From vrnova at gmail.com  Wed Jun  1 08:27:31 2016
From: vrnova at gmail.com (Yanling Liu)
Date: Wed, 1 Jun 2016 08:27:31 -0400
Subject: [ITK-users] MutualInformationAffine example broken
Message-ID: <CACNiyLA4ao+rpVwC3bmFQqP_SC-ihnmF6G5SRQsgtfjYAxhd1A@mail.gmail.com>

Hello,

I downloaded the MutualInformationAffine example from
https://itk.org/Wiki/ITK/Examples/Registration/MutualInformationAffine,
compiled it using ITK 4.9.1 and it reported follow error message:

ExceptionObject caught !

itk::ExceptionObject (0x2030010)
Location: "void itk::MutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::SampleFixedImageDomain(itk::MutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::SpatialSampleContainer&) const [with TFixedImage =
itk::Image<float, 2u>; TMovingImage = itk::Image<float, 2u>;
itk::MutualInformationImageToImageMetric<TFixedImage,
TMovingImage>::SpatialSampleContainer =
std::vector<itk::MutualInformationImageToImageMetric<itk::Image<float, 2u>,
itk::Image<float, 2u> >::SpatialSample,
std::allocator<itk::MutualInformationImageToImageMetric<itk::Image<float,
2u>, itk::Image<float, 2u> >::SpatialSample> >]"
File:
/home/yliu/Imaging/Libraries/ITK/InsightToolkit-4.9.1/install/include/ITK-4.9/itkMutualInformationImageToImageMetric.hxx
Line: 196
Description: itk::ERROR: MutualInformationImageToImageMetric(0x202fd10):
All the sampled point mapped to outside of the moving image

Anyone may help to fix this example? I did not change the source code of
the example at all.

Thanks,

Yanling
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From javij1 at gmail.com  Thu Jun  2 11:39:08 2016
From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=)
Date: Thu, 2 Jun 2016 17:39:08 +0200
Subject: [ITK-users] Set image pixel type and dimension through IOBase
	methods
Message-ID: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com>


Hello,

I have to read a NIfTI file and I don't know which pixel type has (int, 
double, char, etc). Thus, I am using an ImageIOBase object to retrieve 
the image information before loading it. I have followed the code of the 
ITK examples, which is something similar to

// NIfTI IO Factory
itk::NiftiImageIOFactory::RegisterOneFactory();

// Typedefs
typedef itk::ImageIOBase::IOComponentType PixelType;
itk::ImageIOBase::Pointer imageIO = 
itk::ImageIOFactory::CreateImageIO(filename, 
itk::ImageIOFactory::ReadMode);

imageIO->SetFileName(argv[1]);
imageIO->ReadImageInformation();

Here I know the pixel type and the image dimensio through 
"imageIO->GetComponentType()"  and "imageIO->GetDimensions()". Hence, I 
wan to declare an image type with this parameters to work with it on my 
methods.
I would know if there is some way to declare the image without 
performing a long "switch - case double, case int, case ..." code to 
declare the image type, i.e. something similar to this:

// I know this do not compile and it is wrong but something similar
typedef itk::Image<imageIO->GetComponentType(), 
imageIO->GetDimensions()>  ImageType;

Thank you.
Regards.
Javier.


From blowekamp at mail.nih.gov  Thu Jun  2 11:59:36 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 2 Jun 2016 15:59:36 +0000
Subject: [ITK-users] Set image pixel type and dimension through
	IOBase	methods
In-Reply-To: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com>
References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com>
Message-ID: <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov>

Hello,

To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1].

Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python.

Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface.


HTH,
Brad

[1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html

> On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n <javij1 at gmail.com> wrote:
> 
> 
> Hello,
> 
> I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to
> 
> // NIfTI IO Factory
> itk::NiftiImageIOFactory::RegisterOneFactory();
> 
> // Typedefs
> typedef itk::ImageIOBase::IOComponentType PixelType;
> itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode);
> 
> imageIO->SetFileName(argv[1]);
> imageIO->ReadImageInformation();
> 
> Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()"  and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods.
> I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this:
> 
> // I know this do not compile and it is wrong but something similar
> typedef itk::Image<imageIO->GetComponentType(), imageIO->GetDimensions()>  ImageType;
> 
> Thank you.
> Regards.
> Javier.
> 
> _____________________________________
> 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 javij1 at gmail.com  Thu Jun  2 13:02:38 2016
From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=)
Date: Thu, 2 Jun 2016 19:02:38 +0200
Subject: [ITK-users] Set image pixel type and dimension through IOBase
 methods
In-Reply-To: <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov>
References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com>
 <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov>
Message-ID: <e7aba46e-2b2e-4aa7-8f58-81826e7ceb3d@gmail.com>


Thank you for the quick anwser.

I am sorry but I do not clearly see how can I later work with the image 
and with the filters that need the ImageType to declare the object. In 
the [1] example, the "ReadScalarImage" function implements the long 
switch statement code to load the image with the corresponding type. 
However, I cannot return a pointer to the image because depending on the 
case statement, it has one type or another.

Inside each case statement the corresponding image type is known, so 
templated functions can be called and the image type can be inferred for 
each one. This means that I have to embed all my code, my function and 
methods calls inside each case statement to know the ImageType? Surely I 
am not understanding something because I don't believe this approach is 
correct.

Thank you very much.

Regards.

Javier.


El 02/06/2016 a las 17:59, Lowekamp, Bradley (NIH/NLM/LHC) [C] escribi?:
> Hello,
>
> To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1].
>
> Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python.
>
> Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface.
>
>
> HTH,
> Brad
>
> [1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html
>
>> On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n <javij1 at gmail.com> wrote:
>>
>>
>> Hello,
>>
>> I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to
>>
>> // NIfTI IO Factory
>> itk::NiftiImageIOFactory::RegisterOneFactory();
>>
>> // Typedefs
>> typedef itk::ImageIOBase::IOComponentType PixelType;
>> itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode);
>>
>> imageIO->SetFileName(argv[1]);
>> imageIO->ReadImageInformation();
>>
>> Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()"  and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods.
>> I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this:
>>
>> // I know this do not compile and it is wrong but something similar
>> typedef itk::Image<imageIO->GetComponentType(), imageIO->GetDimensions()>  ImageType;
>>
>> Thank you.
>> Regards.
>> Javier.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users


From blowekamp at mail.nih.gov  Thu Jun  2 13:15:15 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 2 Jun 2016 17:15:15 +0000
Subject: [ITK-users] Set image pixel type and dimension through IOBase
 methods
In-Reply-To: <e7aba46e-2b2e-4aa7-8f58-81826e7ceb3d@gmail.com>
References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com>
 <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov>
 <e7aba46e-2b2e-4aa7-8f58-81826e7ceb3d@gmail.com>
Message-ID: <E86126F2-30A4-4B50-B31B-DA5752435FDB@mail.nih.gov>

Hi,

You are correct that you can?t return a typed pointer from the template functions. But not that you should implement your code inside the case statement.

You can implement your code in the templates functions, then call other functions with templates of the type or classes which the type as templates.

HTH,
Brad


> On Jun 2, 2016, at 1:02 PM, Javier Juan Albarrac?n <javij1 at gmail.com> wrote:
> 
> 
> Thank you for the quick anwser.
> 
> I am sorry but I do not clearly see how can I later work with the image and with the filters that need the ImageType to declare the object. In the [1] example, the "ReadScalarImage" function implements the long switch statement code to load the image with the corresponding type. However, I cannot return a pointer to the image because depending on the case statement, it has one type or another.
> 
> Inside each case statement the corresponding image type is known, so templated functions can be called and the image type can be inferred for each one. This means that I have to embed all my code, my function and methods calls inside each case statement to know the ImageType? Surely I am not understanding something because I don't believe this approach is correct.
> 
> Thank you very much.
> 
> Regards.
> 
> Javier.
> 
> 
> El 02/06/2016 a las 17:59, Lowekamp, Bradley (NIH/NLM/LHC) [C] escribi?:
>> Hello,
>> 
>> To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1].
>> 
>> Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python.
>> 
>> Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface.
>> 
>> 
>> HTH,
>> Brad
>> 
>> [1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html
>> 
>>> On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n <javij1 at gmail.com> wrote:
>>> 
>>> 
>>> Hello,
>>> 
>>> I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to
>>> 
>>> // NIfTI IO Factory
>>> itk::NiftiImageIOFactory::RegisterOneFactory();
>>> 
>>> // Typedefs
>>> typedef itk::ImageIOBase::IOComponentType PixelType;
>>> itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode);
>>> 
>>> imageIO->SetFileName(argv[1]);
>>> imageIO->ReadImageInformation();
>>> 
>>> Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()"  and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods.
>>> I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this:
>>> 
>>> // I know this do not compile and it is wrong but something similar
>>> typedef itk::Image<imageIO->GetComponentType(), imageIO->GetDimensions()>  ImageType;
>>> 
>>> Thank you.
>>> Regards.
>>> Javier.
>>> 
>>> _____________________________________
>>> 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 javij1 at gmail.com  Thu Jun  2 13:18:37 2016
From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=)
Date: Thu, 2 Jun 2016 19:18:37 +0200
Subject: [ITK-users] Set image pixel type and dimension through IOBase
 methods
In-Reply-To: <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov>
References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com>
 <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov>
Message-ID: <f2097be9-f7f6-befc-07dd-8ee8da6d552a@gmail.com>


Well, sorry. I just now understand what you are referring. You are 
refering to start to work inside the function "ReadImage" of the [1] 
example (maybe changing his name to some more informative) as if it was 
the "main" function because inside this templated function we have the 
ImageType as the template arg. Yes, it solves my problem.

Anyway, it is a little bit anoying for me. Maybe I can load the image in 
double format to avoid truncation problems and perform a final casting 
to the original type, but surely, in some point I should pass through 
the long switch statement.

Thank you Brad

Javier.


El 02/06/2016 a las 17:59, Lowekamp, Bradley (NIH/NLM/LHC) [C] escribi?:
> Hello,
>
> To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1].
>
> Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python.
>
> Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface.
>
>
> HTH,
> Brad
>
> [1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html
>
>> On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n <javij1 at gmail.com> wrote:
>>
>>
>> Hello,
>>
>> I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to
>>
>> // NIfTI IO Factory
>> itk::NiftiImageIOFactory::RegisterOneFactory();
>>
>> // Typedefs
>> typedef itk::ImageIOBase::IOComponentType PixelType;
>> itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode);
>>
>> imageIO->SetFileName(argv[1]);
>> imageIO->ReadImageInformation();
>>
>> Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()"  and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods.
>> I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this:
>>
>> // I know this do not compile and it is wrong but something similar
>> typedef itk::Image<imageIO->GetComponentType(), imageIO->GetDimensions()>  ImageType;
>>
>> Thank you.
>> Regards.
>> Javier.
>>
>> _____________________________________
>> 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 jchris.fillionr at kitware.com  Fri Jun  3 09:52:10 2016
From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin)
Date: Fri, 3 Jun 2016 09:52:10 -0400
Subject: [ITK-users] [ANN] ITK 4.10.0 has been released!
Message-ID: <CANLz8R4nx=ePB8+J4PSUd+Ot8Ps2QC4Qp-ZHJ5OA=y=ag5AZQA@mail.gmail.com>

The Insight Segmentation and Registration Toolkit (ITK), is an open-source,
cross-platform library for multidimensional image analysis. On behalf of
the Insight Toolkit community, we are proud to announce that ITK 4.10.0 has
been released!

Links to the Sourceforge.net tarballs can be found on the download page:

 http://www.itk.org/ITK/resources/software.html


[image: TwoProjectionRegistrationDiagram.png]


Insight Journal article included as a Remote Module:
TwoProjectionRegistration <http://hdl.handle.net/10380/3245>. Digitally
reconstructed radiographs (DRR) generated as part of the registration are
shown above.



Outline

----------

1. Introduction

2. New Features

3. ITK Changelog

4. ITK Sphinx Examples Changelog

5. ITK Software Guide Changelog


Introduction

-----------------

Developed by an international community, ITK collects best-of-breed
algorithms for registering, segmenting, analyzing, and quantifying
n-dimensional imaging data. The high-quality library facilitates
reproducible research, provides a software resource for teaching image
analysis, and offersis a platform for commercial product development.

A few selected highlights for the 4.10 release include the following:


   -

   New Remote module: TwoProjectionRegistration performs simultaneous
   registration of two projection images to a 3D image volume, which is useful
   for external beam radiotherapy and other applications. It uses Powell?s
   method for optimization and the Siddon-Jacobs fast ray-tracing algorithm.
   -

   First update to internal VNL in five years. Many improvements were made
   to upstream VNL. We now push patches upstream and stay in sync via a Git
   subtree workflow.
   -

   Windows builds now support processing 4GB+ images by default
   -

   GDCM updated for better DICOM support



Congratulations to the 26 contributors to this release. We would especially
like to recognize the new contributors: Andrey Fedorov, Sujin Philip,
Francois Budin, and b'Alvaro Sanchez.

Improved documentation in this release includes new examples on how to
convert between ITK and VTK image data structures
<https://blog.kitware.com/how-to-connect-itk-and-vtk-pipelines/>.
Additionally, a new example demonstrates how to perform vector image
registration with a mean-squares matching metric
<https://itk.org/ITKExamples/src/Registration/Metricsv4/PerformRegistrationOnVectorImages/Documentation.html>.
The ITK Software Guide added documentation on how to add third party
dependencies when creating an ITK module.

This release also brings exciting rapid prototyping improvements to the ITK
Python wrapping. Type specification is no longer necessary during the
creation of most filters. The required type is inferred from a primary
input passed on filter creation. For example, instead of the explicit type
specification:

 median = itk.MedianImageFilter[ImageType, ImageType].New()

 median.SetInput(reader.GetOutput())

It is now possible to call:

 median = itk.MedianImageFilter.New(Input=reader.GetOutput())

Or, the shortened:

 median = itk.MedianImageFilter.New(reader.GetOutput())

Or:

 median = itk.MedianImageFliter.New(reader)

An itk.ImageFileReader can be created by specifying the FileName during
instantiation:

 reader = itk.ImageFileReader.New(FileName=?inputFile.mha?)


Enjoy ITK!


New Features

---------------------

* Wrapping improvements

   -

   ITK_USE_64BITS_IDS supported on Windows
   -

   Faster builds (CastXML calls and build targets reduced by half)
   -

   Faster runtime loading and smaller binary size due to hidden symbol
   visibility
   -

   Wrapping with BUILD_SHARED_LIBS disabled is supported
   -

   Do not link to libpython when possible
   -

   Filter types do not need to be specified when ?Input=inputImage? is
   specified in the constructor
   -

   Improved wrapping class coverage
   -

   Visual Studio 2015 Update 2 Supported
   -

   GCC 6.1 supported


* New Remote Module

   -

   TwoProjectionRegistration
   -

      2D-3D registration designed for radiotherapy
      -

      http://hdl.handle.net/10380/3245


* Core Improvements

   -

   Data and build tool downloads now over HTTPS
   -

   Extended constexpr usage with ITK_CONSTEXPR and ITKCONSTEXPR_FUNC macros
   -

   ITK_USE_64BITS_IDS, required to process 4GB+ images on Windows, now
   enabled by default
   -

   VNL updated and modernized
   -

      CMake configuration major modernization
      -

      vcl has been removed in favor of the standard libraries
      -

      vnl_math_ function avoided in favor of std:: and itk::Math
      -

      VNL had suppressed integer data conversion warnings on Visual Studio
      (C4257); this suppression has been removed and all warnings addressed
      -

   Various improvements for building a module externally against an ITK
   build tree
   -

   CMAKE_POSITION_INDEPENDENT_CODE is enabled by default
   -

   Improved EXERCISE_BASIC_OBJECT_METHODS testing macro


* Filtering Improvements

   -

   RGB pixel support added to itk::ImageToVTKImageFilter
   -

   itk::Box* filters moved out of the Review module
   -

   itk::GaussianDerivativeOperator moved out of the Review module
   -

   MaskLabel is deprecated in N4BiasFieldCorrectionFilter in favor any
   non-zero pixel


* Registration Improvements

   -

   Fixed and moving masks added to the v4 registration methods


* Documentation Improvements

   -

   Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples
   -

   New examples on to convert between ITK and VTK
   -

   New example on how to perform vector image registration
   -

   The ITK Software Guide describes how to add a third-party dependency to
   a module


* Third Party Library Updates

   -

   pygccxml updated to v1.7.3
   -

   GDCM updated to the release branch latest
   -

   VNL updated to latest upstream
   -

   MINC updated to the latest upstream
   -

   SWIG updated to v3.0.8
   -

   PCRE update to v8.38


* Improved code coverage -- we are at 85.0%!

* *Lots* of important bug fixes

* And much more! See details in the log below.


Changes from v4.10rc02..v4.10.0

------------------------------------------------

Bradley Lowekamp (3):
     COMP: Address uninitialized warning of size
     COMP: Devirtualize private methods to prevent instantiation
     COMP: Use well defined ZeroValue for unused initial value.

Hans Johnson (1):
     BUG: try_compile needs to have CMAKE_CXX_STANDARD passed

Hyun Jae Kang (1):
     COMP: Fix unexpected data-cast results of itkCastImageFilter

Jon Haitz Legarreta (1):
     BUG: Fix OpenCV-2.4.9 camera empty image issue.

Matthew McCormick (13):
     COMP: Bump CastXML for GCC 6.1 support.
     STYLE: Improvements to HardConnectedComponentsImageFilter.
     ENH: Add baseline for itkHardConnectedComponentImageFilterTest.
     STYLE: Improvements for itkHardConnectedComponentImageFilterTest
     COMP: HardConnectedComponentImageFilter autological constant out of
range
     DOC: Sphinx examples update to 2016-05-22.
     DOC: Wiki examples update to 2016-05-22.
     COMP: MSVC result of 32-bit shift implicitly converted to 64 bits
     BUG: Disable building the netlib example.
     ENH: Add FloatAddULP
     BUG: Decrement index in BSplineTransform by ULPs.
     BUG: Adjust index decrement in BSplineTransform
     BUG: Remove VNL README left over from subtree merge.

Sumedha Singla (1):
     ENH: WhatModulesITK was not finding modules on Windows


Changes from v4.10rc01..v4.10rc02

------------------------------------------------

Davis Vigneault (1):
     BUG: Improve error checking and testing for ConnectedRegionsMesh

Hyun Jae Kang (2):
     BUG: Address the issue of "Missing Delete" within SwapZeroCornerToIRP.
     COMP: Fixed Mac OSX wrapping configuration warning

Matthew McCormick (6):
     BUG: The ImageFileReader internal pipeline methods should be protected.
     BUG: Use new VNL include directory variables.
     COMP: Add missing NeighborhoodAccessor methods to PhasedArray3D image.
     BUG: Adjust itk.org ExternalData URL.
     COMP: Do not use target_include_directories with CMake 2.8.11.2.
     BUG: Address missing shared_ptr for VS9


Changes from v4.9.0..v4.10rc01

------------------------------------------------

Alvaro Sanchez (1):
     STYLE: moved itkKappaSigmaThresholdImageFilter/Calculator from
Nonunit/Review

Andrey Fedorov (2):
     BUG: Add missing itk_expat_mangle.h install target
     BUG: fix typo in file name

Bill Hoffman (2):
     COMP: fix shared build on Windows when Review is on.
     COMP: work around for VS 2015 optimizer bug causing test failures.

Bill Lorensen (6):
     ENH: Bump version for style fixups.
     ENH: Bump wiki examples version, new remote module process
     ENH: Bump wiki examples version, new remote module process
     STYLE: SuperClass should be Superclass
     COMP: Resolve clang linkage issue
     BUG: Valgrind detected an invalid read

Bradley Lowekamp (21):
     BUG: Compilation problem with GCC 4.1 and explicit instantiation
     ENH: Update Insight Journal handle links to https
     ENH: Adding const qualifier to results
     BUG: Adding missing const qualifier for GetConfusionMatrix method
     BUG: Use Set/GetMacros, fix const correctness and PrintSelf.
     ENH: added inlined Zero and one values for integer NumericTraits
     ENH: Use constexpr for floating point NumericTraits
     ENH: Make NumericTraits functions constexpr for intrinsic
     BUG: Add definition of static constexpr NumericTrait members
     BUG: Declared static constexpr members need to be defined as constexpr
     ENH: ITK_CONSTEXPR_FUNC implies inline
     BUG: Addressing VS10 and VS11 NumericTraits linkage issue
     BUG: Use LargestPossible region for BSpline domain
     BUG: Remove errant file
     COMP: Address warning about this usage in initializer list
     ENH: Prefer ZeroValue function over variable
     STYLE: Use consistent path for try_compiles binary directory
     BUG: Don't use "=" in cmake variable name
     ENH: Test address of NumericTraits One and Zero constexpr
     ENH: Use ITK_USE_64BITS_IDS for windows 64 by default
     ENH: Enable run-time dependency on Python library

Davis Vigneault (4):
     ENH: Update itkFileTools to allow std::string arguments.
     ENH: Add Floored and Truncated Modulus to VNL
     ENH: Add Ternary Operator Image Filter
     STYLE: Prefer static cast

D?enan Zuki? (1):
     ENH: CovariantVector's Normalize returns the norm.

Francois Budin (6):
     PERF: Simplify itkTemplate New() input type identification.
     ENH: Avoid template type specification for image reader in Python
wrapping
     BUG: Missing IOPixelType strings in ImageIOBase
     BUG: Wrapping intermediate files were not automatically updated
     ENH: Reduce number of dependencies for XML files generated for wrapping
     BUG: GCC is limited when calling overloaded base class functions

GCC-XML Upstream (1):
     ENH: pygccxml v1.7.3 (reduced)

GDCM Upstream (1):
     GDCM 2015-09-02 (1efe9e28)

Hans Johnson (27):
     COMP: Static analysis warning
     COMP: Incorrect delete found by static analysis
     PERF:  Avoid temporary std:vector copying.
     COMP: Provide VXL backward compatible includes
     COMP: ITK requires legacy methods
     ENH: Need propagate ITK_LIBRARY_PROPERTIES
     ENH: Added UpdateFromUpstream.sh for VNL
     ENH: Manual copy from vxl/master
     STYLE: vnl_math_[min|max] -> std::[min|max]
     STYLE: Text files should end with a newline
     COMP: Prefer C++11 constexpr when possible
     COMP: Prefer C++11 constexpr when possible
     ENH: Simplify std:: math function definitions
     COMP: Error in constexpr usage
     COMP: Add const to previous const variables
     COMP: SizeValueType can has different definition for itkArray
     ENH: Added utility for modernizing vcl_ to std::
     ENH: Reference vnl_math.h constants directly
     ENH: Avoid using vnl_math_ functions
     COMP: Missing symbol for itkStaticConstMacro
     COMP: Function override missing in BioCell
     ENH: Convert vcl_ to std::
     BUG: Windows vcl_snprintf failures addressed
     COMP: Disabmiguate function calls to SetData
     ENH: Provided static code API for external applications
     COMP: Remove possible type conversion warnings
     ENH: Merge GDCM release branch

Hyun Jae Kang (25):
     COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6
     BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6
     BUG: Fixed the runtime crash of itkTimeProbeTest2
     BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on
OSX 10.6
     BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6
     COMP: Fixed the data conversion warning messages of itkResourceProbe
     BUG: Fixed the runtime crash of itkLabelOverlapMeasuresImageFilterTest
     BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX
10.6
     BUG: Fixed the runtime crash of itkMRIBiasFieldCorrectionFilterTest
     BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1
     BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6
     BUG: Fixed the runtime crash of vnl_test_numeric_traits
     BUG: Fixed the runtime crash of test_pow_log on OSX 10.6
     BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6
     BUG: Fixed the failed test case of itkSTLThreadTest on OS X 10.8
     COMP: Update KWStyle to utilize the latest boost library
     COMP: Fixed the compiler error of ITK on Mingw-w64
     COMP: Temporarily suppress the warning messages of data-conversion on
VS14
     COMP: Put back the disappeared option of "BUILD EXAMPLES".
     BUG: Fix segmentation faults on mingw-W64 x86_64.
     BUG: Fix the failed test of itkCastImageFilterTest on mingw-w64
compiler.
     COMP: Fixed the cmake configuration for ITK_WRAP_DOC
     COMP: Fixed the warning messages on VS14.
     COMP: Add a missing head file at itkNumericTraitsStdVector.h
     COMP: Fix the wraning message of data-conversion

Jean-Christophe Fillion-Robin (4):
     COMP: ITKExternalModule: Support building module without test
directory.
     STYLE: Facilitate maintenance of CastXML generator refactoring
CMakeLists
     COMP: Allow use of multiple "ITK external modules" in the same project.
     STYLE: UseITK: Document static registration of ITK IO factories. See
#3393

Jon Haitz Legarreta (7):
     COMP: Delete unused variable compiler warning.
     ENH: Refactored itkBioCellTest
     ENH: Exercise non-tested itk::Math methods.
     ENH: Improve MersenneTwister class and test.
     ENH: Improve itkFEMLoadPoint coverage.
     ENH: Improve itkVersion class code coverage.
     ENH: Perform class name checks in test macro

KWSys Robot (1):
     KWSys 2016-03-09 (36d8666f)

Lucas Gandel (9):
     ENH: Implement GetNumberOfParameter() in ImageToSpatialObjectMetric
     COMP: Enable wrapping of multiple "ITK external modules" in the same
project
     COMP: Fix CASTXML_EXECUTABLE value for multiple external module
     COMP: Fix external module testing
     COMP: Fix git protocol setup
     ENH: Conditionally add testing for External Modules
     BUG: Fix call to std::max() with different variable types

Manuel Grizonnet (1):
     COMP: add ITKCommon_EXPORT to fix link issues with external
applications

Matthew McCormick (73):
     ENH: Add TwoProjectionRegistration Remote Module.
     ENH: Allow ITKVideoBridgeOpenCV to be built externally.
     COMP: Add export specification for itk::ResourceProbe.
     ENH: Do not force shared libraries when wrapping.
     BUG: BUILD_TESTING should be not advanced.
     ENH: Bump ITK version to 4.10.0.
     DOC: Correct ITKImageNoise description spelling.
     ENH: Wrap FFTNormalizedCorrelationImageFilter.
     BUG: Remove Azure ExternalData resource.
     BUG: ExternalData downloads from midas3.kitware.com only supports
https.
     BUG: Update ExternalData resource.
     BUG: slicer.kitware.com/midas3/ ExternalData will not support http.
     ENH: Add ITK_CUSTOM_LIBRARY_SUFFIX variable.
     ENH: Wrap PipelineMonitorImageFilter.
     BUG: Update MIDAS url for https in archive testing data script.
     ENH: Wrap std::vector< itk::ImageRegion >.
     BUG: Fix wrapping build with DEFAULT_MODULES OFF.
     ENH: Add RGB pixel support to ImageToVTKImageFilter.
     ENH: Add RGB and vector pixel type wrapping for ImageToVTKImageFilter.
     STYLE: Use PixelType and ImageType in Python tests.
     ENH: Avoid template type specification in Python wrapping.
     COMP: Do not use has_key in itkTemplate New.
     DOC: Emphasize that push access is not required to contribute patches.
     ENH: Download SWIG and PCRE from midas3.kitware.com.
     COMP: Ignore build warning from KWStyle's boost.
     BUG: Remove Azure ExternalData resource.
     BUG: ExternalData downloads from midas3.kitware.com only supports
https.
     BUG: slicer.kitware.com/midas3/ ExternalData will not support http.
     ENH: Update the VNL README-ITK.txt subtree commit revision.
     BUG: Mark VXL internal CMake variables as advanced.
     BUG: Run itk_module_target on itknetlib.
     DOC: Direct patches for VXL upstream to the GitHub repository.
     BUG: Run itk_module_target on itknetlib.
     COMP: Account for removal of vcl_* from upstream VXL.
     COMP: Remove itkTypeMacro from BioCellHelper.
     COMP: Convert itkBioCellTest arguments from double to int.
     COMP: Turn off BUILD_DOCUMENTATION for VNL.
     BUG: Install VXL config files to backwards-compatible locations.
     ENH: Remove vcl_complex from the wrapping.
     BUG: Install vnl_export.h and vnl_algo_export.h to previous locations.
     BUG: midas3.kitware.com only supports the https protocol.
     BUG: ImageIOBase SetDimensions should take SizeValueType.
     ENH: Add wrapping for ImagePCAShapeModelEstimator.
     COMP: Do not specify COMPONENTS with find_package(VTK.
     DOC: Fix FFTW warning grammar.
     COMP: Build against system HDF5 1.8.16.
     ENH: Set a default CMAKE_BUILD_TYPE when building a module externally
     COMP: Make initial HDF5 discovery of 1.8.16 quiet.
     ENH: Use hidden symbol visibility for the CPython extension modules.
     ENH: Turn on CMAKE_POSITION_INDEPENDENT_CODE by default.
     BUG: FEMLoadPoint uninitialized value in the constructor.
     BUG: Fix wrapping of complex types in VNL.
     ENH: Bump CMakeLists.txt version 4.9.1.
     COMP: Address ITKCommon Python submodule order.
     BUG: Extend ExternalData_TIMEOUT_ABSOLUTE to 900 seconds.
     BUG: Do not run KWStyle Git config on a release tarball.
     COMP: Ambiguous RGBPixel access in CustomColormapFunction.
     BUG: Prevent division by zero in PhasedArray3DSpecialCoordinatesImage.
     BUG: Initialize azimuth and elevation to pi/2 in PhasedArray3D.
     BUG: Increase MaskLabel backwards compatibility in N4 bias correction.
     ENH: Deprecate MaskLabel in N4BiasFieldCorrectionImageFilter.
     COMP: Update CastXML to support Visual Studio 2015 Update 2.
     COMP: Do not set wrapping library visibility with static builds.
     COMP: Update CastXML to support Visual Studio 2015 Update 2.
     COMP: Broaden the KWStyle warning exception.
     COMP: Update KWStyle version.
     BUG: Do not use the same output file in N4BiasField Test 2,3.
     COMP: Expand EXERCISE_BASIC_OBJECT_METHODS for other GCC versions.
     ENH: Update Cuberille Remote to 2015-05-01.
     ENH: Enable registration of the IOOpenSlide module through CMake.
     ENH: Update itk.org URL's for HTTPS support.
     BUG: Use CastXML built against LLVM with LLVM_ENABLE_TERMINFO OFF.
     BUG: Fix Python wrapping on Windows when ITK_USE_64BIT_IDS is ON.

Michka Popoff (12):
     ENH: Use importlib for python 3.4 instead of imp
     ENH: Update to Swig 3.0.8
     ENH: Update PCRE to version 8.38
     ENH: Wrap RayCastInterpolateImageFunction
     ENH: Wrap RayCastInterpolateImageFunction
     COMP: Remove debug output after vcl_complex removal from wrapping
     ENH: Consolidate .idx file generation with swig .i generation.
     ENH: Update UpdatepygccxmlFromUpstream.sh script
     COMP: Set CastXML path and name for pygccxml 1.7.3
     COMP: Fix RayCastInterpolateImageFunction wrapping for image dim 2
     ENH: Use argparse instead of optparse in igenerator.py
     ENH: Use https URL for OS X castxml binary (for consistency)

Nick Tustison (2):
     ENH:  Add fixed/moving masking in reg. methods.
     ENH:  Making the mask usage consistent with ITK.

Pablo Hernandez-Cerdan (1):
     COMP: Fix warn in FFTW about delete [].

Sean McBride (18):
     COMP: Made script OS X compatible
     COMP: mark GDCM GetSeriesHelper() method as deprecated
     BUG: update script to fetch GDCM from its release-2-4 branch instead
of master
     DOC: Updated comment to reflect new GDCM version
     COMP: Fixed recently introduced build error with deprecated GDCM method
     BUG: Fixed invalid memory access found by ASan
     COMP: Fixed clang warning about macro expansion giving defined
     COMP: Fixed minor dashboards warnings and typos.
     COMP: Fixed a bunch of clang -Wunreachable-code-break warnings
     COMP: fixed some dashboard warnings (dead code, false positive)
     BUG: Fixed off-by-1 error found by ASan
     COMP: Fixed clang -Wcomma warning
     COMP: Introduce ITK_FALLTHROUGH, to suppress switch fall through
warnings
     COMP: Fixed -Wwritable-strings warnings
     COMP: Fixed remaining -Wcomma warnings
     ENH: switch gdcm to release branch, not release-2-4
     COMP: Hack HDF5 to build under ASan & UBSan
     COMP: fixed clang -Wdeprecated-writable-strings warning

Shawn Waldon (1):
     STYLE: move itkGaussianDerivativeOperator

Sujin Philip (1):
     STYLE: Move itkBox* Filters

Sumedha Singla (3):
     ENH: Issue: ITK#3363 Replaced assignment in SetParameters function.
     ENH: Remove unnecessary const_cast
     BUG: Fixed the test itkHDF5ImageIOTest

VXL Maintainers (9):
     VNL 2015-11-22 (ea1d60fb)
     VNL 2016-03-02 (cb31149e)
     VNL 2016-03-13 (ae34f0fc)
     VNL 2016-03-15 (751698ab)
     VNL 2016-03-19 (df10fefa)
     VNL 2016-03-25 (f0040231)
     VNL 2016-03-30 (88f50849)
     VNL 2016-04-22 (0ed18124)
     VNL 2016-04-26 (6b168535)

Vladimir S. FONOV (3):
     MINC 2015-12-17 (dcb93a5f)
     MINC 2016-01-30 (783bca38)
     MINC 2016-02-24 (8632513e)

Ziv Yaniv (1):
     BUG: Interpretation of the Euler angles ZYX or ZXY was not exported.



ITK Sphinx Examples Changelog

---------------------------------------------

D?enan Zuki? (1):
     ENH: Default is current directory. Avoid usage of the class
SeriesHelper.

Matt McCormick (19):
     BUG: Do not depend on the VTK/OpenCV build when system provided.
     ENH: Add ConvertAnitkImageTovtkImageData example.
     ENH: Bump VTK's superbuild version to 7.0.0.
     STYLE: CMake style updates to AddOffsetToIndex/CMakeLists.txt
     ENH: Updates to CreateNewExample.py.in
     ENH: Add ConvertvtkImageDataToAnitkImage example.
     ENH: Update sphinx-bootstrap-theme to v0.4.8
     ENH: Add Python version of StreamAPipeline.
     ENH: Add ConvertAnRGBitkImageTovtkImageData
     ENH: Add a PACE progress bar.
     ENH: Add more Python content to CreateNewExample.py.
     ENH: Add ConvertRGBvtkImageDataToAnitkImage
     BUG: Disable Create3DVolume Python baseline test.
     ENH: Add PerformRegistrationOnVectorImages.
     ENH: Update itk.org URL's for HTTPS support.
     COMP: Use itk::IndexValueType for subdomain index.
     COMP: Bump OpenCV to 3.1.0.
     BUG: Fix superbuild dependencies.
     ENH: Bump ITK to v4.10.0.


ITK Software Guide Changelog

---------------------------------------------

Matt McCormick (6):
     DOC: Correct spelling in the wrapping description.
     BUG: ExternalData servers now use https.
     ENH: Update itk.org URL's for HTTPS support.
     DOC: Adding wrapper .dll's to PATH on Windows is no longer necessary.
     DOC: Document how to add a third-party dependency to a module.
     ENH: Bump ITK ExternalProject to v4.10.0
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From ssult003 at odu.edu  Fri Jun  3 18:01:31 2016
From: ssult003 at odu.edu (Sharmin Sultana)
Date: Fri, 3 Jun 2016 18:01:31 -0400
Subject: [ITK-users] Estimation of initial rotation for Euler3DTransform
Message-ID: <CAKvbS=0aqGPMfyS5tkP=KjqEYZFqnaEryuasARa0MA9+ZC9=ow@mail.gmail.com>

Dear all,

I am trying to register two pointsets where each pointset represents a
curve. I have tried using the IterativeClosestPointRegistration2.cxx
example. But the problem with the results here is that while the
translation seems to be OK, the rotation is not when I do not set an
initial rotation.

According to the user guide, the Euler3DTranform cannot handle for large
rotations, and the user has to provide an initial rotation that is correct
to within 10 or 20 degrees. When I have provided the initial rotations, and
the resulting registered curve seems to be correct. I got the initial
rotations by manually rotating and translating the moving pointset in
Paraview against the fixed pointset using the Transform filter.

Is there a way to automatically estimate the initial rotation required?
Below are the pointsets that I was using.

Fixed PointSet
70.3771 16.9556 -77.8874
69.2143 17.2079 -77.253
68.1514 17.8068 -76.7957
66.9762 18.1519 -76.4658
65.8135 18.6132 -76.2163
64.67 19.0656 -75.7242
63.5119 19.2921 -75.3272
62.3751 19.597 -75.0951
61.2921 19.8394 -74.793
60.2845 20.1405 -74.4514
59.3191 20.3305 -74.1283
58.408 20.3767 -73.9007
57.5404 20.4277 -73.9293
56.8618 20.7408 -73.5224
55.4173 20.853 -72.9256
54.7285 20.8667 -72.693
53.6634 20.0938 -72.5906


Moving PointSet:
-1.158 -9.962 -7.944
-1.026 -9.224 -7.430
-0.883 -8.423 -6.872
-0.757 -7.646 -6.300
-0.640 -6.883 -5.727
-0.518 -6.120 -5.179
-0.406 -5.366 -4.622
-0.352 -4.661 -4.000
-0.291 -3.939 -3.394
-0.185 -3.181 -2.817
-0.042 -2.460 -2.183
0.074 -1.710 -1.531
0.174 -0.927 -0.853
0.296 -0.109 -0.120
0.459 0.737 0.693
0.640 1.647 1.657
0.861 2.763 2.808

Thanks and regards,


-- 
Sharmin Sultana
Old Dominion University
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From egolkar at siswa.ukm.edu.my  Fri Jun  3 22:20:49 2016
From: egolkar at siswa.ukm.edu.my (Favour)
Date: Fri, 3 Jun 2016 19:20:49 -0700 (MST)
Subject: [ITK-users] fatal error:
 'itkScalarChanAndVeseDenseLevelSetImageFilter.h' file not found
In-Reply-To: <1464707791419-37233.post@n7.nabble.com>
References: <1464707791419-37233.post@n7.nabble.com>
Message-ID: <1465006849394-37245.post@n7.nabble.com>

I found the mistake

During compiling ITK, the module_itkReview = ON should be done, in the help
it is just mentioned about vtkGlu module





--
View this message in context: http://itk-users.7.n7.nabble.com/fatal-error-itkScalarChanAndVeseDenseLevelSetImageFilter-h-file-not-found-tp37233p37245.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From tevain at telecom-paristech.fr  Mon Jun  6 05:23:07 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 6 Jun 2016 11:23:07 +0200 (CEST)
Subject: [ITK-users] [ITK] Estimation of initial rotation
	for	Euler3DTransform
In-Reply-To: <CAKvbS=0aqGPMfyS5tkP=KjqEYZFqnaEryuasARa0MA9+ZC9=ow@mail.gmail.com>
References: <CAKvbS=0aqGPMfyS5tkP=KjqEYZFqnaEryuasARa0MA9+ZC9=ow@mail.gmail.com>
Message-ID: <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr>

Hi Sharmin,

If your are able to know which point of dataset 1 correspond to each point of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point [70.3771 16.9556 -77.8874] after registration), then your problem is the one of Absolute Orientation. You could find the exact rotation solving this problem.
You could refer to the Horn method (http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the paper of Besl and McKay which introduce the ICP (http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf) to know how to do it. They are using quaternion for the rotation, but you could retrieve the rotation matrix from it, hence the euler angles (if you know the sequence of rotation, ITK's one is Z->Y->X if I remember correctly). Or you could go with the itkVersorRigid3DTransform.

If you're unable to know the correspondence, you could maybe do a PCA to find principal directions (at least 2) of each curve, take a point in each direction plus the centroid, and resolve the Absolute Orientation with them (you need at least 3 points). But I've never tried it.

HTH,

Tim

 

----- Mail original -----
De: "Sharmin Sultana" <ssult003 at odu.edu>
?: insight-users at itk.org
Envoy?: Samedi 4 Juin 2016 00:01:31
Objet: [ITK] [ITK-users] Estimation of initial rotation for	Euler3DTransform

Dear all, 

I am trying to register two pointsets where each pointset represents a curve. I have tried using the IterativeClosestPointRegistration2.cxx example. But the problem with the results here is that while the translation seems to be OK, the rotation is not when I do not set an initial rotation. 

According to the user guide, the Euler3DTranform cannot handle for large rotations, and the user has to provide an initial rotation that is correct to within 10 or 20 degrees. When I have provided the initial rotations, and the resulting registered curve seems to be correct. I got the initial rotations by manually rotating and translating the moving pointset in Paraview against the fixed pointset using the Transform filter. 

Is there a way to automatically estimate the initial rotation required? Below are the pointsets that I was using. 

Fixed PointSet 
70.3771 16.9556 -77.8874 
69.2143 17.2079 -77.253 
68.1514 17.8068 -76.7957 
66.9762 18.1519 -76.4658 
65.8135 18.6132 -76.2163 
64.67 19.0656 -75.7242 
63.5119 19.2921 -75.3272 
62.3751 19.597 -75.0951 
61.2921 19.8394 -74.793 
60.2845 20.1405 -74.4514 
59.3191 20.3305 -74.1283 
58.408 20.3767 -73.9007 
57.5404 20.4277 -73.9293 
56.8618 20.7408 -73.5224 
55.4173 20.853 -72.9256 
54.7285 20.8667 -72.693 
53.6634 20.0938 -72.5906 

Moving PointSet: 
-1.158 -9.962 -7.944 
-1.026 -9.224 -7.430 
-0.883 -8.423 -6.872 
-0.757 -7.646 -6.300 
-0.640 -6.883 -5.727 
-0.518 -6.120 -5.179 
-0.406 -5.366 -4.622 
-0.352 -4.661 -4.000 
-0.291 -3.939 -3.394 
-0.185 -3.181 -2.817 
-0.042 -2.460 -2.183 
0.074 -1.710 -1.531 
0.174 -0.927 -0.853 
0.296 -0.109 -0.120 
0.459 0.737 0.693 
0.640 1.647 1.657 
0.861 2.763 2.808 

Thanks and regards, 


-- 
Sharmin Sultana 
Old Dominion University 

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From scorpiuni at gmail.com  Mon Jun  6 11:34:51 2016
From: scorpiuni at gmail.com (Robert)
Date: Mon, 6 Jun 2016 08:34:51 -0700 (MST)
Subject: [ITK-users] Levelset not segmenting the shape
Message-ID: <1465227291962-7588954.post@n2.nabble.com>

Hello,
I am working on a semi automatic 3D segmentation using the Geodesic active
contour with shape guidance.
No crashes occur anymore, but something is not right yet, and I can't get
behind the error. Help would be much appreciated.
The following is my code:

https://www.dropbox.com/s/ot8gn0i38mh83ql/GeodesicActiveContourShapePriorLevelSetImageFilter.cxx?dl=0

I preprocess the input image etc, this all seems to work fine judging from
the output images from those filters. (line 194 - 201)
In line 203, I take the output from the underlying levelset (here,
fastmarching), and change the metadata (direction, origin, spacing) to the
one I get from my input image (line 206-209) in order to be even able to set
my levelset as input to the geodesic filter, and I set my feature image as
feature parameter(l 265&266).
I now set some smoothing and geodesic-filter parameters, those are mostly
taken from the example in 2D.
The user gives 3 seedpoints, which should be located inside the shape.
Line 465 is the beginning of the "shape guidance" part.
Here I set my number of PCA images, my mean image, read them, change their
metadata as well, so that in the end, all involved images have the same
origin etc.  (l 468 - 543).  I now set those images as parameters to my
PCAShapeSignedDistanceFunction. 
I now initialize a 3D Euler transform (l 554), a cost function (l 565) and
an optimizer (l.610).
Finally, I give my shape as parameter to the geodesic filter ( l.669).
This should all be correct, right? all the changes in the metadata make
sense as soon as you see the datasets in 3D, they now all occupy exactely
the same space(see imgur pictures). 
However, the result I get is the following:

http://imgur.com/a/aKRuV
Middle picture is the "out" file alone, first and last pic is a 3d render
from the output, and showing the mean image of the structure I want to find
as well as the preprocessed, actual input image.
It seems like my program does not take into account any shape guidance at
all, and it just creates 3 "blobs" originating from my seeds...
Please take the time to have a look at my stuff, I really can't get behind
the mistake I made....
If you'd like to test it for your own, here are some sample pictures (the
ones I used) as well as the command I used to execute the program:
https://www.dropbox.com/sh/j2ognv5y5zv61wu/AABOAn-w4PIlYAq-WSW_lPOMa?dl=0
with
./GeodesicActiveContourShapePriorLevelSetImageFilter CochleaCropped.nrrd
out.nrrd 33 26 14 32 29 13 25 32 12 3 0.6 0.5 0.02 meanImage.nrrd 3
pcImage*.nrrd 10 10 10
Thanks,
Robert



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From scorpiuni at gmail.com  Mon Jun  6 12:30:41 2016
From: scorpiuni at gmail.com (Robert)
Date: Mon, 6 Jun 2016 09:30:41 -0700 (MST)
Subject: [ITK-users] Levelset not segmenting the shape
In-Reply-To: <1465227291962-7588954.post@n2.nabble.com>
References: <1465227291962-7588954.post@n2.nabble.com>
Message-ID: <1465230641527-7588955.post@n2.nabble.com>

What I forgot to mention is:
I played around a while with different sigma values, as well as setting both
propagationScaling and shapePriorScaling terms to 1.0, as well as adjusting
the RMS.
You now can kind of see that the result looks shaped like the cochlea (the
object I want to find), but it is rotated in a weird way, if I use the
actual CT data as backdrop, it does not match. (Rotation-wise).
Also, it still looks kind of "clumpy", I know that the preprocessed images
are low quality, but that's a constraint to deal with, as there is no
micro-CT available. Any tips to enhance this  code errors I can
remove/change?



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From dzenanz at gmail.com  Wed Jun  8 02:50:08 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 8 Jun 2016 08:50:08 +0200
Subject: [ITK-users] MutualInformationAffine example broken
In-Reply-To: <CACNiyLA4ao+rpVwC3bmFQqP_SC-ihnmF6G5SRQsgtfjYAxhd1A@mail.gmail.com>
References: <CACNiyLA4ao+rpVwC3bmFQqP_SC-ihnmF6G5SRQsgtfjYAxhd1A@mail.gmail.com>
Message-ID: <CAPf2UMQfyrJtnt3KfD7JqMrjvCTkLtR=FdJEsyH8yVasfm7eUA@mail.gmail.com>

Hi Yanling,

The usual reason for this is that the images do not overlap in image space,
either with the initial transformation or due to divergence of the
registration. If you run it in debug mode, you will have more information.

Regards,
D?enan
On Jun 1, 2016 14:27, "Yanling Liu" <vrnova at gmail.com> wrote:

> Hello,
>
> I downloaded the MutualInformationAffine example from
> https://itk.org/Wiki/ITK/Examples/Registration/MutualInformationAffine,
> compiled it using ITK 4.9.1 and it reported follow error message:
>
> ExceptionObject caught !
>
> itk::ExceptionObject (0x2030010)
> Location: "void itk::MutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::SampleFixedImageDomain(itk::MutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::SpatialSampleContainer&) const [with TFixedImage =
> itk::Image<float, 2u>; TMovingImage = itk::Image<float, 2u>;
> itk::MutualInformationImageToImageMetric<TFixedImage,
> TMovingImage>::SpatialSampleContainer =
> std::vector<itk::MutualInformationImageToImageMetric<itk::Image<float, 2u>,
> itk::Image<float, 2u> >::SpatialSample,
> std::allocator<itk::MutualInformationImageToImageMetric<itk::Image<float,
> 2u>, itk::Image<float, 2u> >::SpatialSample> >]"
> File:
> /home/yliu/Imaging/Libraries/ITK/InsightToolkit-4.9.1/install/include/ITK-4.9/itkMutualInformationImageToImageMetric.hxx
> Line: 196
> Description: itk::ERROR: MutualInformationImageToImageMetric(0x202fd10):
> All the sampled point mapped to outside of the moving image
>
> Anyone may help to fix this example? I did not change the source code of
> the example at all.
>
> Thanks,
>
> Yanling
>
> _____________________________________
> 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
>
>
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From ssult003 at odu.edu  Wed Jun  8 13:57:51 2016
From: ssult003 at odu.edu (Sharmin Sultana)
Date: Wed, 8 Jun 2016 13:57:51 -0400
Subject: [ITK-users] [ITK] Estimation of initial rotation for
	Euler3DTransform
In-Reply-To: <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr>
References: <CAKvbS=0aqGPMfyS5tkP=KjqEYZFqnaEryuasARa0MA9+ZC9=ow@mail.gmail.com>
 <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr>
Message-ID: <CAKvbS=1dcjiy6v0tO2B6u-2-GY_GgWE5EtTYv+SBKxNd52QEbw@mail.gmail.com>

Hi Tim
Thanks for your reply.
I have somewhat solve the pointset registration problem using
itkVersorRigid3DTransform.
Now the rotation is working fine after applying itk::TransformMeshFilter to
the initial mesh.

But I'm still unable to register those pointset using itk::AffineTransform. I
need to scale the initial mesh. Isn't it possible to apply affine transform
to a pointset or mesh ?

Thanks and Regards.
Sharmin

On Mon, Jun 6, 2016 at 5:23 AM, Timothee Evain <tevain at telecom-paristech.fr>
wrote:

> Hi Sharmin,
>
> If your are able to know which point of dataset 1 correspond to each point
> of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point
> [70.3771 16.9556 -77.8874] after registration), then your problem is the
> one of Absolute Orientation. You could find the exact rotation solving this
> problem.
> You could refer to the Horn method (
> http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the
> paper of Besl and McKay which introduce the ICP (
> http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf)
> to know how to do it. They are using quaternion for the rotation, but you
> could retrieve the rotation matrix from it, hence the euler angles (if you
> know the sequence of rotation, ITK's one is Z->Y->X if I remember
> correctly). Or you could go with the itkVersorRigid3DTransform.
>
> If you're unable to know the correspondence, you could maybe do a PCA to
> find principal directions (at least 2) of each curve, take a point in each
> direction plus the centroid, and resolve the Absolute Orientation with them
> (you need at least 3 points). But I've never tried it.
>
> HTH,
>
> Tim
>
>
>
> ----- Mail original -----
> De: "Sharmin Sultana" <ssult003 at odu.edu>
> ?: insight-users at itk.org
> Envoy?: Samedi 4 Juin 2016 00:01:31
> Objet: [ITK] [ITK-users] Estimation of initial rotation for
>  Euler3DTransform
>
> Dear all,
>
> I am trying to register two pointsets where each pointset represents a
> curve. I have tried using the IterativeClosestPointRegistration2.cxx
> example. But the problem with the results here is that while the
> translation seems to be OK, the rotation is not when I do not set an
> initial rotation.
>
> According to the user guide, the Euler3DTranform cannot handle for large
> rotations, and the user has to provide an initial rotation that is correct
> to within 10 or 20 degrees. When I have provided the initial rotations, and
> the resulting registered curve seems to be correct. I got the initial
> rotations by manually rotating and translating the moving pointset in
> Paraview against the fixed pointset using the Transform filter.
>
> Is there a way to automatically estimate the initial rotation required?
> Below are the pointsets that I was using.
>
> Fixed PointSet
> 70.3771 16.9556 -77.8874
> 69.2143 17.2079 -77.253
> 68.1514 17.8068 -76.7957
> 66.9762 18.1519 -76.4658
> 65.8135 18.6132 -76.2163
> 64.67 19.0656 -75.7242
> 63.5119 19.2921 -75.3272
> 62.3751 19.597 -75.0951
> 61.2921 19.8394 -74.793
> 60.2845 20.1405 -74.4514
> 59.3191 20.3305 -74.1283
> 58.408 20.3767 -73.9007
> 57.5404 20.4277 -73.9293
> 56.8618 20.7408 -73.5224
> 55.4173 20.853 -72.9256
> 54.7285 20.8667 -72.693
> 53.6634 20.0938 -72.5906
>
> Moving PointSet:
> -1.158 -9.962 -7.944
> -1.026 -9.224 -7.430
> -0.883 -8.423 -6.872
> -0.757 -7.646 -6.300
> -0.640 -6.883 -5.727
> -0.518 -6.120 -5.179
> -0.406 -5.366 -4.622
> -0.352 -4.661 -4.000
> -0.291 -3.939 -3.394
> -0.185 -3.181 -2.817
> -0.042 -2.460 -2.183
> 0.074 -1.710 -1.531
> 0.174 -0.927 -0.853
> 0.296 -0.109 -0.120
> 0.459 0.737 0.693
> 0.640 1.647 1.657
> 0.861 2.763 2.808
>
> Thanks and regards,
>
>
> --
> Sharmin Sultana
> Old Dominion University
>
> _____________________________________
> 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
>



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From dzenanz at gmail.com  Thu Jun  9 03:29:55 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 9 Jun 2016 09:29:55 +0200
Subject: [ITK-users] fatal error:
 'itkScalarChanAndVeseDenseLevelSetImageFilter.h' file not found
In-Reply-To: <1465006849394-37245.post@n7.nabble.com>
References: <1464707791419-37233.post@n7.nabble.com>
 <1465006849394-37245.post@n7.nabble.com>
Message-ID: <CAPf2UMS9MtK-tHY4r5QTCf6ATFOgPT0e_yLh2aEkMaryKeHEbw@mail.gmail.com>

Hi Favour,

looking at the up-to-date documentation
<https://itk.org/Doxygen/html/classitk_1_1ScalarChanAndVeseDenseLevelSetImageFilter.html>,
it is clearly visible that this class belongs to Review module, and there
is no mention of VTKGlue. Which documentation were you looking at?

Regards,
D?enan

On Sat, Jun 4, 2016 at 4:20 AM, Favour <egolkar at siswa.ukm.edu.my> wrote:

> I found the mistake
>
> During compiling ITK, the module_itkReview = ON should be done, in the help
> it is just mentioned about vtkGlu module
>
>
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/fatal-error-itkScalarChanAndVeseDenseLevelSetImageFilter-h-file-not-found-tp37233p37245.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
>
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From tevain at telecom-paristech.fr  Thu Jun  9 03:36:48 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Thu, 9 Jun 2016 09:36:48 +0200 (CEST)
Subject: [ITK-users] [ITK] Estimation of initial rotation for
 Euler3DTransform
In-Reply-To: <CAKvbS=1dcjiy6v0tO2B6u-2-GY_GgWE5EtTYv+SBKxNd52QEbw@mail.gmail.com>
References: <CAKvbS=0aqGPMfyS5tkP=KjqEYZFqnaEryuasARa0MA9+ZC9=ow@mail.gmail.com>
 <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr>
 <CAKvbS=1dcjiy6v0tO2B6u-2-GY_GgWE5EtTYv+SBKxNd52QEbw@mail.gmail.com>
Message-ID: <30125847.81064973.1465457808716.JavaMail.zimbra@enst.fr>

If you're able to register with the itkVersorRigid3DTransform and you need scale, just use the itkSimilarity3DTransform, which is an isotropic scaling followed by the VersorRigid3Transform.

HTH,

Tim

----- Mail original -----
De: "Sharmin Sultana" <ssult003 at odu.edu>
?: "Timothee Evain" <tevain at telecom-paristech.fr>
Cc: insight-users at itk.org
Envoy?: Mercredi 8 Juin 2016 19:57:51
Objet: Re: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform

Hi Tim
Thanks for your reply.
I have somewhat solve the pointset registration problem using
itkVersorRigid3DTransform.
Now the rotation is working fine after applying itk::TransformMeshFilter to
the initial mesh.

But I'm still unable to register those pointset using itk::AffineTransform. I
need to scale the initial mesh. Isn't it possible to apply affine transform
to a pointset or mesh ?

Thanks and Regards.
Sharmin

On Mon, Jun 6, 2016 at 5:23 AM, Timothee Evain <tevain at telecom-paristech.fr>
wrote:

> Hi Sharmin,
>
> If your are able to know which point of dataset 1 correspond to each point
> of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point
> [70.3771 16.9556 -77.8874] after registration), then your problem is the
> one of Absolute Orientation. You could find the exact rotation solving this
> problem.
> You could refer to the Horn method (
> http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the
> paper of Besl and McKay which introduce the ICP (
> http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf)
> to know how to do it. They are using quaternion for the rotation, but you
> could retrieve the rotation matrix from it, hence the euler angles (if you
> know the sequence of rotation, ITK's one is Z->Y->X if I remember
> correctly). Or you could go with the itkVersorRigid3DTransform.
>
> If you're unable to know the correspondence, you could maybe do a PCA to
> find principal directions (at least 2) of each curve, take a point in each
> direction plus the centroid, and resolve the Absolute Orientation with them
> (you need at least 3 points). But I've never tried it.
>
> HTH,
>
> Tim
>
>
>
> ----- Mail original -----
> De: "Sharmin Sultana" <ssult003 at odu.edu>
> ?: insight-users at itk.org
> Envoy?: Samedi 4 Juin 2016 00:01:31
> Objet: [ITK] [ITK-users] Estimation of initial rotation for
>  Euler3DTransform
>
> Dear all,
>
> I am trying to register two pointsets where each pointset represents a
> curve. I have tried using the IterativeClosestPointRegistration2.cxx
> example. But the problem with the results here is that while the
> translation seems to be OK, the rotation is not when I do not set an
> initial rotation.
>
> According to the user guide, the Euler3DTranform cannot handle for large
> rotations, and the user has to provide an initial rotation that is correct
> to within 10 or 20 degrees. When I have provided the initial rotations, and
> the resulting registered curve seems to be correct. I got the initial
> rotations by manually rotating and translating the moving pointset in
> Paraview against the fixed pointset using the Transform filter.
>
> Is there a way to automatically estimate the initial rotation required?
> Below are the pointsets that I was using.
>
> Fixed PointSet
> 70.3771 16.9556 -77.8874
> 69.2143 17.2079 -77.253
> 68.1514 17.8068 -76.7957
> 66.9762 18.1519 -76.4658
> 65.8135 18.6132 -76.2163
> 64.67 19.0656 -75.7242
> 63.5119 19.2921 -75.3272
> 62.3751 19.597 -75.0951
> 61.2921 19.8394 -74.793
> 60.2845 20.1405 -74.4514
> 59.3191 20.3305 -74.1283
> 58.408 20.3767 -73.9007
> 57.5404 20.4277 -73.9293
> 56.8618 20.7408 -73.5224
> 55.4173 20.853 -72.9256
> 54.7285 20.8667 -72.693
> 53.6634 20.0938 -72.5906
>
> Moving PointSet:
> -1.158 -9.962 -7.944
> -1.026 -9.224 -7.430
> -0.883 -8.423 -6.872
> -0.757 -7.646 -6.300
> -0.640 -6.883 -5.727
> -0.518 -6.120 -5.179
> -0.406 -5.366 -4.622
> -0.352 -4.661 -4.000
> -0.291 -3.939 -3.394
> -0.185 -3.181 -2.817
> -0.042 -2.460 -2.183
> 0.074 -1.710 -1.531
> 0.174 -0.927 -0.853
> 0.296 -0.109 -0.120
> 0.459 0.737 0.693
> 0.640 1.647 1.657
> 0.861 2.763 2.808
>
> Thanks and regards,
>
>
> --
> Sharmin Sultana
> Old Dominion University
>
> _____________________________________
> 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 tevain at telecom-paristech.fr  Thu Jun  9 03:44:48 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Thu, 9 Jun 2016 09:44:48 +0200 (CEST)
Subject: [ITK-users] [ITK] Estimation of initial rotation for
 Euler3DTransform
In-Reply-To: <CAKvbS=1dcjiy6v0tO2B6u-2-GY_GgWE5EtTYv+SBKxNd52QEbw@mail.gmail.com>
References: <CAKvbS=0aqGPMfyS5tkP=KjqEYZFqnaEryuasARa0MA9+ZC9=ow@mail.gmail.com>
 <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr>
 <CAKvbS=1dcjiy6v0tO2B6u-2-GY_GgWE5EtTYv+SBKxNd52QEbw@mail.gmail.com>
Message-ID: <1772589326.81073485.1465458288560.JavaMail.zimbra@enst.fr>

By the way, I don't know how you're doing your registration, but rather than using meshes, you could go with the itkPointSetToPointSetRegistrationMethod, which seems to be the best fit for your data.

Tim

----- Mail original -----
De: "Sharmin Sultana" <ssult003 at odu.edu>
?: "Timothee Evain" <tevain at telecom-paristech.fr>
Cc: insight-users at itk.org
Envoy?: Mercredi 8 Juin 2016 19:57:51
Objet: Re: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform

Hi Tim
Thanks for your reply.
I have somewhat solve the pointset registration problem using
itkVersorRigid3DTransform.
Now the rotation is working fine after applying itk::TransformMeshFilter to
the initial mesh.

But I'm still unable to register those pointset using itk::AffineTransform. I
need to scale the initial mesh. Isn't it possible to apply affine transform
to a pointset or mesh ?

Thanks and Regards.
Sharmin

On Mon, Jun 6, 2016 at 5:23 AM, Timothee Evain <tevain at telecom-paristech.fr>
wrote:

> Hi Sharmin,
>
> If your are able to know which point of dataset 1 correspond to each point
> of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point
> [70.3771 16.9556 -77.8874] after registration), then your problem is the
> one of Absolute Orientation. You could find the exact rotation solving this
> problem.
> You could refer to the Horn method (
> http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the
> paper of Besl and McKay which introduce the ICP (
> http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf)
> to know how to do it. They are using quaternion for the rotation, but you
> could retrieve the rotation matrix from it, hence the euler angles (if you
> know the sequence of rotation, ITK's one is Z->Y->X if I remember
> correctly). Or you could go with the itkVersorRigid3DTransform.
>
> If you're unable to know the correspondence, you could maybe do a PCA to
> find principal directions (at least 2) of each curve, take a point in each
> direction plus the centroid, and resolve the Absolute Orientation with them
> (you need at least 3 points). But I've never tried it.
>
> HTH,
>
> Tim
>
>
>
> ----- Mail original -----
> De: "Sharmin Sultana" <ssult003 at odu.edu>
> ?: insight-users at itk.org
> Envoy?: Samedi 4 Juin 2016 00:01:31
> Objet: [ITK] [ITK-users] Estimation of initial rotation for
>  Euler3DTransform
>
> Dear all,
>
> I am trying to register two pointsets where each pointset represents a
> curve. I have tried using the IterativeClosestPointRegistration2.cxx
> example. But the problem with the results here is that while the
> translation seems to be OK, the rotation is not when I do not set an
> initial rotation.
>
> According to the user guide, the Euler3DTranform cannot handle for large
> rotations, and the user has to provide an initial rotation that is correct
> to within 10 or 20 degrees. When I have provided the initial rotations, and
> the resulting registered curve seems to be correct. I got the initial
> rotations by manually rotating and translating the moving pointset in
> Paraview against the fixed pointset using the Transform filter.
>
> Is there a way to automatically estimate the initial rotation required?
> Below are the pointsets that I was using.
>
> Fixed PointSet
> 70.3771 16.9556 -77.8874
> 69.2143 17.2079 -77.253
> 68.1514 17.8068 -76.7957
> 66.9762 18.1519 -76.4658
> 65.8135 18.6132 -76.2163
> 64.67 19.0656 -75.7242
> 63.5119 19.2921 -75.3272
> 62.3751 19.597 -75.0951
> 61.2921 19.8394 -74.793
> 60.2845 20.1405 -74.4514
> 59.3191 20.3305 -74.1283
> 58.408 20.3767 -73.9007
> 57.5404 20.4277 -73.9293
> 56.8618 20.7408 -73.5224
> 55.4173 20.853 -72.9256
> 54.7285 20.8667 -72.693
> 53.6634 20.0938 -72.5906
>
> Moving PointSet:
> -1.158 -9.962 -7.944
> -1.026 -9.224 -7.430
> -0.883 -8.423 -6.872
> -0.757 -7.646 -6.300
> -0.640 -6.883 -5.727
> -0.518 -6.120 -5.179
> -0.406 -5.366 -4.622
> -0.352 -4.661 -4.000
> -0.291 -3.939 -3.394
> -0.185 -3.181 -2.817
> -0.042 -2.460 -2.183
> 0.074 -1.710 -1.531
> 0.174 -0.927 -0.853
> 0.296 -0.109 -0.120
> 0.459 0.737 0.693
> 0.640 1.647 1.657
> 0.861 2.763 2.808
>
> Thanks and regards,
>
>
> --
> Sharmin Sultana
> Old Dominion University
>
> _____________________________________
> 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 christopherrmullins at gmail.com  Thu Jun  9 10:14:42 2016
From: christopherrmullins at gmail.com (Christopher Mullins)
Date: Thu, 9 Jun 2016 10:14:42 -0400
Subject: [ITK-users] Build errors in python wrapping of 4.10.0
Message-ID: <CAL1JtzBgoYx3k7xn_pff9s5M9AGLFuKE0ZQJb4Wen0BkAHkzNA@mail.gmail.com>

Hi all,

Apparently my subscription to this list has lapsed and my first email was
rejected (despite receiving the list in my inbox every day).  Sorry if
there's a double post.

I'm getting the following build errors when building ITK 4.10.0 with the
WRAP_PYTHON option ON[1], [3].  Is this a known issue, or is there a
configuration setting I've set improperly?

Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There are
no warnings. See all output details for this machine here [2], and please
let me know if I can provide any others.

The faster I fix this the faster I'll feel comfortable updating the Arch
linux AUR PKGBUILD for ITK, so I appreciate any help you can offer.

Thanks,
Chris



[1] https://open.cdash.org/viewBuildError.php?buildid=4403379
[2] https://open.cdash.org/buildSummary.php?buildid=4403379

[3] To save you a click, and for the sake of archiving, the error is:
/home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:
In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*,
PyObject*)':
/home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65:
error: no matching function for call to
'itk::TriangleHelper<itk::Point<double, 2u> >::TriangleHelper()' result =
(itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
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From marco.giord at gmail.com  Thu Jun  9 10:45:30 2016
From: marco.giord at gmail.com (marco giordano)
Date: Thu, 9 Jun 2016 16:45:30 +0200
Subject: [ITK-users] Read 4D CT cardiac dicom series and save it as a single
 4D nifti file
Message-ID: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>

Hi there,

I need to import a 4D Siemens cardiac CT dataset (3D+ t) from Dicom into
nifti format (or any other format).

The dicom comes as a collection of 2D slices. The 2D slices belonging to
the same volume have the same acquisition time.

I can read the volumes by using the Content Time ("0008|0033") as a
restriction (similarly as in DicomSeriesReadImageWrite2.cxx) but then I do
not understand how I can write the volumes in a single 4D nifti file.

I tried with the VectorImage but it needs the dimension to be specified in
advance which I do not know.

Any help is appreciated.

Regards,


-- 
Marco
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From varasteh at to.infn.it  Thu Jun  9 11:06:26 2016
From: varasteh at to.infn.it (Mohammad Varasteh)
Date: Thu, 9 Jun 2016 08:06:26 -0700 (MST)
Subject: [ITK-users] Read 4D CT cardiac dicom series and save it as a
 single 4D nifti file
In-Reply-To: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>
References: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>
Message-ID: <1465484786789-7588963.post@n2.nabble.com>

Dear Marco,

Actually I do not know how to do it in the ITK but for such cases (if it is
few cases) I normally use "VV: the 4D slicer". You can find it in the
following link:

http://www.creatis.insa-lyon.fr/rio/vv

I hope this will be of some use.

Varasteh



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From scapegoat.sarthak at gmail.com  Thu Jun  9 11:21:18 2016
From: scapegoat.sarthak at gmail.com (Scapegoat Sarthak)
Date: Thu, 9 Jun 2016 11:21:18 -0400
Subject: [ITK-users] Read 4D CT cardiac dicom series and save it as a
 single 4D nifti file
In-Reply-To: <1465484786789-7588963.post@n2.nabble.com>
References: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>
 <1465484786789-7588963.post@n2.nabble.com>
Message-ID: <CANbSmSchv53_pzo3ioB4yrn-Shp=_-UOBBfy0in31XBp54+uDw@mail.gmail.com>

You can do it pretty easily:

Read DICOM using SeriesFileReader and then connect output to a FileWriter
with the file name of your choice (in this case, it would be
"output.nii.gz").

On 9 June 2016 at 11:06, Mohammad Varasteh <varasteh at to.infn.it> wrote:

> Dear Marco,
>
> Actually I do not know how to do it in the ITK but for such cases (if it is
> few cases) I normally use "VV: the 4D slicer". You can find it in the
> following link:
>
> http://www.creatis.insa-lyon.fr/rio/vv
>
> I hope this will be of some use.
>
> Varasteh
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.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
>
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From coyarzunlaura at googlemail.com  Fri Jun 10 05:22:00 2016
From: coyarzunlaura at googlemail.com (Cristina Oyarzun)
Date: Fri, 10 Jun 2016 11:22:00 +0200
Subject: [ITK-users] MICCAI CLIP 2016: DEADLINE EXTENDED!
Message-ID: <CANuPjs20qcVP3rTou3sVqosDhA7Yo+jiEjAtPmtPcmwnWOi0-g@mail.gmail.com>

CALL FOR PAPERS
MICCAI 2016 Workshop on
Clinical Image-based Procedures: Translational Research in Medical Imaging


October 17, 2016
Athens, Greece

Website:http://miccai-clip.org/
==============================
==========================================

SCOPE

 The outstanding proliferation of medical image applications has created a
need for greater study and scrutiny of the clinical application and
validation of such methods. New strategies are essential to ensure a smooth
and effective translation of computational image-based techniques into the
clinic. For these reasons CLIP 2015?s major focus is on translational
research filling the gaps between basic science and clinical applications.
A highlight of the workshop is the subject of strategies for personalized
medicine to enhance diagnosis, treatment and interventions. Authors are
encouraged to submit work centered on specific clinical applications,
including techniques and procedures based on comprehensive clinical image
data. Submissions related to applications already in use and evaluated by
clinical users are particularly encouraged. The event will bring together
world-class specialists to present ways to strengthen links between
computer scientists and engineers, and clinicians.


TOPICS

*Strategies for patient-specific and anatomical modeling to support
planning and interventions

*Clinical studies employing advanced image-guided methods

*Clinical translation and validation of image-guided systems

*Current challenges and emerging techniques in image-based procedures

*Identification of parameters and error analysis in image-based procedures

*Multimodal image integration for modeling, planning and guidance

*Clinical applications in open and minimally invasive procedures




PAPER SUBMISSION

Papers will be limited to eight pages following the MICCAI submission
guidelines. Prospective authors should refer to the Paper Submission
section on the workshop website for details on how to submit papers to be
presented at the workshop.
All submissions will be peer-reviewed by at least 2 members of the program
committee. The selection of the papers will be based on the significance of
results, novelty, technical merit, relevance and clarity of presentation.
Papers will be presented in a day long single track workshop starting with
plenary sessions.
Accepted papers will be published as a proceedings volume in the Springer
Lecture Notes in Computer Science (LNCS) series after the workshop.

WORKSHOP FORMAT

Accepted papers will be presented in a day long single track workshop. The
final program will consist of invited speakers and original papers with
time allocated for discussions. Electronic proceedings will be arranged for
all of the papers presented at the workshop.

IMPORTANT DATES

* June 17, 2016: Paper submission due date
* July 10, 2016: Notification of acceptance
* July 17, 2016: Final camera-ready paper submission deadline

CONTACT

Inquires about the workshop should be sent to the Information Desk (
info at miccai-clip.org).

ORGANIZERS (in alphabetical order)

Klaus Drechsler (Fraunhofer IGD, Germany)
Marius Erdt (Fraunhofer IDM at NTU, Singapore)
Miguel Gonz?lez Ballester (ICREA - Universitat Pompeu Fabra, Spain)
Marius George Linguraru (Children's National Medical Center, USA)
Cristina Oyarzun Laura (Fraunhofer IGD, Germany)
Yoshinobu Sato (Nara Institute of Science and Technology, Japan)
Raj Shekhar (Children's National Medical Center, USA)
Stefan Wesarg (Fraunhofer IGD, Germany)

========================================================================
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From marco.giord at gmail.com  Fri Jun 10 17:31:36 2016
From: marco.giord at gmail.com (marco giordano)
Date: Fri, 10 Jun 2016 23:31:36 +0200
Subject: [ITK-users] Read 4D CT cardiac dicom series and save it as a
 single 4D nifti file
In-Reply-To: <CANbSmSchv53_pzo3ioB4yrn-Shp=_-UOBBfy0in31XBp54+uDw@mail.gmail.com>
References: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>
 <1465484786789-7588963.post@n2.nabble.com>
 <CANbSmSchv53_pzo3ioB4yrn-Shp=_-UOBBfy0in31XBp54+uDw@mail.gmail.com>
Message-ID: <CAF3iUbL6ESHd+j4hWn_HNuuc6aP9XB0LQh7Ub03h=ufvvmJc5w@mail.gmail.com>

Hi there,

Thanks for the suggestions. VV is not really an option since I have to
analyze many cases. I even tried to use VV but it gives me the wrong order
of the slices.

I am trying the  "itk::ImageSeriesReader" (right?) but it is complaining
that "Position is not unique".  I think it refers to the fact that the
slices in my "series" have the "same location". Not sure this is meant to
transform 2D into 4D if it expects different locations, maybe it is for 2D
into 3D. Any idea?

Regards

2016-06-09 17:21 GMT+02:00 Scapegoat Sarthak <scapegoat.sarthak at gmail.com>:

> You can do it pretty easily:
>
> Read DICOM using SeriesFileReader and then connect output to a FileWriter
> with the file name of your choice (in this case, it would be
> "output.nii.gz").
>
>
> On 9 June 2016 at 11:06, Mohammad Varasteh <varasteh at to.infn.it> wrote:
>
>> Dear Marco,
>>
>> Actually I do not know how to do it in the ITK but for such cases (if it
>> is
>> few cases) I normally use "VV: the 4D slicer". You can find it in the
>> following link:
>>
>> http://www.creatis.insa-lyon.fr/rio/vv
>>
>> I hope this will be of some use.
>>
>> Varasteh
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>


-- 
Marco Giordano
SKYPE:marcogiord81
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From lasso at queensu.ca  Sat Jun 11 00:25:23 2016
From: lasso at queensu.ca (Andras Lasso)
Date: Sat, 11 Jun 2016 04:25:23 +0000
Subject: [ITK-users] [ITK] Read 4D CT cardiac dicom series and save it
 as a single 4D nifti file
In-Reply-To: <CAF3iUbL6ESHd+j4hWn_HNuuc6aP9XB0LQh7Ub03h=ufvvmJc5w@mail.gmail.com>
References: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>
 <1465484786789-7588963.post@n2.nabble.com>
 <CANbSmSchv53_pzo3ioB4yrn-Shp=_-UOBBfy0in31XBp54+uDw@mail.gmail.com>,
 <CAF3iUbL6ESHd+j4hWn_HNuuc6aP9XB0LQh7Ub03h=ufvvmJc5w@mail.gmail.com>
Message-ID: <DM2PR07MB350E83D9D05861C13533DF0D8510@DM2PR07MB350.namprd07.prod.outlook.com>

3D Slicer can load some 4D CTs a 3D+t sequence and you cab save it as a 4D nrrd. You may give it a try. If it doesn't work for your sequence then report the problem on the slicer-users mailing list. If you can provide a sample data set then slicer developers most likely will be able to make it work.

Andras

From: marco giordano<mailto:marco.giord at gmail.com>
Sent: June 10, 2016 17:32
To: Scapegoat Sarthak<mailto:scapegoat.sarthak at gmail.com>
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file

Hi there,

Thanks for the suggestions. VV is not really an option since I have to analyze many cases. I even tried to use VV but it gives me the wrong order of the slices.

I am trying the  "itk::ImageSeriesReader" (right?) but it is complaining that "Position is not unique".  I think it refers to the fact that the slices in my "series" have the "same location". Not sure this is meant to transform 2D into 4D if it expects different locations, maybe it is for 2D into 3D. Any idea?

Regards

2016-06-09 17:21 GMT+02:00 Scapegoat Sarthak <scapegoat.sarthak at gmail.com<mailto:scapegoat.sarthak at gmail.com>>:
You can do it pretty easily:

Read DICOM using SeriesFileReader and then connect output to a FileWriter with the file name of your choice (in this case, it would be "output.nii.gz").


On 9 June 2016 at 11:06, Mohammad Varasteh <varasteh at to.infn.it<mailto:varasteh at to.infn.it>> wrote:
Dear Marco,

Actually I do not know how to do it in the ITK but for such cases (if it is
few cases) I normally use "VV: the 4D slicer". You can find it in the
following link:

http://www.creatis.insa-lyon.fr/rio/vv

I hope this will be of some use.

Varasteh



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
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


_____________________________________
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




--
Marco Giordano
SKYPE:marcogiord81
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From zhuangming.shen at sphic.org.cn  Sun Jun 12 01:33:13 2016
From: zhuangming.shen at sphic.org.cn (=?utf-8?B?5rKI5bqE5piO?=)
Date: Sun, 12 Jun 2016 05:33:13 +0000
Subject: [ITK-users] Issue on itk.QuadEdgeMeshCellTraitsInfo
Message-ID: <1465709590989.57546@sphic.org.cn>

?Hi all,


When I used python-supported ITK 4.10.0 to get the types of itk.QuadEdgeMeshCellTraitsInfo for the first time, I got two warnings


Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
<itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
Options:


If I run itk.QuadEdgeMeshCellTraitsInfo.GetTypes() again or use ITK 4.9.1 instead, it just displays

<itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
Options:


So what's the problem? What is the unknown parameter? Has someone met this issue? Thanks.


Regards,

Zhuangming Shen







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From y.borokh at gmail.com  Wed Jun 15 06:00:14 2016
From: y.borokh at gmail.com (Yurii Borokh)
Date: Wed, 15 Jun 2016 03:00:14 -0700 (MST)
Subject: [ITK-users] Fast image creation from a signed distance function
Message-ID: <1465984814443-7588969.post@n2.nabble.com>

Hi all,I'm searching for a filter that could effectively create an image from
a signed distance function.Of course, it can be done straightforwardly by
calculation of distance in each pixel. But I would like to minimize the
number of calls to distance function since it's implemented via RBF and
calls are rather expensive. Does ITK has some kind of such functionality?Any
hints would be appreciated.Regards,Yurii



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Fast-image-creation-from-a-signed-distance-function-tp7588969.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From michkapopoff at gmail.com  Wed Jun 15 17:12:06 2016
From: michkapopoff at gmail.com (Michka Popoff)
Date: Wed, 15 Jun 2016 23:12:06 +0200
Subject: [ITK-users] Build errors in python wrapping of 4.10.0
In-Reply-To: <CAL1JtzBgoYx3k7xn_pff9s5M9AGLFuKE0ZQJb4Wen0BkAHkzNA@mail.gmail.com>
References: <CAL1JtzBgoYx3k7xn_pff9s5M9AGLFuKE0ZQJb4Wen0BkAHkzNA@mail.gmail.com>
Message-ID: <D452B2C7-BD65-426B-BC46-A10C642DB70A@gmail.com>

Hi

I think this bug is not known. I had a look and could reproduce it with gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X.
GCC 6 is using c++14 by default, but even with c++11 you would probably get the problem.
The problem is also there with the latest commit from the master branch.

Please note that we probably never tested Python Wrappings with c++11, even not speaking of c++14.

The problem seems to have appeared with this patch:
https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395

I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy constructor, and was able to compile
with gcc 6. But it may just a side effect of that patch which is now only appearing with c++ >= 11.
It is weird that the problem seems to be only for the itkTriangleHelper class.

I will have to look what is the difference in the files generated for swig and what is exactly failing,
though I do not know how long it will take me. I hope I can do this this weekend.

Thanks

Michka


> On 09 Jun 2016, at 16:14, Christopher Mullins <christopherrmullins at gmail.com> wrote:
> 
> Hi all,
> 
> Apparently my subscription to this list has lapsed and my first email was rejected (despite receiving the list in my inbox every day).  Sorry if there's a double post.
> 
> I'm getting the following build errors when building ITK 4.10.0 with the WRAP_PYTHON option ON[1], [3].  Is this a known issue, or is there a configuration setting I've set improperly?  
> 
> Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There are no warnings. See all output details for this machine here [2], and please let me know if I can provide any others.
> 
> The faster I fix this the faster I'll feel comfortable updating the Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer.
> 
> Thanks,
> Chris
> 
> 
> 
> [1] https://open.cdash.org/viewBuildError.php?buildid=4403379
> [2] https://open.cdash.org/buildSummary.php?buildid=4403379
> 
> [3] To save you a click, and for the sake of archiving, the error is:
> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)': /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65: error: no matching function for call to 'itk::TriangleHelper<itk::Point<double, 2u> >::TriangleHelper()' result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
> _____________________________________
> 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 hans-johnson at uiowa.edu  Wed Jun 15 17:22:06 2016
From: hans-johnson at uiowa.edu (Johnson, Hans J)
Date: Wed, 15 Jun 2016 21:22:06 +0000
Subject: [ITK-users] Build errors in python wrapping of 4.10.0
In-Reply-To: <D452B2C7-BD65-426B-BC46-A10C642DB70A@gmail.com>
References: <CAL1JtzBgoYx3k7xn_pff9s5M9AGLFuKE0ZQJb4Wen0BkAHkzNA@mail.gmail.com>
 <D452B2C7-BD65-426B-BC46-A10C642DB70A@gmail.com>
Message-ID: <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu>

I?m trying to reproduce now.

Hans


-- 


On 6/15/16, 4:12 PM, "Insight-users on behalf of Michka Popoff" <insight-users-bounces at itk.org on behalf of michkapopoff at gmail.com> wrote:

>Hi
>
>I think this bug is not known. I had a look and could reproduce it with gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X.
>GCC 6 is using c++14 by default, but even with c++11 you would probably get the problem.
>The problem is also there with the latest commit from the master branch.
>
>Please note that we probably never tested Python Wrappings with c++11, even not speaking of c++14.
>
>The problem seems to have appeared with this patch:
>https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395
>
>I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy constructor, and was able to compile
>with gcc 6. But it may just a side effect of that patch which is now only appearing with c++ >= 11.
>It is weird that the problem seems to be only for the itkTriangleHelper class.
>
>I will have to look what is the difference in the files generated for swig and what is exactly failing,
>though I do not know how long it will take me. I hope I can do this this weekend.
>
>Thanks
>
>Michka
>
>
>> On 09 Jun 2016, at 16:14, Christopher Mullins <christopherrmullins at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> Apparently my subscription to this list has lapsed and my first email was rejected (despite receiving the list in my inbox every day).  Sorry if there's a double post.
>> 
>> I'm getting the following build errors when building ITK 4.10.0 with the WRAP_PYTHON option ON[1], [3].  Is this a known issue, or is there a configuration setting I've set improperly?  
>> 
>> Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There are no warnings. See all output details for this machine here [2], and please let me know if I can provide any others.
>> 
>> The faster I fix this the faster I'll feel comfortable updating the Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer.
>> 
>> Thanks,
>> Chris
>> 
>> 
>> 
>> [1] https://open.cdash.org/viewBuildError.php?buildid=4403379
>> [2] https://open.cdash.org/buildSummary.php?buildid=4403379
>> 
>> [3] To save you a click, and for the sake of archiving, the error is:
>> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)': /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65: error: no matching function for call to 'itk::TriangleHelper<itk::Point<double, 2u> >::TriangleHelper()' result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>
>_____________________________________
>Powered by www.kitware.com
>
>Visit other Kitware open-source projects at
>http://www.kitware.com/opensource/opensource.html
>
>Kitware offers ITK Training Courses, for more information visit:
>http://www.kitware.com/products/protraining.php
>
>Please keep messages on-topic and check the ITK FAQ at:
>http://www.itk.org/Wiki/ITK_FAQ
>
>Follow this link to subscribe/unsubscribe:
>http://public.kitware.com/mailman/listinfo/insight-users


From paniwani at gmail.com  Fri Jun 17 02:28:08 2016
From: paniwani at gmail.com (paniwani)
Date: Thu, 16 Jun 2016 23:28:08 -0700 (MST)
Subject: [ITK-users] Simple ITK Python not working on Mac El Capitan (10.11)
Message-ID: <1466144888365-37265.post@n7.nabble.com>

Hi,

I was using simple ITK with python in my application with no problems until
I recently upgraded to El Capitan on my Mac. Since then, I have received
error messages regarding 64-bit issues. I've tried to reinstall simple ITK
multiple times using the python binaries as stated here
https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both
pip and easy_install. However, I continue to run into issues running
simpleITK.

I am on OSX El Capitan (10.11) and Python 2.7.

Here is the output when I try to install the latest via pip and and use it:

 

I also tried to download a separate binary which I thought would be more
applicable for El Capitan (Mac OSX v10.11):

SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl

However, I received the same error message:



Any help to get simpleITK in python working again would be appreciated.
Thanks in advance!

Neil







--
View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Fri Jun 17 08:05:49 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 17 Jun 2016 12:05:49 +0000
Subject: [ITK-users] Simple ITK Python not working on Mac El Capitan
 (10.11)
In-Reply-To: <1466144888365-37265.post@n7.nabble.com>
References: <1466144888365-37265.post@n7.nabble.com>
Message-ID: <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov>

Hello,

You probably what this file:
https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl

Also you probably didn?t have the latest version of pip, try using updating to the latest version. It is recommended not to change the system version but instead use a virtual environment as described in the wiki documentation.

Aside from that general advice, I can?t help specifically because you did not provide sufficient details. Such as which python you are using ( system, anaconda) or it?s version, nor do you provide the command to install SimpleITK or the output.

HTH,
Brad


> On Jun 17, 2016, at 2:28 AM, paniwani <paniwani at gmail.com> wrote:
> 
> Hi,
> 
> I was using simple ITK with python in my application with no problems until
> I recently upgraded to El Capitan on my Mac. Since then, I have received
> error messages regarding 64-bit issues. I've tried to reinstall simple ITK
> multiple times using the python binaries as stated here
> https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both
> pip and easy_install. However, I continue to run into issues running
> simpleITK.
> 
> I am on OSX El Capitan (10.11) and Python 2.7.
> 
> Here is the output when I try to install the latest via pip and and use it:
> 
> 
> 
> I also tried to download a separate binary which I thought would be more
> applicable for El Capitan (Mac OSX v10.11):
> 
> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
> 
> However, I received the same error message:
> 
> 
> 
> Any help to get simpleITK in python working again would be appreciated.
> Thanks in advance!
> 
> Neil
> 
> 
> 
> 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265.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 coyarzunlaura at googlemail.com  Fri Jun 17 11:31:59 2016
From: coyarzunlaura at googlemail.com (Cristina Oyarzun)
Date: Fri, 17 Jun 2016 17:31:59 +0200
Subject: [ITK-users] MICCAI CLIP 2016: DEADLINE EXTENDED!
Message-ID: <CANuPjs1MD+x1n_EG+4tmGrRpCV0ovdfKXuYQ=iBBhpp2C=c0NQ@mail.gmail.com>

CALL FOR PAPERS
MICCAI 2016 Workshop on
Clinical Image-based Procedures: Translational Research in Medical Imaging


October 17, 2016
Athens, Greece

Website:http://miccai-clip.org/
==============================
==========================================

SCOPE

 The outstanding proliferation of medical image applications has created a
need for greater study and scrutiny of the clinical application and
validation of such methods. New strategies are essential to ensure a smooth
and effective translation of computational image-based techniques into the
clinic. For these reasons CLIP 2015?s major focus is on translational
research filling the gaps between basic science and clinical applications.
A highlight of the workshop is the subject of strategies for personalized
medicine to enhance diagnosis, treatment and interventions. Authors are
encouraged to submit work centered on specific clinical applications,
including techniques and procedures based on comprehensive clinical image
data. Submissions related to applications already in use and evaluated by
clinical users are particularly encouraged. The event will bring together
world-class specialists to present ways to strengthen links between
computer scientists and engineers, and clinicians.


TOPICS

*Strategies for patient-specific and anatomical modeling to support
planning and interventions

*Clinical studies employing advanced image-guided methods

*Clinical translation and validation of image-guided systems

*Current challenges and emerging techniques in image-based procedures

*Identification of parameters and error analysis in image-based procedures

*Multimodal image integration for modeling, planning and guidance

*Clinical applications in open and minimally invasive procedures




PAPER SUBMISSION

Papers will be limited to eight pages following the MICCAI submission
guidelines. Prospective authors should refer to the Paper Submission
section on the workshop website for details on how to submit papers to be
presented at the workshop.
All submissions will be peer-reviewed by at least 2 members of the program
committee. The selection of the papers will be based on the significance of
results, novelty, technical merit, relevance and clarity of presentation.
Papers will be presented in a day long single track workshop starting with
plenary sessions.
Accepted papers will be published as a proceedings volume in the Springer
Lecture Notes in Computer Science (LNCS) series after the workshop.

WORKSHOP FORMAT

Accepted papers will be presented in a day long single track workshop. The
final program will consist of invited speakers and original papers with
time allocated for discussions. Electronic proceedings will be arranged for
all of the papers presented at the workshop.

IMPORTANT DATES

* June 24, 2016: Paper submission due date
* July 10, 2016: Notification of acceptance
* July 17, 2016: Final camera-ready paper submission deadline

CONTACT

Inquires about the workshop should be sent to the Information Desk (
info at miccai-clip.org).

ORGANIZERS (in alphabetical order)

Klaus Drechsler (Fraunhofer IGD, Germany)
Marius Erdt (Fraunhofer IDM at NTU, Singapore)
Miguel Gonz?lez Ballester (ICREA - Universitat Pompeu Fabra, Spain)
Marius George Linguraru (Children's National Medical Center, USA)
Cristina Oyarzun Laura (Fraunhofer IGD, Germany)
Yoshinobu Sato (Nara Institute of Science and Technology, Japan)
Raj Shekhar (Children's National Medical Center, USA)
Stefan Wesarg (Fraunhofer IGD, Germany)

========================================================================
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From paniwani at gmail.com  Fri Jun 17 11:20:28 2016
From: paniwani at gmail.com (paniwani)
Date: Fri, 17 Jun 2016 08:20:28 -0700 (MST)
Subject: [ITK-users] Simple ITK Python not working on Mac El Capitan
 (10.11)
In-Reply-To: <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov>
References: <1466144888365-37265.post@n7.nabble.com>
 <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov>
Message-ID: <1466176828948-37268.post@n7.nabble.com>

Hi, 

It appears the code that I pasted did not show up in the email version of
the mailing list. I've re-pasted below. I'm using system Python 2.7 and Mac
OSX El Capitan. Thank you!

-----

I was using simple ITK with python in my application with no problems until
I recently upgraded to El Capitan on my Mac. Since then, I have received
error messages regarding 64-bit issues. I've tried to reinstall simple ITK
multiple times using the python binaries as stated here
https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both
pip and easy_install. However, I continue to run into issues running
simpleITK. 

I am on OSX El Capitan (10.11) and Python 2.7. 

Here is the output when I try to install the latest via pip and and use it: 

?  Downloads sudo pip install  --trusted-host www.simpleitk.org -f
http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30
SimpleITK
The directory '/Users/neil/Library/Caches/pip/http' or its parent directory
is not owned by the current user and the cache has been disabled. Please
check the permissions and owner of that directory. If executing pip with
sudo, you may want sudo's -H flag.
The directory '/Users/neil/Library/Caches/pip' or its parent directory is
not owned by the current user and caching wheels has been disabled. check
the permissions and owner of that directory. If executing pip with sudo, you
may want sudo's -H flag.
Collecting SimpleITK
  Downloading
https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
(72.6MB)
    100% |????????????????????????????????| 72.6MB 41.9MB/s 
Installing collected packages: SimpleITK
Successfully installed SimpleITK-0.9.1
?  Downloads python
Python 2.7.10 (default, Oct 23 2015, 19:19:21) 
[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import SimpleITK as sitk
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in
<module>
    from .SimpleITK import *
  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28,
in <module>
    _SimpleITK = swig_import_helper()
  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24,
in swig_import_helper
    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no
appropriate 64-bit architecture (see "man python" for running in 32-bit
mode)
>>> 

I also tried to download a separate binary which I thought would be more
applicable for El Capitan (Mac OSX v10.11): 

SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl 

However, I received the same error message: 

?  Downloads sudo pip install
SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
The directory '/Users/neil/Library/Caches/pip/http' or its parent directory
is not owned by the current user and the cache has been disabled. Please
check the permissions and owner of that directory. If executing pip with
sudo, you may want sudo's -H flag.
The directory '/Users/neil/Library/Caches/pip' or its parent directory is
not owned by the current user and caching wheels has been disabled. check
the permissions and owner of that directory. If executing pip with sudo, you
may want sudo's -H flag.
Processing
./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
Installing collected packages: SimpleITK
Successfully installed SimpleITK-0.9.0
?  Downloads python
Python 2.7.10 (default, Oct 23 2015, 19:19:21) 
[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import SimpleITK as sitk
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in
<module>
    from .SimpleITK import *
  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28,
in <module>
    _SimpleITK = swig_import_helper()
  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24,
in swig_import_helper
    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no
appropriate 64-bit architecture (see "man python" for running in 32-bit
mode)
>>> 

Any help to get simpleITK in python working again would be appreciated.
Thanks in advance! 

Neil 



--
View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Fri Jun 17 14:05:25 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 17 Jun 2016 18:05:25 +0000
Subject: [ITK-users] Simple ITK Python not working on Mac El Capitan
 (10.11)
In-Reply-To: <1466176828948-37268.post@n7.nabble.com>
References: <1466144888365-37265.post@n7.nabble.com>
 <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov>
 <1466176828948-37268.post@n7.nabble.com>
Message-ID: <E92C22EE-76E2-42B8-82C5-DA8D24EE7986@mail.nih.gov>

Hi,

Where did you get you python from? You are using a version from /Library/Framework/Python.frameworks, which is not the system version.

The error with the first command gives you a suggestion on how to solve the problem. 

The second error appears to be a binary compatibility issue with the distribution you have of python.

Please read the guidance on the wiki with the different distributions of python, along with following the recommendation to setup a virtual environment.

https://itk.org/Wiki/SimpleITK/GettingStarted

Good luck,
Brad




> On Jun 17, 2016, at 11:20 AM, paniwani <paniwani at gmail.com> wrote:
> 
> Hi, 
> 
> It appears the code that I pasted did not show up in the email version of
> the mailing list. I've re-pasted below. I'm using system Python 2.7 and Mac
> OSX El Capitan. Thank you!
> 
> -----
> 
> I was using simple ITK with python in my application with no problems until
> I recently upgraded to El Capitan on my Mac. Since then, I have received
> error messages regarding 64-bit issues. I've tried to reinstall simple ITK
> multiple times using the python binaries as stated here
> https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both
> pip and easy_install. However, I continue to run into issues running
> simpleITK. 
> 
> I am on OSX El Capitan (10.11) and Python 2.7. 
> 
> Here is the output when I try to install the latest via pip and and use it: 
> 
> ?  Downloads sudo pip install  --trusted-host www.simpleitk.org -f
> http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30
> SimpleITK
> The directory '/Users/neil/Library/Caches/pip/http' or its parent directory
> is not owned by the current user and the cache has been disabled. Please
> check the permissions and owner of that directory. If executing pip with
> sudo, you may want sudo's -H flag.
> The directory '/Users/neil/Library/Caches/pip' or its parent directory is
> not owned by the current user and caching wheels has been disabled. check
> the permissions and owner of that directory. If executing pip with sudo, you
> may want sudo's -H flag.
> Collecting SimpleITK
>  Downloading
> https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
> (72.6MB)
>    100% |????????????????????????????????| 72.6MB 41.9MB/s 
> Installing collected packages: SimpleITK
> Successfully installed SimpleITK-0.9.1
> ?  Downloads python
> Python 2.7.10 (default, Oct 23 2015, 19:19:21) 
> [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import SimpleITK as sitk
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in
> <module>
>    from .SimpleITK import *
>  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28,
> in <module>
>    _SimpleITK = swig_import_helper()
>  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24,
> in swig_import_helper
>    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no
> appropriate 64-bit architecture (see "man python" for running in 32-bit
> mode)
>>>> 
> 
> I also tried to download a separate binary which I thought would be more
> applicable for El Capitan (Mac OSX v10.11): 
> 
> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl 
> 
> However, I received the same error message: 
> 
> ?  Downloads sudo pip install
> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
> The directory '/Users/neil/Library/Caches/pip/http' or its parent directory
> is not owned by the current user and the cache has been disabled. Please
> check the permissions and owner of that directory. If executing pip with
> sudo, you may want sudo's -H flag.
> The directory '/Users/neil/Library/Caches/pip' or its parent directory is
> not owned by the current user and caching wheels has been disabled. check
> the permissions and owner of that directory. If executing pip with sudo, you
> may want sudo's -H flag.
> Processing
> ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
> Installing collected packages: SimpleITK
> Successfully installed SimpleITK-0.9.0
> ?  Downloads python
> Python 2.7.10 (default, Oct 23 2015, 19:19:21) 
> [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import SimpleITK as sitk
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in
> <module>
>    from .SimpleITK import *
>  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28,
> in <module>
>    _SimpleITK = swig_import_helper()
>  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24,
> in swig_import_helper
>    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no
> appropriate 64-bit architecture (see "man python" for running in 32-bit
> mode)
>>>> 
> 
> Any help to get simpleITK in python working again would be appreciated.
> Thanks in advance! 
> 
> Neil 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.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 paniwani at gmail.com  Fri Jun 17 14:55:26 2016
From: paniwani at gmail.com (paniwani)
Date: Fri, 17 Jun 2016 11:55:26 -0700 (MST)
Subject: [ITK-users] Simple ITK Python not working on Mac El Capitan
 (10.11)
In-Reply-To: <E92C22EE-76E2-42B8-82C5-DA8D24EE7986@mail.nih.gov>
References: <1466144888365-37265.post@n7.nabble.com>
 <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov>
 <1466176828948-37268.post@n7.nabble.com>
 <E92C22EE-76E2-42B8-82C5-DA8D24EE7986@mail.nih.gov>
Message-ID: <CAC5GmLvT8aF6SnX2uhS6TBSEy0pH81Y9AdwdHCObdNh_bM6O9g@mail.gmail.com>

I had several versions of Python installed. I removed the version at
/Library/Frameworks and reinstalled Python 2.7 using Homebrew. I then
followed the advice of the guide and setup a virtual environment within my
project (called ecvenv), installed pip, upgraded pip, and used it to
install SimpleITK. It installed the one you recommended earlier, v0.9.1.

(ecvenv) *?  **econtour* *git:(**master**) **?* pip install  --trusted-host
www.simpleitk.org -f
http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30
SimpleITK

Collecting SimpleITK

  Downloading
https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
(72.6MB)

    100% |????????????????????????????????| 72.6MB 43.5MB/s

Installing collected packages: SimpleITK

Successfully installed SimpleITK-0.9.1


However, I continue to run into a "Fatal Python Error" when trying to load
simple itk from within python. See below:

(ecvenv) *?  **econtour* *git:(**master**) **?* which python

/Users/neil/work/Meteor/econtour/ecvenv/bin/python

(ecvenv) *?  **econtour* *git:(**master**) **?* which pip

/Users/neil/work/Meteor/econtour/ecvenv/bin/pip

(ecvenv) *?  **econtour* *git:(**master**) **?* pip list

pip (8.1.2)

setuptools (23.0.0)

SimpleITK (0.9.1)

wheel (0.29.0)

(ecvenv) *?  **econtour* *git:(**master**) **?* python

Python 2.7.11 (default, Jan 22 2016, 08:29:18)

[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import SimpleITK as sitk

Fatal Python error: PyThreadState_Get: no current thread

[1]    2805 abort      python




On Fri, Jun 17, 2016 at 9:56 AM, Bradley Lowekamp [via ITK - Users] <
ml-node+s7n37269h95 at n7.nabble.com> wrote:

> Hi,
>
> Where did you get you python from? You are using a version from
> /Library/Framework/Python.frameworks, which is not the system version.
>
> The error with the first command gives you a suggestion on how to solve
> the problem.
>
> The second error appears to be a binary compatibility issue with the
> distribution you have of python.
>
> Please read the guidance on the wiki with the different distributions of
> python, along with following the recommendation to setup a virtual
> environment.
>
> https://itk.org/Wiki/SimpleITK/GettingStarted
>
> Good luck,
> Brad
>
>
>
>
> > On Jun 17, 2016, at 11:20 AM, paniwani <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=37269&i=0>> wrote:
> >
> > Hi,
> >
> > It appears the code that I pasted did not show up in the email version
> of
> > the mailing list. I've re-pasted below. I'm using system Python 2.7 and
> Mac
> > OSX El Capitan. Thank you!
> >
> > -----
> >
> > I was using simple ITK with python in my application with no problems
> until
> > I recently upgraded to El Capitan on my Mac. Since then, I have received
> > error messages regarding 64-bit issues. I've tried to reinstall simple
> ITK
> > multiple times using the python binaries as stated here
> > https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with
> both
> > pip and easy_install. However, I continue to run into issues running
> > simpleITK.
> >
> > I am on OSX El Capitan (10.11) and Python 2.7.
> >
> > Here is the output when I try to install the latest via pip and and use
> it:
> >
> > ?  Downloads sudo pip install  --trusted-host www.simpleitk.org -f
> > http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30
> > SimpleITK
> > The directory '/Users/neil/Library/Caches/pip/http' or its parent
> directory
> > is not owned by the current user and the cache has been disabled. Please
> > check the permissions and owner of that directory. If executing pip with
> > sudo, you may want sudo's -H flag.
> > The directory '/Users/neil/Library/Caches/pip' or its parent directory
> is
> > not owned by the current user and caching wheels has been disabled.
> check
> > the permissions and owner of that directory. If executing pip with sudo,
> you
> > may want sudo's -H flag.
> > Collecting SimpleITK
> >  Downloading
> >
> https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
> > (72.6MB)
> >    100% |????????????????????????????????| 72.6MB 41.9MB/s
> > Installing collected packages: SimpleITK
> > Successfully installed SimpleITK-0.9.1
> > ?  Downloads python
> > Python 2.7.10 (default, Oct 23 2015, 19:19:21)
> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import SimpleITK as sitk
> > Traceback (most recent call last):
> >  File "<stdin>", line 1, in <module>
> >  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1,
> in
> > <module>
> >    from .SimpleITK import *
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 28,
> > in <module>
> >    _SimpleITK = swig_import_helper()
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 24,
> > in swig_import_helper
> >    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python:
> no
> > appropriate 64-bit architecture (see "man python" for running in 32-bit
> > mode)
> >>>>
> >
> > I also tried to download a separate binary which I thought would be more
> > applicable for El Capitan (Mac OSX v10.11):
> >
> >
> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>
> >
> > However, I received the same error message:
> >
> > ?  Downloads sudo pip install
> >
> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>
> > The directory '/Users/neil/Library/Caches/pip/http' or its parent
> directory
> > is not owned by the current user and the cache has been disabled. Please
> > check the permissions and owner of that directory. If executing pip with
> > sudo, you may want sudo's -H flag.
> > The directory '/Users/neil/Library/Caches/pip' or its parent directory
> is
> > not owned by the current user and caching wheels has been disabled.
> check
> > the permissions and owner of that directory. If executing pip with sudo,
> you
> > may want sudo's -H flag.
> > Processing
> >
> ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>
> > Installing collected packages: SimpleITK
> > Successfully installed SimpleITK-0.9.0
> > ?  Downloads python
> > Python 2.7.10 (default, Oct 23 2015, 19:19:21)
> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import SimpleITK as sitk
> > Traceback (most recent call last):
> >  File "<stdin>", line 1, in <module>
> >  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1,
> in
> > <module>
> >    from .SimpleITK import *
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 28,
> > in <module>
> >    _SimpleITK = swig_import_helper()
> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
> 24,
> > in swig_import_helper
> >    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python:
> no
> > appropriate 64-bit architecture (see "man python" for running in 32-bit
> > mode)
> >>>>
> >
> > Any help to get simpleITK in python working again would be appreciated.
> > Thanks in advance!
> >
> > Neil
> >
> >
> >
> > --
> > View this message in context:
> http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.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
>
> _____________________________________
> 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
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
>
> http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37269.html
> To unsubscribe from Simple ITK Python not working on Mac El Capitan
> (10.11), click here
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=37265&code=cGFuaXdhbmlAZ21haWwuY29tfDM3MjY1fC0xOTE2MTYxMTkw>
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>



-- 
Neil Panjwani
Duke University | B.S.E. 2010
Tel: (760) 486-0765




--
View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37270.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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From paniwani at gmail.com  Fri Jun 17 16:11:49 2016
From: paniwani at gmail.com (paniwani)
Date: Fri, 17 Jun 2016 13:11:49 -0700 (MST)
Subject: [ITK-users] Simple ITK Python not working on Mac El Capitan
 (10.11)
In-Reply-To: <E92C22EE-76E2-42B8-82C5-DA8D24EE7986@mail.nih.gov>
References: <1466144888365-37265.post@n7.nabble.com>
 <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov>
 <1466176828948-37268.post@n7.nabble.com>
 <E92C22EE-76E2-42B8-82C5-DA8D24EE7986@mail.nih.gov>
Message-ID: <CAC5GmLvKrFD-hYdHr40FzVMn_4ziwrFFdmvhgdY3o6_OfU=N-g@mail.gmail.com>

I eventually got it working by re-installing python as above and then using
homebrew to install simple itk. Thanks for your help!

Neil

On Fri, Jun 17, 2016 at 1:03 PM, Neil Panjwani <paniwani at gmail.com> wrote:

> I had several versions of Python installed. I removed the version at
> /Library/Frameworks and reinstalled Python 2.7 using Homebrew. I then
> followed the advice of the guide and setup a virtual environment within my
> project (called ecvenv), installed pip, upgraded pip, and used it to
> install SimpleITK. It installed the one you recommended earlier, v0.9.1.
>
> (ecvenv) *?  **econtour* *git:(**master**) **?* pip install
> --trusted-host www.simpleitk.org -f
> http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30
> SimpleITK
>
> Collecting SimpleITK
>
>   Downloading
> https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
> (72.6MB)
>
>     100% |????????????????????????????????| 72.6MB 43.5MB/s
>
> Installing collected packages: SimpleITK
>
> Successfully installed SimpleITK-0.9.1
>
>
> However, I continue to run into a "Fatal Python Error" when trying to load
> simple itk from within python. See below:
>
> (ecvenv) *?  **econtour* *git:(**master**) **?* which python
>
> /Users/neil/work/Meteor/econtour/ecvenv/bin/python
>
> (ecvenv) *?  **econtour* *git:(**master**) **?* which pip
>
> /Users/neil/work/Meteor/econtour/ecvenv/bin/pip
>
> (ecvenv) *?  **econtour* *git:(**master**) **?* pip list
>
> pip (8.1.2)
>
> setuptools (23.0.0)
>
> SimpleITK (0.9.1)
>
> wheel (0.29.0)
>
> (ecvenv) *?  **econtour* *git:(**master**) **?* python
>
> Python 2.7.11 (default, Jan 22 2016, 08:29:18)
>
> [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin
>
> Type "help", "copyright", "credits" or "license" for more information.
>
> >>> import SimpleITK as sitk
>
> Fatal Python error: PyThreadState_Get: no current thread
>
> [1]    2805 abort      python
>
>
>
>
> On Fri, Jun 17, 2016 at 9:56 AM, Bradley Lowekamp [via ITK - Users] <
> ml-node+s7n37269h95 at n7.nabble.com> wrote:
>
>> Hi,
>>
>> Where did you get you python from? You are using a version from
>> /Library/Framework/Python.frameworks, which is not the system version.
>>
>> The error with the first command gives you a suggestion on how to solve
>> the problem.
>>
>> The second error appears to be a binary compatibility issue with the
>> distribution you have of python.
>>
>> Please read the guidance on the wiki with the different distributions of
>> python, along with following the recommendation to setup a virtual
>> environment.
>>
>> https://itk.org/Wiki/SimpleITK/GettingStarted
>>
>> Good luck,
>> Brad
>>
>>
>>
>>
>> > On Jun 17, 2016, at 11:20 AM, paniwani <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=37269&i=0>> wrote:
>> >
>> > Hi,
>> >
>> > It appears the code that I pasted did not show up in the email version
>> of
>> > the mailing list. I've re-pasted below. I'm using system Python 2.7 and
>> Mac
>> > OSX El Capitan. Thank you!
>> >
>> > -----
>> >
>> > I was using simple ITK with python in my application with no problems
>> until
>> > I recently upgraded to El Capitan on my Mac. Since then, I have
>> received
>> > error messages regarding 64-bit issues. I've tried to reinstall simple
>> ITK
>> > multiple times using the python binaries as stated here
>> > https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with
>> both
>> > pip and easy_install. However, I continue to run into issues running
>> > simpleITK.
>> >
>> > I am on OSX El Capitan (10.11) and Python 2.7.
>> >
>> > Here is the output when I try to install the latest via pip and and use
>> it:
>> >
>> > ?  Downloads sudo pip install  --trusted-host www.simpleitk.org -f
>> > http://www.simpleitk.org/SimpleITK/resources/software.html --timeout
>> 30
>> > SimpleITK
>> > The directory '/Users/neil/Library/Caches/pip/http' or its parent
>> directory
>> > is not owned by the current user and the cache has been disabled.
>> Please
>> > check the permissions and owner of that directory. If executing pip
>> with
>> > sudo, you may want sudo's -H flag.
>> > The directory '/Users/neil/Library/Caches/pip' or its parent directory
>> is
>> > not owned by the current user and caching wheels has been disabled.
>> check
>> > the permissions and owner of that directory. If executing pip with
>> sudo, you
>> > may want sudo's -H flag.
>> > Collecting SimpleITK
>> >  Downloading
>> >
>> https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl
>> > (72.6MB)
>> >    100% |????????????????????????????????| 72.6MB 41.9MB/s
>> > Installing collected packages: SimpleITK
>> > Successfully installed SimpleITK-0.9.1
>> > ?  Downloads python
>> > Python 2.7.10 (default, Oct 23 2015, 19:19:21)
>> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
>> > Type "help", "copyright", "credits" or "license" for more information.
>> >>>> import SimpleITK as sitk
>> > Traceback (most recent call last):
>> >  File "<stdin>", line 1, in <module>
>> >  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line
>> 1, in
>> > <module>
>> >    from .SimpleITK import *
>> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
>> 28,
>> > in <module>
>> >    _SimpleITK = swig_import_helper()
>> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
>> 24,
>> > in swig_import_helper
>> >    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python:
>> no
>> > appropriate 64-bit architecture (see "man python" for running in 32-bit
>> > mode)
>> >>>>
>> >
>> > I also tried to download a separate binary which I thought would be
>> more
>> > applicable for El Capitan (Mac OSX v10.11):
>> >
>> >
>> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>>
>> >
>> > However, I received the same error message:
>> >
>> > ?  Downloads sudo pip install
>> >
>> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>>
>> > The directory '/Users/neil/Library/Caches/pip/http' or its parent
>> directory
>> > is not owned by the current user and the cache has been disabled.
>> Please
>> > check the permissions and owner of that directory. If executing pip
>> with
>> > sudo, you may want sudo's -H flag.
>> > The directory '/Users/neil/Library/Caches/pip' or its parent directory
>> is
>> > not owned by the current user and caching wheels has been disabled.
>> check
>> > the permissions and owner of that directory. If executing pip with
>> sudo, you
>> > may want sudo's -H flag.
>> > Processing
>> >
>> ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl
>>
>> > Installing collected packages: SimpleITK
>> > Successfully installed SimpleITK-0.9.0
>> > ?  Downloads python
>> > Python 2.7.10 (default, Oct 23 2015, 19:19:21)
>> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
>> > Type "help", "copyright", "credits" or "license" for more information.
>> >>>> import SimpleITK as sitk
>> > Traceback (most recent call last):
>> >  File "<stdin>", line 1, in <module>
>> >  File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line
>> 1, in
>> > <module>
>> >    from .SimpleITK import *
>> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
>> 28,
>> > in <module>
>> >    _SimpleITK = swig_import_helper()
>> >  File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line
>> 24,
>> > in swig_import_helper
>> >    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python:
>> no
>> > appropriate 64-bit architecture (see "man python" for running in 32-bit
>> > mode)
>> >>>>
>> >
>> > Any help to get simpleITK in python working again would be appreciated.
>> > Thanks in advance!
>> >
>> > Neil
>> >
>> >
>> >
>> > --
>> > View this message in context:
>> http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.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
>>
>> _____________________________________
>> 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
>>
>>
>> ------------------------------
>> If you reply to this email, your message will be added to the discussion
>> below:
>>
>> http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37269.html
>> To unsubscribe from Simple ITK Python not working on Mac El Capitan
>> (10.11), click here
>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=37265&code=cGFuaXdhbmlAZ21haWwuY29tfDM3MjY1fC0xOTE2MTYxMTkw>
>> .
>> NAML
>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>
>
>
>
> --
> Neil Panjwani
> Duke University | B.S.E. 2010
> Tel: (760) 486-0765
>



-- 
Neil Panjwani
Duke University | B.S.E. 2010
Tel: (760) 486-0765




--
View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37271.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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From javij1 at gmail.com  Sat Jun 18 19:59:34 2016
From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=)
Date: Sun, 19 Jun 2016 01:59:34 +0200
Subject: [ITK-users] ImageI iterators same walk order simultaneously
Message-ID: <3b8ffc92-0aeb-11ba-d4c1-a946ee8ee3c1@gmail.com>


Hello,

I want to traverse an image that points to an intra-cranial mask, and 
perform an operation on other image only in the voxels where the 
intra-cranial mask are true. I wrote the following code:

itk::ImageRegionConstIterator<MaskType> iteratorMask(mask, 
mask->GetLargestPossibleRegion());
itk::ImageRegionIterator<MapType> iteratorMap(map, 
map->GetLargestPossibleRegion());

iteratorMask.GoToBegin();
iteratorMap.GoToBegin();
while (!iteratorMask.IsAtEnd())
{
      if (iteratorMask.Get())
      {
          iteratorMap.Set(i);
           ++i;
       }
       ++iteratorMask;
       ++iteratorMap;

}

My question is: can I be sure that, with this implementation both 
iterators point to the same voxel of the image simultaneously? Or should 
I use itk::ImageRegionConstIteratorWithIndex on "mask" and modify "map" 
through the "SetPixel" method? I have read that "SetPixel" and 
"GetPixel" methods are slow and not preferred against iterators. It is 
possible to implement this operation only with iterators?

Thank you very much

Regards.

Javier.



From tevain at telecom-paristech.fr  Mon Jun 20 04:41:42 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 20 Jun 2016 10:41:42 +0200 (CEST)
Subject: [ITK-users] [ITK] ImageI iterators same walk order
 simultaneously
In-Reply-To: <3b8ffc92-0aeb-11ba-d4c1-a946ee8ee3c1@gmail.com>
References: <3b8ffc92-0aeb-11ba-d4c1-a946ee8ee3c1@gmail.com>
Message-ID: <166575769.10455174.1466412102217.JavaMail.zimbra@enst.fr>

Hi Javier,

You can use iterators to do so without problems, given that you ensure that:
- The two images are in the same reference frame (i.e. axes represent the same directions in both).
- The ImageRegions to parse are identical .
Otherwise you will lose the correpondence between the images.

HTH,

Tim

----- Mail original -----
De: "Javier Juan Albarrac?n" <javij1 at gmail.com>
?: insight-users at itk.org
Envoy?: Dimanche 19 Juin 2016 01:59:34
Objet: [ITK] [ITK-users] ImageI iterators same walk order simultaneously


Hello,

I want to traverse an image that points to an intra-cranial mask, and 
perform an operation on other image only in the voxels where the 
intra-cranial mask are true. I wrote the following code:

itk::ImageRegionConstIterator<MaskType> iteratorMask(mask, 
mask->GetLargestPossibleRegion());
itk::ImageRegionIterator<MapType> iteratorMap(map, 
map->GetLargestPossibleRegion());

iteratorMask.GoToBegin();
iteratorMap.GoToBegin();
while (!iteratorMask.IsAtEnd())
{
      if (iteratorMask.Get())
      {
          iteratorMap.Set(i);
           ++i;
       }
       ++iteratorMask;
       ++iteratorMap;

}

My question is: can I be sure that, with this implementation both 
iterators point to the same voxel of the image simultaneously? Or should 
I use itk::ImageRegionConstIteratorWithIndex on "mask" and modify "map" 
through the "SetPixel" method? I have read that "SetPixel" and 
"GetPixel" methods are slow and not preferred against iterators. It is 
possible to implement this operation only with iterators?

Thank you very much

Regards.

Javier.


_____________________________________
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
_______________________________________________
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From hebennink at gmail.com  Mon Jun 20 09:49:58 2016
From: hebennink at gmail.com (Edwin Bennink)
Date: Mon, 20 Jun 2016 15:49:58 +0200
Subject: [ITK-users] WrapITK question: how to cast images with RGB or
 complex float pixel types to a Numpy array?
Message-ID: <CAJbB22F1qO5MgCrN1GQZkyDn8e_EoT7f1kUdmp7WOYB3PhyN5w@mail.gmail.com>

Hello,


I am searching for a way to access pixel data of unsigned char RGBPixel
images and complex float images in Numpy through PyBuffer.

I guess that it should be possible to cast these images to a vector type
and access the data without copying, but I can't figure out how. PyBuffer
doesn't support RGB or complex images, and it feels stupid to decompose and
recompose into a vector image.

What would be a neat solution to this problem? Thanks!


Edwin Bennink
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From scapegoat.sarthak at gmail.com  Mon Jun 20 10:31:59 2016
From: scapegoat.sarthak at gmail.com (Scapegoat Sarthak)
Date: Mon, 20 Jun 2016 10:31:59 -0400
Subject: [ITK-users] ResampleDICOM Assertion Error
Message-ID: <CANbSmSdFbdPxf5fGyNCJHoUir8p+3cn5WmMo-pXVQcvjPoWRbA@mail.gmail.com>

Hello All,

I have been trying (unsuccessfully) to write a DICOM series with
non-integer slopes. I have seen in an earlier community post (reference -
http://public.kitware.com/pipermail/community/2014-September/007143.html)
about the exact same issue and it is still not resolved (I am running
version 4.9.0.

Can someone from the moderators' side confirm in which version this has
been taken care of (if at all)?

Thanks,
Sarthak
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From blowekamp at mail.nih.gov  Mon Jun 20 11:18:24 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 20 Jun 2016 15:18:24 +0000
Subject: [ITK-users] [ITK] WrapITK question: how to cast images with RGB
 or complex float pixel types to a Numpy array?
In-Reply-To: <CAJbB22F1qO5MgCrN1GQZkyDn8e_EoT7f1kUdmp7WOYB3PhyN5w@mail.gmail.com>
References: <CAJbB22F1qO5MgCrN1GQZkyDn8e_EoT7f1kUdmp7WOYB3PhyN5w@mail.gmail.com>
Message-ID: <0E306F74-4017-4F1F-BFE4-CD0624909082@mail.nih.gov>

Hello,

In C++ ITK I would just use the CastImageFilter inplace to convert from RGBPixel to a vector type. But that doesn?t seemed to be wrapped:

https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageFilterBase/wrapping/itkCastImageFilter.wrap

I would look into extending the pyBuffer to support the RGBPixel type:

https://github.com/tobiasmaier/itkPyBuffer/blob/master/wrapping/itkPyBuffer.wrap

There should be some information documenting this in the ITK software guide:
https://itk.org/ITK/help/documentation.html

HTH,
Brad

On Jun 20, 2016, at 9:49 AM, Edwin Bennink <hebennink at gmail.com<mailto:hebennink at gmail.com>> wrote:

Hello,


I am searching for a way to access pixel data of unsigned char RGBPixel images and complex float images in Numpy through PyBuffer.

I guess that it should be possible to cast these images to a vector type and access the data without copying, but I can't figure out how. PyBuffer doesn't support RGB or complex images, and it feels stupid to decompose and recompose into a vector image.

What would be a neat solution to this problem? Thanks!


Edwin Bennink
_____________________________________
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
_______________________________________________
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http://public.kitware.com/mailman/listinfo/community

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From jmalsoaz at yahoo.fr  Tue Jun 21 02:33:19 2016
From: jmalsoaz at yahoo.fr (Malsoaz James)
Date: Tue, 21 Jun 2016 06:33:19 +0000 (UTC)
Subject: [ITK-users] Licensing question
References: <1039149860.11159873.1466490799507.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <1039149860.11159873.1466490799507.JavaMail.yahoo@mail.yahoo.com>

Hi,
I would like to use ITK in a commercial application but I have some questions about the Apache2 license.?Should I include somewhere the ITK copyright in my application? In source code? In related documents?
Currently I'm using version 4.8. I made minor modifications in source file of ITK to fit my needs. Should I publish these changes?
Thank you for your answer.Best regards,
James
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From kolin9105 at gmail.com  Tue Jun 21 11:52:31 2016
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 21 Jun 2016 22:52:31 +0700
Subject: [ITK-users] help me
Message-ID: <CAEiw7u7ye+6xgS9ndrLxOnuUo2rnkx3XmLZ0hzRuYsDTOUSsMA@mail.gmail.com>

hello everyone..
I need your help.
I am a beginner in itk and I need confidence connected for my riset.
now I am very confused about a function SeedX and SeedY in confidence
connected.
can you give what is the usefulness of SeedX and SeedY because
when I set Seed X and seed Y in confidence connected segmentation the
picture would be change.
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From jhlegarreta at vicomtech.org  Tue Jun 21 17:19:47 2016
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Tue, 21 Jun 2016 23:19:47 +0200
Subject: [ITK-users] help me
In-Reply-To: <CAEiw7u7ye+6xgS9ndrLxOnuUo2rnkx3XmLZ0hzRuYsDTOUSsMA@mail.gmail.com>
References: <CAEiw7u7ye+6xgS9ndrLxOnuUo2rnkx3XmLZ0hzRuYsDTOUSsMA@mail.gmail.com>
Message-ID: <CAAKhGh9GWGSzggtKeEdvPPRTZBWaiOcLUfT5kJ3y9nuFKSyrBw@mail.gmail.com>

Hi Miekolin,
the itk::ConfidenceConnectedImageFilter [1] (if that is the one you are
using) requires a seed (or point inside the structure of interest in your
image) to start developing its segmentation algorihm.

Having a look at the implementation itself [2], there are no such SeedX or
SeedY functions, but rather one named SetSeed, which makes sense given that
ITK is a toolkit to deal with N-dimensional images.

Reading the software guide [3] is a must when beginning to work with ITK.
The filter you are supposedly using is explained in section 4.1.4, p.354.

HTH
JON HAITZ

[1]
https://itk.org/Doxygen/html/classitk_1_1ConfidenceConnectedImageFilter.html
[2]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Segmentation/RegionGrowing/include/itkConfidenceConnectedImageFilter.hxx
[3] https://itk.org/ItkSoftwareGuide.pdf


_____________________________________
> 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
>
>
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From marco.giord at gmail.com  Wed Jun 22 04:38:06 2016
From: marco.giord at gmail.com (marco giordano)
Date: Wed, 22 Jun 2016 10:38:06 +0200
Subject: [ITK-users] [ITK] Read 4D CT cardiac dicom series and save it
 as a single 4D nifti file
In-Reply-To: <DM2PR07MB350E83D9D05861C13533DF0D8510@DM2PR07MB350.namprd07.prod.outlook.com>
References: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>
 <1465484786789-7588963.post@n2.nabble.com>
 <CANbSmSchv53_pzo3ioB4yrn-Shp=_-UOBBfy0in31XBp54+uDw@mail.gmail.com>
 <CAF3iUbL6ESHd+j4hWn_HNuuc6aP9XB0LQh7Ub03h=ufvvmJc5w@mail.gmail.com>
 <DM2PR07MB350E83D9D05861C13533DF0D8510@DM2PR07MB350.namprd07.prod.outlook.com>
Message-ID: <CAF3iUbK7k5Yd8KW3PTbXwPPdS7mNNkTWnamKg6x8wszXJJBMew@mail.gmail.com>

Dear Andras, all,
I did try with 3D Slicer but the 4D sequence is not loaded correctly
(slices are not loaded in the right order). One issue that I see is that
each Dicom series is actually a semi-volume (e.g. the upper or lower part
of a volume) thus it requires some merging of the data before writing. I am
writing some code even though I thought there would be more examples of
similar import routine developed in the past. I will keep you posted if i
make any progress
regards



2016-06-11 6:25 GMT+02:00 Andras Lasso <lasso at queensu.ca>:

> 3D Slicer can load some 4D CTs a 3D+t sequence and you cab save it as a 4D
> nrrd. You may give it a try. If it doesn't work for your sequence then
> report the problem on the slicer-users mailing list. If you can provide a
> sample data set then slicer developers most likely will be able to make it
> work.
>
>
>
> Andras
>
>
>
> *From: *marco giordano <marco.giord at gmail.com>
> *Sent: *June 10, 2016 17:32
> *To: *Scapegoat Sarthak <scapegoat.sarthak at gmail.com>
> *Cc: *insight-users at itk.org
> *Subject: *Re: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save
> it as a single 4D nifti file
>
>
> Hi there,
>
> Thanks for the suggestions. VV is not really an option since I have to
> analyze many cases. I even tried to use VV but it gives me the wrong order
> of the slices.
>
> I am trying the  "itk::ImageSeriesReader" (right?) but it is complaining
> that "Position is not unique".  I think it refers to the fact that the
> slices in my "series" have the "same location". Not sure this is meant to
> transform 2D into 4D if it expects different locations, maybe it is for 2D
> into 3D. Any idea?
>
> Regards
>
> 2016-06-09 17:21 GMT+02:00 Scapegoat Sarthak <scapegoat.sarthak at gmail.com>
> :
>
>> You can do it pretty easily:
>>
>> Read DICOM using SeriesFileReader and then connect output to a FileWriter
>> with the file name of your choice (in this case, it would be
>> "output.nii.gz").
>>
>>
>> On 9 June 2016 at 11:06, Mohammad Varasteh <varasteh at to.infn.it> wrote:
>>
>>> Dear Marco,
>>>
>>> Actually I do not know how to do it in the ITK but for such cases (if it
>>> is
>>> few cases) I normally use "VV: the 4D slicer". You can find it in the
>>> following link:
>>>
>>> http://www.creatis.insa-lyon.fr/rio/vv
>>>
>>> I hope this will be of some use.
>>>
>>> Varasteh
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.html
>>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
> --
> Marco Giordano
> SKYPE:marcogiord81
>



-- 
Marco Giordano
SKYPE:marcogiord81
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From dzenanz at gmail.com  Wed Jun 22 06:33:41 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 22 Jun 2016 12:33:41 +0200
Subject: [ITK-users] [ITK] Fast image creation from a signed distance
	function
In-Reply-To: <1465984814443-7588969.post@n2.nabble.com>
References: <1465984814443-7588969.post@n2.nabble.com>
Message-ID: <CAPf2UMQi0Y+cysNawzKppJ4swhDTgw7z8BqVMJwF3GpQyQ=pTw@mail.gmail.com>

Hi Yurii,

if you can provide 0 level pixels, the rest can be computed using e.g.
Maurer
<https://itk.org/Doxygen/html/classitk_1_1SignedMaurerDistanceMapImageFilter.html>
filter.

Regards

On Wed, Jun 15, 2016 at 12:00 PM, Yurii Borokh <y.borokh at gmail.com> wrote:

> Hi all,I'm searching for a filter that could effectively create an image
> from
> a signed distance function.Of course, it can be done straightforwardly by
> calculation of distance in each pixel. But I would like to minimize the
> number of calls to distance function since it's implemented via RBF and
> calls are rather expensive. Does ITK has some kind of such
> functionality?Any
> hints would be appreciated.Regards,Yurii
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/Fast-image-creation-from-a-signed-distance-function-tp7588969.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From dzenanz at gmail.com  Wed Jun 22 06:46:05 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 22 Jun 2016 12:46:05 +0200
Subject: [ITK-users] Licensing question
In-Reply-To: <1039149860.11159873.1466490799507.JavaMail.yahoo@mail.yahoo.com>
References: <1039149860.11159873.1466490799507.JavaMail.yahoo.ref@mail.yahoo.com>
 <1039149860.11159873.1466490799507.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <CAPf2UMQx8X_HAAFmY0=39sFK8oa-GEVgPKXuPCzA8kuL5z58zA@mail.gmail.com>

TL;DR version:
http://www.apache.org/foundation/license-faq.html#WhatDoesItMEAN

Regards,
D?enan

On Tue, Jun 21, 2016 at 8:33 AM, Malsoaz James via Insight-users <
insight-users at itk.org> wrote:

> Hi,
>
> I would like to use ITK in a commercial application but I have some
> questions about the Apache2 license.
> Should I include somewhere the ITK copyright in my application? In source
> code? In related documents?
>
> Currently I'm using version 4.8. I made minor modifications in source file
> of ITK to fit my needs. Should I publish these changes?
>
> Thank you for your answer.
> Best regards,
>
> James
>
> _____________________________________
> 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
>
>
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From shrikantvc at gmail.com  Wed Jun 22 11:50:48 2016
From: shrikantvc at gmail.com (shrikant)
Date: Wed, 22 Jun 2016 08:50:48 -0700 (MST)
Subject: [ITK-users] image registration in MATALAB vs ITK.
Message-ID: <1466610648735-7588990.post@n2.nabble.com>

Hi,

I am new to ITK, i have working MATLAB registration as a below code. Please
note that here I am registering fixed image with high features and moving
image with very low signal.

[optimizer,metric]=imregconfig('multimodal');
tr1 = imregtform(movingImage, fixedImageResized, 'translation', optimizer,
metric);

I need to convert into ITK 4 code. I am using below ITK code 
  
  typedef itk::ImageRegistrationMethodv4<ITKImageType, ITKImageType,
TransformType> RegistrationType;
  RegistrationType::Pointer registration = RegistrationType::New();
  RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel;
  RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel;
  MetricType::Pointer metric = MetricType::New();

  metric->SetNumberOfHistogramBins(50);
  metric->SetUseMovingImageGradientFilter(true);
  metric->SetUseFixedImageGradientFilter(true);
  registration->SetMetric(metric);


  RSGDOptimizerType::Pointer smartOptimizer = RSGDOptimizerType::New();
  smartOptimizer->SetLearningRate(0.5);
  smartOptimizer->SetMaximumStepSizeInPhysicalUnits(0.001);
  smartOptimizer->SetMinimumStepLength(0.0001);
  smartOptimizer->SetNumberOfIterations(100);
  smartOptimizer->ReturnBestParametersAndValueOn();
  smartOptimizer->SetRelaxationFactor(0.5);
  registration->SetOptimizer(smartOptimizer);


  registration->SetNumberOfLevels(1);

  shrinkFactorsPerLevel.SetSize(1);
  shrinkFactorsPerLevel[0] = 1;
  registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel);
  smoothingSigmasPerLevel.SetSize(1);
  smoothingSigmasPerLevel[0] = 0;
  registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel);


  registration->SetMetricSamplingStrategy(RegistrationType::REGULAR);
  registration->SetMetricSamplingPercentage(100);

  registration->Update();

  TransformType::ParametersType finalParameters =  
registration->GetOutput()->Get()->GetParameters();
  yTranslation = finalParameters[1];

Here I am getting huge differences like, -0.33 (ITK) vs -1.20(MATLAB) mm. If
I see visually then matlab results look more correct.

Any idea what is going wrong here?

Any help would be highly appreciated.




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/image-registration-in-MATALAB-vs-ITK-tp7588990.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From chinander at gmail.com  Wed Jun 22 13:40:11 2016
From: chinander at gmail.com (Mike Chinander)
Date: Wed, 22 Jun 2016 12:40:11 -0500
Subject: [ITK-users] Wrap new filter for CSharp
Message-ID: <CAEb_q0fO+ZNnqeonxu4JvNPu1hZwQEk9dCczck-xD2UNvMAEbQ@mail.gmail.com>

Are the instructions here [1] applicable to wrapping filters for CSharp?
I'd like to use the SiddonJacobsRayCastInterpolateImageFunction in C# from
a SimpleITK Superbuild.

Thanks,

--Mike Chinander

[1]
https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1500009.5
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From dan.muel at gmail.com  Wed Jun 22 23:27:36 2016
From: dan.muel at gmail.com (Dan Mueller)
Date: Thu, 23 Jun 2016 12:57:36 +0930
Subject: [ITK-users] Wrap new filter for CSharp
In-Reply-To: <CAEb_q0fO+ZNnqeonxu4JvNPu1hZwQEk9dCczck-xD2UNvMAEbQ@mail.gmail.com>
References: <CAEb_q0fO+ZNnqeonxu4JvNPu1hZwQEk9dCczck-xD2UNvMAEbQ@mail.gmail.com>
Message-ID: <CAPNvZ5YnyRRm6dGzo0MMayXFeK8JxRUSeiGG_tsGcxBMKR4Z5w@mail.gmail.com>

Hi Mike,

No, the link you reference is for ITK wrappers, not SimpleITK (ITK and
SimpleITK are different -- SimpleITK is built on top of ITK).

If you want to wrap this filter in SimpleITK, the following links may be
helpful:
https://itk.org/SimpleITKDoxygen/html/FilterTemplatesPage.html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874546/

Cheers, Dan
On 23 Jun 2016 3:10 am, "Mike Chinander" <chinander at gmail.com> wrote:

> Are the instructions here [1] applicable to wrapping filters for CSharp?
> I'd like to use the SiddonJacobsRayCastInterpolateImageFunction in C# from
> a SimpleITK Superbuild.
>
> Thanks,
>
> --Mike Chinander
>
> [1]
> https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1500009.5
>
> _____________________________________
> 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
>
>
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From marco.giord at gmail.com  Thu Jun 23 09:15:44 2016
From: marco.giord at gmail.com (marco giordano)
Date: Thu, 23 Jun 2016 15:15:44 +0200
Subject: [ITK-users] [ITK] Read 4D CT cardiac dicom series and save it
 as a single 4D nifti file
In-Reply-To: <CAF3iUbK7k5Yd8KW3PTbXwPPdS7mNNkTWnamKg6x8wszXJJBMew@mail.gmail.com>
References: <CAF3iUb+vc=58hXotfiVG1U7NgABwFV2Yu3bO98a7PyEaL=B6Pw@mail.gmail.com>
 <1465484786789-7588963.post@n2.nabble.com>
 <CANbSmSchv53_pzo3ioB4yrn-Shp=_-UOBBfy0in31XBp54+uDw@mail.gmail.com>
 <CAF3iUbL6ESHd+j4hWn_HNuuc6aP9XB0LQh7Ub03h=ufvvmJc5w@mail.gmail.com>
 <DM2PR07MB350E83D9D05861C13533DF0D8510@DM2PR07MB350.namprd07.prod.outlook.com>
 <CAF3iUbK7k5Yd8KW3PTbXwPPdS7mNNkTWnamKg6x8wszXJJBMew@mail.gmail.com>
Message-ID: <CAF3iUbJfXAUmdYivOdQZ5U3ZJBq2UOh4F7RzdOg8_b9r-NNPVQ@mail.gmail.com>

Hi there,

I managed to read the 4D CT cardiac dataset by importing each volume
separately and writing it in a 4D image with an iterator. It assumes the
origin of the first series  is the correct one. With some adaptations it
can read also semi-volumes and stitch them together (still in progress) .I
share the routine here, maybe it is useful to someone:

https://github.com/marcogiord/esercizi/blob/master/itk/DicomRead4DTimeSeries_SingleDicomVolumes.cpp

Marco
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From blowekamp at mail.nih.gov  Thu Jun 23 10:21:44 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 23 Jun 2016 14:21:44 +0000
Subject: [ITK-users] image registration in MATALAB vs ITK.
In-Reply-To: <1466610648735-7588990.post@n2.nabble.com>
References: <1466610648735-7588990.post@n2.nabble.com>
Message-ID: <D825266B-7C80-4A59-83A0-221DD2A6ACAA@mail.nih.gov>

Hello,

One key feature of ITK is that is does just about everything with respect to physical space, as opposed to considering things just a matrix of numbers.

This can make setting up the parameters data dependent and tricker. There is the scales estimator which can be used to help certain aspects of this [1], but this then interacts with your learning rate.

Also make sure to use the callbacks to print the parameters and metric value during the optimization [2].

You need to study the optimization process and algorithm to determine why its not covering correctly.

HTH,
Brad



[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration1.cxx#L442-L450
[2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration1.cxx#L469-L471

> On Jun 22, 2016, at 11:50 AM, shrikant <shrikantvc at gmail.com> wrote:
> 
> Hi,
> 
> I am new to ITK, i have working MATLAB registration as a below code. Please
> note that here I am registering fixed image with high features and moving
> image with very low signal.
> 
> [optimizer,metric]=imregconfig('multimodal');
> tr1 = imregtform(movingImage, fixedImageResized, 'translation', optimizer,
> metric);
> 
> I need to convert into ITK 4 code. I am using below ITK code 
> 
>  typedef itk::ImageRegistrationMethodv4<ITKImageType, ITKImageType,
> TransformType> RegistrationType;
>  RegistrationType::Pointer registration = RegistrationType::New();
>  RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel;
>  RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel;
>  MetricType::Pointer metric = MetricType::New();
> 
>  metric->SetNumberOfHistogramBins(50);
>  metric->SetUseMovingImageGradientFilter(true);
>  metric->SetUseFixedImageGradientFilter(true);
>  registration->SetMetric(metric);
> 
> 
>  RSGDOptimizerType::Pointer smartOptimizer = RSGDOptimizerType::New();
>  smartOptimizer->SetLearningRate(0.5);
>  smartOptimizer->SetMaximumStepSizeInPhysicalUnits(0.001);
>  smartOptimizer->SetMinimumStepLength(0.0001);
>  smartOptimizer->SetNumberOfIterations(100);
>  smartOptimizer->ReturnBestParametersAndValueOn();
>  smartOptimizer->SetRelaxationFactor(0.5);
>  registration->SetOptimizer(smartOptimizer);
> 
> 
>  registration->SetNumberOfLevels(1);
> 
>  shrinkFactorsPerLevel.SetSize(1);
>  shrinkFactorsPerLevel[0] = 1;
>  registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel);
>  smoothingSigmasPerLevel.SetSize(1);
>  smoothingSigmasPerLevel[0] = 0;
>  registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel);
> 
> 
>  registration->SetMetricSamplingStrategy(RegistrationType::REGULAR);
>  registration->SetMetricSamplingPercentage(100);
> 
>  registration->Update();
> 
>  TransformType::ParametersType finalParameters =  
> registration->GetOutput()->Get()->GetParameters();
>  yTranslation = finalParameters[1];
> 
> Here I am getting huge differences like, -0.33 (ITK) vs -1.20(MATLAB) mm. If
> I see visually then matlab results look more correct.
> 
> Any idea what is going wrong here?
> 
> Any help would be highly appreciated.
> 
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/image-registration-in-MATALAB-vs-ITK-tp7588990.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 sg.ele.eng at gmail.com  Sun Jun 26 01:57:16 2016
From: sg.ele.eng at gmail.com (Sara Gh)
Date: Sun, 26 Jun 2016 01:57:16 -0400
Subject: [ITK-users] SimpleITK - Resampling Coronal Image in the Axial View
Message-ID: <CACjcMuasgTMj+=-BFO_vLUT6kWE73FBA6PewcLSFZNFm4Se7Sg@mail.gmail.com>

Hello experts,

I have two MRI scans: Axial and Coronal
# *imageA* : Axial MRI scan, size : 256x256x56 (256mmx256mmx168mm) ,
 spacing: 1,1,3  ( slice gap : 1  =>  slice thickness : 2)
# *imageC* : Coronal MRI scan, size : 256x256x68 (256mmx256mmx204mm) ,
 spacing: 1,1,3  ( slice gap : 1  =>  slice thickness : 2)

I am trying to view Coronal image from the axial view i.e. resampling
Coronal image using the direction of Axial image. Here is my code:

resample = sitk.ResampleImageFilter()
resample.SetReferenceImage(imageC)
resample.SetOutputDirection(imageA.GetDirection())
resample.SetOutputOrigin(imageA.GetOrigin())
imageCA = resample.Execute(imageC)
sitk.Show(imageCA)

# Result: imageCA: size : 256x256x68 (256mmx256mmx204mm), spacing: 1,1,3

I believe I have missed something because, in my idea, the size of
resampled coronal image (imageCA) should be 68x256x256 (204mmx256mmx256mm) with
the spacing [3,1,1].

I also tried to set the OutputSpacing to [3,1,1], but the size of the
imageCA changes to 256x256x68 (768mmx256mmx68mm).

I would be thankful if someone could help me in this regard.

Best regards,
Sara Gh
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From ibr_ex at yahoo.com  Sun Jun 26 11:40:33 2016
From: ibr_ex at yahoo.com (ibraheem aldhamari)
Date: Sun, 26 Jun 2016 15:40:33 +0000 (UTC)
Subject: [ITK-users] SimilarityIndexImageFilter, always zero output
References: <1186939577.686552.1466955633640.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <1186939577.686552.1466955633640.JavaMail.yahoo@mail.yahoo.com>

Hi all,Is there any example for using?itkSimilarityIndexImageFilter ? I keep getting zero for SimilarityIndex value even for the same image.
I appreciate your suggestions!? Ibrahim
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From ibr_ex at yahoo.com  Sun Jun 26 14:34:11 2016
From: ibr_ex at yahoo.com (ibraheem aldhamari)
Date: Sun, 26 Jun 2016 18:34:11 +0000 (UTC)
Subject: [ITK-users] SimilarityIndexImageFilter, always zero output
In-Reply-To: <1186939577.686552.1466955633640.JavaMail.yahoo@mail.yahoo.com>
References: <1186939577.686552.1466955633640.JavaMail.yahoo.ref@mail.yahoo.com>
 <1186939577.686552.1466955633640.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <1327306736.1941581.1466966051303.JavaMail.yahoo@mail.yahoo.com>

Sorry, I forgot to call update();now it works :).?Ibrahim

      From: ibraheem aldhamari via Insight-users <insight-users at itk.org>
 To: "insight-users at itk.org" <insight-users at itk.org> 
 Sent: Sunday, June 26, 2016 5:40 PM
 Subject: [ITK-users] SimilarityIndexImageFilter, always zero output
   
Hi all,Is there any example for using?itkSimilarityIndexImageFilter ? I keep getting zero for SimilarityIndex value even for the same image.
I appreciate your suggestions!? Ibrahim
_____________________________________
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


  
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From cervellone at gmail.com  Sun Jun 26 16:07:46 2016
From: cervellone at gmail.com (cervellone at gmail.com)
Date: Sun, 26 Jun 2016 22:07:46 +0200
Subject: [ITK-users] Import itk always takes ages and results in warnings
Message-ID: <CAO8H67PxXkXJgLSoKST2gOdfH2jRYmuL4D0hkE9RUVU-FGGU3A@mail.gmail.com>

Hello all,

Is there a way to speed up the import of itk in an application and the
suppression of the warnings I get every time I run the python script ?

Thank you all
JP


Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo<
3,float,float,unsigned long,unsigned long,unsigned
char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned
long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned
long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned
long,unsigned long,bool,bool,true > > >,std::set< unsigned long
>,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >'
in template 'itk::CellInterface'
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From tevain at telecom-paristech.fr  Mon Jun 27 05:40:01 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 27 Jun 2016 11:40:01 +0200 (CEST)
Subject: [ITK-users] [ITK] SimpleITK - Resampling Coronal Image in the
 Axial	View
In-Reply-To: <CACjcMuasgTMj+=-BFO_vLUT6kWE73FBA6PewcLSFZNFm4Se7Sg@mail.gmail.com>
References: <CACjcMuasgTMj+=-BFO_vLUT6kWE73FBA6PewcLSFZNFm4Se7Sg@mail.gmail.com>
Message-ID: <1561329490.15991909.1467020401395.JavaMail.zimbra@enst.fr>

Hello,

First of all, it depends on the patient position in the data, but usually the X axis describe the left/right direction, the Y axis the anterior/posterior direction and the Z axis the top/bottom one.
So I would expect the resampled imageC size to be 256x68x256 rather than 68x256x256.

Then, I think you should try to transform your imageC to be in the imageA orientation. Let say the imageA have a LPS coordinate system. 
If the imageC :
-first direction represents the axis going from the patient's right to the patient's left
-second direction represents the axis going from the patient's top to the patient's bottom
-third direction represents the axis going from the patient's front to the patient's rear
Then you should rotate the imageC by a -pi/2 angle around the X axis.

You could use the Euler3DTransform to get this rotation.
Then you feed the resample filter with this transform, plus the needed parameters (origin, spacing, size,...), and you should be able to have your resampled data.
Just be sure to fully understand the transformation you're making (I recommend the ResampleImageFilter part of the ITK guide which is quite useful).

HTH,

Tim


----- Mail original -----
De: "Sara Gh" <sg.ele.eng at gmail.com>
?: insight-users at itk.org
Envoy?: Dimanche 26 Juin 2016 07:57:16
Objet: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the Axial	View

Hello experts, 

I have two MRI scans: Axial and Coronal 
# imageA : Axial MRI scan, size : 256x256x56 (256mmx256mmx168mm) , spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 ) 
# imageC : Coronal MRI scan, size : 256x256x68 (256mmx256mmx204mm) , spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 ) 

I am trying to view Coronal image from the axial view i.e. resampling Coronal image using the direction of Axial image. Here is my code: 

resample = sitk.ResampleImageFilter() 
resample.SetReferenceImage(imageC) 
resample.SetOutputDirection(imageA.GetDirection()) 
resample.SetOutputOrigin(imageA.GetOrigin()) 
imageCA = resample.Execute(imageC) 
sitk.Show(imageCA) 

# Result: imageCA: size : 256x256x68 (256mmx256mmx204mm), spacing: 1,1,3 

I believe I have missed something because, in my idea, the size of resampled coronal image (imageCA) should be 68x256x256 ( 204mmx256mmx256mm) with the spacing [3,1,1] . 

I also tried to set the OutputSpacing to [3,1,1], but the size of the imageCA changes to 256x256x68 (768mmx256mmx68mm). 

I would be thankful if someone could help me in this regard. 

Best regards, 
Sara Gh 

_____________________________________
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 michkapopoff at gmail.com  Mon Jun 27 16:03:30 2016
From: michkapopoff at gmail.com (Michka Popoff)
Date: Mon, 27 Jun 2016 22:03:30 +0200
Subject: [ITK-users] Import itk always takes ages and results in warnings
In-Reply-To: <CAO8H67PxXkXJgLSoKST2gOdfH2jRYmuL4D0hkE9RUVU-FGGU3A@mail.gmail.com>
References: <CAO8H67PxXkXJgLSoKST2gOdfH2jRYmuL4D0hkE9RUVU-FGGU3A@mail.gmail.com>
Message-ID: <A651064C-2610-47EF-9DDE-914666F048D1@gmail.com>

Hi

to reduce the import time, one solution would be to reduce the number of wrapped modules
and types (and image/vector dimensions). If you re-build ITK by disabling the things you
don?t need, there will be less things to load.

I have some ideas on how to improve the import situation but never came to it, so
not sure anybody has been working intensively on that.

For the warnings, we need to fix them in ITK.
The QuadEdgeMeshCellTraitsInfo class is probably not be usable as is.

If you want to hide the warnings, you can use (like for other python warnings):

import warnings
warnings.simplefilter(?ignore", Warning)

You can reset the filter after the import.

That should to it.


Michka

> On 26 Jun 2016, at 22:07, cervellone at gmail.com wrote:
> 
> Hello all, 
> 
> Is there a way to speed up the import of itk in an application and the suppression of the warnings I get every time I run the python script ?
> 
> Thank you all 
> JP
> 
> 
> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
> 
> 
> _____________________________________
> 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 michkapopoff at gmail.com  Mon Jun 27 16:25:05 2016
From: michkapopoff at gmail.com (Michka Popoff)
Date: Mon, 27 Jun 2016 22:25:05 +0200
Subject: [ITK-users] Issue on itk.QuadEdgeMeshCellTraitsInfo
In-Reply-To: <1465709590989.57546@sphic.org.cn>
References: <1465709590989.57546@sphic.org.cn>
Message-ID: <C3D62BAE-8248-4854-93E1-27B7D49386EC@gmail.com>

Hi

thanks for reporting this. I also could reproduce the warnings.
I opened a bug for this here so we can keep track of it:
https://issues.itk.org/jira/browse/ITK-3448

The same error was also reported on the mailing list yesterday.
If you just want to hide the warning you can use:

import warnings
warnings.simplefilter(?ignore", Warning)

If you need to use QuadEdgeMeshCellTraitsInfo with Python,
somebody will need to fix this. I already gave it a shot, but
this may take some time. Not sure I will be able to look at
this until next week.

Thanks

Michka



> On 12 Jun 2016, at 07:33, ??? <zhuangming.shen at sphic.org.cn> wrote:
> 
> ?Hi all,
> 
> When I used python-supported ITK 4.10.0 to get the types of itk.QuadEdgeMeshCellTraitsInfo for the first time, I got two warnings
> 
> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
> <itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
> Options:
> 
> 
> If I run itk.QuadEdgeMeshCellTraitsInfo.GetTypes() again or use ITK 4.9.1 instead, it just displays
> 
> <itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
> Options:
> 
> 
> So what's the problem? What is the unknown parameter? Has someone met this issue? Thanks.
> 
> 
> Regards,
> 
> Zhuangming Shen
> 
> 
> 
> 
> 
> 
> 
> _____________________________________
> 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 cervellone at gmail.com  Tue Jun 28 04:59:08 2016
From: cervellone at gmail.com (cervellone at gmail.com)
Date: Tue, 28 Jun 2016 10:59:08 +0200
Subject: [ITK-users] Import itk always takes ages and results in warnings
In-Reply-To: <A651064C-2610-47EF-9DDE-914666F048D1@gmail.com>
References: <CAO8H67PxXkXJgLSoKST2gOdfH2jRYmuL4D0hkE9RUVU-FGGU3A@mail.gmail.com>
 <A651064C-2610-47EF-9DDE-914666F048D1@gmail.com>
Message-ID: <CAO8H67PRxGby0gt0ZzSUYMU0O=e+C1Gw1Pj4zvXSMsLs4+7esg@mail.gmail.com>

Dear Michka
Thank you for your reply.

I will take that into consideration when building ITK next time.
Unfortunately there is little comprehensive guide to what all those options
in cmake really mean or do, so id rather build more than less.
Also VTK is pretty heavy in term of modules, and I have the impression that
it is noticeably faster.
Best
JP

On Mon, Jun 27, 2016 at 10:03 PM, Michka Popoff <michkapopoff at gmail.com>
wrote:

> Hi
>
> to reduce the import time, one solution would be to reduce the number of
> wrapped modules
> and types (and image/vector dimensions). If you re-build ITK by disabling
> the things you
> don?t need, there will be less things to load.
>
> I have some ideas on how to improve the import situation but never came to
> it, so
> not sure anybody has been working intensively on that.
>
> For the warnings, we need to fix them in ITK.
> The QuadEdgeMeshCellTraitsInfo class is probably not be usable as is.
>
> If you want to hide the warnings, you can use (like for other python
> warnings):
>
> import warnings
> warnings.simplefilter(?ignore", Warning)
>
> You can reset the filter after the import.
>
> That should to it.
>
>
> Michka
>
> > On 26 Jun 2016, at 22:07, cervellone at gmail.com wrote:
> >
> > Hello all,
> >
> > Is there a way to speed up the import of itk in an application and the
> suppression of the warnings I get every time I run the python script ?
> >
> > Thank you all
> > JP
> >
> >
> > Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo<
> 3,float,float,unsigned long,unsigned long,unsigned
> char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned
> long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned
> long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned
> long,unsigned long,bool,bool,true > > >,std::set< unsigned long
> >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >'
> in template 'itk::CellInterface'
> >
> >
> > _____________________________________
> > 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
>
>
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From blowekamp at mail.nih.gov  Tue Jun 28 08:47:07 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 28 Jun 2016 12:47:07 +0000
Subject: [ITK-users] Import itk always takes ages and results in warnings
In-Reply-To: <CAO8H67PRxGby0gt0ZzSUYMU0O=e+C1Gw1Pj4zvXSMsLs4+7esg@mail.gmail.com>
References: <CAO8H67PxXkXJgLSoKST2gOdfH2jRYmuL4D0hkE9RUVU-FGGU3A@mail.gmail.com>
 <A651064C-2610-47EF-9DDE-914666F048D1@gmail.com>
 <CAO8H67PRxGby0gt0ZzSUYMU0O=e+C1Gw1Pj4zvXSMsLs4+7esg@mail.gmail.com>
Message-ID: <53A818A2-9662-45F8-BFEE-39FB05A28A5D@mail.nih.gov>

Hi JP,

Native ITK wrapping has a powerful set of features which include using template like classes. This allows for easy customization of the build and direct control over the input and output type of many filter. This does come at the cost of having a very large interface and currently long import time.

Have you looked into SimpleITK? It has a smaller interface, and less flexibility but it does load quite quickly (.3s) into Python.

HTH,
Brad

On Jun 28, 2016, at 4:59 AM, cervellone at gmail.com<mailto:cervellone at gmail.com> wrote:

Dear Michka
Thank you for your reply.

I will take that into consideration when building ITK next time.
Unfortunately there is little comprehensive guide to what all those options in cmake really mean or do, so id rather build more than less.
Also VTK is pretty heavy in term of modules, and I have the impression that it is noticeably faster.
Best
JP

On Mon, Jun 27, 2016 at 10:03 PM, Michka Popoff <michkapopoff at gmail.com<mailto:michkapopoff at gmail.com>> wrote:
Hi

to reduce the import time, one solution would be to reduce the number of wrapped modules
and types (and image/vector dimensions). If you re-build ITK by disabling the things you
don?t need, there will be less things to load.

I have some ideas on how to improve the import situation but never came to it, so
not sure anybody has been working intensively on that.

For the warnings, we need to fix them in ITK.
The QuadEdgeMeshCellTraitsInfo class is probably not be usable as is.

If you want to hide the warnings, you can use (like for other python warnings):

import warnings
warnings.simplefilter(?ignore", Warning)

You can reset the filter after the import.

That should to it.


Michka

> On 26 Jun 2016, at 22:07, cervellone at gmail.com<mailto:cervellone at gmail.com> wrote:
>
> Hello all,
>
> Is there a way to speed up the import of itk in an application and the suppression of the warnings I get every time I run the python script ?
>
> Thank you all
> JP
>
>
> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
>
>
> _____________________________________
> 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


_____________________________________
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

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From scorpiuni at gmail.com  Tue Jun 28 15:52:09 2016
From: scorpiuni at gmail.com (Robert)
Date: Tue, 28 Jun 2016 12:52:09 -0700 (MST)
Subject: [ITK-users] Filters in 3D
Message-ID: <1467143529556-7589004.post@n2.nabble.com>

Hello,

 I have a general question about 3D filters, especially about the
SignedDanielssonDistanceMapImageFilter.
Does this filter work Slice by Slice when using 3-dimensional data, or does
the calculation of the euclidian distance take into account the 3
coordinates of a voxel? I guess sometimes the result would be quite similar,
but I constructed some examples on paper where there would be a difference.
Is there any place where this is marked down for the different filters?

Thanks in advance,
Robert



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Filters-in-3D-tp7589004.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From basafa at clearguidemedical.com  Tue Jun 28 16:08:00 2016
From: basafa at clearguidemedical.com (ebasafa)
Date: Tue, 28 Jun 2016 13:08:00 -0700 (MST)
Subject: [ITK-users] Filters in 3D
In-Reply-To: <1467143529556-7589004.post@n2.nabble.com>
References: <1467143529556-7589004.post@n2.nabble.com>
Message-ID: <1467144480931-7589005.post@n2.nabble.com>

Hi Robert,

As far as I know, all ITK filters are templated over the input/output image
type(s), which means you set the dimensions as you define the image types to
work with. I don't have experience with that particular filter, but seems
like it's no exception.

That being said, there is a filter that lets you apply a filter or a bunch
of filters on individual slices of an input volume
(itkSliceBySliceImageFilter). Basically you assign to it input image(s) and
filter(s) and it applies those filter(s) on individual slices of those
image(s). Obviously, those filters need to be able to work with images of
one dimension less than your input image.

I presume the results will differ if a filter that calculates distances is
applied on 2D vs 3D images.

HTH
Ehsan


Robert wrote
> Hello,
> 
>  I have a general question about 3D filters, especially about the
> SignedDanielssonDistanceMapImageFilter.
> Does this filter work Slice by Slice when using 3-dimensional data, or
> does the calculation of the euclidian distance take into account the 3
> coordinates of a voxel? I guess sometimes the result would be quite
> similar, but I constructed some examples on paper where there would be a
> difference. Is there any place where this is marked down for the different
> filters?
> 
> Thanks in advance,
> Robert





--
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From scorpiuni at gmail.com  Tue Jun 28 16:21:44 2016
From: scorpiuni at gmail.com (Robert)
Date: Tue, 28 Jun 2016 13:21:44 -0700 (MST)
Subject: [ITK-users] Filters in 3D
In-Reply-To: <1467144480931-7589005.post@n2.nabble.com>
References: <1467143529556-7589004.post@n2.nabble.com>
 <1467144480931-7589005.post@n2.nabble.com>
Message-ID: <1467145304984-7589006.post@n2.nabble.com>

Thanks for the fast reply, however, this does not yet quite answer my
question.
I used the filter, as you said, with dimension 3 inside my code. I know
about the Slice by Slice Filter, however, I want to know how it works
specifically when using the template for dimension 3.
I mean, I could apply it slice by slice, then apply it with dimension 3 and
then calculate the difference, but I thought that maybe someone already
tested this once ;)
Basically, my question is if the template for dimension 3 uses the Slice by
Slice approach, or if it uses "real" 3d coordinates.

Thanks for you reply however.



--
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From matt.mccormick at kitware.com  Tue Jun 28 18:16:17 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 28 Jun 2016 18:16:17 -0400
Subject: [ITK-users] ResampleDICOM Assertion Error
In-Reply-To: <CANbSmSdFbdPxf5fGyNCJHoUir8p+3cn5WmMo-pXVQcvjPoWRbA@mail.gmail.com>
References: <CANbSmSdFbdPxf5fGyNCJHoUir8p+3cn5WmMo-pXVQcvjPoWRbA@mail.gmail.com>
Message-ID: <CALzTN-SZzgMCiV9EXcrF8DNbgg7Wbc_H1tZDopfE6+1-eYCNLg@mail.gmail.com>

Hi Sarthak,

ITK 4.10.0 was updated to use the GDCM release branch. Please try
4.10.0 and let us know how it goes.

Thanks,
Matt

On Mon, Jun 20, 2016 at 10:31 AM, Scapegoat Sarthak
<scapegoat.sarthak at gmail.com> wrote:
> Hello All,
>
> I have been trying (unsuccessfully) to write a DICOM series with non-integer
> slopes. I have seen in an earlier community post (reference -
> http://public.kitware.com/pipermail/community/2014-September/007143.html)
> about the exact same issue and it is still not resolved (I am running
> version 4.9.0.
>
> Can someone from the moderators' side confirm in which version this has been
> taken care of (if at all)?
>
> Thanks,
> Sarthak
>
> _____________________________________
> 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 dzenanz at gmail.com  Wed Jun 29 09:52:06 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 29 Jun 2016 09:52:06 -0400
Subject: [ITK-users] Filters in 3D
In-Reply-To: <1467145304984-7589006.post@n2.nabble.com>
References: <1467143529556-7589004.post@n2.nabble.com>
 <1467144480931-7589005.post@n2.nabble.com>
 <1467145304984-7589006.post@n2.nabble.com>
Message-ID: <CAPf2UMTBDxmS4VWR9JMbdVkXQtAY13sjcRbRfPwX_02FfR-X2Q@mail.gmail.com>

Hi Robert,

Danielsson's and Maurer's filters use real 3D coordinates for distances.

Regards,
D?enan

On Tue, Jun 28, 2016 at 4:21 PM, Robert <scorpiuni at gmail.com> wrote:

> Thanks for the fast reply, however, this does not yet quite answer my
> question.
> I used the filter, as you said, with dimension 3 inside my code. I know
> about the Slice by Slice Filter, however, I want to know how it works
> specifically when using the template for dimension 3.
> I mean, I could apply it slice by slice, then apply it with dimension 3 and
> then calculate the difference, but I thought that maybe someone already
> tested this once ;)
> Basically, my question is if the template for dimension 3 uses the Slice by
> Slice approach, or if it uses "real" 3d coordinates.
>
> Thanks for you reply however.
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/Filters-in-3D-tp7589004p7589006.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
>
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From matt.mccormick at kitware.com  Wed Jun 29 11:30:22 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 29 Jun 2016 11:30:22 -0400
Subject: [ITK-users] Licensing question
In-Reply-To: <CAPf2UMQx8X_HAAFmY0=39sFK8oa-GEVgPKXuPCzA8kuL5z58zA@mail.gmail.com>
References: <1039149860.11159873.1466490799507.JavaMail.yahoo.ref@mail.yahoo.com>
 <1039149860.11159873.1466490799507.JavaMail.yahoo@mail.yahoo.com>
 <CAPf2UMQx8X_HAAFmY0=39sFK8oa-GEVgPKXuPCzA8kuL5z58zA@mail.gmail.com>
Message-ID: <CALzTN-Tr5rvMKvRsXnoP9O4d2+ysHr+4D+Pb8nwzMyp5EYDiDA@mail.gmail.com>

Hi James,

If your modifications would be useful to others, your contributions
are welcome. Please see

  https://itk.org/Wiki/ITK/Git/Develop

for the process.

Thanks,
Matt

On Wed, Jun 22, 2016 at 6:46 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> TL;DR version:
> http://www.apache.org/foundation/license-faq.html#WhatDoesItMEAN
>
> Regards,
> D?enan
>
> On Tue, Jun 21, 2016 at 8:33 AM, Malsoaz James via Insight-users
> <insight-users at itk.org> wrote:
>>
>> Hi,
>>
>> I would like to use ITK in a commercial application but I have some
>> questions about the Apache2 license.
>> Should I include somewhere the ITK copyright in my application? In source
>> code? In related documents?
>>
>> Currently I'm using version 4.8. I made minor modifications in source file
>> of ITK to fit my needs. Should I publish these changes?
>>
>> Thank you for your answer.
>> Best regards,
>>
>> James
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From christopherrmullins at gmail.com  Thu Jun 30 11:55:03 2016
From: christopherrmullins at gmail.com (Christopher Mullins)
Date: Thu, 30 Jun 2016 11:55:03 -0400
Subject: [ITK-users] Build errors in python wrapping of 4.10.0
In-Reply-To: <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu>
References: <CAL1JtzBgoYx3k7xn_pff9s5M9AGLFuKE0ZQJb4Wen0BkAHkzNA@mail.gmail.com>
 <D452B2C7-BD65-426B-BC46-A10C642DB70A@gmail.com>
 <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu>
Message-ID: <CAL1JtzDwp5dx-yKpk52OxTg6h0gLt_xMg-c0ZUCpkF_cJ3hk2A@mail.gmail.com>

Hi all,

Thanks for the help on this.  I've been traveling and haven't had much time
to investigate, but I believe Michka is correct.  It looks like the build
is successful with the -std=c++98 flag, and only one test fails [1].  I'll
test the python wrapping and report back if anything terrible happens -- if
not I'll bump the AUR PKGBUILD.  Thanks again,

Chris

[1] https://open.cdash.org/buildSummary.php?buildid=4435570

On Wed, Jun 15, 2016 at 5:22 PM, Johnson, Hans J <hans-johnson at uiowa.edu>
wrote:

> I?m trying to reproduce now.
>
> Hans
>
>
> --
>
>
> On 6/15/16, 4:12 PM, "Insight-users on behalf of Michka Popoff" <
> insight-users-bounces at itk.org on behalf of michkapopoff at gmail.com> wrote:
>
> >Hi
> >
> >I think this bug is not known. I had a look and could reproduce it with
> gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X.
> >GCC 6 is using c++14 by default, but even with c++11 you would probably
> get the problem.
> >The problem is also there with the latest commit from the master branch.
> >
> >Please note that we probably never tested Python Wrappings with c++11,
> even not speaking of c++14.
> >
> >The problem seems to have appeared with this patch:
> >
> https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395
> >
> >I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy
> constructor, and was able to compile
> >with gcc 6. But it may just a side effect of that patch which is now only
> appearing with c++ >= 11.
> >It is weird that the problem seems to be only for the itkTriangleHelper
> class.
> >
> >I will have to look what is the difference in the files generated for
> swig and what is exactly failing,
> >though I do not know how long it will take me. I hope I can do this this
> weekend.
> >
> >Thanks
> >
> >Michka
> >
> >
> >> On 09 Jun 2016, at 16:14, Christopher Mullins <
> christopherrmullins at gmail.com> wrote:
> >>
> >> Hi all,
> >>
> >> Apparently my subscription to this list has lapsed and my first email
> was rejected (despite receiving the list in my inbox every day).  Sorry if
> there's a double post.
> >>
> >> I'm getting the following build errors when building ITK 4.10.0 with
> the WRAP_PYTHON option ON[1], [3].  Is this a known issue, or is there a
> configuration setting I've set improperly?
> >>
> >> Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There
> are no warnings. See all output details for this machine here [2], and
> please let me know if I can provide any others.
> >>
> >> The faster I fix this the faster I'll feel comfortable updating the
> Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer.
> >>
> >> Thanks,
> >> Chris
> >>
> >>
> >>
> >> [1] https://open.cdash.org/viewBuildError.php?buildid=4403379
> >> [2] https://open.cdash.org/buildSummary.php?buildid=4403379
> >>
> >> [3] To save you a click, and for the sake of archiving, the error is:
> >>
> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:
> In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*,
> PyObject*)':
> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65:
> error: no matching function for call to
> 'itk::TriangleHelper<itk::Point<double, 2u> >::TriangleHelper()' result =
> (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
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> >http://www.kitware.com/products/protraining.php
> >
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