>>> 
>>> 	vtkSmartPointer<vtkSTLWriter> stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
>>> 	
>>> 	stlWriter->SetInput( polyDatareader->GetOutput());
>>> 	stlWriter->SetFileName("D:/QEoutput.stl");
>>> 	stlWriter->SetFileTypeToASCII();
>>> 	stlWriter->Write();
>>> 	
>>> 	//Here it stops and taking long time 
>>> 
>>> 	return 0;
>>> 
>>> 	
>>> }
>>> ////
>>> 
>>> 
>>> 
>>> On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>> Hi Arnaud,
>>> 
>>> Thanks for your reply and valuable suggestions.
>>> 
>>> Number of points in my input mesh are 78928.In my pipeline I am already cleaning the polydata using vtkCleanPolyData filter.I will check the speed improvement and results with delaunay conforming turned OFF.
>>> 
>>> Thank you
>>> 
>>> 
>>> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>> Hi Malik,
>>> 
>>> First of all, I would recommend using MeshFileReader instead of VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near future?).
>>> 
>>> Regarding now the smoothing procedure in itself. This class definitively misses some documentation and I will be adding some in the next few days (mainly extracted from the corresponding insight journal).
>>> 
>>> At the end of each iteration, when the delaunay conforming flag is turned ON, the conformation is performed. So depending on the mesh configuration, mesh size and number of iterations, it can take ages?
>>> How large is your input mesh (number of points)?
>>> 
>>> You can also check results, by running first a smoothing without delaunay conforming, then apply a delaunay conforming on the output. Results won't be as nice, but you should get significant speed improvement.
>>> Another possibility is to first do a clean poly data in vtk, with a small threshold to remove small edges in the input meshes (which results in lots of edge flipping after smoothing).
>>> 
>>> HTH
>>> Arnaud
>>> 
>>> 
>>> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>> 
>>>> Hi All,
>>>> 
>>>> Can anyone suggest me if anything wrong I am doing in this below pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in release mode) at itkVtkPolydataReader .
>>>> 
>>>> 
>>>> ////
>>>> 
>>>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;
>>>> 	
>>>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>>> 
>>>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>> 
>>>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>>>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>>>> 
>>>> //VTKPolyDataWriterType::Pointer ItkToVtkWriter=VTKPolyDataWriterType::New();
>>>> VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();
>>>> 
>>>> VtkToItkReader->SetFileName("abc.vtk");
>>>> VtkToItkReader->Update();	
>>>> 
>>>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>>>> SmoothingQuadEdgeMeshFilter;
>>>> 
>>>>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =   SmoothingQuadEdgeMeshFilter::New();
>>>> 	
>>>> 
>>>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>>>> QEMeshSmoother->SetNumberOfIterations(5 );
>>>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>> QEMeshSmoother->SetDelaunayConforming(true );
>>>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );	
>>>> 	
>>>> QEMeshSmoother->Update();
>>>> 
>>>> ////
>>>> 
>>>> 
>>>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>> Thanks Bill for your answer.
>>>> 
>>>> The reason I am using this pipeline is that SmoothingQEMeshFilter has an additional parameter for smoothing which is delaunay conforming which helps to optimize aspect ratio of triangles while smoothing and thus produces better output.Is there anything similar filter in the vtk pipeline.I used vtkWindowedSincPolydatafilter which is not giving the output as good as QEMeshSmoothing filter.
>>>> 
>>>> Thanks for your help 
>>>> 
>>>> 
>>>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>> 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
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Regards:
>>>> Mallik
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> 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
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Regards:
>>> Mallik
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Regards:
>>> Mallik
>>> 
>> 
>> 
>> 
>> 
>> -- 
>> Regards:
>> Mallik
>> 
>> <temp.vtk>
> 
> 
> 
> 
> -- 
> Regards:
> Mallik
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140820/c5b9e42f/attachment.html>

From arnaudgelas at gmail.com  Wed Aug 20 10:28:58 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 20 Aug 2014 16:28:58 +0200
Subject: [ITK-users] combining N images
Message-ID: <CAK3qF+-QpDPqbCRjMABOu7gTyVfQ48DoHH7A7CzUxgvkBRE-jg@mail.gmail.com>

Hi all,

I am trying to combine N images together into a single image of the same
dimension.

These N images have the same direction, but can have different origin,
start index, spacing, size (there is no overlap). Then gaps in between
images would be filled with a given constant value.

Is there such a filter? or assuming I have already resampled all images to
a common ground, is there a filter to do this?

Thanks,
Arnaud
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140820/854d2a75/attachment.html>

From joseignacio.prieto at gmail.com  Wed Aug 20 11:00:51 2014
From: joseignacio.prieto at gmail.com (Jose Ignacio Prieto)
Date: Wed, 20 Aug 2014 11:00:51 -0400
Subject: [ITK-users] Composite Filter with variable stdvector of filters
	inside
Message-ID: <CANkppu5b2vBFN96F7fx7MCSmRH8aqA14AUOCn7rbUtGFCWemAw@mail.gmail.com>

Hi all,
I am trying to create a composite filter for a 4D dataset that will use
different cascaded 2D filters on the inside. For this, I have created a
double std vector that holds all the 2D filters. I have also set some param
setters for this filters (that perform a double for inside, setting the
param to each filter and then calling modified() on the outside one). I
have another method called UpdateNumberofFilters, that depending on 2 ints
(num of Z slices, num of T timeframes) will push back more filters to the
2D array of filters.
My problem is that I dont know which function should call the
UpdateNumofFilters. It should be done before the setters but after the
constructor and after setting those two ints. I want to design it so that
if I change a param after calling update I dont have to run the whole
filter again, so I dont want it to be under the GenerateData() method.

Thank you very much for your insights.

Ignacio Prieto

 --
Ignacio Prieto
Research Assistant
Biomedical Imaging Center
Pontificia Universida Catolica de Chile
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140820/1fb6f961/attachment-0001.html>

From mercikd at thomas.edu  Wed Aug 20 11:48:43 2014
From: mercikd at thomas.edu (Dan Mercik)
Date: Wed, 20 Aug 2014 15:48:43 +0000
Subject: [ITK-users] Tiling Side by Side Question
Message-ID: <5a78d43e709547e49519d34f2e74838e@T9.tcnet.thomas.edu>

Hey,



        In my program I'm using a If Else statement to decide which direction I want my images to tile. So far, the If statement works if I want my images to tile horizontally, but It not working vertically. In my code if I input 1 my images would tile horizontally, anything input other than 1 should display my images vertically. Do anyone happen to see the problem in my if Else statement?





Daniel Mercik

Computer Science Major

Service Desk Technician

Thomas College
-------------- next part --------------
A non-text attachment was scrubbed...
Name: sidebyside tiling.JPG
Type: image/jpeg
Size: 67308 bytes
Desc: sidebyside tiling.JPG
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140820/19b30aa8/attachment.jpe>

From arnaudgelas at gmail.com  Wed Aug 20 11:51:19 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 20 Aug 2014 17:51:19 +0200
Subject: [ITK-users] combining N images
In-Reply-To: <CAK07tM-wbff17T17w6Cu8b6d8-pTatizXLT7KGkpCmS9tPy=DQ@mail.gmail.com>
References: <CAK3qF+-QpDPqbCRjMABOu7gTyVfQ48DoHH7A7CzUxgvkBRE-jg@mail.gmail.com>
 <CAK07tM-wbff17T17w6Cu8b6d8-pTatizXLT7KGkpCmS9tPy=DQ@mail.gmail.com>
Message-ID: <CAK3qF+8XCGByndYiKGfLqDwie+2PkipByMovDod7QAq04Nwrmg@mail.gmail.com>

Hi,

I do not want to add images, it is more something like pasting but I do not
know in advance what would be the output image size, but it would be at
least the bounding box of all images...

Arnaud

On Wednesday, August 20, 2014, Mordig, Maximilian Oliver <
maximilian_oliver.mordig at roche.com> wrote:

> Once you have resampled all images, you can use the itk AddFilter.
>
>
> On Wed, Aug 20, 2014 at 4:28 PM, Arnaud Gelas <arnaudgelas at gmail.com
> <javascript:_e(%7B%7D,'cvml','arnaudgelas at gmail.com');>> wrote:
>
>> Hi all,
>>
>> I am trying to combine N images together into a single image of the same
>> dimension.
>>
>> These N images have the same direction, but can have different origin,
>> start index, spacing, size (there is no overlap). Then gaps in between
>> images would be filled with a given constant value.
>>
>> Is there such a filter? or assuming I have already resampled all images
>> to a common ground, is there a filter to do this?
>>
>> Thanks,
>> Arnaud
>>
>> _____________________________________
>> 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 <javascript:_e(%7B%7D,'cvml','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/20140820/36254472/attachment-0001.html>

From brad at lowekamp.net  Wed Aug 20 12:53:18 2014
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Wed, 20 Aug 2014 12:53:18 -0400
Subject: [ITK-users] [ITK]  combining N images
In-Reply-To: <CAK3qF+8XCGByndYiKGfLqDwie+2PkipByMovDod7QAq04Nwrmg@mail.gmail.com>
References: <CAK3qF+-QpDPqbCRjMABOu7gTyVfQ48DoHH7A7CzUxgvkBRE-jg@mail.gmail.com>
 <CAK07tM-wbff17T17w6Cu8b6d8-pTatizXLT7KGkpCmS9tPy=DQ@mail.gmail.com>
 <CAK3qF+8XCGByndYiKGfLqDwie+2PkipByMovDod7QAq04Nwrmg@mail.gmail.com>
Message-ID: <41BB5486-E3F6-4196-8E58-C59F514C8800@mail.nih.gov>

This may be of some use:

https://github.com/blowekamp/itkStreamingSinc/blob/master/include/itkBoundingRegionImageSinc.h

> On Aug 20, 2014, at 11:51 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> 
> Hi,
> 
> I do not want to add images, it is more something like pasting but I do not know in advance what would be the output image size, but it would be at least the bounding box of all images...
> 
> Arnaud
> 
>> On Wednesday, August 20, 2014, Mordig, Maximilian Oliver <maximilian_oliver.mordig at roche.com> wrote:
>> Once you have resampled all images, you can use the itk AddFilter.
>> 
>> 
>>> On Wed, Aug 20, 2014 at 4:28 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>> Hi all,
>>> 
>>> I am trying to combine N images together into a single image of the same dimension.
>>> 
>>> These N images have the same direction, but can have different origin, start index, spacing, size (there is no overlap). Then gaps in between images would be filled with a given constant value.
>>> 
>>> Is there such a filter? or assuming I have already resampled all images to a common ground, is there a filter to do this?
>>> 
>>> Thanks,
>>> Arnaud
>>> 
>>> 
>>> _____________________________________
>>> 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
> _______________________________________________
> 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/20140820/62b3c5de/attachment.html>

From yxp233 at postech.ac.kr  Wed Aug 20 13:07:38 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Thu, 21 Aug 2014 02:07:38 +0900
Subject: [ITK-users] Compiling ITK for GPU support
In-Reply-To: <1405141094987070.021539.ptmail03@ptmail03>
References: <1405141094987070.021539.ptmail03@ptmail03>
Message-ID: <023f01cfbc99$3ecc2c60$bc648520$@ac.kr>

Hello,

 

I would like to develop GPU based program for image processing, so I tried to compile ITK with GPU support. 

 

My question is whether I shall install 3rd party program like CUDDA first?

 

Thank you.

 

Xiaopeng

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140821/49f6e98b/attachment.html>

From grothausmann.roman at mh-hannover.de  Thu Aug 21 03:30:02 2014
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Thu, 21 Aug 2014 09:30:02 +0200
Subject: [ITK-users] Tiling Side by Side Question
In-Reply-To: <5a78d43e709547e49519d34f2e74838e@T9.tcnet.thomas.edu>
References: <5a78d43e709547e49519d34f2e74838e@T9.tcnet.thomas.edu>
Message-ID: <53F59FFA.2070002@mh-hannover.de>

Hm, haven't used that filter before but I'd think that you need to change 
layout[2] to layout[1].

On 20/08/14 17:48, Dan Mercik wrote:
> Hey,
>
>
>
> In my program I'm using a If Else statement to decide which direction I want
> my images to tile. So far, the If statement works if I want my images to tile
> horizontally, but It not working vertically. In my code if I input 1 my
> images would tile horizontally, anything input other than 1 should display my
> images vertically. Do anyone happen to see the problem in my if Else
> statement?
>
>
>
>
>
> Daniel Mercik
>
> Computer Science Major
>
> Service Desk Technician
>
> Thomas College
>
>
>
> _____________________________________ 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 michkapopoff at gmail.com  Thu Aug 21 03:37:31 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Thu, 21 Aug 2014 09:37:31 +0200
Subject: [ITK-users] Tiling Side by Side Question
In-Reply-To: <53F59FFA.2070002@mh-hannover.de>
References: <5a78d43e709547e49519d34f2e74838e@T9.tcnet.thomas.edu>
 <53F59FFA.2070002@mh-hannover.de>
Message-ID: <8BA6CC8C-BAFC-496A-8FA3-B2998B9745B6@gmail.com>

Yes, layout[2] is for the third direction, when you do a stack.
Do not set layout[2], as you set your FixedArray to be 2 dimensional. (else you should do itk::FixedArray< unsigned int, 3 >  layout;

So for vertical tiling it is:
layout[0] = 0;
layout[1] = i + 1;

Michka

On 21 ao?t 2014, at 09:30, Dr. Roman Grothausmann <grothausmann.roman at mh-hannover.de> wrote:

> Hm, haven't used that filter before but I'd think that you need to change layout[2] to layout[1].
> 
> On 20/08/14 17:48, Dan Mercik wrote:
>> Hey,
>> 
>> 
>> 
>> In my program I'm using a If Else statement to decide which direction I want
>> my images to tile. So far, the If statement works if I want my images to tile
>> horizontally, but It not working vertically. In my code if I input 1 my
>> images would tile horizontally, anything input other than 1 should display my
>> images vertically. Do anyone happen to see the problem in my if Else
>> statement?
>> 
>> 
>> 
>> 
>> 
>> Daniel Mercik
>> 
>> Computer Science Major
>> 
>> Service Desk Technician
>> 
>> Thomas College
>> 
>> 
>> 
>> _____________________________________ 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
> _____________________________________
> 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 yuetian926 at 163.com  Thu Aug 21 04:55:17 2014
From: yuetian926 at 163.com (Yuetian Liu)
Date: Thu, 21 Aug 2014 16:55:17 +0800 (CST)
Subject: [ITK-users] How to fusion the MR volume to the CT volume
Message-ID: <40b48479.b227.147f7c6f61b.Coremail.yuetian926@163.com>



Hi itkusers,


Recently I want to fuse the MR volume to the CT volume, but I search the itk mailist. 
I haven;t known how to realise it. And there isn't example in the InsightSoftwareGuide-4.5.0.pdf
and InsightSphinxExamplesPDF-4.5.0.pdf. 
So I want to ask how to fuse the MR volume to the CT volume by itk.


Thank you for helping me! 


Best 
Yuetian
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140821/7184ce12/attachment.html>

From yuetian926 at 163.com  Thu Aug 21 04:44:11 2014
From: yuetian926 at 163.com (Yuetian Liu)
Date: Thu, 21 Aug 2014 16:44:11 +0800 (CST)
Subject: [ITK-users] How to fusion the MR volume to the CT volume
Message-ID: <49b24f0c.ad8d.147f7bccdd9.Coremail.yuetian926@163.com>

Hi itkusers,


Recently I want to fuse the MR volume to the CT volume, but I search the itk mailist. 
I haven;t known how to realise it. And there isn't example in the InsightSoftwareGuide-4.5.0.pdf
and InsightSphinxExamplesPDF-4.5.0.pdf. 
So I want to ask how to fuse the MR volume to the CT volume by itk.


Thank you for helping me! 


Best 
Yuetian
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140821/72f0dbd7/attachment.html>

From arnaudgelas at gmail.com  Thu Aug 21 06:47:17 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 21 Aug 2014 12:47:17 +0200
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <CADJSx6xChSVq447yw4pbOuYtHPKaRDpmZoRqoxj92ejdtazzRg@mail.gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
 <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
 <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>
 <305E1509-8EF7-4770-9236-3D639B9BF155@gmail.com>
 <CADJSx6xG6tUTOnkbD3ekPQZ5Pdj-hLWS9r7QGbSNjWxCg5HzJg@mail.gmail.com>
 <D1EA86D9-549D-4245-B667-83A93735C0BC@gmail.com>
 <CADJSx6xABVRSoQRQ98Uoh9+Fraz19BwG3XbqR5JhTCBHcgCr+g@mail.gmail.com>
 <8E777677-5A6C-47A1-9ED6-030C85AB48B5@gmail.com>
 <CADJSx6xChSVq447yw4pbOuYtHPKaRDpmZoRqoxj92ejdtazzRg@mail.gmail.com>
Message-ID: <D4FDB533-282B-4F99-836E-EB2582AA1E1D@gmail.com>

Hi,

As of now, there is no progress event on this filter, so it is normal nothing happened.

I'll submit another patch for progress event later today.

To review the patch, you need to create an account on gerrit:

	http://review.source.kitware.com

Then you ca volunteer to the review patch, you can add comments, accept, refuse?
Else once you are registered, you can send me an email and I will add you as a reviewer.

Best,
Arnaud

On Aug 21, 2014, at 12:11 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:

> Hi,
>  I am trying observe the progressEvent by using AddObserver method of this filter but I couldn't. Could you check the below code once.
> 
> And one more thing,Could you guide me what exactly I have to do to Review the patch you have submitted.
> 
> Thank you
> 
> 
> ///progress
> 
> #include<iostream>
> #include<string>
> 
> #include <itkMeshFileWriter.h>
> #include <itkMeshFileReader.h>
> #include <itkMeshIOFactory.h>
> #include <itkMeshIOBase.h>
> #include "itkMesh.h"
> #include "itkQuadEdgeMesh.h"
> #include "itkQuadEdgeMeshTraits.h"
> #include "itkSmoothingQuadEdgeMeshFilter.h"
> #include "itkCommand.h"
> 
> class MyCommand : public itk::Command
> {
>   public:
>     itkNewMacro( MyCommand );
>  
>   public:
>  
>     void Execute(itk::Object *caller, const itk::EventObject & event)
>     {
>       Execute( (const itk::Object *)caller, event);
>     }
>  
>     void Execute(const itk::Object * object, const itk::EventObject & event)
>     {
>       std::cout << "Command called." << std::endl;
> 
> 	  if( typeid( itk::ProgressEvent ) ==  typeid( event ) )
>        {
> 		   ::itk::ProcessObject::ConstPointer  process = 
>              dynamic_cast< const itk::ProcessObject *>( object/*caller*/ );
> 
>            const int value = static_cast<int>(process->GetProgress() * 100 );
> 		   std::cout<<"progress:"<<value<<std::endl;   
> 		  	  
> 
>       
>        }
> 
>     }
>  
> };
> 
> int main( int argc, char* argv[] )
> {
> 
> 	/*if( argc < 2 )
>     {
>     std::cerr << "Usage: " << std::endl;
>     std::cerr << argv[0] << "  inputImageFile   outputImageFile   flipAxisX   flipAxisY" << std::endl;
>     return EXIT_FAILURE;
>     }*/
> 
> 	std::string Inputfilename="D:\\temp.vtk";
>   typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits; 
>   typedef itk::QuadEdgeMesh< double, 3,qetraits > MeshType;
>   
>   itk::OnesMatrixCoefficients< MeshType > coeff0;
>   typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >SmoothingQuadEdgeMeshFilter;
>     
>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother = SmoothingQuadEdgeMeshFilter::New();
>  
>   typedef itk::MeshFileReader<MeshType> MeshReaderType;
>   MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>   Meshreader->SetFileName( Inputfilename.c_str()/*argv[1]*/ );
>  // Meshreader->Update();
>   
>   
>   MyCommand::Pointer myCommand = MyCommand::New();
> 
>   QEMeshSmoother->SetInput(Meshreader->GetOutput() );
>   QEMeshSmoother->SetNumberOfIterations( 1 );
>   QEMeshSmoother->SetRelaxationFactor( 0.5 );
>   QEMeshSmoother->SetDelaunayConforming(true);
>   QEMeshSmoother->SetCoefficientsMethod( &coeff0 ); 
>   QEMeshSmoother->AddObserver(itk::ProgressEvent, myCommand);
>   
>  // QEMeshSmoother->Update();
>   std::string Outputfilename="D:\\tempOut2.vtk";
>     
>   typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>   MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>   Meshwriter->SetFileName(Outputfilename.c_str() /*argv[2]*/ );
>   Meshwriter->SetInput(QEMeshSmoother->GetOutput());
> 
>   try
>   {
>     Meshwriter->Update();
>   }
>   catch( itk::ExceptionObject& e )
>   {
>     std::cerr << e.what() << std::endl;
>   }
> 
>   return 0;
> 
>   
> } 
> 
> 
> On Wed, Aug 20, 2014 at 7:33 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Hi,
> 
> I have just submitted this patch for the documentation, can you please review it?
> 
> 	http://review.source.kitware.com/#/c/16755/
> 
> I was running this code on Mac i5 with 4GB RAM, with both ITK and this program compiled in Debug?
> 
> Best,
> Arnaud
> 
> On Aug 7, 2014, at 5:20 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> 
>> Hi Arnaud,
>> 
>> Thanks,Can you please tell me your machine confuguration. I am running 4GB RAM,i3  on windows7.
>> I have downloaded your project and tried to execute it and it is still the same problem Which I was facing earlier.Any suggestions .....
>> 
>> thank you 
>> 
>> 
>> On Thu, Aug 7, 2014 at 8:10 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> It takes 29s on my machine in debug to run 5 iterations with Delaunay conforming set to true
>> 
>> https://gist.github.com/arnaudgelas/0f20ebdaf53956f79997
>> 
>> 
>> On Aug 7, 2014, at 3:45 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>> 
>>> File path is correct.if it is '\'(backward slash) we have to add "D:\\" .since I used '/' it's not required to add "//".
>>> 
>>> please find the attached  .vtk file 
>>> 
>>> Thanks
>>> 
>>> 
>>> On Thu, Aug 7, 2014 at 7:01 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>> Shouldn't it be D://temp.vtk ? Isn't it missing one '/' ?
>>> 
>>> Can you send this vtk file?
>>> 
>>> 
>>> On Aug 7, 2014, at 3:23 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>> 
>>>> Hi Arnaud,
>>>> 
>>>> Kindly have a look in the below code ,the problem  is that even after QEMeshFilter output is saved as .stl file ,the program is still running for long time.I have observed in my tests that MeshFileReader seems to be the culprit. Any suggestions ?
>>>> 
>>>> /////
>>>> #include<iostream>
>>>> #include<string>
>>>> 
>>>> #include <vtkPolyDataWriter.h>
>>>> #include <vtkPolyDataReader.h>
>>>> #include <itkMeshFileWriter.h>
>>>> #include <itkMeshFileReader.h>
>>>> #include <itkMeshIOFactory.h>
>>>> #include <itkMeshIOBase.h>
>>>> #include <vtkTriangleFilter.h>
>>>> #include <vtkCleanPolyData.h>
>>>> #include "itkMesh.h"
>>>> #include "itkQuadEdgeMesh.h"
>>>> #include "itkQuadEdgeMeshTraits.h"
>>>> #include "itkSmoothingQuadEdgeMeshFilter.h"
>>>> #include "vtkSTLWriter.h"
>>>> #include <vtkSmartPointer.h>
>>>> 
>>>> int main()
>>>> {
>>>> 	std::string Inputfilename="D:/temp.vtk";   //number of points of this mesh file is around 78K
>>>> 
>>>> 	typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;	
>>>> 	typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>>> 	
>>>> 	itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>> 	typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >SmoothingQuadEdgeMeshFilter;
>>>>     
>>>> 	vtkSmartPointer<vtkPolyDataWriter> polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
>>>> 	vtkSmartPointer<vtkPolyDataReader> polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();
>>>>    
>>>>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother = SmoothingQuadEdgeMeshFilter::New();
>>>> 	
>>>>    /* polyDatareader->SetFileName(Inputfilename.c_str() );
>>>> 	polyDatareader->ReleaseDataFlagOn();
>>>> 	polyDatareader->Update();*/
>>>> 
>>>> 	/*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
>>>>     vtkSmartPointer<vtkTriangleFilter>::New();
>>>>     triangleFilter->SetInput(polyDatareader->GetOutput());
>>>>     triangleFilter->Update();*/
>>>>   
>>>> 	//
>>>> 	/* vtkSmartPointer<vtkCleanPolyData> clean = vtkSmartPointer<vtkCleanPolyData>::New();
>>>> 	#if (VTK_MAJOR_VERSION < 6)
>>>> 	 clean->SetInput(triangleFilter->GetOutput() );
>>>> 	#else
>>>>        clean->SetInputData(triangleFilter->GetOutput() );
>>>> 	#endif
>>>> 	
>>>>     clean->ConvertPolysToLinesOff();
>>>>     clean->ConvertLinesToPointsOff();
>>>>     clean->Update();
>>>> 
>>>> 	std::string Inputfilename2="D:/cleaned.vtk";*/
>>>> 
>>>> 	////
>>>> 	/*polyDatawriter->SetInput(clean->GetOutput());	
>>>> 	polyDatawriter->SetFileName(Inputfilename2.c_str());
>>>> 	polyDatawriter->ReleaseDataFlagOn();
>>>> 	polyDatawriter->Write(); */ 
>>>>   
>>>> 	typedef itk::MeshFileReader<MeshType> MeshReaderType;
>>>> 	MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>>>>        Meshreader->SetFileName(Inputfilename.c_str( ));
>>>> 	Meshreader->Update();
>>>> 
>>>> 	/*MeshType::Pointer mesh =  Meshreader->GetOutput();
>>>>          mesh->DisconnectPipeline();*/
>>>> 	
>>>> 
>>>> 	QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
>>>> 	QEMeshSmoother->SetNumberOfIterations(1 );
>>>> 	QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>> 	QEMeshSmoother->SetDelaunayConforming(true);
>>>> 	QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>>> 
>>>> 	QEMeshSmoother->ReleaseDataFlagOn();
>>>> 
>>>> 	QEMeshSmoother->Update();	
>>>>     
>>>> 	std::string Outputfilename="D:/tempOut.vtk";
>>>> 
>>>> 	typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>>>> 	MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>>>>        Meshwriter->SetFileName(Outputfilename.c_str( ));
>>>> 	Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>>>>        Meshwriter->Update();	
>>>> 
>>>> 	polyDatareader->SetFileName(Outputfilename.c_str() );
>>>> 	polyDatareader->ReleaseDataFlagOn();
>>>> 	polyDatareader->Update();
>>>> 
>>>> 	vtkSmartPointer<vtkSTLWriter> stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
>>>> 	
>>>> 	stlWriter->SetInput( polyDatareader->GetOutput());
>>>> 	stlWriter->SetFileName("D:/QEoutput.stl");
>>>> 	stlWriter->SetFileTypeToASCII();
>>>> 	stlWriter->Write();
>>>> 	
>>>> 	//Here it stops and taking long time 
>>>> 
>>>> 	return 0;
>>>> 
>>>> 	
>>>> }
>>>> ////
>>>> 
>>>> 
>>>> 
>>>> On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>> Hi Arnaud,
>>>> 
>>>> Thanks for your reply and valuable suggestions.
>>>> 
>>>> Number of points in my input mesh are 78928.In my pipeline I am already cleaning the polydata using vtkCleanPolyData filter.I will check the speed improvement and results with delaunay conforming turned OFF.
>>>> 
>>>> Thank you
>>>> 
>>>> 
>>>> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>> Hi Malik,
>>>> 
>>>> First of all, I would recommend using MeshFileReader instead of VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near future?).
>>>> 
>>>> Regarding now the smoothing procedure in itself. This class definitively misses some documentation and I will be adding some in the next few days (mainly extracted from the corresponding insight journal).
>>>> 
>>>> At the end of each iteration, when the delaunay conforming flag is turned ON, the conformation is performed. So depending on the mesh configuration, mesh size and number of iterations, it can take ages?
>>>> How large is your input mesh (number of points)?
>>>> 
>>>> You can also check results, by running first a smoothing without delaunay conforming, then apply a delaunay conforming on the output. Results won't be as nice, but you should get significant speed improvement.
>>>> Another possibility is to first do a clean poly data in vtk, with a small threshold to remove small edges in the input meshes (which results in lots of edge flipping after smoothing).
>>>> 
>>>> HTH
>>>> Arnaud
>>>> 
>>>> 
>>>> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>> 
>>>>> Hi All,
>>>>> 
>>>>> Can anyone suggest me if anything wrong I am doing in this below pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in release mode) at itkVtkPolydataReader .
>>>>> 
>>>>> 
>>>>> ////
>>>>> 
>>>>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;
>>>>> 	
>>>>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>>>> 
>>>>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>>> 
>>>>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>>>>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>>>>> 
>>>>> //VTKPolyDataWriterType::Pointer ItkToVtkWriter=VTKPolyDataWriterType::New();
>>>>> VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();
>>>>> 
>>>>> VtkToItkReader->SetFileName("abc.vtk");
>>>>> VtkToItkReader->Update();	
>>>>> 
>>>>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>>>>> SmoothingQuadEdgeMeshFilter;
>>>>> 
>>>>>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =   SmoothingQuadEdgeMeshFilter::New();
>>>>> 	
>>>>> 
>>>>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>>>>> QEMeshSmoother->SetNumberOfIterations(5 );
>>>>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>>> QEMeshSmoother->SetDelaunayConforming(true );
>>>>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );	
>>>>> 	
>>>>> QEMeshSmoother->Update();
>>>>> 
>>>>> ////
>>>>> 
>>>>> 
>>>>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>>> Thanks Bill for your answer.
>>>>> 
>>>>> The reason I am using this pipeline is that SmoothingQEMeshFilter has an additional parameter for smoothing which is delaunay conforming which helps to optimize aspect ratio of triangles while smoothing and thus produces better output.Is there anything similar filter in the vtk pipeline.I used vtkWindowedSincPolydatafilter which is not giving the output as good as QEMeshSmoothing filter.
>>>>> 
>>>>> Thanks for your help 
>>>>> 
>>>>> 
>>>>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>>> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Regards:
>>>>> Mallik
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> 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
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Regards:
>>>> Mallik
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Regards:
>>>> Mallik
>>>> 
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Regards:
>>> Mallik
>>> 
>>> <temp.vtk>
>> 
>> 
>> 
>> 
>> -- 
>> Regards:
>> Mallik
>> 
> 
> 
> 
> 
> -- 
> Regards:
> Mallik
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140821/e3b32421/attachment.html>

From arnaudgelas at gmail.com  Thu Aug 21 07:00:52 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 21 Aug 2014 13:00:52 +0200
Subject: [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
In-Reply-To: <D4FDB533-282B-4F99-836E-EB2582AA1E1D@gmail.com>
References: <CADJSx6xP6x6O0f63QKWAv_JQcjNSeX0+=RqraP9kzL9t1Q6ALg@mail.gmail.com>
 <CADZJ4hNCJWdC-hKWu0ouv6vvfPNABSKau_7xo4=+eVU7RyjppA@mail.gmail.com>
 <CADJSx6ysawyiJ5e=2wDZTyrDMkX6tufkUubd-DFZJqiHQc6GJQ@mail.gmail.com>
 <CADZJ4hN_ur5_Sc6aaKHPGVwNgBAsUi=XeD+xi=qmtO8MYc+vdw@mail.gmail.com>
 <CADJSx6zYy5n06d_ieFe2VaAgRFXYC=2aL8db0VNs4sEmsW6CPw@mail.gmail.com>
 <CADJSx6xNv1iQ-Yetd8oh+G_n0nRabGmRjL5UPK2ySu1B1+LT-A@mail.gmail.com>
 <20566F1B-1B71-411D-8C31-B25D4B24397A@gmail.com>
 <CADJSx6wS9fd0ChzOA-2+4__0csmYnSayPkBmRjr2Jis=CCee7w@mail.gmail.com>
 <CADJSx6xX_7non0ncNunJ3t_WeZExbzYyMG5KpndbFr1kSC=+TA@mail.gmail.com>
 <305E1509-8EF7-4770-9236-3D639B9BF155@gmail.com>
 <CADJSx6xG6tUTOnkbD3ekPQZ5Pdj-hLWS9r7QGbSNjWxCg5HzJg@mail.gmail.com>
 <D1EA86D9-549D-4245-B667-83A93735C0BC@gmail.com>
 <CADJSx6xABVRSoQRQ98Uoh9+Fraz19BwG3XbqR5JhTCBHcgCr+g@mail.gmail.com>
 <8E777677-5A6C-47A1-9ED6-030C85AB48B5@gmail.com>
 <CADJSx6xChSVq447yw4pbOuYtHPKaRDpmZoRqoxj92ejdtazzRg@mail.gmail.com>
 <D4FDB533-282B-4F99-836E-EB2582AA1E1D@gmail.com>
Message-ID: <997CA50D-FE3F-4620-BBDD-CCCD9EB440E0@gmail.com>

Here is the patch (for progress report):

	http://review.source.kitware.com/#/c/16769/

On Aug 21, 2014, at 12:47 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi,
> 
> As of now, there is no progress event on this filter, so it is normal nothing happened.
> 
> I'll submit another patch for progress event later today.
> 
> To review the patch, you need to create an account on gerrit:
> 
> 	http://review.source.kitware.com
> 
> Then you ca volunteer to the review patch, you can add comments, accept, refuse?
> Else once you are registered, you can send me an email and I will add you as a reviewer.
> 
> Best,
> Arnaud
> 
> On Aug 21, 2014, at 12:11 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
> 
>> Hi,
>>  I am trying observe the progressEvent by using AddObserver method of this filter but I couldn't. Could you check the below code once.
>> 
>> And one more thing,Could you guide me what exactly I have to do to Review the patch you have submitted.
>> 
>> Thank you
>> 
>> 
>> ///progress
>> 
>> #include<iostream>
>> #include<string>
>> 
>> #include <itkMeshFileWriter.h>
>> #include <itkMeshFileReader.h>
>> #include <itkMeshIOFactory.h>
>> #include <itkMeshIOBase.h>
>> #include "itkMesh.h"
>> #include "itkQuadEdgeMesh.h"
>> #include "itkQuadEdgeMeshTraits.h"
>> #include "itkSmoothingQuadEdgeMeshFilter.h"
>> #include "itkCommand.h"
>> 
>> class MyCommand : public itk::Command
>> {
>>   public:
>>     itkNewMacro( MyCommand );
>>  
>>   public:
>>  
>>     void Execute(itk::Object *caller, const itk::EventObject & event)
>>     {
>>       Execute( (const itk::Object *)caller, event);
>>     }
>>  
>>     void Execute(const itk::Object * object, const itk::EventObject & event)
>>     {
>>       std::cout << "Command called." << std::endl;
>> 
>> 	  if( typeid( itk::ProgressEvent ) ==  typeid( event ) )
>>        {
>> 		   ::itk::ProcessObject::ConstPointer  process = 
>>              dynamic_cast< const itk::ProcessObject *>( object/*caller*/ );
>> 
>>            const int value = static_cast<int>(process->GetProgress() * 100 );
>> 		   std::cout<<"progress:"<<value<<std::endl;   
>> 		  	  
>> 
>>       
>>        }
>> 
>>     }
>>  
>> };
>> 
>> int main( int argc, char* argv[] )
>> {
>> 
>> 	/*if( argc < 2 )
>>     {
>>     std::cerr << "Usage: " << std::endl;
>>     std::cerr << argv[0] << "  inputImageFile   outputImageFile   flipAxisX   flipAxisY" << std::endl;
>>     return EXIT_FAILURE;
>>     }*/
>> 
>> 	std::string Inputfilename="D:\\temp.vtk";
>>   typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits; 
>>   typedef itk::QuadEdgeMesh< double, 3,qetraits > MeshType;
>>   
>>   itk::OnesMatrixCoefficients< MeshType > coeff0;
>>   typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >SmoothingQuadEdgeMeshFilter;
>>     
>>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother = SmoothingQuadEdgeMeshFilter::New();
>>  
>>   typedef itk::MeshFileReader<MeshType> MeshReaderType;
>>   MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>>   Meshreader->SetFileName( Inputfilename.c_str()/*argv[1]*/ );
>>  // Meshreader->Update();
>>   
>>   
>>   MyCommand::Pointer myCommand = MyCommand::New();
>> 
>>   QEMeshSmoother->SetInput(Meshreader->GetOutput() );
>>   QEMeshSmoother->SetNumberOfIterations( 1 );
>>   QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>   QEMeshSmoother->SetDelaunayConforming(true);
>>   QEMeshSmoother->SetCoefficientsMethod( &coeff0 ); 
>>   QEMeshSmoother->AddObserver(itk::ProgressEvent, myCommand);
>>   
>>  // QEMeshSmoother->Update();
>>   std::string Outputfilename="D:\\tempOut2.vtk";
>>     
>>   typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>>   MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>>   Meshwriter->SetFileName(Outputfilename.c_str() /*argv[2]*/ );
>>   Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>> 
>>   try
>>   {
>>     Meshwriter->Update();
>>   }
>>   catch( itk::ExceptionObject& e )
>>   {
>>     std::cerr << e.what() << std::endl;
>>   }
>> 
>>   return 0;
>> 
>>   
>> } 
>> 
>> 
>> On Wed, Aug 20, 2014 at 7:33 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> Hi,
>> 
>> I have just submitted this patch for the documentation, can you please review it?
>> 
>> 	http://review.source.kitware.com/#/c/16755/
>> 
>> I was running this code on Mac i5 with 4GB RAM, with both ITK and this program compiled in Debug?
>> 
>> Best,
>> Arnaud
>> 
>> On Aug 7, 2014, at 5:20 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>> 
>>> Hi Arnaud,
>>> 
>>> Thanks,Can you please tell me your machine confuguration. I am running 4GB RAM,i3  on windows7.
>>> I have downloaded your project and tried to execute it and it is still the same problem Which I was facing earlier.Any suggestions .....
>>> 
>>> thank you 
>>> 
>>> 
>>> On Thu, Aug 7, 2014 at 8:10 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>> It takes 29s on my machine in debug to run 5 iterations with Delaunay conforming set to true
>>> 
>>> https://gist.github.com/arnaudgelas/0f20ebdaf53956f79997
>>> 
>>> 
>>> On Aug 7, 2014, at 3:45 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>> 
>>>> File path is correct.if it is '\'(backward slash) we have to add "D:\\" .since I used '/' it's not required to add "//".
>>>> 
>>>> please find the attached  .vtk file 
>>>> 
>>>> Thanks
>>>> 
>>>> 
>>>> On Thu, Aug 7, 2014 at 7:01 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>> Shouldn't it be D://temp.vtk ? Isn't it missing one '/' ?
>>>> 
>>>> Can you send this vtk file?
>>>> 
>>>> 
>>>> On Aug 7, 2014, at 3:23 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>> 
>>>>> Hi Arnaud,
>>>>> 
>>>>> Kindly have a look in the below code ,the problem  is that even after QEMeshFilter output is saved as .stl file ,the program is still running for long time.I have observed in my tests that MeshFileReader seems to be the culprit. Any suggestions ?
>>>>> 
>>>>> /////
>>>>> #include<iostream>
>>>>> #include<string>
>>>>> 
>>>>> #include <vtkPolyDataWriter.h>
>>>>> #include <vtkPolyDataReader.h>
>>>>> #include <itkMeshFileWriter.h>
>>>>> #include <itkMeshFileReader.h>
>>>>> #include <itkMeshIOFactory.h>
>>>>> #include <itkMeshIOBase.h>
>>>>> #include <vtkTriangleFilter.h>
>>>>> #include <vtkCleanPolyData.h>
>>>>> #include "itkMesh.h"
>>>>> #include "itkQuadEdgeMesh.h"
>>>>> #include "itkQuadEdgeMeshTraits.h"
>>>>> #include "itkSmoothingQuadEdgeMeshFilter.h"
>>>>> #include "vtkSTLWriter.h"
>>>>> #include <vtkSmartPointer.h>
>>>>> 
>>>>> int main()
>>>>> {
>>>>> 	std::string Inputfilename="D:/temp.vtk";   //number of points of this mesh file is around 78K
>>>>> 
>>>>> 	typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;	
>>>>> 	typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>>>> 	
>>>>> 	itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>>> 	typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >SmoothingQuadEdgeMeshFilter;
>>>>>     
>>>>> 	vtkSmartPointer<vtkPolyDataWriter> polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
>>>>> 	vtkSmartPointer<vtkPolyDataReader> polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();
>>>>>    
>>>>>     SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother = SmoothingQuadEdgeMeshFilter::New();
>>>>> 	
>>>>>    /* polyDatareader->SetFileName(Inputfilename.c_str() );
>>>>> 	polyDatareader->ReleaseDataFlagOn();
>>>>> 	polyDatareader->Update();*/
>>>>> 
>>>>> 	/*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
>>>>>     vtkSmartPointer<vtkTriangleFilter>::New();
>>>>>     triangleFilter->SetInput(polyDatareader->GetOutput());
>>>>>     triangleFilter->Update();*/
>>>>>   
>>>>> 	//
>>>>> 	/* vtkSmartPointer<vtkCleanPolyData> clean = vtkSmartPointer<vtkCleanPolyData>::New();
>>>>> 	#if (VTK_MAJOR_VERSION < 6)
>>>>> 	 clean->SetInput(triangleFilter->GetOutput() );
>>>>> 	#else
>>>>>        clean->SetInputData(triangleFilter->GetOutput() );
>>>>> 	#endif
>>>>> 	
>>>>>     clean->ConvertPolysToLinesOff();
>>>>>     clean->ConvertLinesToPointsOff();
>>>>>     clean->Update();
>>>>> 
>>>>> 	std::string Inputfilename2="D:/cleaned.vtk";*/
>>>>> 
>>>>> 	////
>>>>> 	/*polyDatawriter->SetInput(clean->GetOutput());	
>>>>> 	polyDatawriter->SetFileName(Inputfilename2.c_str());
>>>>> 	polyDatawriter->ReleaseDataFlagOn();
>>>>> 	polyDatawriter->Write(); */ 
>>>>>   
>>>>> 	typedef itk::MeshFileReader<MeshType> MeshReaderType;
>>>>> 	MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>>>>>        Meshreader->SetFileName(Inputfilename.c_str( ));
>>>>> 	Meshreader->Update();
>>>>> 
>>>>> 	/*MeshType::Pointer mesh =  Meshreader->GetOutput();
>>>>>          mesh->DisconnectPipeline();*/
>>>>> 	
>>>>> 
>>>>> 	QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
>>>>> 	QEMeshSmoother->SetNumberOfIterations(1 );
>>>>> 	QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>>> 	QEMeshSmoother->SetDelaunayConforming(true);
>>>>> 	QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>>>> 
>>>>> 	QEMeshSmoother->ReleaseDataFlagOn();
>>>>> 
>>>>> 	QEMeshSmoother->Update();	
>>>>>     
>>>>> 	std::string Outputfilename="D:/tempOut.vtk";
>>>>> 
>>>>> 	typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>>>>> 	MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>>>>>        Meshwriter->SetFileName(Outputfilename.c_str( ));
>>>>> 	Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>>>>>        Meshwriter->Update();	
>>>>> 
>>>>> 	polyDatareader->SetFileName(Outputfilename.c_str() );
>>>>> 	polyDatareader->ReleaseDataFlagOn();
>>>>> 	polyDatareader->Update();
>>>>> 
>>>>> 	vtkSmartPointer<vtkSTLWriter> stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
>>>>> 	
>>>>> 	stlWriter->SetInput( polyDatareader->GetOutput());
>>>>> 	stlWriter->SetFileName("D:/QEoutput.stl");
>>>>> 	stlWriter->SetFileTypeToASCII();
>>>>> 	stlWriter->Write();
>>>>> 	
>>>>> 	//Here it stops and taking long time 
>>>>> 
>>>>> 	return 0;
>>>>> 
>>>>> 	
>>>>> }
>>>>> ////
>>>>> 
>>>>> 
>>>>> 
>>>>> On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>>> Hi Arnaud,
>>>>> 
>>>>> Thanks for your reply and valuable suggestions.
>>>>> 
>>>>> Number of points in my input mesh are 78928.In my pipeline I am already cleaning the polydata using vtkCleanPolyData filter.I will check the speed improvement and results with delaunay conforming turned OFF.
>>>>> 
>>>>> Thank you
>>>>> 
>>>>> 
>>>>> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>>> Hi Malik,
>>>>> 
>>>>> First of all, I would recommend using MeshFileReader instead of VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near future?).
>>>>> 
>>>>> Regarding now the smoothing procedure in itself. This class definitively misses some documentation and I will be adding some in the next few days (mainly extracted from the corresponding insight journal).
>>>>> 
>>>>> At the end of each iteration, when the delaunay conforming flag is turned ON, the conformation is performed. So depending on the mesh configuration, mesh size and number of iterations, it can take ages?
>>>>> How large is your input mesh (number of points)?
>>>>> 
>>>>> You can also check results, by running first a smoothing without delaunay conforming, then apply a delaunay conforming on the output. Results won't be as nice, but you should get significant speed improvement.
>>>>> Another possibility is to first do a clean poly data in vtk, with a small threshold to remove small edges in the input meshes (which results in lots of edge flipping after smoothing).
>>>>> 
>>>>> HTH
>>>>> Arnaud
>>>>> 
>>>>> 
>>>>> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>>> 
>>>>>> Hi All,
>>>>>> 
>>>>>> Can anyone suggest me if anything wrong I am doing in this below pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5 mins in release mode) at itkVtkPolydataReader .
>>>>>> 
>>>>>> 
>>>>>> ////
>>>>>> 
>>>>>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double > qetraits;
>>>>>> 	
>>>>>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>>>>> 
>>>>>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>>>> 
>>>>>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>>>>>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>>>>>> 
>>>>>> //VTKPolyDataWriterType::Pointer ItkToVtkWriter=VTKPolyDataWriterType::New();
>>>>>> VTKPolyDataReaderType::Pointer VtkToItkReader=VTKPolyDataReaderType::New();
>>>>>> 
>>>>>> VtkToItkReader->SetFileName("abc.vtk");
>>>>>> VtkToItkReader->Update();	
>>>>>> 
>>>>>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>>>>>> SmoothingQuadEdgeMeshFilter;
>>>>>> 
>>>>>>  SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =   SmoothingQuadEdgeMeshFilter::New();
>>>>>> 	
>>>>>> 
>>>>>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>>>>>> QEMeshSmoother->SetNumberOfIterations(5 );
>>>>>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>>>> QEMeshSmoother->SetDelaunayConforming(true );
>>>>>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );	
>>>>>> 	
>>>>>> QEMeshSmoother->Update();
>>>>>> 
>>>>>> ////
>>>>>> 
>>>>>> 
>>>>>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>>>>>> Thanks Bill for your answer.
>>>>>> 
>>>>>> The reason I am using this pipeline is that SmoothingQEMeshFilter has an additional parameter for smoothing which is delaunay conforming which helps to optimize aspect ratio of triangles while smoothing and thus produces better output.Is there anything similar filter in the vtk pipeline.I used vtkWindowedSincPolydatafilter which is not giving the output as good as QEMeshSmoothing filter.
>>>>>> 
>>>>>> Thanks for your help 
>>>>>> 
>>>>>> 
>>>>>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>>>> 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
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> -- 
>>>>>> Regards:
>>>>>> Mallik
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> -- 
>>>>>> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Regards:
>>>>> Mallik
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Regards:
>>>>> Mallik
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Regards:
>>>> Mallik
>>>> 
>>>> <temp.vtk>
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Regards:
>>> Mallik
>>> 
>> 
>> 
>> 
>> 
>> -- 
>> Regards:
>> Mallik
>> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140821/7ba72bc7/attachment-0001.html>

From maximilian_oliver.mordig at roche.com  Thu Aug 21 10:52:53 2014
From: maximilian_oliver.mordig at roche.com (maximilian)
Date: Thu, 21 Aug 2014 07:52:53 -0700 (PDT)
Subject: [ITK-users] Modifying ValueAt function of SpatialObject
Message-ID: <1408632773158-7586101.post@n2.nabble.com>

Dear all,

I am using the itk::SpatialObjectToImageFilter to convert a
GroupSpatialObject (collection of several spatial objects) to an image. This
filter is fine, however, if several spatial objects overlap at a location,
the image's pixel value of that location is the first value returned by any
spatial object in GroupSpatialObject (the ValueAt function is implemented in
SpatialObject.hxx and iterates through its children; if one children
matches, its value is immediately returned). I wanted the change the
ValueAt() function to add up all the values returned by the ValueAt function
if several SpatialObjects overlap at a location.


To change the behavior, I have to inherit my new class, let's call it A,
from GroupSpatialObject (collection of SpatialObjects) and redefine the
method ValueAt(). The ValueAt() function in A has to be very similar to the
ValueAt() defined in SpatialObject, but add up the values returned by its
children spatial objects (instead of returning just the first match as it is
currently implemented). The problem is that I need access m_TreeNode that is
a list of all children (i.e. all objects contained in the
GroupSpatialObject) to get the values of each child. However, m_TreeNode is
declared private in the SpatialObject class. How can I circumvent this?

Of course, I could copy-paste SpatialObject into a new class, but I consider
this a very ugly solution, because I have to do so for all derived classes
(like GroupSpatialObject, among others).


Regards,
Maximilian



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Modifying-ValueAt-function-of-SpatialObject-tp7586101.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From bilgincc at gmail.com  Thu Aug 21 13:33:53 2014
From: bilgincc at gmail.com (Cagatay Bilgin)
Date: Thu, 21 Aug 2014 10:33:53 -0700
Subject: [ITK-users] Different output with dense and sparse level set
	representations
Message-ID: <CAHoiV3aK+kG_EM=6XPBOH2jOCo+dvHvCHovKNH7i0U7cNtBKTQ@mail.gmail.com>

Hello everybody,

I continue with my exploration of the new level set framework. I have
modified one of the examples and have an advection field in the positive x
direction. I would expect the initial contour to move in that direction and
that's the case with the sparse representation. Using the dense
representation however, only half of the contour moves to my surprise. Is
this a bug or I am missing something here. Here is the code and the cmake
file and snapshots of the movements.

[image: Inline image 2][image: Inline image 1]


#include "itkBinaryImageToLevelSetImageAdaptor.h"
#include "itkLevelSetContainer.h"
#include "itkLevelSetEquationPropagationTerm.h"
#include "itkLevelSetEquationAdvectionTerm.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 "itkWhitakerSparseLevelSetImage.h"
#include "itkLevelSetSparseImage.h"

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

void CreateSquareImage(FIT::Pointer image, FIT::Pointer prop, FIT::Pointer
advec)
{
    FIT::RegionType region;
    FIT::IndexType start;
    start[0] = 0;
    start[1] = 0;

    FIT::SizeType size;
    size[0] = 100;
    size[1] = 100;

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

    image->SetRegions(region);
    image->Allocate();
    image->FillBuffer(0);

    //constant grow in all directions
    prop->SetRegions(image->GetLargestPossibleRegion());
    prop->Allocate();
    prop->FillBuffer(1);

    //advec will increase in positive x direction
    advec->SetRegions(image->GetLargestPossibleRegion());
    advec->Allocate();
    advec->FillBuffer(0);

    // Set pixels in a square to one value
    for(unsigned int x = 35; x < 65; x++){
        for(unsigned int y = 35; y < 65; y++){
            FIT::IndexType pixelIndex;
            pixelIndex[0] = x;
            pixelIndex[1] = y;

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

    //advection in positive x direction
    for(unsigned int x = 0; x < 100; x++){
        for(unsigned int y = 0; y < 100; y++){
            FIT::IndexType pixelIndex;
            pixelIndex[0] = x;
            pixelIndex[1] = y;

            advec->SetPixel(pixelIndex, x);
        }
    }
}


/*
 */
int main(int argc, char* argv[] )
{
    using namespace itk;
    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;
    }

    FIT::Pointer input = FIT::New();
    FIT::Pointer prop  = FIT::New();
    FIT::Pointer advec  = FIT::New();

    CreateSquareImage(input, prop, advec);

    int numberOfIterations = atoi(argv[1]);

    typedef float LSPT;
    typedef Image< LSPT, 2 >    LSIT;
    typedef LevelSetDenseImage< LSIT >  LST;
    //typedef WhitakerSparseLevelSetImage< LSPT, 2 > LST;

    typedef LST::OutputRealType  LSOutputT;

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

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

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

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

    typedef LevelSetEquationAdvectionTerm<FIT, LSContainerT>  AdvecT;
    AdvecT::Pointer advectionTerm = AdvecT::New();
    advectionTerm->SetInput(advec);
    advectionTerm->SetCoefficient(atof(argv[3]));

    typedef LevelSetEquationCurvatureTerm<FIT, LSContainerT>  CurvT;
    CurvT::Pointer curvatureTerm = CurvT::New();
    curvatureTerm->SetCoefficient(atof(argv[4]));

    // Create term container (equation rhs)
    typedef LevelSetEquationTermContainer< FIT, LSContainerT >
TermContainerT;
    TermContainerT::Pointer termContainer = TermContainerT::New();
    termContainer->SetLevelSetContainer(levelSetContainer );
    termContainer->SetInput(input );
    termContainer->AddTerm(0, curvatureTerm );
    termContainer->AddTerm(1, advectionTerm );
    termContainer->AddTerm(2, propagationTerm );

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

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

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

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

    typedef LevelSetIterationUpdateCommand< LSEvolT, VisT >
IterationUpdateCommandType;
    IterationUpdateCommandType::Pointer iterationUpdateCommand =
IterationUpdateCommandType::New();
    iterationUpdateCommand->SetFilterToUpdate(visualizer );
    iterationUpdateCommand->SetUpdatePeriod(1 );

    evolution->AddObserver(IterationEvent(), iterationUpdateCommand );
    evolution->Update();

    return EXIT_SUCCESS;
}


cmake_minimum_required(VERSION 2.8)
project(Motion)

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})

Params used for the experiment:
Ran sparse representation with
./Motion 15 0 1 1

Ran dense representation with
./Motion 15 0 1 0


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/20140821/a2bfd8a6/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: sparse_00015.png
Type: image/png
Size: 2848 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140821/a2bfd8a6/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dense_00010.png
Type: image/png
Size: 2737 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140821/a2bfd8a6/attachment-0001.png>

From matt.mccormick at kitware.com  Thu Aug 21 17:54:56 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 21 Aug 2014 17:54:56 -0400
Subject: [ITK-users] Friday gathering
Message-ID: <CALzTN-RiENMmYwR+7NMg7squ4esWbDc4PWxHtHFHfR=1rdSv5A@mail.gmail.com>

Hi,

I will not be able to host or attend the regular gathering tomorrow.
If someone is interested in hosting, please do so.

Thanks,
Matt

From arnaudgelas at gmail.com  Fri Aug 22 02:58:34 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Fri, 22 Aug 2014 08:58:34 +0200
Subject: [ITK-users] [ITK]  combining N images
In-Reply-To: <41BB5486-E3F6-4196-8E58-C59F514C8800@mail.nih.gov>
References: <CAK3qF+-QpDPqbCRjMABOu7gTyVfQ48DoHH7A7CzUxgvkBRE-jg@mail.gmail.com>
 <CAK07tM-wbff17T17w6Cu8b6d8-pTatizXLT7KGkpCmS9tPy=DQ@mail.gmail.com>
 <CAK3qF+8XCGByndYiKGfLqDwie+2PkipByMovDod7QAq04Nwrmg@mail.gmail.com>
 <41BB5486-E3F6-4196-8E58-C59F514C8800@mail.nih.gov>
Message-ID: <CAK3qF+_htTdda3=N7LQD2ESBFSKvL__sh8Lb8P9-AG+p0Zjg-Q@mail.gmail.com>

Hi Brad,

Thanks for the link! It helped me to get on track...
In the end, it was not that complicated to do all in one filter (let me
know if anyone is interested).

Arnaud


On Wed, Aug 20, 2014 at 6:53 PM, Bradley Lowekamp <brad at lowekamp.net> wrote:

> This may be of some use:
>
>
> https://github.com/blowekamp/itkStreamingSinc/blob/master/include/itkBoundingRegionImageSinc.h
>
> On Aug 20, 2014, at 11:51 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>
> Hi,
>
> I do not want to add images, it is more something like pasting but I do
> not know in advance what would be the output image size, but it would be at
> least the bounding box of all images...
>
> Arnaud
>
> On Wednesday, August 20, 2014, Mordig, Maximilian Oliver <
> maximilian_oliver.mordig at roche.com> wrote:
>
>> Once you have resampled all images, you can use the itk AddFilter.
>>
>>
>> On Wed, Aug 20, 2014 at 4:28 PM, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I am trying to combine N images together into a single image of the same
>>> dimension.
>>>
>>> These N images have the same direction, but can have different origin,
>>> start index, spacing, size (there is no overlap). Then gaps in between
>>> images would be filled with a given constant value.
>>>
>>> Is there such a filter? or assuming I have already resampled all images
>>> to a common ground, is there a filter to do this?
>>>
>>> Thanks,
>>> Arnaud
>>>
>>> _____________________________________
>>> 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
>
> _______________________________________________
> 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/20140822/47df5d3b/attachment.html>

From vincent.ngai at gmail.com  Fri Aug 22 03:30:44 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Fri, 22 Aug 2014 15:30:44 +0800
Subject: [ITK-users] Silly question on itk::Matrix
Message-ID: <CAC3nAP3dkMaEr-gzjhf4WrX-Q2gv5_keTCRYs_1bJ1K4sAHEJQ@mail.gmail.com>

Hi all, pardon me for this silly question on itk::Matrix. Why do I need to
transpose a translation matrix after I copy the [x,y,z] translation values
to the matrix[3].

I know conceptually it should not really matter whether its row or col
major so long as you can
post multiply or pre multiply with another vector. But the way operator*()
works only allows for
Matrix * P, and when I test the simple case of TranslationMatrix * Point, I
would have to transpose the matrix. If I could also do Point *
TranslationMatrix, then i wouldn't need to transpose.

Any ideas?

-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140822/a701a2a3/attachment.html>

From millerjv at gmail.com  Fri Aug 22 07:14:11 2014
From: millerjv at gmail.com (Jim Miller)
Date: Fri, 22 Aug 2014 07:14:11 -0400
Subject: [ITK-users] Silly question on itk::Matrix
In-Reply-To: <CAC3nAP3dkMaEr-gzjhf4WrX-Q2gv5_keTCRYs_1bJ1K4sAHEJQ@mail.gmail.com>
References: <CAC3nAP3dkMaEr-gzjhf4WrX-Q2gv5_keTCRYs_1bJ1K4sAHEJQ@mail.gmail.com>
Message-ID: <0BBC89C9-0F67-48F1-99F4-AC89AF5C394B@gmail.com>

ITK standard is that points are column vectors. Thus, matrix times a point a point is defined as Mat * P

Jim

> On Aug 22, 2014, at 3:30 AM, vincent ngai <vincent.ngai at gmail.com> wrote:
> 
> Hi all, pardon me for this silly question on itk::Matrix. Why do I need to transpose a translation matrix after I copy the [x,y,z] translation values to the matrix[3].
> 
> I know conceptually it should not really matter whether its row or col major so long as you can 
> post multiply or pre multiply with another vector. But the way operator*() works only allows for
> Matrix * P, and when I test the simple case of TranslationMatrix * Point, I would have to transpose the matrix. If I could also do Point * TranslationMatrix, then i wouldn't need to transpose.
> 
> Any ideas?
> 
> -- 
> 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

From joseignacio.prieto at gmail.com  Fri Aug 22 19:45:37 2014
From: joseignacio.prieto at gmail.com (Jose Ignacio Prieto)
Date: Fri, 22 Aug 2014 19:45:37 -0400
Subject: [ITK-users] 2D polygon stack to 3d mesh
Message-ID: <CANkppu7H-iZxtwPfLO4k2McaT43Ggwm6wtwbusrr7zz=Q5uGbQ@mail.gmail.com>

Hi all,
I am dubious to which mail list use. I have an array of 2d snake
segmentations for the left ventricle( a std vector of 20 rows with a closed
convex 2d polygon each row) on ITK and I would like it to turn it into a
mesh that can be visualized. Should I use QuadMeshEdge and then a Delaunay
in ITk, or use Delaunay methods in VTK. Or maybe I should write an ad-hoc
method given that the points are sorted so a triangle can be made with two
consecutive polygon points and the closest one on the following slice.

Thank you very much,

Ignacio Prieto

--
Ignacio Prieto
Research Assistant
Biomedical Imaging Center
Pontificia Universidad Catolica de Chile
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140822/2faf45f5/attachment.html>

From vincent.ngai at gmail.com  Fri Aug 22 21:49:32 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Sat, 23 Aug 2014 09:49:32 +0800
Subject: [ITK-users] Silly question on itk::Matrix
In-Reply-To: <0BBC89C9-0F67-48F1-99F4-AC89AF5C394B@gmail.com>
References: <CAC3nAP3dkMaEr-gzjhf4WrX-Q2gv5_keTCRYs_1bJ1K4sAHEJQ@mail.gmail.com>
 <0BBC89C9-0F67-48F1-99F4-AC89AF5C394B@gmail.com>
Message-ID: <CAC3nAP16d-rqWs0PkdWJkK+gryjqOEJ0_NZWyMwF_GS7oD+S6Q@mail.gmail.com>

Ah yes, so my question is why is the [] accessor not column major? If
points are columns, the matrix elements for the Tx,Ty,Tz translation
components should also be columnar? It just seems like extra work to need
to get the matrix transpose just to do a Mat * P

Regards,
Vincent


On Fri, Aug 22, 2014 at 7:14 PM, Jim Miller <millerjv at gmail.com> wrote:

> ITK standard is that points are column vectors. Thus, matrix times a point
> a point is defined as Mat * P
>
> Jim
>
> > On Aug 22, 2014, at 3:30 AM, vincent ngai <vincent.ngai at gmail.com>
> wrote:
> >
> > Hi all, pardon me for this silly question on itk::Matrix. Why do I need
> to transpose a translation matrix after I copy the [x,y,z] translation
> values to the matrix[3].
> >
> > I know conceptually it should not really matter whether its row or col
> major so long as you can
> > post multiply or pre multiply with another vector. But the way
> operator*() works only allows for
> > Matrix * P, and when I test the simple case of TranslationMatrix *
> Point, I would have to transpose the matrix. If I could also do Point *
> TranslationMatrix, then i wouldn't need to transpose.
> >
> > Any ideas?
> >
> > --
> > 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
>



-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140823/62f530df/attachment.html>

From millerjv at gmail.com  Sat Aug 23 08:12:10 2014
From: millerjv at gmail.com (Jim Miller)
Date: Sat, 23 Aug 2014 08:12:10 -0400
Subject: [ITK-users] Silly question on itk::Matrix
In-Reply-To: <CAC3nAP16d-rqWs0PkdWJkK+gryjqOEJ0_NZWyMwF_GS7oD+S6Q@mail.gmail.com>
References: <CAC3nAP3dkMaEr-gzjhf4WrX-Q2gv5_keTCRYs_1bJ1K4sAHEJQ@mail.gmail.com>
 <0BBC89C9-0F67-48F1-99F4-AC89AF5C394B@gmail.com>
 <CAC3nAP16d-rqWs0PkdWJkK+gryjqOEJ0_NZWyMwF_GS7oD+S6Q@mail.gmail.com>
Message-ID: <E7985D50-B42B-46A0-88A5-5782580D864F@gmail.com>

Matrices and images are row major order.  Points and vectors are column vectors. 

No transpose is necessary.  You can index element by element directly to set the column you want. 

Row major ordering is more popular than column major ordering. I think there are regional preferences as to the"proper" way. I also think electrical engineers prefer one way whereas mechanical engineers prefer the other. Probably is partially based on how disciplines view the composition of coordinate frames (inside out or outside in). 

Some systems allow you to use either convention. We found that leads to a lot of confusion and errors. So 15 years ago, when we started ITK, we chose to pick a single standard for the code. 

Jim

> On Aug 22, 2014, at 9:49 PM, vincent ngai <vincent.ngai at gmail.com> wrote:
> 
> Ah yes, so my question is why is the [] accessor not column major? If points are columns, the matrix elements for the Tx,Ty,Tz translation components should also be columnar? It just seems like extra work to need to get the matrix transpose just to do a Mat * P
> 
> Regards,
> Vincent
> 
> 
>> On Fri, Aug 22, 2014 at 7:14 PM, Jim Miller <millerjv at gmail.com> wrote:
>> ITK standard is that points are column vectors. Thus, matrix times a point a point is defined as Mat * P
>> 
>> Jim
>> 
>> > On Aug 22, 2014, at 3:30 AM, vincent ngai <vincent.ngai at gmail.com> wrote:
>> >
>> > Hi all, pardon me for this silly question on itk::Matrix. Why do I need to transpose a translation matrix after I copy the [x,y,z] translation values to the matrix[3].
>> >
>> > I know conceptually it should not really matter whether its row or col major so long as you can
>> > post multiply or pre multiply with another vector. But the way operator*() works only allows for
>> > Matrix * P, and when I test the simple case of TranslationMatrix * Point, I would have to transpose the matrix. If I could also do Point * TranslationMatrix, then i wouldn't need to transpose.
>> >
>> > Any ideas?
>> >
>> > --
>> > 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
> 
> 
> 
> -- 
> Regards,
> Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140823/56303acb/attachment.html>

From vincent.ngai at gmail.com  Sun Aug 24 22:38:37 2014
From: vincent.ngai at gmail.com (vincent ngai)
Date: Mon, 25 Aug 2014 10:38:37 +0800
Subject: [ITK-users] Silly question on itk::Matrix
In-Reply-To: <E7985D50-B42B-46A0-88A5-5782580D864F@gmail.com>
References: <CAC3nAP3dkMaEr-gzjhf4WrX-Q2gv5_keTCRYs_1bJ1K4sAHEJQ@mail.gmail.com>
 <0BBC89C9-0F67-48F1-99F4-AC89AF5C394B@gmail.com>
 <CAC3nAP16d-rqWs0PkdWJkK+gryjqOEJ0_NZWyMwF_GS7oD+S6Q@mail.gmail.com>
 <E7985D50-B42B-46A0-88A5-5782580D864F@gmail.com>
Message-ID: <CAC3nAP2hgYfLR+3WxUjG9Rnt81b1Wst9cE-O6fzogfXCsJpfVg@mail.gmail.com>

Hi Jim, thanks for the background, that clarified things for me.

Regards,
Vincent


On Sat, Aug 23, 2014 at 8:12 PM, Jim Miller <millerjv at gmail.com> wrote:

> Matrices and images are row major order.  Points and vectors are column
> vectors.
>
> No transpose is necessary.  You can index element by element directly to
> set the column you want.
>
> Row major ordering is more popular than column major ordering. I think
> there are regional preferences as to the"proper" way. I also think
> electrical engineers prefer one way whereas mechanical engineers prefer the
> other. Probably is partially based on how disciplines view the composition
> of coordinate frames (inside out or outside in).
>
> Some systems allow you to use either convention. We found that leads to a
> lot of confusion and errors. So 15 years ago, when we started ITK, we chose
> to pick a single standard for the code.
>
> Jim
>
> On Aug 22, 2014, at 9:49 PM, vincent ngai <vincent.ngai at gmail.com> wrote:
>
> Ah yes, so my question is why is the [] accessor not column major? If
> points are columns, the matrix elements for the Tx,Ty,Tz translation
> components should also be columnar? It just seems like extra work to need
> to get the matrix transpose just to do a Mat * P
>
> Regards,
> Vincent
>
>
> On Fri, Aug 22, 2014 at 7:14 PM, Jim Miller <millerjv at gmail.com> wrote:
>
>> ITK standard is that points are column vectors. Thus, matrix times a
>> point a point is defined as Mat * P
>>
>> Jim
>>
>> > On Aug 22, 2014, at 3:30 AM, vincent ngai <vincent.ngai at gmail.com>
>> wrote:
>> >
>> > Hi all, pardon me for this silly question on itk::Matrix. Why do I need
>> to transpose a translation matrix after I copy the [x,y,z] translation
>> values to the matrix[3].
>> >
>> > I know conceptually it should not really matter whether its row or col
>> major so long as you can
>> > post multiply or pre multiply with another vector. But the way
>> operator*() works only allows for
>> > Matrix * P, and when I test the simple case of TranslationMatrix *
>> Point, I would have to transpose the matrix. If I could also do Point *
>> TranslationMatrix, then i wouldn't need to transpose.
>> >
>> > Any ideas?
>> >
>> > --
>> > 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
>>
>
>
>
> --
> Regards,
> Vincent
>
>


-- 
Regards,
Vincent
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140825/423b1480/attachment.html>

From CHernando at telespazio.es  Mon Aug 25 04:36:44 2014
From: CHernando at telespazio.es (Carlos Hernando Ramiro)
Date: Mon, 25 Aug 2014 10:36:44 +0200
Subject: [ITK-users] UseAllPixelsOn with Mutual Information
In-Reply-To: <800D4DFDAF353641B990F5CEB49F05E179B9C9@GORDONS.aurensis.com>
References: <800D4DFDAF353641B990F5CEB49F05E179B9C9@GORDONS.aurensis.com>
Message-ID: <53FAF59C.3040602@telespazio.es>

Dear all,

is seems that the method UseAllPixelsOn() does not work for the class 
itkMutualInformationImageToImageMetric. Then, what I can do to assure 
that all the pixels of an specific region are used to calculate this 
metric? Is there any alternative to UseAllPixelsOn()?


Best regards
Carlos

From chernando at telespazio.es  Mon Aug 25 05:20:45 2014
From: chernando at telespazio.es (carlos)
Date: Mon, 25 Aug 2014 02:20:45 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
	transformation
In-Reply-To: <1408375248616-7586081.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
Message-ID: <1408958445955-7586112.post@n2.nabble.com>

Dear Jan,

I think that you can use the metric without optimizer, but that you need a
transformation and an interpolator. You can use the translation transform
(and the interpolator you prefer, although it will not influence):
typedef itk::MutualInformationImageToImageMetric<ImageType, ImageType>
MIMetricType;
MIMetricType::Pointer MImetric;
typedef itk::TranslationTransform< double, ImageDimension > TransformType;
TransformType::Pointer transform = TransformType::New();
MImetric->SetTransform(transform);

and then call GetValue with the translation parameters [0,0]
MIMetricType::TransformParametersType
displacementMI(transform->ParametersDimension);
displacementMI[0] = 0;
displacementMI[1] = 0;
MImetric->GetValue(displacementMI);


Best regards
Carlos



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586112.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From dlrdave at aol.com  Mon Aug 25 10:34:13 2014
From: dlrdave at aol.com (David Cole)
Date: Mon, 25 Aug 2014 10:34:13 -0400 (EDT)
Subject: [ITK-users] FDA agile practices guidance
In-Reply-To: <53EBA560.208@gmail.com>
References: <53EBA560.208@gmail.com>
Message-ID: <8D18E88C674FD6D-1E58-23933@webmail-m289.sysops.aol.com>

> anyone know about resources about FDA guidances for implementing 
agile
> practices in the development of medical device software? In concrete,
> the document AAMI TIR45:2012 is the one I am seeking online.

Well, it's for sale at ansi.org for $150:

     
http://webstore.ansi.org/RecordDetail.aspx?sku=AAMI+TIR45%3A2012+%28AAMI+TIR+45%3A2012%29

I couldn't find it anywhere else online.


HTH,
David C.


From payalprajapati2808 at gmail.com  Mon Aug 25 13:01:36 2014
From: payalprajapati2808 at gmail.com (mahi)
Date: Mon, 25 Aug 2014 10:01:36 -0700 (PDT)
Subject: [ITK-users] Problem in computing Eigenvalue for swir band of hdf
 taken by Imager payload
Message-ID: <1408986096189-34456.post@n7.nabble.com>

Hello All,

I am new to ITK.I want to compute eigenvalue of SWIR band of .h5 File.I have
tried it  using itkSymmetricEigenAnalysis and   vnl_symmetric_eigen .Both
Programs work fine for a .tiff file(which i am using for experimental
purpose) having dimension 256*256 and it works fine. SWIR band has dimension
of 11220*11264. so I made it of 11264*11264 by padding extra zeros at rows
starting from 11221. My problem is when i apply both program on this
extended matrix it shows no error but also doesnt give any output.It gets
stuck...Am i going in a right direction or not?Why this happen?I have
attached both code. itk_image_to_matrix.cxx
<http://itk-users.7.n7.nabble.com/file/n34456/itk_image_to_matrix.cxx>  

newsvd.cxx <http://itk-users.7.n7.nabble.com/file/n34456/newsvd.cxx>  
Q_matrixfinal.cxx
<http://itk-users.7.n7.nabble.com/file/n34456/Q_matrixfinal.cxx>  

Any help would be appriciated.

Thank You,
Payal




--
View this message in context: http://itk-users.7.n7.nabble.com/Problem-in-computing-Eigenvalue-for-swir-band-of-hdf-taken-by-Imager-payload-tp34456.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From mercikd at thomas.edu  Mon Aug 25 14:44:28 2014
From: mercikd at thomas.edu (Dan Mercik)
Date: Mon, 25 Aug 2014 18:44:28 +0000
Subject: [ITK-users] Tiling Side by Side Question
Message-ID: <5d84846dd31f482d88152b7c19c56632@T9.tcnet.thomas.edu>

Hey,

            I have 7 images to tile but only want 2  images to  be tile horizontally and  the other 5 other images to be tile vertically. When I declare the layouts like

layout[0] = 2;

layout[1] = 5;

The x axis is always being filled. Is it possible to not fill that tile with an image?



Daniel Mercik

Computer Science Major

Service Desk Technician

Thomas College

From millerjv at gmail.com  Mon Aug 25 15:42:04 2014
From: millerjv at gmail.com (Jim Miller)
Date: Mon, 25 Aug 2014 15:42:04 -0400
Subject: [ITK-users] Tiling Side by Side Question
In-Reply-To: <5d84846dd31f482d88152b7c19c56632@T9.tcnet.thomas.edu>
References: <5d84846dd31f482d88152b7c19c56632@T9.tcnet.thomas.edu>
Message-ID: <A80BA66C-5947-48D5-BE66-8C55D337B65F@gmail.com>

In this, I think you want to cascade two TileImage filters. One to tile the first two images horizontally. The second to Tile that result with your others vertically. 

Jim

> On Aug 25, 2014, at 2:44 PM, Dan Mercik <mercikd at thomas.edu> wrote:
> 
> Hey,
> 
>            I have 7 images to tile but only want 2  images to  be tile horizontally and  the other 5 other images to be tile vertically. When I declare the layouts like
> 
> layout[0] = 2;
> 
> layout[1] = 5;
> 
> The x axis is always being filled. Is it possible to not fill that tile with an image?
> 
> 
> 
> Daniel Mercik
> 
> Computer Science Major
> 
> Service Desk Technician
> 
> Thomas College
> _____________________________________
> 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 Aug 25 23:46:52 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 25 Aug 2014 23:46:52 -0400
Subject: [ITK-users] Composite Filter with variable stdvector of filters
	inside
In-Reply-To: <CANkppu5b2vBFN96F7fx7MCSmRH8aqA14AUOCn7rbUtGFCWemAw@mail.gmail.com>
References: <CANkppu5b2vBFN96F7fx7MCSmRH8aqA14AUOCn7rbUtGFCWemAw@mail.gmail.com>
Message-ID: <CALzTN-RYBYBxrgvJr6eT=XkiewvkuXee1ZC2y=wq+Za5L=Zzow@mail.gmail.com>

Hi Ignacio,

If I understand corrections, this may do want is desired:

void SetNumberOfZSlices( int slices )
{
if( m_NumberOfZSlices != slices )
  {
  this->m_NumberOfZSlices = slices;
  this->UpdateNumberOfFilters();
  this->Modified();
  }
}

and a similar implementation for SetNumberOfTimeFrames().

Hope this helps,
Matt

On Wed, Aug 20, 2014 at 11:00 AM, Jose Ignacio Prieto
<joseignacio.prieto at gmail.com> wrote:
> Hi all,
> I am trying to create a composite filter for a 4D dataset that will use
> different cascaded 2D filters on the inside. For this, I have created a
> double std vector that holds all the 2D filters. I have also set some param
> setters for this filters (that perform a double for inside, setting the
> param to each filter and then calling modified() on the outside one). I have
> another method called UpdateNumberofFilters, that depending on 2 ints (num
> of Z slices, num of T timeframes) will push back more filters to the 2D
> array of filters.
> My problem is that I dont know which function should call the
> UpdateNumofFilters. It should be done before the setters but after the
> constructor and after setting those two ints. I want to design it so that if
> I change a param after calling update I dont have to run the whole filter
> again, so I dont want it to be under the GenerateData() method.
>
> Thank you very much for your insights.
>
> Ignacio Prieto
>
>  --
> Ignacio Prieto
> Research Assistant
> Biomedical Imaging Center
> Pontificia Universida Catolica de Chile
>
>
>
> _____________________________________
> 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 jan.bergmeier at imes.uni-hannover.de  Tue Aug 26 09:08:26 2014
From: jan.bergmeier at imes.uni-hannover.de (jan)
Date: Tue, 26 Aug 2014 06:08:26 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
	transformation
In-Reply-To: <1408958445955-7586112.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <1408958445955-7586112.post@n2.nabble.com>
Message-ID: <1409058506727-7586118.post@n2.nabble.com>

Dear Carlos,
thank you for your help. i'm still experiencing some difficulties. I tried
your proposed way like this:

    typedef itk::MutualInformationImageToImageMetric< UChar2DImageType,
UChar2DImageType > MetricType;
    typedef itk::TranslationTransform< double, 2 > TransformType;
    typedef itk::GradientDescentOptimizer OptimizerType;
    MetricType::Pointer metric = MetricType::New();
    TransformType::Pointer transform = TransformType::New();

    MetricType::TransformParametersType displacement(
transform->ParametersDimension );
    displacement[0] = 0.0;
    displacement[1] = 0.0;

    metric->SetFixedImage( fixedImage );
    metric->SetMovingImage( movingImage);
    metric->SetTransform( transform );
    metric->GetValue( displacement );

When I am trying to get the MI-value with the displacement parameters, my
program crashes.



i tried another way with an optimizer that does only one iteration:

    typedef itk::TranslationTransform< double, 2 > TransformType;
    typedef itk::GradientDescentOptimizer OptimizerType;
    typedef itk::LinearInterpolateImageFunction< UChar2DImageType, double >
InterpolatorType;
    typedef itk::ImageRegistrationMethod< UChar2DImageType, UChar2DImageType
> RegistrationType;
    typedef itk::MutualInformationImageToImageMetric< UChar2DImageType,
UChar2DImageType > MetricType;
    typedef RegistrationType::ParametersType ParametersType;

    TransformType::Pointer transform = TransformType::New();
    OptimizerType::Pointer optimizer = OptimizerType::New();
    InterpolatorType::Pointer interpolator = InterpolatorType::New();
    RegistrationType::Pointer registration = RegistrationType::New();
    MetricType::Pointer metric = MetricType::New();

    registration->SetOptimizer( optimizer );
    registration->SetTransform( transform );
    registration->SetInterpolator( interpolator );
    registration->SetMetric( metric );

    registration->SetFixedImage( fixedImage );
    registration->SetMovingImage( movingImage );

    ParametersType initialParameters( transform->GetNumberOfParameters() );
    initialParameters[0] = 0.0;
    initialParameters[1] = 0.0;

    registration->SetInitialTransformParameters( initialParameters );

    optimizer->SetNumberOfIterations( 1 );

    try
    {
        registration->Update();
    }
    catch( itk::ExceptionObject & err )
    {
        std::cout << "ExceptionObject caught !" << std::endl;
        std::cout << err << std::endl;
    }

    double bestValue = optimizer->GetValue();

The problem here is that I get the following Error:

     "Description: itk::ERROR:
MutualInformationImageToImageMetric(0x48e0860): Standard deviation is too
small"



Any suggestions for a convenient solution?

Thanks, 
Jan



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586118.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From gass at vision.ee.ethz.ch  Tue Aug 26 09:22:33 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Tue, 26 Aug 2014 15:22:33 +0200
Subject: [ITK-users] MutualInformationImageToImageMetric without
	transformation
In-Reply-To: <1408375248616-7586081.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
Message-ID: <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>

Hi Jan,

ITK also offers a convenient identity transform for this:

http://www.itk.org/Doxygen/html/classitk_1_1IdentityTransform.html

Hope that helps,
Tobias


2014-08-18 17:20 GMT+02:00 jan <jan.bergmeier at imes.uni-hannover.de>:

> Hello,
>
> I want to perform a registration between two images without any
> transformation or optimization. I like to use the
> itk::MutualInformationImageToImageMetric. As I understand the itk metric,
> you have to use a transformation, an optimizer, an interpolator and so on.
>
> I want to compare one image to a set of images with mutual information as
> metric.
>
> So basically, I like to use the   GetValue()   method, without giving any
> parameters to it. Is there a way to do that, or another way to get just one
> mutual information value between two images?
>
> Thanks in advance,
>
> Jan
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081.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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140826/4a0f05cc/attachment.html>

From jan.bergmeier at imes.uni-hannover.de  Tue Aug 26 09:31:46 2014
From: jan.bergmeier at imes.uni-hannover.de (jan)
Date: Tue, 26 Aug 2014 06:31:46 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
 transformation
In-Reply-To: <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
Message-ID: <1409059906690-7586120.post@n2.nabble.com>

Hi,

my attempt with the identity transform would be this:

    typedef itk::IdentityTransform< double, 2 > TransformType;
    typedef itk::MutualInformationImageToImageMetric< UChar2DImageType,
UChar2DImageType > MetricType;

    TransformType::Pointer transform = TransformType::New();
    MetricType::Pointer metric = MetricType::New();

    metric->SetFixedImage( fixedImage );
    metric->SetMovingImage( movingImage );
    metric->GetValue( transform->GetParameters() );

For me it's the same problem. The program crashes when I use GetValue(). It
seems to me as if the parameters need to be OptimizerParameters....

Thanks,
Jan



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586120.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From gass at vision.ee.ethz.ch  Tue Aug 26 09:36:46 2014
From: gass at vision.ee.ethz.ch (Tobias Gass)
Date: Tue, 26 Aug 2014 15:36:46 +0200
Subject: [ITK-users] MutualInformationImageToImageMetric without
	transformation
In-Reply-To: <1409059906690-7586120.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
 <1409059906690-7586120.post@n2.nabble.com>
Message-ID: <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>

Have you checked whether your images are physically overlapping?

You could also try to change the number of MI samples to avoid accidentally
sampling only from homogeneous regions.

Best of luck,
Tobias


2014-08-26 15:31 GMT+02:00 jan <jan.bergmeier at imes.uni-hannover.de>:

> Hi,
>
> my attempt with the identity transform would be this:
>
>     typedef itk::IdentityTransform< double, 2 > TransformType;
>     typedef itk::MutualInformationImageToImageMetric< UChar2DImageType,
> UChar2DImageType > MetricType;
>
>     TransformType::Pointer transform = TransformType::New();
>     MetricType::Pointer metric = MetricType::New();
>
>     metric->SetFixedImage( fixedImage );
>     metric->SetMovingImage( movingImage );
>     metric->GetValue( transform->GetParameters() );
>
> For me it's the same problem. The program crashes when I use GetValue(). It
> seems to me as if the parameters need to be OptimizerParameters....
>
> Thanks,
> Jan
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586120.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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140826/d1794932/attachment.html>

From joseignacio.prieto at gmail.com  Tue Aug 26 09:38:16 2014
From: joseignacio.prieto at gmail.com (Jose Ignacio Prieto)
Date: Tue, 26 Aug 2014 09:38:16 -0400
Subject: [ITK-users] Composite Filter with variable stdvector of filters
	inside
In-Reply-To: <CALzTN-RYBYBxrgvJr6eT=XkiewvkuXee1ZC2y=wq+Za5L=Zzow@mail.gmail.com>
References: <CANkppu5b2vBFN96F7fx7MCSmRH8aqA14AUOCn7rbUtGFCWemAw@mail.gmail.com>
 <CALzTN-RYBYBxrgvJr6eT=XkiewvkuXee1ZC2y=wq+Za5L=Zzow@mail.gmail.com>
Message-ID: <CANkppu6TEftnReOJ6qbDFxHwCkmvcF=7PSS+k7BbWL0oZhzX5w@mail.gmail.com>

Thanks Matt, my problem was that I didn't know when to call this methods. I
finally put them into GenerateInputRequestedRegion and this way seems to be
called before Update(). I don't know under what conditions
GenerateInputRequestedRegion is called, for example if a parameter is
changed after an update call, will it be called again or only GenerateData
would be called. Is there a good developer manual? The ITK user manual
seems a little short on this.

Thanks

Ignacio Prieto


On Mon, Aug 25, 2014 at 11:46 PM, Matt McCormick <matt.mccormick at kitware.com
> wrote:

> Hi Ignacio,
>
> If I understand corrections, this may do want is desired:
>
> void SetNumberOfZSlices( int slices )
> {
> if( m_NumberOfZSlices != slices )
>   {
>   this->m_NumberOfZSlices = slices;
>   this->UpdateNumberOfFilters();
>   this->Modified();
>   }
> }
>
> and a similar implementation for SetNumberOfTimeFrames().
>
> Hope this helps,
> Matt
>
> On Wed, Aug 20, 2014 at 11:00 AM, Jose Ignacio Prieto
> <joseignacio.prieto at gmail.com> wrote:
> > Hi all,
> > I am trying to create a composite filter for a 4D dataset that will use
> > different cascaded 2D filters on the inside. For this, I have created a
> > double std vector that holds all the 2D filters. I have also set some
> param
> > setters for this filters (that perform a double for inside, setting the
> > param to each filter and then calling modified() on the outside one). I
> have
> > another method called UpdateNumberofFilters, that depending on 2 ints
> (num
> > of Z slices, num of T timeframes) will push back more filters to the 2D
> > array of filters.
> > My problem is that I dont know which function should call the
> > UpdateNumofFilters. It should be done before the setters but after the
> > constructor and after setting those two ints. I want to design it so
> that if
> > I change a param after calling update I dont have to run the whole filter
> > again, so I dont want it to be under the GenerateData() method.
> >
> > Thank you very much for your insights.
> >
> > Ignacio Prieto
> >
> >  --
> > Ignacio Prieto
> > Research Assistant
> > Biomedical Imaging Center
> > Pontificia Universida Catolica de Chile
> >
> >
> >
> > _____________________________________
> > 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
> >
>



-- 
Jos? Ignacio Prieto
celular(nuevo): 94348182
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140826/c10a9b5c/attachment.html>

From jan.bergmeier at imes.uni-hannover.de  Tue Aug 26 10:17:05 2014
From: jan.bergmeier at imes.uni-hannover.de (jan)
Date: Tue, 26 Aug 2014 07:17:05 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
 transformation
In-Reply-To: <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
 <1409059906690-7586120.post@n2.nabble.com>
 <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>
Message-ID: <1409062625902-7586123.post@n2.nabble.com>

Increasing the NumberOfSpatialSamples fixes the way with the one-iteration
optimizer but unfortunately not the attempts without the optimizer (which I
would prefer, since I like to keep it simple).



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586123.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From joseignacio.prieto at gmail.com  Tue Aug 26 11:35:50 2014
From: joseignacio.prieto at gmail.com (Jose Ignacio Prieto)
Date: Tue, 26 Aug 2014 11:35:50 -0400
Subject: [ITK-users] Create PolygonToMeshFilter
Message-ID: <CANkppu4z5KvydhVi_uM0dvO+ZgU4RzzrAXv-X6UaY2rsu3k+og@mail.gmail.com>

Hi all,
I am trying to create a filter that receives many 2D polygons in the form
of PolyLineParametricPath (which in turn has an itkImage as input) and
returns an itkMesh for later visualization. I have completed the
GenerateData() method by calling internally to
itkAutomaticTopologyMeshSource. The problem seems to be that before
GenerateData, the filter fails in itkPointSet::CopyInformation (because it
tries to cast the polygon as a mesh). I discovered that the call stack
comes from UpdateOutputInformation on my PolygonToMeshFilter and then
GenerateOutputInformation, then itkMesh::CopyInformation and
itkPointset::CopyInformation.
I think I should edit my PolygonToMesh::GenerateOutputInformation() but I
don't know how. Inside it I just called
Superclass::GenerateOutputInformation.
My filter PolygonToMeshFilter is a copy of MeshToMesh filter and inherits
from MeshSource. Maybe I should inherit from anothe filter.
Thank you very much

Ignacio Prieto

--
Ignacio Prieto
Research Assistant
Biomedical Imaging Center
Pontificia Universidad Catolica de Chile
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140826/b952893b/attachment.html>

From matt.mccormick at kitware.com  Tue Aug 26 11:38:34 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 26 Aug 2014 11:38:34 -0400
Subject: [ITK-users] Composite Filter with variable stdvector of filters
	inside
In-Reply-To: <CANkppu6TEftnReOJ6qbDFxHwCkmvcF=7PSS+k7BbWL0oZhzX5w@mail.gmail.com>
References: <CANkppu5b2vBFN96F7fx7MCSmRH8aqA14AUOCn7rbUtGFCWemAw@mail.gmail.com>
 <CALzTN-RYBYBxrgvJr6eT=XkiewvkuXee1ZC2y=wq+Za5L=Zzow@mail.gmail.com>
 <CANkppu6TEftnReOJ6qbDFxHwCkmvcF=7PSS+k7BbWL0oZhzX5w@mail.gmail.com>
Message-ID: <CALzTN-TXjp-vMXVxjD4rzjDB1QNNFwbab+ZR2Aac_O+gz5Laiw@mail.gmail.com>

Hi Ignacio,

GenerateInputRequestedRegion() may be a good place, too.

When an Update() is called, GenerateInputRequestedRegion() will get
called during the pipeline update if the filter's Modified time
indicates this is necessary.  If the filter needs to be updated, the
GenerateData will also get called as appropriate.

The best manual I am aware of is the ITK Software Guide [1].  More
information on this subject comes in Section 8.3.2 Details of Pipeline
Execution and section 8.3 Streaming Large Data.

HTH,
Matt

[1] http://sourceforge.net/projects/itk/files/itk/4.6/InsightSoftwareGuide-Book1-4.6.0.pdf/download

On Tue, Aug 26, 2014 at 9:38 AM, Jose Ignacio Prieto
<joseignacio.prieto at gmail.com> wrote:
> Thanks Matt, my problem was that I didn't know when to call this methods. I
> finally put them into GenerateInputRequestedRegion and this way seems to be
> called before Update(). I don't know under what conditions
> GenerateInputRequestedRegion is called, for example if a parameter is
> changed after an update call, will it be called again or only GenerateData
> would be called. Is there a good developer manual? The ITK user manual seems
> a little short on this.
>
> Thanks
>
> Ignacio Prieto
>
>
> On Mon, Aug 25, 2014 at 11:46 PM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>>
>> Hi Ignacio,
>>
>> If I understand corrections, this may do want is desired:
>>
>> void SetNumberOfZSlices( int slices )
>> {
>> if( m_NumberOfZSlices != slices )
>>   {
>>   this->m_NumberOfZSlices = slices;
>>   this->UpdateNumberOfFilters();
>>   this->Modified();
>>   }
>> }
>>
>> and a similar implementation for SetNumberOfTimeFrames().
>>
>> Hope this helps,
>> Matt
>>
>> On Wed, Aug 20, 2014 at 11:00 AM, Jose Ignacio Prieto
>> <joseignacio.prieto at gmail.com> wrote:
>> > Hi all,
>> > I am trying to create a composite filter for a 4D dataset that will use
>> > different cascaded 2D filters on the inside. For this, I have created a
>> > double std vector that holds all the 2D filters. I have also set some
>> > param
>> > setters for this filters (that perform a double for inside, setting the
>> > param to each filter and then calling modified() on the outside one). I
>> > have
>> > another method called UpdateNumberofFilters, that depending on 2 ints
>> > (num
>> > of Z slices, num of T timeframes) will push back more filters to the 2D
>> > array of filters.
>> > My problem is that I dont know which function should call the
>> > UpdateNumofFilters. It should be done before the setters but after the
>> > constructor and after setting those two ints. I want to design it so
>> > that if
>> > I change a param after calling update I dont have to run the whole
>> > filter
>> > again, so I dont want it to be under the GenerateData() method.
>> >
>> > Thank you very much for your insights.
>> >
>> > Ignacio Prieto
>> >
>> >  --
>> > Ignacio Prieto
>> > Research Assistant
>> > Biomedical Imaging Center
>> > Pontificia Universida Catolica de Chile
>> >
>> >
>> >
>> > _____________________________________
>> > 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
>> >
>
>
>
>
> --
> Jos? Ignacio Prieto
> celular(nuevo): 94348182

From joseignacio.prieto at gmail.com  Tue Aug 26 11:56:27 2014
From: joseignacio.prieto at gmail.com (Jose Ignacio Prieto)
Date: Tue, 26 Aug 2014 11:56:27 -0400
Subject: [ITK-users] Create PolygonToMeshFilter
In-Reply-To: <CANkppu4z5KvydhVi_uM0dvO+ZgU4RzzrAXv-X6UaY2rsu3k+og@mail.gmail.com>
References: <CANkppu4z5KvydhVi_uM0dvO+ZgU4RzzrAXv-X6UaY2rsu3k+og@mail.gmail.com>
Message-ID: <CANkppu5xKnqsYhPJanoG6t4xqDhPXm11sYUyZVuiSTjr+oGXoA@mail.gmail.com>

I solved it partially but don't know why it works. I just set
GenerateOutputInformation(){} on my .h file as it is done on
itkSpatialObjecToPointSetFilter so it goes straight to
GenerateInputRequestedRegion.



On Tue, Aug 26, 2014 at 11:35 AM, Jose Ignacio Prieto <
joseignacio.prieto at gmail.com> wrote:

> Hi all,
> I am trying to create a filter that receives many 2D polygons in the form
> of PolyLineParametricPath (which in turn has an itkImage as input) and
> returns an itkMesh for later visualization. I have completed the
> GenerateData() method by calling internally to
> itkAutomaticTopologyMeshSource. The problem seems to be that before
> GenerateData, the filter fails in itkPointSet::CopyInformation (because it
> tries to cast the polygon as a mesh). I discovered that the call stack
> comes from UpdateOutputInformation on my PolygonToMeshFilter and then
> GenerateOutputInformation, then itkMesh::CopyInformation and
> itkPointset::CopyInformation.
> I think I should edit my PolygonToMesh::GenerateOutputInformation() but I
> don't know how. Inside it I just called
> Superclass::GenerateOutputInformation.
> My filter PolygonToMeshFilter is a copy of MeshToMesh filter and inherits
> from MeshSource. Maybe I should inherit from anothe filter.
> Thank you very much
>
> Ignacio Prieto
>
> --
> Ignacio Prieto
> Research Assistant
> Biomedical Imaging Center
> Pontificia Universidad Catolica de Chile
>



-- 
Jos? Ignacio Prieto
celular(nuevo): 94348182
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140826/228e2a06/attachment.html>

From chernando at telespazio.es  Wed Aug 27 04:55:38 2014
From: chernando at telespazio.es (carlos)
Date: Wed, 27 Aug 2014 01:55:38 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
 transformation
In-Reply-To: <1409062625902-7586123.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
 <1409059906690-7586120.post@n2.nabble.com>
 <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>
 <1409062625902-7586123.post@n2.nabble.com>
Message-ID: <1409129738759-7586127.post@n2.nabble.com>

When the program crashes, no error appears?

Take also into account, that having the same size does not mean always that
they overlap. You have to check also their origin and spacing in case they
have different physical locations.

Regarding the standard deviation issue, if you previously normalize the
image, then a standard deviation of 0.4 works, please see this example:
http://www.itk.org/Doxygen/html/RegistrationITKv4_2ImageRegistration2_8cxx-example.html
 



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586127.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From maximilian_oliver.mordig at roche.com  Wed Aug 27 08:29:12 2014
From: maximilian_oliver.mordig at roche.com (maximilian)
Date: Wed, 27 Aug 2014 05:29:12 -0700 (PDT)
Subject: [ITK-users] Problem with itk::ImageToHistogramFilter
Message-ID: <1409142552492-7586128.post@n2.nabble.com>

I am having problems with the itk::ImageToHistogramFilter.

I am generating ellipses that I want to add to an image that already
contains some ellipses (in each iteration step, I add one ellipse to an
image being the result of previous iterations). To see if the new ellipse
overlaps by more than (let's say) 10%, I use the ImageToHistogramFilter.
The previous image has objects that all have pixel values of 1. The newly
added ellipse has value of 2. So, to get the number of overlapping pixels, I
add up both images and I count the number of pixels = 3 in that image.

I set the histogram bin minimum to 0 (background) and the histogram bin
maximum to 3 (+ some constant c) and the number of bins such that the step
is = 1 (here, it is 3 + c). However, when I output the average frequencies
associated to each bin, I get values between 0 and 2 (number like 1.92) and
not between 0 and 3 + c (see output of program of attached file). Why?

GenerateCells.cxx
<http://itk-insight-users.2283740.n2.nabble.com/file/n7586128/GenerateCells.cxx>  



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problem-with-itk-ImageToHistogramFilter-tp7586128.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From alaamegawer at yahoo.com  Wed Aug 27 09:17:25 2014
From: alaamegawer at yahoo.com (alaamegawer)
Date: Wed, 27 Aug 2014 06:17:25 -0700 (PDT)
Subject: [ITK-users] itkConnectedThresholdImageFilter modification for
 airway segmentation module
In-Reply-To: <CA+i5_QQDeqdxyisDXhm1Mv=QH8rXa4LiJ0qPe_ezGoUexEEnDA@mail.gmail.com>
References: <CA+i5_QTzJunHoAB5cZjE=Z=qA=XgyhzY-bsd=AAUaKS2dhXznA@mail.gmail.com>
 <CALzTN-Q1T8WsvxK5y0uakqTwt_EHbVgV7QNPq4sQqqpTW_tPZQ@mail.gmail.com>
 <CA+i5_QQDeqdxyisDXhm1Mv=QH8rXa4LiJ0qPe_ezGoUexEEnDA@mail.gmail.com>
Message-ID: <1409145445368-7586129.post@n2.nabble.com>

i wanna segment the airway tree from lung image so please if you segment it
can you please send me the source code  if that available. 



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/itkConnectedThresholdImageFilter-modification-for-airway-segmentation-module-tp7584078p7586129.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From alaamegawer at yahoo.com  Wed Aug 27 09:40:43 2014
From: alaamegawer at yahoo.com (alaamegawer)
Date: Wed, 27 Aug 2014 06:40:43 -0700 (PDT)
Subject: [ITK-users] Airway tree segmentation and segmentation dark object
	from an image
Message-ID: <1409146843926-7586130.post@n2.nabble.com>

Hi All 

I wanna segment the airway tree from Thoracic CT image. my algorithm depends
on
1- segment the center of the trachea then
2 apply 3D region growing to segment the trachea the main bronchi .

i start segmenting the center of the trachea by applying iterative threshold
and after that i stopped because i don't know how to get the dark region
from the bright region as found in the attachment file.

so Please help me to segment this point and if you have another way to
segment the airway please let me know .
<http://itk-insight-users.2283740.n2.nabble.com/file/n7586130/trachea.png> 
<http://itk-insight-users.2283740.n2.nabble.com/file/n7586130/trachea.png> 



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Airway-tree-segmentation-and-segmentation-dark-object-from-an-image-tp7586130.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From pattersonnp.work at gmail.com  Wed Aug 27 12:28:19 2014
From: pattersonnp.work at gmail.com (Nick Patterson)
Date: Wed, 27 Aug 2014 17:28:19 +0100
Subject: [ITK-users] ResampleDICOM example and DCMTK
Message-ID: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>


Hi,
 
I have been trying to test the ResampledDICOM ITK example using DCMTK instead of GDCM. I have attached the code below. The code compiles and runs, but does not output the resultant files - which is strange, as all of the expected parameters are good (i.e. number of files, origin of image, image dimensions etc).

Can anyone possibly comment on any possible reason why the code execute without error, but does not result in any output files?

Regards, Nick



#include "itkVersion.h"
#include "itkImage.h"
#include "itkMinimumMaximumImageFilter.h"
#include "itkDCMTKImageIO.h"
#include "itkDCMTKSeriesFileNames.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"
#include "itkResampleImageFilter.h"
#include "itkShiftScaleImageFilter.h"
#include "itkIdentityTransform.h"
#include "itkLinearInterpolateImageFunction.h"
#include <itksys/SystemTools.hxx>
#include "dcmdata/dcuid.h"
#include <string>

static void CopyDictionary (itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict);

int main( int argc, char* argv[] )
{
  // Validate input parameters
  if( argc < 4 )
    {
    std::cerr << "Usage: "
              << argv[0]
              << " InputDicomDirectory OutputDicomDirectory spacing_x spacing_y spacing_z"
              << std::endl;
    return EXIT_FAILURE;
    }

  const unsigned int InputDimension = 3;
  const unsigned int OutputDimension = 2;

  typedef signed short PixelType;

  typedef itk::Image< PixelType, InputDimension > InputImageType;
  typedef itk::Image< PixelType, OutputDimension > OutputImageType;
  typedef itk::ImageSeriesReader< InputImageType >ReaderType;
  typedef itk::DCMTKImageIO ImageIOType;
  typedef itk::DCMTKSeriesFileNames InputNamesGeneratorType;
  typedef itk::NumericSeriesFileNames OutputNamesGeneratorType;
  typedef itk::IdentityTransform< double, InputDimension > TransformType;
  typedef itk::LinearInterpolateImageFunction< InputImageType, double > InterpolatorType;
  typedef itk::ResampleImageFilter< InputImageType, InputImageType > ResampleFilterType;
  typedef itk::ShiftScaleImageFilter< InputImageType, InputImageType > ShiftScaleType;
  typedef itk::ImageSeriesWriter< InputImageType, OutputImageType > SeriesWriterType;

////////////////////////////////////////////////
// 1) Read the input series

  ImageIOType::Pointer gdcmIO = ImageIOType::New();
  InputNamesGeneratorType::Pointer inputNames = InputNamesGeneratorType::New();
  inputNames->SetInputDirectory( argv[1] );

  const ReaderType::FileNamesContainer & filenames = inputNames->GetInputFileNames();

  ReaderType::Pointer reader = ReaderType::New();

  reader->SetImageIO( gdcmIO );
  reader->SetFileNames( filenames );
  try
    {
    reader->Update();
    }
  catch (itk::ExceptionObject &excp)
    {
    std::cerr << "Exception thrown while reading the series" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

////////////////////////////////////////////////
// 2) Resample the series
  InterpolatorType::Pointer interpolator = InterpolatorType::New();

  TransformType::Pointer transform = TransformType::New();
  transform->SetIdentity();

  const InputImageType::SpacingType& inputSpacing = reader->GetOutput()->GetSpacing();
  const InputImageType::RegionType& inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
  const InputImageType::SizeType& inputSize =  inputRegion.GetSize();

  std::cout << "The input series in directory " << argv[1]
            << " has " << filenames.size() << " files with spacing "
            << inputSpacing
            << std::endl;

  // Compute the size of the output. The user specifies a spacing on
  // the command line. If the spacing is 0, the input spacing will be
  // used. The size (# of pixels) in the output is recomputed using
  // the ratio of the input and output sizes.
  InputImageType::SpacingType outputSpacing;
  outputSpacing[0] = atof(argv[3]);
  outputSpacing[1] = atof(argv[4]);
  outputSpacing[2] = atof(argv[5]);

  bool changeInSpacing = false;
  for (unsigned int i = 0; i < 3; i++)
    {
    if (outputSpacing[i] == 0.0)
      {
      outputSpacing[i] = inputSpacing[i];
      }
    else
      {
      changeInSpacing = true;
      }
    }
  InputImageType::SizeType   outputSize;
  typedef InputImageType::SizeType::SizeValueType SizeValueType;
  outputSize[0] = static_cast<SizeValueType>(inputSize[0] * inputSpacing[0] / outputSpacing[0] + .5);
  outputSize[1] = static_cast<SizeValueType>(inputSize[1] * inputSpacing[1] / outputSpacing[1] + .5);
  outputSize[2] = static_cast<SizeValueType>(inputSize[2] * inputSpacing[2] / outputSpacing[2] + .5);

  ResampleFilterType::Pointer resampler = ResampleFilterType::New();
    resampler->SetInput( reader->GetOutput() );
    resampler->SetTransform( transform );
    resampler->SetInterpolator( interpolator );
    resampler->SetOutputOrigin ( reader->GetOutput()->GetOrigin());
    resampler->SetOutputSpacing ( outputSpacing );
    resampler->SetOutputDirection ( reader->GetOutput()->GetDirection());
    resampler->SetSize ( outputSize );
    resampler->Update ();


////////////////////////////////////////////////
// 3) Create a MetaDataDictionary for each slice.

  // Copy the dictionary from the first image and override slice
  // specific fields
  ReaderType::DictionaryRawPointer inputDict = (*(reader->GetMetaDataDictionaryArray()))[0];
  ReaderType::DictionaryArrayType outputArray;

  // To keep the new series in the same study as the original we need
  // to keep the same study UID. But we need new series and frame of
  // reference UID's.

  char seriesUID[100];
  dcmGenerateUniqueIdentifier(seriesUID);

  char frameOfReferenceUID[100];
  dcmGenerateUniqueIdentifier(frameOfReferenceUID);

  std::string studyUID;
  std::string sopClassUID;
  itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
  itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
 // gdcmIO->KeepOriginalUIDOn();

  for (unsigned int f = 0; f < outputSize[2]; f++)
    {
    // Create a new dictionary for this slice
    ReaderType::DictionaryRawPointer dict = new ReaderType::DictionaryType;

    // Copy the dictionary from the first slice
    CopyDictionary (*inputDict, *dict);

    // Set the UID's for the study, series, SOP  and frame of reference
    itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);
    itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0052", frameOfReferenceUID);

    char sopInstanceUID[100];
    dcmGenerateUniqueIdentifier(sopInstanceUID);

    itk::EncapsulateMetaData<std::string>(*dict,"0008|0018", sopInstanceUID);
    itk::EncapsulateMetaData<std::string>(*dict,"0002|0003", sopInstanceUID);

    // Change fields that are slice specific
    itksys_ios::ostringstream value;
    value.str("");
    value << f + 1;

    // Image Number
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());

    // Series Description - Append new description to current series
    // description
    std::string oldSeriesDesc;
    itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);

    value.str("");
    value << oldSeriesDesc << ": Resampled with pixel spacing " << outputSpacing[0] << ", "<< outputSpacing[1] << ", "<< outputSpacing[2];
    // This is an long string and there is a 64 character limit in the
    // standard
    unsigned lengthDesc = value.str().length();

    std::string seriesDesc( value.str(), 0,lengthDesc > 64 ? 64 : lengthDesc);
    itk::EncapsulateMetaData<std::string>(*dict,"0008|103e", seriesDesc);

    // Series Number
    value.str("");
    value << 1001;
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0011", value.str());

    // Derivation Description - How this image was derived
    value.str("");
    for (int i = 0; i < argc; i++)
      {
      value << argv[i] << " ";
      }
    value << ": " << ITK_SOURCE_VERSION;

    lengthDesc = value.str().length();
    std::string derivationDesc( value.str(), 0, lengthDesc > 1024 ? 1024 : lengthDesc);
    itk::EncapsulateMetaData<std::string>(*dict,"0008|2111", derivationDesc);

    // Image Position Patient: This is calculated by computing the
    // physical coordinate of the first pixel in each slice.
    InputImageType::PointType position;
    InputImageType::IndexType index;
    index[0] = 0;
    index[1] = 0;
    index[2] = f;
    resampler->GetOutput()->TransformIndexToPhysicalPoint(index, position);

    value.str("");
    value << position[0] << "\\" << position[1] << "\\" << position[2];
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str());
    // Slice Location: For now, we store the z component of the Image
    // Position Patient.
    value.str("");
    value << position[2];
    itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());

    if (changeInSpacing)
      {
      // Slice Thickness: For now, we store the z spacing
      value.str("");
      value << outputSpacing[2];
      itk::EncapsulateMetaData<std::string>(*dict,"0018|0050",value.str());
      // Spacing Between Slices
      itk::EncapsulateMetaData<std::string>(*dict,"0018|0088",value.str());
      }

    // Save the dictionary
     outputArray.push_back(dict);
    }

////////////////////////////////////////////////
// 4) Shift data to undo the effect of a rescale intercept by the
//    DICOM reader
  std::string interceptTag("0028|1052");
  typedef itk::MetaDataObject< std::string > MetaDataStringType;
  itk::MetaDataObjectBase::Pointer entry = (*inputDict)[interceptTag];

  MetaDataStringType::ConstPointer interceptValue = dynamic_cast<const MetaDataStringType *>( entry.GetPointer() ) ;

  int interceptShift = 0;

  if( interceptValue )
    {
    std::string tagValue = interceptValue->GetMetaDataObjectValue();
    interceptShift = -atoi ( tagValue.c_str() );
    }

  ShiftScaleType::Pointer shiftScale = ShiftScaleType::New();
  shiftScale->SetInput( resampler->GetOutput());
  shiftScale->SetShift( interceptShift );

////////////////////////////////////////////////
// 5) Write the new DICOM series

  // Make the output directory and generate the file names.
  itksys::SystemTools::MakeDirectory( argv[2] );

  // Generate the file names
  OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
  std::string seriesFormat(argv[2]);
  seriesFormat = seriesFormat + "IM%d.dcm";
  outputNames->SetSeriesFormat (seriesFormat.c_str());
  outputNames->SetStartIndex (1);
  outputNames->SetEndIndex (outputSize[2]);
  std::cout << "Output Size: " << outputSize[2] << std::endl;
  std::cout << outputNames->GetFileNames().at(0) << std::endl;

  SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
  seriesWriter->SetInput( shiftScale->GetOutput() );
  seriesWriter->SetImageIO( gdcmIO );
  seriesWriter->SetFileNames( outputNames->GetFileNames() );
  seriesWriter->SetMetaDataDictionaryArray( &outputArray );

  std::cout << seriesWriter->GetImageIO()->GetOrigin(0) << " " << seriesWriter->GetImageIO()->GetOrigin(1) <<
               " " << seriesWriter->GetImageIO()->GetOrigin(2) << std::endl;

  try
    {
        seriesWriter->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
        std::cerr << "Exception thrown while writing the series " << std::endl;
        std::cerr << excp << std::endl;
        return EXIT_FAILURE;
    }
  std::cout << "The output series in directory " << argv[2] << " has " << outputSize[2] << " files with spacing "<< outputSpacing << std::endl;
  return EXIT_SUCCESS;
}

void CopyDictionary (itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict)
{
  typedef itk::MetaDataDictionary DictionaryType;
  DictionaryType::ConstIterator itr = fromDict.Begin();
  DictionaryType::ConstIterator end = fromDict.End();
  typedef itk::MetaDataObject< std::string > MetaDataStringType;



  while( itr != end )
    {
    itk::MetaDataObjectBase::Pointer  entry = itr->second;
    MetaDataStringType::Pointer entryvalue = dynamic_cast<MetaDataStringType *>( entry.GetPointer() ) ;
    if( entryvalue )
      {
      std::string tagkey   = itr->first;
      std::string tagvalue = entryvalue->GetMetaDataObjectValue();
      itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
      }
    ++itr;
    }
}

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140827/350a059f/attachment-0001.html>

From matt.mccormick at kitware.com  Wed Aug 27 13:30:56 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 27 Aug 2014 13:30:56 -0400
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-R3iUdTM7DaEc9xr0Nr_dNUh_jk0yKF6E-cQa8rNPXy4A@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss,
design, and learn with your fellow
ITK community members.


On Thursday (tomorow), 9 AM Eastern USA time, there will be a Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/u/0/events/cj4tf2heirsligiim1blh9j3498


On Friday, 10 AM Eastern USA time, an ITK development teleconference,

  (866) 546-4138 USA or
  +1 (404) 602-0798 International
  Access code 5687046#


All are welcome.  Hope to talk to you then!

From jan.bergmeier at imes.uni-hannover.de  Thu Aug 28 07:43:45 2014
From: jan.bergmeier at imes.uni-hannover.de (jan)
Date: Thu, 28 Aug 2014 04:43:45 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
 transformation
In-Reply-To: <1409129738759-7586127.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
 <1409059906690-7586120.post@n2.nabble.com>
 <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>
 <1409062625902-7586123.post@n2.nabble.com>
 <1409129738759-7586127.post@n2.nabble.com>
Message-ID: <1409226225974-7586133.post@n2.nabble.com>

Hey,

no error appears when the program crashes.
i checked the origin and the spacing. Both are the same for both images.


Thanks, 
Jan



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586133.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From jan.bergmeier at imes.uni-hannover.de  Thu Aug 28 09:24:40 2014
From: jan.bergmeier at imes.uni-hannover.de (jan)
Date: Thu, 28 Aug 2014 06:24:40 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
 transformation
In-Reply-To: <1409226225974-7586133.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
 <1409059906690-7586120.post@n2.nabble.com>
 <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>
 <1409062625902-7586123.post@n2.nabble.com>
 <1409129738759-7586127.post@n2.nabble.com>
 <1409226225974-7586133.post@n2.nabble.com>
Message-ID: <1409232280489-7586134.post@n2.nabble.com>

Hi, I will use this way, because it's the most convenient that's working for
me.

    //Typedefs
    typedef itk::IdentityTransform< double, 2 > TransformType;
    typedef itk::GradientDescentOptimizer OptimizerType;
    typedef itk::LinearInterpolateImageFunction< UChar2DImageType, double >
InterpolatorType;
    typedef itk::MutualInformationImageToImageMetric< UChar2DImageType,
UChar2DImageType > MiMetricType;
    typedef itk::ImageRegistrationMethod< UChar2DImageType, UChar2DImageType
> RegistrationType;

    //Create registration components
    TransformType::Pointer transform = TransformType::New();
    OptimizerType::Pointer optimizer = OptimizerType::New();
    InterpolatorType::Pointer interpolator = InterpolatorType::New();
    RegistrationType::Pointer registration = RegistrationType::New();
    
    //Configure transform
    transform->SetIdentity();

    //Configure optimizer
    optimizer->SetNumberOfIterations( 1 );
    
    //Configure metric
    MetricType::Pointer metric = MetricType::New();
    metric->SetNumberOfSpatialSamples( 1000 );

    //Set up registration
    registration->SetOptimizer( optimizer );
    registration->SetTransform( transform );
    registration->SetInterpolator( interpolator );
    registration->SetMetric( metric );

    registration->SetFixedImage( fixedImageIn );
    registration->SetMovingImage( movingImageIn );
    registration->SetInitialTransformParameters( transform->GetParameters()
);

    //Perform registration
    try
    {
        registration->Update();
    }
    catch( itk::ExceptionObject & err )
    {
        std::cout << "ExceptionObject caught !" << std::endl;
        std::cout << err << std::endl;
    }

    //Get output
    double bestValue = optimizer->GetValue();

Thank you all for your help,

Jan



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586134.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Thu Aug 28 22:35:03 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 28 Aug 2014 22:35:03 -0400
Subject: [ITK-users] [ITK-dev] Create PolygonToMeshFilter
In-Reply-To: <CANkppu5xKnqsYhPJanoG6t4xqDhPXm11sYUyZVuiSTjr+oGXoA@mail.gmail.com>
References: <CANkppu4z5KvydhVi_uM0dvO+ZgU4RzzrAXv-X6UaY2rsu3k+og@mail.gmail.com>
 <CANkppu5xKnqsYhPJanoG6t4xqDhPXm11sYUyZVuiSTjr+oGXoA@mail.gmail.com>
Message-ID: <CALzTN-R8dDD8u1RkXowL9zi+iUoiizhECDH8nUYqw5kNJQMadw@mail.gmail.com>

Hi Ignacio,

The default implementation of GenerateOutputInformation() in
itk::ProcessObject is to call ::CopyInformation() on all the pipeline
objects from the input to the output DataObjects.  The information
that is copied for itk::PointSet / itk::Mesh is related to Region's
(see their implementations of ::CopyInformation()).  You may write a
GenerateOutputInformation() that sets these regions, or you could
leave the default values given in the constructors, which is what the
SpatialObjectToPointSetFilter does.

Hope this helps,
Matt

On Tue, Aug 26, 2014 at 11:56 AM, Jose Ignacio Prieto
<joseignacio.prieto at gmail.com> wrote:
> I solved it partially but don't know why it works. I just set
> GenerateOutputInformation(){} on my .h file as it is done on
> itkSpatialObjecToPointSetFilter so it goes straight to
> GenerateInputRequestedRegion.
>
>
>
> On Tue, Aug 26, 2014 at 11:35 AM, Jose Ignacio Prieto
> <joseignacio.prieto at gmail.com> wrote:
>>
>> Hi all,
>> I am trying to create a filter that receives many 2D polygons in the form
>> of PolyLineParametricPath (which in turn has an itkImage as input) and
>> returns an itkMesh for later visualization. I have completed the
>> GenerateData() method by calling internally to
>> itkAutomaticTopologyMeshSource. The problem seems to be that before
>> GenerateData, the filter fails in itkPointSet::CopyInformation (because it
>> tries to cast the polygon as a mesh). I discovered that the call stack comes
>> from UpdateOutputInformation on my PolygonToMeshFilter and then
>> GenerateOutputInformation, then itkMesh::CopyInformation and
>> itkPointset::CopyInformation.
>> I think I should edit my PolygonToMesh::GenerateOutputInformation() but I
>> don't know how. Inside it I just called
>> Superclass::GenerateOutputInformation.
>> My filter PolygonToMeshFilter is a copy of MeshToMesh filter and inherits
>> from MeshSource. Maybe I should inherit from anothe filter.
>> Thank you very much
>>
>> Ignacio Prieto
>>
>> --
>> Ignacio Prieto
>> Research Assistant
>> Biomedical Imaging Center
>> Pontificia Universidad Catolica de Chile
>
>
>
>
> --
> Jos? Ignacio Prieto
> celular(nuevo): 94348182
>
> _______________________________________________
> 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
>

From matt.mccormick at kitware.com  Thu Aug 28 22:39:54 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 28 Aug 2014 22:39:54 -0400
Subject: [ITK-users] MutualInformationImageToImageMetric without
	transformation
In-Reply-To: <1409232280489-7586134.post@n2.nabble.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
 <1409059906690-7586120.post@n2.nabble.com>
 <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>
 <1409062625902-7586123.post@n2.nabble.com>
 <1409129738759-7586127.post@n2.nabble.com>
 <1409226225974-7586133.post@n2.nabble.com>
 <1409232280489-7586134.post@n2.nabble.com>
Message-ID: <CALzTN-SGCgVfa8mUoS3hZNSBtbx75iSV8J7vLyRkPXGwiFnuKQ@mail.gmail.com>

Hi Jan,

Make sure to call Initialize() [1].  See also the
MeanSquareImageMetric1.cxx file from the Examples/ directory.

Hope this helps,
Matt

[1] http://www.itk.org/Insight/Doxygen/html/classitk_1_1ImageToImageMetric.html#a2bd5955a3bedf31e701aed3ee1d4e473

On Thu, Aug 28, 2014 at 9:24 AM, jan <jan.bergmeier at imes.uni-hannover.de> wrote:
> Hi, I will use this way, because it's the most convenient that's working for
> me.
>
>     //Typedefs
>     typedef itk::IdentityTransform< double, 2 > TransformType;
>     typedef itk::GradientDescentOptimizer OptimizerType;
>     typedef itk::LinearInterpolateImageFunction< UChar2DImageType, double >
> InterpolatorType;
>     typedef itk::MutualInformationImageToImageMetric< UChar2DImageType,
> UChar2DImageType > MiMetricType;
>     typedef itk::ImageRegistrationMethod< UChar2DImageType, UChar2DImageType
>> RegistrationType;
>
>     //Create registration components
>     TransformType::Pointer transform = TransformType::New();
>     OptimizerType::Pointer optimizer = OptimizerType::New();
>     InterpolatorType::Pointer interpolator = InterpolatorType::New();
>     RegistrationType::Pointer registration = RegistrationType::New();
>
>     //Configure transform
>     transform->SetIdentity();
>
>     //Configure optimizer
>     optimizer->SetNumberOfIterations( 1 );
>
>     //Configure metric
>     MetricType::Pointer metric = MetricType::New();
>     metric->SetNumberOfSpatialSamples( 1000 );
>
>     //Set up registration
>     registration->SetOptimizer( optimizer );
>     registration->SetTransform( transform );
>     registration->SetInterpolator( interpolator );
>     registration->SetMetric( metric );
>
>     registration->SetFixedImage( fixedImageIn );
>     registration->SetMovingImage( movingImageIn );
>     registration->SetInitialTransformParameters( transform->GetParameters()
> );
>
>     //Perform registration
>     try
>     {
>         registration->Update();
>     }
>     catch( itk::ExceptionObject & err )
>     {
>         std::cout << "ExceptionObject caught !" << std::endl;
>         std::cout << err << std::endl;
>     }
>
>     //Get output
>     double bestValue = optimizer->GetValue();
>
> Thank you all for your help,
>
> Jan
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586134.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 g.bogle at auckland.ac.nz  Fri Aug 29 04:09:30 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 08:09:30 +0000
Subject: [ITK-users] Strange Visual Studio 2012 problem
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>

I've been using Visual Studio 10 for a few years without any problems.  Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my programs with the new libraries the build fails with (for example) this message:

crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h': No such file or directory

Looking at the Project Properties I see in Additional Include Directories: crop.cpp(18): \include\ITK-4.5
For some reason cmake has not used the ITK_DIR prefix.  In addition I see in Linker > Additional Dependencies that all the ITK libraries are expected to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory, although in this case the ITK_DIR prefix has been used.

This is a bit of a mess.  I presume the problem lies with cmake.  My version is 2.8.12.2, which I would have thought was recent enough - maybe it's too recent.  Has anyone else run into this problem, and is there a solution?

Thanks
Gib
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/c45d30cd/attachment.html>

From indianzeppelin at gmail.com  Fri Aug 29 04:29:47 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Fri, 29 Aug 2014 09:29:47 +0100
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
Message-ID: <CAA+VR6iaSPHvpJ71XGZ73DpOn5hiV1aOS0W_RTNn9Vs0euGSEw@mail.gmail.com>

Could you paste the part of your CMakeLists.txt where you find/include/link
ITK?


On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:

>  I've been using Visual Studio 10 for a few years without any problems.
> Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I
> have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK
> environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my
> programs with the new libraries the build fails with (for example) this
> message:
>
> crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h':
> No such file or directory
>
> Looking at the Project Properties I see in Additional Include Directories:
> crop.cpp(18): \include\ITK-4.5
> For some reason cmake has not used the ITK_DIR prefix.  In addition I see
> in Linker > Additional Dependencies that all the ITK libraries are expected
> to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory,
> although in this case the ITK_DIR prefix has been used.
>
> This is a bit of a mess.  I presume the problem lies with cmake.  My
> version is 2.8.12.2, which I would have thought was recent enough - maybe
> it's too recent.  Has anyone else run into this problem, and is there a
> solution?
>
> Thanks
> Gib
>
> _____________________________________
> 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
>
>


-- 
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/c6bdc3dc/attachment.html>

From g.bogle at auckland.ac.nz  Fri Aug 29 05:10:05 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 09:10:05 +0000
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>

I just remembered that I forgot to paste that:

cmake_minimum_required(VERSION 2.6)

PROJECT(crop)
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)

set(PROJECTNAME "crop")
ADD_EXECUTABLE(${PROJECTNAME} crop.cpp)
TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} )
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com]
Sent: Friday, 29 August 2014 8:25 p.m.
To: Gib Bogle
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

Could you paste the part of your CMakeLists.txt where you find/include ITK?


On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I've been using Visual Studio 10 for a few years without any problems.  Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my programs with the new libraries the build fails with (for example) this message:

crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h': No such file or directory

Looking at the Project Properties I see in Additional Include Directories: crop.cpp(18): \include\ITK-4.5
For some reason cmake has not used the ITK_DIR prefix.  In addition I see in Linker > Additional Dependencies that all the ITK libraries are expected to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory, although in this case the ITK_DIR prefix has been used.

This is a bit of a mess.  I presume the problem lies with cmake.  My version is 2.8.12.2, which I would have thought was recent enough - maybe it's too recent.  Has anyone else run into this problem, and is there a solution?

Thanks
Gib

_____________________________________
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




--
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/492c8f07/attachment.html>

From indianzeppelin at gmail.com  Fri Aug 29 05:29:51 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Fri, 29 Aug 2014 10:29:51 +0100
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>
Message-ID: <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>

That looks alright. Did you try MESSAGE (${ITK_USE_FILE}) and MESSAGE
(${ITK_INCLUDE_DIRS})?


On Fri, Aug 29, 2014 at 10:10 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:

>  I just remembered that I forgot to paste that:
>
>
> cmake_minimum_required(VERSION 2.6)
>
> PROJECT(crop)
> FIND_PACKAGE(ITK)
> IF(ITK_FOUND)
> INCLUDE(${ITK_USE_FILE})
> ELSE(ITK_FOUND)
> MESSAGE(FATAL_ERROR
> "ITK not found. Please set ITK_DIR.")
> ENDIF(ITK_FOUND)
>
> set(PROJECTNAME "crop")
> ADD_EXECUTABLE(${PROJECTNAME} crop.cpp)
> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} )
>  ------------------------------
> *From:* Girish Mallya Udupi [indianzeppelin at gmail.com]
> *Sent:* Friday, 29 August 2014 8:25 p.m.
> *To:* Gib Bogle
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem
>
>   Could you paste the part of your CMakeLists.txt where you find/include
> ITK?
>
>
> On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>
>>  I've been using Visual Studio 10 for a few years without any problems.
>> Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I
>> have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK
>> environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my
>> programs with the new libraries the build fails with (for example) this
>> message:
>>
>> crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h':
>> No such file or directory
>>
>> Looking at the Project Properties I see in Additional Include
>> Directories: crop.cpp(18): \include\ITK-4.5
>> For some reason cmake has not used the ITK_DIR prefix.  In addition I see
>> in Linker > Additional Dependencies that all the ITK libraries are expected
>> to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory,
>> although in this case the ITK_DIR prefix has been used.
>>
>> This is a bit of a mess.  I presume the problem lies with cmake.  My
>> version is 2.8.12.2, which I would have thought was recent enough - maybe
>> it's too recent.  Has anyone else run into this problem, and is there a
>> solution?
>>
>> Thanks
>> Gib
>>
>> _____________________________________
>> 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
>>
>>
>
>
>  --
> Regards,
> Girish
>



-- 
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/76826f73/attachment.html>

From g.bogle at auckland.ac.nz  Fri Aug 29 05:33:19 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 09:33:19 +0000
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D132E1@uxcn10-tdc01.UoA.auckland.ac.nz>

OK, I just did that, and got:

D:/InsightToolkit-4.5.2/CMake/UseITK.cmake
/include/ITK-4.5

________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com]
Sent: Friday, 29 August 2014 9:29 p.m.
To: Gib Bogle
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

That looks alright. Did you try MESSAGE (${ITK_USE_FILE}) and MESSAGE (${ITK_INCLUDE_DIRS})?


On Fri, Aug 29, 2014 at 10:10 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I just remembered that I forgot to paste that:


cmake_minimum_required(VERSION 2.6)

PROJECT(crop)
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)

set(PROJECTNAME "crop")
ADD_EXECUTABLE(${PROJECTNAME} crop.cpp)
TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} )
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com<mailto:indianzeppelin at gmail.com>]
Sent: Friday, 29 August 2014 8:25 p.m.
To: Gib Bogle
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

Could you paste the part of your CMakeLists.txt where you find/include ITK?


On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I've been using Visual Studio 10 for a few years without any problems.  Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my programs with the new libraries the build fails with (for example) this message:

crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h': No such file or directory

Looking at the Project Properties I see in Additional Include Directories: crop.cpp(18): \include\ITK-4.5
For some reason cmake has not used the ITK_DIR prefix.  In addition I see in Linker > Additional Dependencies that all the ITK libraries are expected to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory, although in this case the ITK_DIR prefix has been used.

This is a bit of a mess.  I presume the problem lies with cmake.  My version is 2.8.12.2, which I would have thought was recent enough - maybe it's too recent.  Has anyone else run into this problem, and is there a solution?

Thanks
Gib

_____________________________________
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




--
Regards,
Girish



--
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/53dd39e7/attachment.html>

From g.bogle at auckland.ac.nz  Fri Aug 29 05:47:46 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 09:47:46 +0000
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D132F3@uxcn10-tdc01.UoA.auckland.ac.nz>

Hold everything, Girish!  I see that D:\ITK-VS11-x64 does not have the directory structure of an ITK installation, from which I conclude that I did something wrong.  I am now checking the build of ITK and will report back.
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com]
Sent: Friday, 29 August 2014 9:29 p.m.
To: Gib Bogle
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

That looks alright. Did you try MESSAGE (${ITK_USE_FILE}) and MESSAGE (${ITK_INCLUDE_DIRS})?


On Fri, Aug 29, 2014 at 10:10 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I just remembered that I forgot to paste that:


cmake_minimum_required(VERSION 2.6)

PROJECT(crop)
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)

set(PROJECTNAME "crop")
ADD_EXECUTABLE(${PROJECTNAME} crop.cpp)
TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} )
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com<mailto:indianzeppelin at gmail.com>]
Sent: Friday, 29 August 2014 8:25 p.m.
To: Gib Bogle
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

Could you paste the part of your CMakeLists.txt where you find/include ITK?


On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I've been using Visual Studio 10 for a few years without any problems.  Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my programs with the new libraries the build fails with (for example) this message:

crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h': No such file or directory

Looking at the Project Properties I see in Additional Include Directories: crop.cpp(18): \include\ITK-4.5
For some reason cmake has not used the ITK_DIR prefix.  In addition I see in Linker > Additional Dependencies that all the ITK libraries are expected to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory, although in this case the ITK_DIR prefix has been used.

This is a bit of a mess.  I presume the problem lies with cmake.  My version is 2.8.12.2, which I would have thought was recent enough - maybe it's too recent.  Has anyone else run into this problem, and is there a solution?

Thanks
Gib

_____________________________________
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




--
Regards,
Girish



--
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/999f6c99/attachment.html>

From g.bogle at auckland.ac.nz  Fri Aug 29 05:57:24 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 09:57:24 +0000
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D13306@uxcn10-tdc01.UoA.auckland.ac.nz>

Now I'm more confused.  I thought that D:\ITK-VS11-x64 didn't look like an ITK installation directory because on my other machine there are only the subdirectories 'bin', 'include', 'lib', and 'share', while on the new machine I have those and many more, including 'CMakeFiles', 'config', 'ExternalData', 'Modules', 'Utilities'.  But I did Build Install again and it left things unchanged.  So it appears that the ITK install has changed from ITK-4.0 to ITK-4.5.

Should I go back to 4.0?  Life was simpler then...
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com]
Sent: Friday, 29 August 2014 9:29 p.m.
To: Gib Bogle
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

That looks alright. Did you try MESSAGE (${ITK_USE_FILE}) and MESSAGE (${ITK_INCLUDE_DIRS})?


On Fri, Aug 29, 2014 at 10:10 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I just remembered that I forgot to paste that:


cmake_minimum_required(VERSION 2.6)

PROJECT(crop)
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)

set(PROJECTNAME "crop")
ADD_EXECUTABLE(${PROJECTNAME} crop.cpp)
TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} )
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com<mailto:indianzeppelin at gmail.com>]
Sent: Friday, 29 August 2014 8:25 p.m.
To: Gib Bogle
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

Could you paste the part of your CMakeLists.txt where you find/include ITK?


On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I've been using Visual Studio 10 for a few years without any problems.  Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my programs with the new libraries the build fails with (for example) this message:

crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h': No such file or directory

Looking at the Project Properties I see in Additional Include Directories: crop.cpp(18): \include\ITK-4.5
For some reason cmake has not used the ITK_DIR prefix.  In addition I see in Linker > Additional Dependencies that all the ITK libraries are expected to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory, although in this case the ITK_DIR prefix has been used.

This is a bit of a mess.  I presume the problem lies with cmake.  My version is 2.8.12.2, which I would have thought was recent enough - maybe it's too recent.  Has anyone else run into this problem, and is there a solution?

Thanks
Gib

_____________________________________
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




--
Regards,
Girish



--
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/0bdc6434/attachment.html>

From g.bogle at auckland.ac.nz  Fri Aug 29 06:16:14 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 10:16:14 +0000
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D13319@uxcn10-tdc01.UoA.auckland.ac.nz>

I just checked the build configuration in cmake and everything looks fine.
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com]
Sent: Friday, 29 August 2014 9:29 p.m.
To: Gib Bogle
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

That looks alright. Did you try MESSAGE (${ITK_USE_FILE}) and MESSAGE (${ITK_INCLUDE_DIRS})?


On Fri, Aug 29, 2014 at 10:10 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I just remembered that I forgot to paste that:


cmake_minimum_required(VERSION 2.6)

PROJECT(crop)
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)

set(PROJECTNAME "crop")
ADD_EXECUTABLE(${PROJECTNAME} crop.cpp)
TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} )
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com<mailto:indianzeppelin at gmail.com>]
Sent: Friday, 29 August 2014 8:25 p.m.
To: Gib Bogle
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem

Could you paste the part of your CMakeLists.txt where you find/include ITK?


On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
I've been using Visual Studio 10 for a few years without any problems.  Now I have a new machine with Visual Studio 11 (i.e. 2012) installed.  I have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.  The ITK environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to build my programs with the new libraries the build fails with (for example) this message:

crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h': No such file or directory

Looking at the Project Properties I see in Additional Include Directories: crop.cpp(18): \include\ITK-4.5
For some reason cmake has not used the ITK_DIR prefix.  In addition I see in Linker > Additional Dependencies that all the ITK libraries are expected to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent directory, although in this case the ITK_DIR prefix has been used.

This is a bit of a mess.  I presume the problem lies with cmake.  My version is 2.8.12.2, which I would have thought was recent enough - maybe it's too recent.  Has anyone else run into this problem, and is there a solution?

Thanks
Gib

_____________________________________
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




--
Regards,
Girish



--
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/191ec97b/attachment-0001.html>

From indianzeppelin at gmail.com  Fri Aug 29 06:35:44 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Fri, 29 Aug 2014 11:35:44 +0100
Subject: [ITK-users] [ITK]  Strange Visual Studio 2012 problem
In-Reply-To: <BD80F91C3E2E394894ED4780703D7F9E81D13319@uxcn10-tdc01.UoA.auckland.ac.nz>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13289@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAA+VR6gsp+M8kjM8LE=H=Hdm0yzejXSjKVTnX2hR-5+Lghy-ag@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D132BC@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAA+VR6jjwhXaTWS_1HYNGWtkXWGd8hqBbDknfqC2-L8JCtErKQ@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D13319@uxcn10-tdc01.UoA.auckland.ac.nz>
Message-ID: <CAA+VR6inxtePZ_5HY8vqo3khEaDbknH7p7Y4DAfsnjhmojWUJQ@mail.gmail.com>

Ok, I've never actually built the "INSTALL" project and the oldest ITK
version I have used is ITK-4.5.1. The folders you see ('CMakeFiles' etc)
look normal to me since those are present in the build folder. Anyway, it
might be worth trying to build ITK again using the following simple steps.
(You might be aware of all the steps, but mentioning them all here just for
the sake of completeness).

1) Create a root folder e.g., D:\ITK-4.5
2) Create two folders in the root folder "src" and "bin"
3) Put the ITK source tree in the src folder. So this folder would have the
main ITK CMakeLists.txt.
4) Configure and generate using CMake with "D:\ITK-4.5\src" as source
folder and "D:\ITK-4.5\bin" as binary directory
5) Then open the ITK.sln from "D:\ITK-4.5\bin" and build the solution.
6) Once built, edit the ITK environment variable ITK_DIR  to point to "
D:\ITK-4.5\bin"

I've never faced any problem using ITK in my projects after building it
this way. I am still a beginner, so someone more knowledgeable could point
out what exactly the problem was with your build.



On Fri, Aug 29, 2014 at 11:16 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:

>  I just checked the build configuration in cmake and everything looks
> fine.
>  ------------------------------
> *From:* Girish Mallya Udupi [indianzeppelin at gmail.com]
> *Sent:* Friday, 29 August 2014 9:29 p.m.
>
> *To:* Gib Bogle
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem
>
>   That looks alright. Did you try MESSAGE (${ITK_USE_FILE}) and MESSAGE
> (${ITK_INCLUDE_DIRS})?
>
>
> On Fri, Aug 29, 2014 at 10:10 AM, Gib Bogle <g.bogle at auckland.ac.nz>
> wrote:
>
>>  I just remembered that I forgot to paste that:
>>
>>
>> cmake_minimum_required(VERSION 2.6)
>>
>> PROJECT(crop)
>> FIND_PACKAGE(ITK)
>> IF(ITK_FOUND)
>> INCLUDE(${ITK_USE_FILE})
>> ELSE(ITK_FOUND)
>> MESSAGE(FATAL_ERROR
>> "ITK not found. Please set ITK_DIR.")
>> ENDIF(ITK_FOUND)
>>
>> set(PROJECTNAME "crop")
>> ADD_EXECUTABLE(${PROJECTNAME} crop.cpp)
>> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} )
>>   ------------------------------
>> *From:* Girish Mallya Udupi [indianzeppelin at gmail.com]
>> *Sent:* Friday, 29 August 2014 8:25 p.m.
>> *To:* Gib Bogle
>> *Cc:* insight-users at itk.org
>> *Subject:* Re: [ITK] [ITK-users] Strange Visual Studio 2012 problem
>>
>>    Could you paste the part of your CMakeLists.txt where you
>> find/include ITK?
>>
>>
>> On Fri, Aug 29, 2014 at 9:09 AM, Gib Bogle <g.bogle at auckland.ac.nz>
>> wrote:
>>
>>>  I've been using Visual Studio 10 for a few years without any
>>> problems.  Now I have a new machine with Visual Studio 11 (i.e. 2012)
>>> installed.  I have built ITK 64-bit, and installed it in D:\ITK-VS11-x64.
>>> The ITK environment variable ITK_DIR = D:\ITK-VS11-x64.  When I try to
>>> build my programs with the new libraries the build fails with (for example)
>>> this message:
>>>
>>> crop.cpp(18): fatal error C1083: Cannot open include file: 'itkImage.h':
>>> No such file or directory
>>>
>>> Looking at the Project Properties I see in Additional Include
>>> Directories: crop.cpp(18): \include\ITK-4.5
>>> For some reason cmake has not used the ITK_DIR prefix.  In addition I
>>> see in Linker > Additional Dependencies that all the ITK libraries are
>>> expected to be in D:\ITK-VS11-x64\lib\Release\ - another nonexistent
>>> directory, although in this case the ITK_DIR prefix has been used.
>>>
>>> This is a bit of a mess.  I presume the problem lies with cmake.  My
>>> version is 2.8.12.2, which I would have thought was recent enough - maybe
>>> it's too recent.  Has anyone else run into this problem, and is there a
>>> solution?
>>>
>>> Thanks
>>> Gib
>>>
>>> _____________________________________
>>> 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
>>>
>>>
>>
>>
>>  --
>> Regards,
>> Girish
>>
>
>
>
>  --
> Regards,
> Girish
>



-- 
Regards,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/d6e4cebe/attachment.html>

From jan.bergmeier at imes.uni-hannover.de  Fri Aug 29 09:10:41 2014
From: jan.bergmeier at imes.uni-hannover.de (jan)
Date: Fri, 29 Aug 2014 06:10:41 -0700 (PDT)
Subject: [ITK-users] MutualInformationImageToImageMetric without
 transformation
In-Reply-To: <CALzTN-SGCgVfa8mUoS3hZNSBtbx75iSV8J7vLyRkPXGwiFnuKQ@mail.gmail.com>
References: <1408375248616-7586081.post@n2.nabble.com>
 <CAKy7kk0h5KgoWGgCwbAA+mtTU0p7-u4k+=dQ+PmgNXSEmR_n7Q@mail.gmail.com>
 <1409059906690-7586120.post@n2.nabble.com>
 <CAKy7kk1WEEdpC72+z-0S9kLUnt5ZFZj3+_XuM696hPzLkrsm2Q@mail.gmail.com>
 <1409062625902-7586123.post@n2.nabble.com>
 <1409129738759-7586127.post@n2.nabble.com>
 <1409226225974-7586133.post@n2.nabble.com>
 <1409232280489-7586134.post@n2.nabble.com>
 <CALzTN-SGCgVfa8mUoS3hZNSBtbx75iSV8J7vLyRkPXGwiFnuKQ@mail.gmail.com>
Message-ID: <1409317841331-7586146.post@n2.nabble.com>

Thanks Matt,

this example was exactly what I was searching in the first place.

My new minimal version is now this:

    typedef itk::MutualInformationImageToImageMetric< UChar2DImageType,
UChar2DImageType > MetricType;
    typedef itk::LinearInterpolateImageFunction< UChar2DImageType, double >
InterpolatorType;
    typedef itk::IdentityTransform< double, 2 > TransformType;

    MetricType::Pointer metric = MetricType::New();
    TransformType::Pointer transform = TransformType::New();
    InterpolatorType::Pointer interpolator = InterpolatorType::New();

    metric->SetFixedImage( fixedImage );
    metric->SetMovingImage( movingImage );
    metric->SetFixedImageRegion( fixedImage->GetLargestPossibleRegion() );
    metric->SetTransform( transform );
    metric->SetInterpolator( interpolator );
    metric->SetNumberOfSpatialSamples( 1000 );

    metric->Initialize();
    double mutualInformation = metric->GetValue( transform->GetParameters()
);

Regards,
Jan



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/MutualInformationImageToImageMetric-without-transformation-tp7586081p7586146.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Fri Aug 29 12:24:39 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 29 Aug 2014 12:24:39 -0400
Subject: [ITK-users] Problem with itk::ImageToHistogramFilter
In-Reply-To: <1409142552492-7586128.post@n2.nabble.com>
References: <1409142552492-7586128.post@n2.nabble.com>
Message-ID: <CALzTN-T=Ugr6EEG=_MJp+MpjK8-DT1VVZ5j5oOWGWMFUYoyFBA@mail.gmail.com>

Hi Maximilian,

It is necessary to call

  imageToHistogramFilter->SetAutoMinimumMaximum( false );

 http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1ImageToHistogramFilter.html#ab0f2c568bbb0ec3ff22e27e10b6af295

Usually, the range of values are computed from the input image.

HTH,
Matt

On Wed, Aug 27, 2014 at 8:29 AM, maximilian
<maximilian_oliver.mordig at roche.com> wrote:
> I am having problems with the itk::ImageToHistogramFilter.
>
> I am generating ellipses that I want to add to an image that already
> contains some ellipses (in each iteration step, I add one ellipse to an
> image being the result of previous iterations). To see if the new ellipse
> overlaps by more than (let's say) 10%, I use the ImageToHistogramFilter.
> The previous image has objects that all have pixel values of 1. The newly
> added ellipse has value of 2. So, to get the number of overlapping pixels, I
> add up both images and I count the number of pixels = 3 in that image.
>
> I set the histogram bin minimum to 0 (background) and the histogram bin
> maximum to 3 (+ some constant c) and the number of bins such that the step
> is = 1 (here, it is 3 + c). However, when I output the average frequencies
> associated to each bin, I get values between 0 and 2 (number like 1.92) and
> not between 0 and 3 + c (see output of program of attached file). Why?
>
> GenerateCells.cxx
> <http://itk-insight-users.2283740.n2.nabble.com/file/n7586128/GenerateCells.cxx>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Problem-with-itk-ImageToHistogramFilter-tp7586128.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 g.bogle at auckland.ac.nz  Fri Aug 29 16:00:48 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 20:00:48 +0000
Subject: [ITK-users] VS 2012
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D13396@uxcn10-tdc01.UoA.auckland.ac.nz>

Has anyone built ITK-4.5 with Visual Studio 2012?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140829/68671022/attachment.html>

From g.bogle at auckland.ac.nz  Fri Aug 29 17:15:36 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Fri, 29 Aug 2014 21:15:36 +0000
Subject: [ITK-users] [ITK]  VS 2012
In-Reply-To: <CAKzA029VgQfLALnpAtKY1ndXCouqfGd6_OFsP2CT-ne9PHa4bw@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13396@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAKzA029VgQfLALnpAtKY1ndXCouqfGd6_OFsP2CT-ne9PHa4bw@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D133C7@uxcn10-tdc01.UoA.auckland.ac.nz>

When I build ITK-4.0 with VS2010, Build INSTALL creates the directory that I specified, with four subdirectories: bin. include, lib, share.  I set ITK_DIR to the install directory, and my programs build correctly.
When I build ITK-4.5 with VS2012, Build INSTALL creates the install directory with a completely different structure, with many additional files and subdirectories, and if ITK_DIR is set to this install directory program builds fail.  To build my programs successfully I need to set ITK_DIR to the name of the ITK build directory.

What I'm trying to ascertain is whether this is the result of an ITK change or a VS change.

When you build ITK-3.20 with VS2012 do you do Build INSTALL, and if so what does the install directory look like?
________________________________
From: ???'?? ?????? [nekto1989 at gmail.com]
Sent: Saturday, 30 August 2014 8:52 a.m.
To: Gib Bogle
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] VS 2012

Hi,

Same way as 3.20-vs2010 or 3.20-vs2012.


2014-08-29 23:00 GMT+03:00 Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>>:
Has anyone built ITK-4.5 with Visual Studio 2012?

_____________________________________
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/20140829/6b369e27/attachment.html>

From drescherjm at gmail.com  Fri Aug 29 20:46:16 2014
From: drescherjm at gmail.com (John Drescher)
Date: Fri, 29 Aug 2014 20:46:16 -0400
Subject: [ITK-users] Fwd:  VS 2012
In-Reply-To: <CAEhu1-5CB53SircqJRVF82omPqgahcrN1wkv2=cdmV07vBmUjQ@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13396@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAEhu1-5CB53SircqJRVF82omPqgahcrN1wkv2=cdmV07vBmUjQ@mail.gmail.com>
Message-ID: <CAEhu1-6U6tuVR2_UZAF4npTKaTCJULMN18EXFt8d91NqNr=_+A@mail.gmail.com>

---------- Forwarded message ----------
From: John Drescher <drescherjm at gmail.com>
Date: Fri, Aug 29, 2014 at 8:45 PM
Subject: Re: [ITK-users] VS 2012
To: Gib Bogle <g.bogle at auckland.ac.nz>


On Fri, Aug 29, 2014 at 4:00 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> Has anyone built ITK-4.5 with Visual Studio 2012?

Yes dozens of times with no issues at all..

John


-- 
John M. Drescher

From drescherjm at gmail.com  Fri Aug 29 21:19:48 2014
From: drescherjm at gmail.com (John Drescher)
Date: Fri, 29 Aug 2014 21:19:48 -0400
Subject: [ITK-users] VS 2012
In-Reply-To: <BD80F91C3E2E394894ED4780703D7F9E81D13418@uxcn10-tdc01.UoA.auckland.ac.nz>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13396@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAEhu1-5CB53SircqJRVF82omPqgahcrN1wkv2=cdmV07vBmUjQ@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D13418@uxcn10-tdc01.UoA.auckland.ac.nz>
Message-ID: <CAEhu1-7aV6yZatHQYNJLhNhENWyfN9kC74=8829c_nZiVq31iA@mail.gmail.com>

> Do you do Build INSTALL in the VS IDE?  If so, what does your install directory look like, i.e. what are the subdirectories?

I do not build INSTALL ever because that prevents me from using both
Release and Debug. I build itk using cmake --build from the command
line.

John

From g.bogle at auckland.ac.nz  Fri Aug 29 21:33:15 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Sat, 30 Aug 2014 01:33:15 +0000
Subject: [ITK-users] VS 2012
In-Reply-To: <CAEhu1-7aV6yZatHQYNJLhNhENWyfN9kC74=8829c_nZiVq31iA@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13396@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAEhu1-5CB53SircqJRVF82omPqgahcrN1wkv2=cdmV07vBmUjQ@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D13418@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAEhu1-7aV6yZatHQYNJLhNhENWyfN9kC74=8829c_nZiVq31iA@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D1342B@uxcn10-tdc01.UoA.auckland.ac.nz>

It seems that there is a problem with Build INSTALL.  The build itself is fine, and I can use it if I set ITK_DIR to the build directory, but the installation done with Build INSTALL is not usable.  It's probably a cmake issue, since the wrong paths for include and library files are configured in the VS project file.

I'm pursuing this issue because having different build procedures on different machines is a recipe for confusion down the line, when I've forgotten what I had to do to get things working.  It's puzzling to me that Kitware now have a divergence between ITK and VTK build-install procedures - the Build INSTALL path works with VTK.
________________________________________
From: John Drescher [drescherjm at gmail.com]
Sent: Saturday, 30 August 2014 1:19 p.m.
To: Gib Bogle; Insight-Users
Subject: Re: [ITK-users] VS 2012

> Do you do Build INSTALL in the VS IDE?  If so, what does your install directory look like, i.e. what are the subdirectories?

I do not build INSTALL ever because that prevents me from using both
Release and Debug. I build itk using cmake --build from the command
line.

John

From indianzeppelin at gmail.com  Sat Aug 30 02:40:24 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Sat, 30 Aug 2014 07:40:24 +0100
Subject: [ITK-users] VS 2012
In-Reply-To: <BD80F91C3E2E394894ED4780703D7F9E81D1342B@uxcn10-tdc01.UoA.auckland.ac.nz>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13396@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAEhu1-5CB53SircqJRVF82omPqgahcrN1wkv2=cdmV07vBmUjQ@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D13418@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAEhu1-7aV6yZatHQYNJLhNhENWyfN9kC74=8829c_nZiVq31iA@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D1342B@uxcn10-tdc01.UoA.auckland.ac.nz>
Message-ID: <CAA+VR6iZLBrNoZuH+-7VTWpim11YGQVDmg5G5_YtOEdPrqAKrQ@mail.gmail.com>

I don't think this is an ITK version issue. I built INSTALL for ITK-4.5.1
and ITK-4.6.0 using VS2010 and the install directories have only those
sub-directories that you mentioned (bin. include, lib, share).
Also, did you try the latest CMake 3.0.1? Just a couple of weeks ago, I
faced an issue (can't remember the specific details) when building my
project using 2.8.12 while 3.0.1 worked without any problems.


On Sat, Aug 30, 2014 at 2:33 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:

> It seems that there is a problem with Build INSTALL.  The build itself is
> fine, and I can use it if I set ITK_DIR to the build directory, but the
> installation done with Build INSTALL is not usable.  It's probably a cmake
> issue, since the wrong paths for include and library files are configured
> in the VS project file.
>
> I'm pursuing this issue because having different build procedures on
> different machines is a recipe for confusion down the line, when I've
> forgotten what I had to do to get things working.  It's puzzling to me that
> Kitware now have a divergence between ITK and VTK build-install procedures
> - the Build INSTALL path works with VTK.
> ________________________________________
> From: John Drescher [drescherjm at gmail.com]
> Sent: Saturday, 30 August 2014 1:19 p.m.
> To: Gib Bogle; Insight-Users
> Subject: Re: [ITK-users] VS 2012
>
> > Do you do Build INSTALL in the VS IDE?  If so, what does your install
> directory look like, i.e. what are the subdirectories?
>
> I do not build INSTALL ever because that prevents me from using both
> Release and Debug. I build itk using cmake --build from the command
> line.
>
> John
> _____________________________________
> 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,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140830/bc87ef43/attachment.html>

From g.bogle at auckland.ac.nz  Sat Aug 30 05:59:17 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Sat, 30 Aug 2014 09:59:17 +0000
Subject: [ITK-users] VS 2012
In-Reply-To: <CAA+VR6iZLBrNoZuH+-7VTWpim11YGQVDmg5G5_YtOEdPrqAKrQ@mail.gmail.com>
References: <BD80F91C3E2E394894ED4780703D7F9E81D13396@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAEhu1-5CB53SircqJRVF82omPqgahcrN1wkv2=cdmV07vBmUjQ@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D13418@uxcn10-tdc01.UoA.auckland.ac.nz>
 <CAEhu1-7aV6yZatHQYNJLhNhENWyfN9kC74=8829c_nZiVq31iA@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E81D1342B@uxcn10-tdc01.UoA.auckland.ac.nz>,
 <CAA+VR6iZLBrNoZuH+-7VTWpim11YGQVDmg5G5_YtOEdPrqAKrQ@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E81D13455@uxcn10-tdc01.UoA.auckland.ac.nz>

Thanks Girish!  I installed cmake 3.0.1 and rebuilt ITK, and now it all works as expected.  Whew!

Gib
________________________________
From: Girish Mallya Udupi [indianzeppelin at gmail.com]
Sent: Saturday, 30 August 2014 6:40 p.m.
To: Gib Bogle
Cc: John Drescher; Insight-Users
Subject: Re: [ITK-users] VS 2012

I don't think this is an ITK version issue. I built INSTALL for ITK-4.5.1 and ITK-4.6.0 using VS2010 and the install directories have only those sub-directories that you mentioned (bin. include, lib, share).
Also, did you try the latest CMake 3.0.1? Just a couple of weeks ago, I faced an issue (can't remember the specific details) when building my project using 2.8.12 while 3.0.1 worked without any problems.


On Sat, Aug 30, 2014 at 2:33 AM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
It seems that there is a problem with Build INSTALL.  The build itself is fine, and I can use it if I set ITK_DIR to the build directory, but the installation done with Build INSTALL is not usable.  It's probably a cmake issue, since the wrong paths for include and library files are configured in the VS project file.

I'm pursuing this issue because having different build procedures on different machines is a recipe for confusion down the line, when I've forgotten what I had to do to get things working.  It's puzzling to me that Kitware now have a divergence between ITK and VTK build-install procedures - the Build INSTALL path works with VTK.
________________________________________
From: John Drescher [drescherjm at gmail.com<mailto:drescherjm at gmail.com>]
Sent: Saturday, 30 August 2014 1:19 p.m.
To: Gib Bogle; Insight-Users
Subject: Re: [ITK-users] VS 2012

> Do you do Build INSTALL in the VS IDE?  If so, what does your install directory look like, i.e. what are the subdirectories?

I do not build INSTALL ever because that prevents me from using both
Release and Debug. I build itk using cmake --build from the command
line.

John
_____________________________________
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,
Girish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140830/db1ada61/attachment.html>

From marco.ulge at gmail.com  Sat Aug 30 06:16:57 2014
From: marco.ulge at gmail.com (Marco Ulge)
Date: Sat, 30 Aug 2014 03:16:57 -0700 (PDT)
Subject: [ITK-users]  Convert Matrix to itk::Image
Message-ID: <1409393816990-34497.post@n7.nabble.com>

Hello,

I used the vnl_matrix_ref class to extract the matrix from the itk::Image
and then perform some calculations. What i need to do now, is convert the
matrix back to an itk::Image and i read that i should use the
itkImportImageFilter class to achieve this. I am having difficulties
understanding what should be my input to SetImportPointer method. Can anyone
help me with this?

Regards,

Marco



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Convert-Matrix-to-itk-Image-tp34497.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From millerjv at gmail.com  Sat Aug 30 08:23:20 2014
From: millerjv at gmail.com (Jim Miller)
Date: Sat, 30 Aug 2014 08:23:20 -0400
Subject: [ITK-users] Convert Matrix to itk::Image
In-Reply-To: <1409393816990-34497.post@n7.nabble.com>
References: <1409393816990-34497.post@n7.nabble.com>
Message-ID: <F3A01485-8A0F-4F11-A0CC-422DA294EE38@gmail.com>

You pass the pointer to the pixels you want to ITK image to wrap. There is a Boolean in the methods to control whether ITK should manage the memory from that point forward (deleting the pixels when the ITK Image is destroyed) or whether you want your program to maintain control of that memory block and you will be carefule to ensure the buffer is freed at the appropriate time. 

Jim

> On Aug 30, 2014, at 6:16 AM, Marco Ulge <marco.ulge at gmail.com> wrote:
> 
> Hello,
> 
> I used the vnl_matrix_ref class to extract the matrix from the itk::Image
> and then perform some calculations. What i need to do now, is convert the
> matrix back to an itk::Image and i read that i should use the
> itkImportImageFilter class to achieve this. I am having difficulties
> understanding what should be my input to SetImportPointer method. Can anyone
> help me with this?
> 
> Regards,
> 
> Marco
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Convert-Matrix-to-itk-Image-tp34497.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 wechen5 at vt.edu  Sat Aug 30 18:36:29 2014
From: wechen5 at vt.edu (blueridge)
Date: Sat, 30 Aug 2014 15:36:29 -0700 (PDT)
Subject: [ITK-users] Using RGB file for GMM module
Message-ID: <1409438189857-34499.post@n7.nabble.com>

Is it possible to use ImageToListSampleAdaptor to convert RGB image to a list
of samples and then use ExpectationMaximizationMixtureModelEstimator to
estimate components of this RGB image?

thanks



--
View this message in context: http://itk-users.7.n7.nabble.com/Using-RGB-file-for-GMM-module-tp34499.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From pattersonnp.work at gmail.com  Sun Aug 31 16:06:53 2014
From: pattersonnp.work at gmail.com (NPatterson)
Date: Sun, 31 Aug 2014 13:06:53 -0700 (PDT)
Subject: [ITK-users] ResampleDICOM example and DCMTK
In-Reply-To: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
Message-ID: <1409515613801-7586158.post@n2.nabble.com>

Hi, I wondered if anyone could test the code attached in the thread header
"ResampleDICOM example and DCMTK" regarding the use of DCMTK for DICOM
reading writing in ITK. I adapted the ResampleDICOM example to work with
DCMTK instead of GDCM, and although I get no errors, I also do not get any
output dicom images. If someone has the time to test this code to see if
they observe the same behaviour/or can suggest a fix, I would be very
appreciative.

Regards, Nick.



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-ResampleDICOM-example-and-DCMTK-tp7586131p7586158.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From wechen5 at vt.edu  Sun Aug 31 16:40:52 2014
From: wechen5 at vt.edu (blueridge)
Date: Sun, 31 Aug 2014 13:40:52 -0700 (PDT)
Subject: [ITK-users] ExpectationMaximizationMixtureModelEstimator use of
 WeightedMeanSampleFilter
In-Reply-To: <alpine.LRH.2.01.1307180912460.17648@hymn01.u.washington.edu>
References: <alpine.LRH.2.01.1307011708160.17648@hymn01.u.washington.edu>
 <alpine.LRH.2.01.1307101605510.17648@hymn01.u.washington.edu>
 <alpine.LRH.2.01.1307180912460.17648@hymn01.u.washington.edu>
Message-ID: <1409517652082-34501.post@n7.nabble.com>

It's kind of late, but just for the record since I ran into same error
message.

My problem was that I did not initialize the component parameters correctly,
( I did not initialize it at all, use default constructor, with set all
zeros), then the weights of first iteration are all zeros, which triggers
the error message.





--
View this message in context: http://itk-users.7.n7.nabble.com/ExpectationMaximizationMixtureModelEstimator-error-tp31798p34501.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Sun Aug 31 17:38:39 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 31 Aug 2014 17:38:39 -0400
Subject: [ITK-users] ResampleDICOM example and DCMTK
In-Reply-To: <1409515613801-7586158.post@n2.nabble.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
Message-ID: <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>

Hi Nick,

Nothing stands out from inspecting the code.  Could you please send an
example dataset?

Thanks,
Matt

On Sun, Aug 31, 2014 at 4:06 PM, NPatterson <pattersonnp.work at gmail.com> wrote:
> Hi, I wondered if anyone could test the code attached in the thread header
> "ResampleDICOM example and DCMTK" regarding the use of DCMTK for DICOM
> reading writing in ITK. I adapted the ResampleDICOM example to work with
> DCMTK instead of GDCM, and although I get no errors, I also do not get any
> output dicom images. If someone has the time to test this code to see if
> they observe the same behaviour/or can suggest a fix, I would be very
> appreciative.
>
> Regards, Nick.
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-ResampleDICOM-example-and-DCMTK-tp7586131p7586158.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