From dzenanz at gmail.com Mon Aug 1 09:38:18 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 1 Aug 2016 09:38:18 -0400 Subject: [ITK-dev] ITK wrapping with VS2013 Message-ID: Hi Brad and everybody, I am trying to build ITK with Ultrasound module, FFTW and wrapping for Python. This builds without errors on Linux, but on Windows I run into issues: 165> Building Custom Rule C:/Libs/InsightToolkit-4.10.0/Modules/External/ITKUltrasound/wrapping/CMakeLists.txt ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(720): warning 476: Initialization using std::initializer_list. ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(793): warning 476: Initialization using std::initializer_list. 165>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): error MSB6006: "cmd.exe" exited with code 28. The same error happens with ITK 4.10.0 and ITK git from 10 days ago. Can someone shed some light on the error and how to fix it? Regards, D?enan -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Mon Aug 1 11:21:16 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 1 Aug 2016 11:21:16 -0400 Subject: [ITK-dev] ITK fails to compile after recent update Message-ID: Folks, My clang compile of ITK fails to compile. clang version: Apple clang version 3.0 (tags/Apple/clang-211.12) (based on LLVM 3.0svn) Error: In file included from /Users/lorensen/ProjectsGIT/ITK/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler_detection.h:160: /Users/lorensen/ProjectsGIT/ITK/Modules/ThirdParty/VNL/src/vxl/vcl/compilers/VXL_COMPILER_INFO_Clang_CXX.h:6:8: error: #error Unsupported compiler version # error Unsupported compiler version Bill From blowekamp at mail.nih.gov Wed Aug 10 13:14:28 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 10 Aug 2016 17:14:28 +0000 Subject: [ITK-dev] Midas mirror script Message-ID: <2C043DCE-BEA2-44CC-AAD5-96B75EDF2A16@mail.nih.gov> Hello, I am looking to mirror the SimpleITK directory of the midas3.kitware.com MIDAS server. Are there any scripts around to aid in this? Thanks, Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: From taylor at braun-jones.org Mon Aug 15 18:21:37 2016 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 15 Aug 2016 18:21:37 -0400 Subject: [ITK-dev] Unable to login to review.source.kitware.com Message-ID: Hi all, I'm trying to login to Kitware's Gerrit instance in order to submit an ITK patch and getting the following message after I approve access to my GitHub account information: [image: Inline image 1] Any ideas? The GitHub account I'm using is nocnokneo with primary email address taylor at braun-jones.org Thanks in advance, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 10932 bytes Desc: not available URL: From taylor at braun-jones.org Mon Aug 15 18:32:00 2016 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 15 Aug 2016 18:32:00 -0400 Subject: [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: On Mon, Aug 15, 2016 at 6:21 PM, Taylor Braun-Jones wrote: > > I'm trying to login to Kitware's Gerrit instance in order to submit an ITK patch and getting the following message after I approve access to my GitHub account information: > > Any ideas? The GitHub account I'm using is nocnokneo with primary email address taylor at braun-jones.org I just noticed the note on the ITK wiki about OAuth access: > OAuth currently requests R/W access to GitHub repositories. However, none of the repositories will be modified. My Github account is a member of a private Github organization with private repos. Could this be the source of the problem? From dzenanz at gmail.com Tue Aug 16 10:23:24 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 16 Aug 2016 10:23:24 -0400 Subject: [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: Hi Taylor, did the issue go away by now? Regards, D?enan On Mon, Aug 15, 2016 at 6:32 PM, Taylor Braun-Jones wrote: > On Mon, Aug 15, 2016 at 6:21 PM, Taylor Braun-Jones > wrote: > > > > I'm trying to login to Kitware's Gerrit instance in order to submit an > ITK patch and getting the following message after I approve access to my > GitHub account information: > > > > Any ideas? The GitHub account I'm using is nocnokneo with primary email > address taylor at braun-jones.org > > I just noticed the note on the ITK wiki about OAuth access: > > > OAuth currently requests R/W access to GitHub repositories. However, > none of the repositories will be modified. > > My Github account is a member of a private Github organization with > private repos. Could this be the source of the problem? > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Aug 16 11:00:37 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Aug 2016 11:00:37 -0400 Subject: [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: Hi Taylor, The error comes up for folks with an older account where a sign in did not occur during the transition from OpenID to GitHub OAuth. The administrators will reset your old account, and you will be good to go. Thanks, Matt On Mon, Aug 15, 2016 at 6:21 PM, Taylor Braun-Jones wrote: > Hi all, > > I'm trying to login to Kitware's Gerrit instance in order to submit an ITK > patch and getting the following message after I approve access to my GitHub > account information: > > [image: Inline image 1] > > Any ideas? The GitHub account I'm using is nocnokneo with primary email > address taylor at braun-jones.org > > Thanks in advance, > Taylor > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 10932 bytes Desc: not available URL: From taylor at braun-jones.org Tue Aug 16 11:15:12 2016 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Tue, 16 Aug 2016 11:15:12 -0400 Subject: [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: On Tue, Aug 16, 2016 at 11:00 AM, Matt McCormick wrote: > The error comes up for folks with an older account where a sign in did not > occur during the transition from OpenID to GitHub OAuth. > > The administrators will reset your old account, and you will be good to go. > Great, thank you. I'll wait for that account reset to go through. Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Aug 22 12:57:36 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 Aug 2016 12:57:36 -0400 Subject: [ITK-dev] Midas mirror script In-Reply-To: <2C043DCE-BEA2-44CC-AAD5-96B75EDF2A16@mail.nih.gov> References: <2C043DCE-BEA2-44CC-AAD5-96B75EDF2A16@mail.nih.gov> Message-ID: Hi Brad, I am not aware of a script to download / mirror a directory on midas3.kitware.com. However, last week we performed a one-time mirror of the ITK Community on midas3.kitware.com (including all the SimpleITK data), to the Girder instance on data.kitware.com: https://data.kitware.com/#collection/57b5c9e58d777f126827f5a1/folder/57b5dd988d777f10f2695f32 There is a command line and Python client that can be used to locally mirror the data: http://girder.readthedocs.io/en/latest/python-client.html A patch is in progress to add testing data support to the ExternalData CMake module: http://review.source.kitware.com/#/c/21468/ An important difference to note between Girder and Midas is that Girder does not support different revisions for the same file. HTH, Matt On Wed, Aug 10, 2016 at 1:14 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Hello, > > I am looking to mirror the SimpleITK directory of the midas3.kitware.com > MIDAS server. Are there any scripts around to aid in this? > > Thanks, > Brad > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > From blowekamp at mail.nih.gov Mon Aug 22 15:49:22 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Mon, 22 Aug 2016 19:49:22 +0000 Subject: [ITK-dev] CircleCi for ITK? Message-ID: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> Hello, I have gotten CircleCi to compile and test SimpleITK[1]. Occasionally it runs into some memory problems linking, but I was able to over come the time constraint by compiling the library and tests by utilizing distcc with multiple containers, then dividing the testing across the containers. Based on that work, I was able to do a similar thing for ITK and created a pull request on github with the current status[2]. I would like to discontinue the current ITK continuous builds. The current continuous build should be able to be replaced with the some of the Continuous Integration services available online in a modern on demand basis. The next step would be to update the script to report to CDash correctly. I would also note that this may be a better way to test many External/Remote ITK modules as it would avoid the maintaince of multiple docker images. Brad [1] https://circleci.com/gh/SimpleITK/SimpleITK [2] https://github.com/InsightSoftwareConsortium/ITK/pull/14 From bill.lorensen at gmail.com Mon Aug 22 16:11:51 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 22 Aug 2016 16:11:51 -0400 Subject: [ITK-dev] [ITK] CircleCi for ITK? In-Reply-To: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> References: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> Message-ID: Certainly needs integration into ctest. I find the current reporting to be confusing. On Mon, Aug 22, 2016 at 3:49 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Hello, > > I have gotten CircleCi to compile and test SimpleITK[1]. Occasionally it runs into some memory problems linking, but I was able to over come the time constraint by compiling the library and tests by utilizing distcc with multiple containers, then dividing the testing across the containers. > > Based on that work, I was able to do a similar thing for ITK and created a pull request on github with the current status[2]. > > I would like to discontinue the current ITK continuous builds. The current continuous build should be able to be replaced with the some of the Continuous Integration services available online in a modern on demand basis. The next step would be to update the script to report to CDash correctly. > > I would also note that this may be a better way to test many External/Remote ITK modules as it would avoid the maintaince of multiple docker images. > > Brad > > [1] https://circleci.com/gh/SimpleITK/SimpleITK > [2] https://github.com/InsightSoftwareConsortium/ITK/pull/14 > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -- Unpaid intern in BillsBasement at noware dot com From matt.mccormick at kitware.com Mon Aug 22 16:16:58 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 Aug 2016 16:16:58 -0400 Subject: [ITK-dev] CircleCi for ITK? In-Reply-To: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> References: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> Message-ID: Thanks for looking into this, Brad. The CircleCI service has been enabled for the ITK repository: https://circleci.com/gh/InsightSoftwareConsortium/ITK It would be great to have Continuous builds via this service. Of course, we still need the current Gerrit/Jenkins system for code review, Windows builds, and CDash integration. Thanks, Matt On Mon, Aug 22, 2016 at 3:49 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Hello, > > I have gotten CircleCi to compile and test SimpleITK[1]. Occasionally it runs into some memory problems linking, but I was able to over come the time constraint by compiling the library and tests by utilizing distcc with multiple containers, then dividing the testing across the containers. > > Based on that work, I was able to do a similar thing for ITK and created a pull request on github with the current status[2]. > > I would like to discontinue the current ITK continuous builds. The current continuous build should be able to be replaced with the some of the Continuous Integration services available online in a modern on demand basis. The next step would be to update the script to report to CDash correctly. > > I would also note that this may be a better way to test many External/Remote ITK modules as it would avoid the maintaince of multiple docker images. > > Brad > > [1] https://circleci.com/gh/SimpleITK/SimpleITK > [2] https://github.com/InsightSoftwareConsortium/ITK/pull/14 > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers From k.marstal at erasmusmc.nl Tue Aug 23 12:04:43 2016 From: k.marstal at erasmusmc.nl (K.K. Marstal) Date: Tue, 23 Aug 2016 16:04:43 +0000 Subject: [ITK-dev] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler Message-ID: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl> Hello, As discussed in this gerrit ticket http://review.source.kitware.com/#/c/20900 the recent change to itkGetStaticConstMacro hides the ImageBase::ImageDimension symbol for linking in some cases. While the problem seemed to have been solved in that particular case, I am getting the same error compiling SimpleITK and linking against the Python wrapper on Mac OS X with GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5) compiler. The issue is fixed if I change line 780 of itkMacro.h "itkStaticConstMacro(name,type,value) static ITK_CONSTEXPR type name = value" back the version of itk 4.8.2, namely "#define itkStaticConstMacro(name, type, value) enum { name = value }". To clarify, the problem seem to be with ITK, not with SimpleITK. Kind Regards, Kasper Marstal -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Aug 23 15:10:09 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 23 Aug 2016 19:10:09 +0000 Subject: [ITK-dev] [ITK] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler In-Reply-To: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl> References: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl> Message-ID: <5CE651EE-994F-42A2-936F-71D71BA748EF@mail.nih.gov> Hello, Do you have a specific version of SimpleITK and ITK and Xcode which cause this problem? The current SimpleITK master with Xcode 7.3 seems ok to me. Brad On Aug 23, 2016, at 12:04 PM, K.K. Marstal > wrote: Hello, As discussed in this gerrit ticket http://review.source.kitware.com/#/c/20900 the recent change to itkGetStaticConstMacro hides the ImageBase::ImageDimension symbol for linking in some cases. While the problem seemed to have been solved in that particular case, I am getting the same error compiling SimpleITK and linking against the Python wrapper on Mac OS X with GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5) compiler. The issue is fixed if I change line 780 of itkMacro.h "itkStaticConstMacro(name,type,value) static ITK_CONSTEXPR type name = value" back the version of itk 4.8.2, namely "#define itkStaticConstMacro(name, type, value) enum { name = value }". To clarify, the problem seem to be with ITK, not with SimpleITK. Kind Regards, Kasper Marstal _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From andinet.enqu at kitware.com Tue Aug 23 20:15:34 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Tue, 23 Aug 2016 20:15:34 -0400 Subject: [ITK-dev] ANN:Kitware is hiring software developers for ITK and 3D Slicer Message-ID: Apologies for duplicate postings. =================== Hi folks, Kitware is seeking to hire highly skilled software developers to assist us in creating high quality software by utilizing and extending ITK and 3D Slicer for our research and commercial collaborations. If you are interested in this opportunity, please consider applying. Software Developer for ITK and Slicer http://tinyurl.com/h3e6ukh Another opportunity in the Medical Computing group: Research and Development Involving Machine Learning and Medical Image Analysis http://tinyurl.com/hy58kq8 For other job openings including internships at Kitware, please check http://jobs.kitware.com/opportunities.html -- Andinet Enquobahrie, Ph.D., MBA Assistant Director of Medical Computing Kitware, Inc. http://www.kitware.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From k.marstal at erasmusmc.nl Wed Aug 24 06:26:25 2016 From: k.marstal at erasmusmc.nl (K.K. Marstal) Date: Wed, 24 Aug 2016 10:26:25 +0000 Subject: [ITK-dev] [ITK] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler In-Reply-To: <5CE651EE-994F-42A2-936F-71D71BA748EF@mail.nih.gov> References: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl>, <5CE651EE-994F-42A2-936F-71D71BA748EF@mail.nih.gov> Message-ID: <1868B119ADBA1240A7DB9DF965237231D98B9A97@EXCH-HE03.erasmusmc.nl> I am using xcode 7.3.1, ITK v4.10, and SimpleITK v0.10.0. I should clarify that SimpleITK itself compiles and links allright, but the error happens when linking against my own extensions to SimpleITK (https://github.com/kaspermarstal/SimpleElastix). The way itkStaticConstMacro and the ImageDimension is used here here https://github.com/kaspermarstal/elastix/blob/641c83af7f97dfe2397e26e832cdda76e166fd14/src/Core/Main/elxElastixFilter.h#L80-L81 seems to hide the ImageDimension symbol during linking, much in the same way as in the referenced gerrit discussion. There are workarounds of course, just thought you should know. Kasper ________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Tuesday, August 23, 2016 9:10 PM To: K.K. Marstal Cc: insight-developers at itk.org Subject: Re: [ITK] [ITK-dev] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler Hello, Do you have a specific version of SimpleITK and ITK and Xcode which cause this problem? The current SimpleITK master with Xcode 7.3 seems ok to me. Brad On Aug 23, 2016, at 12:04 PM, K.K. Marstal > wrote: Hello, As discussed in this gerrit ticket http://review.source.kitware.com/#/c/20900 the recent change to itkGetStaticConstMacro hides the ImageBase::ImageDimension symbol for linking in some cases. While the problem seemed to have been solved in that particular case, I am getting the same error compiling SimpleITK and linking against the Python wrapper on Mac OS X with GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5) compiler. The issue is fixed if I change line 780 of itkMacro.h "itkStaticConstMacro(name,type,value) static ITK_CONSTEXPR type name = value" back the version of itk 4.8.2, namely "#define itkStaticConstMacro(name, type, value) enum { name = value }". To clarify, the problem seem to be with ITK, not with SimpleITK. Kind Regards, Kasper Marstal _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From sepideh.movaghati at gmail.com Mon Aug 29 13:54:45 2016 From: sepideh.movaghati at gmail.com (sepideh movaghati) Date: Mon, 29 Aug 2016 13:54:45 -0400 Subject: [ITK-dev] Source of Non-deterministic behavior of Registration v4 Message-ID: Hi, I posted the same issue on insight-users initially but then I thought it would be more relevant to developers mailing list. I was observing an unexpected non-deterministic behavior while changing the order of completely unrelated registrations. In the following example, my test revealed that transform and transform' are not identical: transform = Register(image1, image2); vs. transform-foo = Register(image-foo1, image-foo2); transform' = Register(image1, image2); I looked into the source of this non-deterministic behavior while making sure the metric sampling strategy has been set to Regular. Eventually I found the cause of the problem in itkRegistrationParametersScaleEstimator class. In this class there are two functions SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the sampling strategy is chosen based on the Transformation type. For example if the transformation is of type displacement field or BSpline, it uses all of the samples. If transformation is any regular affine or rigid transformation (child of class MatrixOffsetTransformBase) it performs corner sampling. However, if the transformation is none of the known ones, it uses Random Sampling. In my test I was using one level rigid transformation (v4). But here is were the problem happens: in itkImageRegistrationMethodv4.hxx the Metric transformation (MovingTransform) always set to a CompositeTransform! Therefore, ScaleEstimator cannot detect the transformation type and it always fall into "else" which is using Random Sampling! It does not matter if you do a multilevel registration or not. The transformation is always of type CompositeTransform. By changing the sampling strategy in ScaleEstimator class from Random to a regular sampling, the non-deterministic behavior is gone and transform and transform' in the above example become identical. I would appreciate if you let me know if I was correct about this issue and whether we can consider this a bug and hope to get it fixed for the upcoming versions. Thanks a lot for your consideration in advance, Sepide -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Mon Aug 29 14:06:46 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Mon, 29 Aug 2016 18:06:46 +0000 Subject: [ITK-dev] Source of Non-deterministic behavior of Registration v4 In-Reply-To: References: Message-ID: Hello, There should be a way to set the seed to a fixed value. Sorry I don?t have anything more specific, but grep through ITK for ?SetSeed? and there should be some tests or examples which do this. If you set a consistent seed before performing a registration ( inside your Register method ) it may solve your problem. HTH, Brad > On Aug 29, 2016, at 1:54 PM, sepideh movaghati wrote: > > Hi, > > I posted the same issue on insight-users initially but then I thought it would be more relevant to developers mailing list. > > I was observing an unexpected non-deterministic behavior while changing the order of completely unrelated registrations. In the following example, my test revealed that transform and transform' are not identical: > > transform = Register(image1, image2); > > vs. > > transform-foo = Register(image-foo1, image-foo2); > transform' = Register(image1, image2); > > > I looked into the source of this non-deterministic behavior while making sure the metric sampling strategy has been set to Regular. > Eventually I found the cause of the problem in itkRegistrationParametersScaleEstimator class. In this class there are two functions SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the sampling strategy is chosen based on the Transformation type. For example if the transformation is of type displacement field or BSpline, it uses all of the samples. If transformation is any regular affine or rigid transformation (child of class MatrixOffsetTransformBase) it performs corner sampling. However, if the transformation is none of the known ones, it uses Random Sampling. > > In my test I was using one level rigid transformation (v4). But here is were the problem happens: in itkImageRegistrationMethodv4.hxx the Metric transformation (MovingTransform) always set to a CompositeTransform! Therefore, ScaleEstimator cannot detect the transformation type and it always fall into "else" which is using Random Sampling! It does not matter if you do a multilevel registration or not. The transformation is always of type CompositeTransform. > > By changing the sampling strategy in ScaleEstimator class from Random to a regular sampling, the non-deterministic behavior is gone and transform and transform' in the above example become identical. > > I would appreciate if you let me know if I was correct about this issue and whether we can consider this a bug and hope to get it fixed for the upcoming versions. > > Thanks a lot for your consideration in advance, > Sepide > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers