From marco.dev.open at gmail.com Tue Aug 4 08:04:33 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Tue, 4 Aug 2015 16:34:33 +0430 Subject: [ITK-dev] converting metaimage format to nrrd Message-ID: Hi dears, Is way to convert metaimage (.mhd and .raw )format to .nrrd format ? Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Aug 4 10:21:21 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 4 Aug 2015 10:21:21 -0400 Subject: [ITK-dev] converting metaimage format to nrrd In-Reply-To: References: Message-ID: Hi Marco, This example may be useful: http://itk.org/ITKExamples/src/IO/ImageBase/ConvertFileFormats/Documentation.html HTH, Matt On Tue, Aug 4, 2015 at 8:04 AM, Marco Dev wrote: > Hi dears, > Is way to convert metaimage (.mhd and .raw )format to .nrrd format ? > Thanks in advance. > > > _______________________________________________ > 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 marco.dev.open at gmail.com Wed Aug 5 06:11:59 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Wed, 5 Aug 2015 14:41:59 +0430 Subject: [ITK-dev] converting metaimage format to nrrd In-Reply-To: References: Message-ID: Thanks about your help . On Tue, Aug 4, 2015 at 6:51 PM, Matt McCormick wrote: > Hi Marco, > > This example may be useful: > > > http://itk.org/ITKExamples/src/IO/ImageBase/ConvertFileFormats/Documentation.html > > HTH, > Matt > > On Tue, Aug 4, 2015 at 8:04 AM, Marco Dev > wrote: > > Hi dears, > > Is way to convert metaimage (.mhd and .raw )format to .nrrd format ? > > Thanks in advance. > > > > > > _______________________________________________ > > 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 david.m.welch at gmail.com Wed Aug 5 12:51:12 2015 From: david.m.welch at gmail.com (David Welch) Date: Wed, 05 Aug 2015 11:51:12 -0500 Subject: [ITK-dev] converting metaimage format to nrrd In-Reply-To: References: Message-ID: These pages are also a lot of help: http://www.cmake.org/Wiki/Getting_Started_with_the_NRRD_Format http://teem.sourceforge.net/nrrd/format.html Cheers, Dave From: Marco Dev Date: Wednesday, August 5, 2015 at 5:11 AM To: Matt McCormick Cc: "vtkusers at vtk.org", ITK Subject: Re: [ITK-dev] converting metaimage format to nrrd Thanks about your help . On Tue, Aug 4, 2015 at 6:51 PM, Matt McCormick wrote: Hi Marco, This example may be useful: http://itk.org/ITKExamples/src/IO/ImageBase/ConvertFileFormats/Documentation.html HTH, Matt On Tue, Aug 4, 2015 at 8:04 AM, Marco Dev wrote: > Hi dears, > Is way to convert metaimage (.mhd and .raw )format to .nrrd format ? > Thanks in advance. > > > _______________________________________________ > 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 Thu Aug 6 10:28:47 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 6 Aug 2015 10:28:47 -0400 Subject: [ITK-dev] Ubuntu 14 Test failure bisect results In-Reply-To: <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov> References: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov> <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov> Message-ID: Hi Brad, I have been doing some Experimental builds on the dashboard. So far, the test failures are repeatable with GCC / Binutils in Ubuntu 14.04 with BUILD_SHARED_LIBS OFF, but not BUILD_SHARED_LIBS ON. I am working on a patch... :-) Thanks, Matt On Thu, Aug 6, 2015 at 9:33 AM, Bradley Lowekamp wrote: > Matt, > > What were the results of this experiment? It'd be nice to clean up the release branch of these failing tests. > > And I want to steal the correct solution for SimpleITK too :) > > Brad > > On Jul 31, 2015, at 3:29 PM, Matt McCormick wrote: > >> Hi Brad, >> >> Thanks for investigating and getting great information out of git bisect. >> >> I developed the patch on Gentoo with GCC 4.8.4 / binutils 2.24, and I >> have not seen any issues. The eldorado builds on the dashboard are >> all Ubuntu 14.04.2, too. I will start an Experimental build with >> BUILD_SHARED_LIBS set on eldorado to be sure it can be reproduced. >> >> Thanks, >> Matt >> >> On Fri, Jul 31, 2015 at 1:03 PM, Bradley Lowekamp >> wrote: >>> Matt, >>> >>> I was digging into these test failures: >>> >>> https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451 >>> >>> Here are the results of the git bisect: >>> >>> 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit >>> commit 674acdb2dd5546b7045f7253c84e4f9f237405e8 >>> Author: Matt McCormick >>> Date: Sun May 31 21:00:55 2015 -0400 >>> >>> ENH: Use gold linker on Linux with GCC. >>> >>> >>> >>> The gold linker is approximately three times as fast as the default >>> linker. >>> Enable it with GCC 4.8 and newer where it was tested. The gold linker >>> only >>> works with ELF executables, so it is only enabled for Linux. >>> >>> >>> >>> Timing tests: >>> >>> >>> >>> Static libs link time: >>> >>> >>> >>> ld: 452 sec >>> ld-gold: 179 sec >>> >>> >>> >>> Shared libs link time, wrapping enabled: >>> >>> >>> >>> ld: 164 sec >>> ld-gold: 48 sec >>> >>> >>> >>> Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c >>> >>> Disabling ld-gold seems to fix the problem. >>> >>> Versions: >>> >>> blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version >>> gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4 >>> Copyright (C) 2013 Free Software Foundation, Inc. >>> This is free software; see the source for copying conditions. There is NO >>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>> >>> blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version >>> GNU ld (GNU Binutils for Ubuntu) 2.24 >>> Copyright 2013 Free Software Foundation, Inc. >>> This program is free software; you may redistribute it under the terms of >>> the GNU General Public License version 3 or (at your option) a later >>> version. >>> This program has absolutely no warranty. >>> >>> blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a >>> No LSB modules are available. >>> Distributor ID: Ubuntu >>> Description: Ubuntu 14.04.2 LTS >>> Release: 14.04 >>> Codename: trusty >>> >>> >>> Currently we have a check for using gold with > 4.8.3: >>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206 >>> >>> But looking at this change: >>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e >>> >>> We should have know about these related test failures: >>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e >>> >>> So what do you recall about what versions of GCC ld-gold works on? >>> >>> Thanks, >>> Brad >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> > From blowekamp at mail.nih.gov Thu Aug 6 09:33:36 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 06 Aug 2015 09:33:36 -0400 Subject: [ITK-dev] Ubuntu 14 Test failure bisect results In-Reply-To: References: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov> Message-ID: <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov> Matt, What were the results of this experiment? It'd be nice to clean up the release branch of these failing tests. And I want to steal the correct solution for SimpleITK too :) Brad On Jul 31, 2015, at 3:29 PM, Matt McCormick wrote: > Hi Brad, > > Thanks for investigating and getting great information out of git bisect. > > I developed the patch on Gentoo with GCC 4.8.4 / binutils 2.24, and I > have not seen any issues. The eldorado builds on the dashboard are > all Ubuntu 14.04.2, too. I will start an Experimental build with > BUILD_SHARED_LIBS set on eldorado to be sure it can be reproduced. > > Thanks, > Matt > > On Fri, Jul 31, 2015 at 1:03 PM, Bradley Lowekamp > wrote: >> Matt, >> >> I was digging into these test failures: >> >> https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451 >> >> Here are the results of the git bisect: >> >> 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit >> commit 674acdb2dd5546b7045f7253c84e4f9f237405e8 >> Author: Matt McCormick >> Date: Sun May 31 21:00:55 2015 -0400 >> >> ENH: Use gold linker on Linux with GCC. >> >> >> >> The gold linker is approximately three times as fast as the default >> linker. >> Enable it with GCC 4.8 and newer where it was tested. The gold linker >> only >> works with ELF executables, so it is only enabled for Linux. >> >> >> >> Timing tests: >> >> >> >> Static libs link time: >> >> >> >> ld: 452 sec >> ld-gold: 179 sec >> >> >> >> Shared libs link time, wrapping enabled: >> >> >> >> ld: 164 sec >> ld-gold: 48 sec >> >> >> >> Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c >> >> Disabling ld-gold seems to fix the problem. >> >> Versions: >> >> blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version >> gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4 >> Copyright (C) 2013 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >> >> blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version >> GNU ld (GNU Binutils for Ubuntu) 2.24 >> Copyright 2013 Free Software Foundation, Inc. >> This program is free software; you may redistribute it under the terms of >> the GNU General Public License version 3 or (at your option) a later >> version. >> This program has absolutely no warranty. >> >> blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a >> No LSB modules are available. >> Distributor ID: Ubuntu >> Description: Ubuntu 14.04.2 LTS >> Release: 14.04 >> Codename: trusty >> >> >> Currently we have a check for using gold with > 4.8.3: >> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206 >> >> But looking at this change: >> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e >> >> We should have know about these related test failures: >> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e >> >> So what do you recall about what versions of GCC ld-gold works on? >> >> Thanks, >> Brad >> >> >> >> >> >> >> >> >> >> >> From matt.mccormick at kitware.com Thu Aug 6 12:10:43 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 6 Aug 2015 12:10:43 -0400 Subject: [ITK-dev] Ubuntu 14 Test failure bisect results In-Reply-To: References: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov> <8EC6E57A-1ED3-4909-A1AA-81EA4E83DFA5@mail.nih.gov> Message-ID: Here is the patch: http://review.source.kitware.com/#/c/20068/ Interestingly, the test failures are not repeatable on Gentoo with the same versions of GCC / binutils. Matt On Thu, Aug 6, 2015 at 10:28 AM, Matt McCormick wrote: > Hi Brad, > > I have been doing some Experimental builds on the dashboard. So far, > the test failures are repeatable with GCC / Binutils in Ubuntu 14.04 > with BUILD_SHARED_LIBS OFF, but not BUILD_SHARED_LIBS ON. I am > working on a patch... :-) > > Thanks, > Matt > > On Thu, Aug 6, 2015 at 9:33 AM, Bradley Lowekamp wrote: >> Matt, >> >> What were the results of this experiment? It'd be nice to clean up the release branch of these failing tests. >> >> And I want to steal the correct solution for SimpleITK too :) >> >> Brad >> >> On Jul 31, 2015, at 3:29 PM, Matt McCormick wrote: >> >>> Hi Brad, >>> >>> Thanks for investigating and getting great information out of git bisect. >>> >>> I developed the patch on Gentoo with GCC 4.8.4 / binutils 2.24, and I >>> have not seen any issues. The eldorado builds on the dashboard are >>> all Ubuntu 14.04.2, too. I will start an Experimental build with >>> BUILD_SHARED_LIBS set on eldorado to be sure it can be reproduced. >>> >>> Thanks, >>> Matt >>> >>> On Fri, Jul 31, 2015 at 1:03 PM, Bradley Lowekamp >>> wrote: >>>> Matt, >>>> >>>> I was digging into these test failures: >>>> >>>> https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451 >>>> >>>> Here are the results of the git bisect: >>>> >>>> 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit >>>> commit 674acdb2dd5546b7045f7253c84e4f9f237405e8 >>>> Author: Matt McCormick >>>> Date: Sun May 31 21:00:55 2015 -0400 >>>> >>>> ENH: Use gold linker on Linux with GCC. >>>> >>>> >>>> >>>> The gold linker is approximately three times as fast as the default >>>> linker. >>>> Enable it with GCC 4.8 and newer where it was tested. The gold linker >>>> only >>>> works with ELF executables, so it is only enabled for Linux. >>>> >>>> >>>> >>>> Timing tests: >>>> >>>> >>>> >>>> Static libs link time: >>>> >>>> >>>> >>>> ld: 452 sec >>>> ld-gold: 179 sec >>>> >>>> >>>> >>>> Shared libs link time, wrapping enabled: >>>> >>>> >>>> >>>> ld: 164 sec >>>> ld-gold: 48 sec >>>> >>>> >>>> >>>> Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c >>>> >>>> Disabling ld-gold seems to fix the problem. >>>> >>>> Versions: >>>> >>>> blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version >>>> gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4 >>>> Copyright (C) 2013 Free Software Foundation, Inc. >>>> This is free software; see the source for copying conditions. There is NO >>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>>> >>>> blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version >>>> GNU ld (GNU Binutils for Ubuntu) 2.24 >>>> Copyright 2013 Free Software Foundation, Inc. >>>> This program is free software; you may redistribute it under the terms of >>>> the GNU General Public License version 3 or (at your option) a later >>>> version. >>>> This program has absolutely no warranty. >>>> >>>> blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a >>>> No LSB modules are available. >>>> Distributor ID: Ubuntu >>>> Description: Ubuntu 14.04.2 LTS >>>> Release: 14.04 >>>> Codename: trusty >>>> >>>> >>>> Currently we have a check for using gold with > 4.8.3: >>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206 >>>> >>>> But looking at this change: >>>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e >>>> >>>> We should have know about these related test failures: >>>> https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e >>>> >>>> So what do you recall about what versions of GCC ld-gold works on? >>>> >>>> Thanks, >>>> Brad >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >> From marco.dev.open at gmail.com Thu Aug 13 02:47:37 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Thu, 13 Aug 2015 11:17:37 +0430 Subject: [ITK-dev] converting coordinate system Message-ID: Hi dears, I have some itk image filter for translating from image coordinate system to world coordinate system Means I want to convert Dicom image position and another tag information such as pixel spacing orientation to world coordinate for Itk coordinate these are difference in position How can do this convert Thanks in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Thu Aug 13 11:40:53 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 13 Aug 2015 17:40:53 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 Message-ID: Hi all, I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I get the following link error [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 [...] lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to 'itk::VideoIOBase::VideoIOBase()' lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to 'itk::VideoIOBase::~VideoIOBase()' lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to 'typeinfo for itk::VideoIOBase' collect2: error: ld returned 1 exit status I have checked these methods are implemented in itkVideoIOBase.cxx... Any idea? Thanks Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Aug 13 12:41:01 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 13 Aug 2015 12:41:01 -0400 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Hi Arnaud, Is this with building the examples with the superbuild? I think I was getting this error, too. Here is a patch that should address it: http://review.source.kitware.com/#/c/20077/ Thanks, Matt On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas wrote: > Hi all, > > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I get > the following link error > > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 > > [...] > > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > 'itk::VideoIOBase::VideoIOBase()' > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > 'itk::VideoIOBase::~VideoIOBase()' > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > 'typeinfo for itk::VideoIOBase' > collect2: error: ld returned 1 exit status > > I have checked these methods are implemented in itkVideoIOBase.cxx... > > Any idea? > > Thanks > Arnaud > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://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 mohammedrashadkm at gmail.com Thu Aug 13 14:55:19 2015 From: mohammedrashadkm at gmail.com (Rashad M) Date: Thu, 13 Aug 2015 20:55:19 +0200 Subject: [ITK-dev] regarding ImageFileReader::GenerateOutputInformation() Message-ID: Hello all, The documentation of itk::ProcessObject::GenerateOutputInformation( ) says Generate the information describing the output data. [1]. The GenerateOutputInformation() in itkImageFileReader first create all instances of ImageIO and setup direction, spacing, etc.. If I understand correctly, the GenerateOutputInformation in the image file reader is called by UpdateOutputInformation( ) To my question, If I call reader->UpdateOutputInformation() for first time it calls reader->GenerateOutputInformation() as described in docs[2]. Now If I have a second call to reader->UpdateOutputInformation( ) ? Will it again go to GenerateOutputInformation() and createAllInstances of imageio , do the same thing again! In itkProcessObject.cxx, there is the below documentation * Call GenerateOutputInformation for subclass specific information. * Since UpdateOutputInformation propagates all the way up the pipeline, * we need to be careful here to call GenerateOutputInformation only if * necessary. Otherwise, we may cause this source to be modified which * will cause it to execute again on the next update. How can I prevent it from calling it again in class sub class of itk::ImageSource? [1] http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#abe61fb6b7de8c443e7af1561bd722736 -- Regards, Rashad -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Aug 13 15:11:32 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 13 Aug 2015 15:11:32 -0400 Subject: [ITK-dev] regarding ImageFileReader::GenerateOutputInformation() In-Reply-To: References: Message-ID: <3284837D-9DD6-48A1-A65D-5ED81EC1A95B@mail.nih.gov> Hello Rashad, If you call ImageFileReader::UpdateOutputInformation() 2 times is "should" only call GenerateOutputInformation once. The key to this behavior is the management of the timestamps in the process object classes done here [1]. What is required for this to work correctly is that the only the correct object get modified in these pipeline methods. When an object is modified the timestamp should be updated, and downstream processes get marked as out of date. The best way to make sure your ImageSource does not get call twice is to write a test, that makes sure the process object's MTime does not change in GenerateOutputInformation call. HTH, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/9f88e4e3b388ee2f1c1c006ae36de0613d305284/Modules/Core/Common/src/itkProcessObject.cxx#L1431-L1542 On Aug 13, 2015, at 2:55 PM, Rashad M wrote: > Hello all, > > The documentation of itk::ProcessObject::GenerateOutputInformation( ) says > Generate the information describing the output data. [1]. The GenerateOutputInformation() in itkImageFileReader first create all instances of ImageIO and setup direction, spacing, etc.. > > If I understand correctly, the GenerateOutputInformation in the image file reader is called by UpdateOutputInformation( ) > > To my question, > If I call reader->UpdateOutputInformation() for first time it calls > reader->GenerateOutputInformation() as described in docs[2]. > > Now If I have a second call to reader->UpdateOutputInformation( ) ? > > Will it again go to GenerateOutputInformation() and createAllInstances of imageio , do the same thing again! > > In itkProcessObject.cxx, there is the below documentation > > * Call GenerateOutputInformation for subclass specific information. > * Since UpdateOutputInformation propagates all the way up the pipeline, > * we need to be careful here to call GenerateOutputInformation only if > * necessary. Otherwise, we may cause this source to be modified which > * will cause it to execute again on the next update. > > How can I prevent it from calling it again in class sub class of itk::ImageSource? > > [1]http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#abe61fb6b7de8c443e7af1561bd722736 > > > -- > Regards, > Rashad > _______________________________________________ > 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 Thu Aug 13 18:13:24 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 13 Aug 2015 18:13:24 -0400 Subject: [ITK-dev] converting coordinate system In-Reply-To: References: Message-ID: Hello, All computations in ITK are done in the world coordinate system, i.e. the physical coordinates. To convert an image coordinate, i.e. the index coordinates, use the TransformIndexToPhysicalPoint [1] method on itk::Image. This takes into account image orientation and spacing. HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#ab003313ba1a078d89a832dc0a35d2efa On Thu, Aug 13, 2015 at 2:47 AM, Marco Dev wrote: > Hi dears, > I have some itk image filter for translating from image coordinate system to > world coordinate system > Means I want to convert Dicom image position and another tag information > such as pixel spacing orientation to world coordinate for Itk coordinate > these are difference in position > How can do this convert > Thanks in advance > > _______________________________________________ > 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 arnaudgelas at gmail.com Fri Aug 14 02:21:19 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 14 Aug 2015 08:21:19 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Hi Matt, It happened while directly building ITK with OpenCV 2.4.9, without any superbuild... Thanks for the patch, but that does not solve it... I wonder if it could have something to do with the new linking system (note it uses COMPILE_DEPENDS) ? Thanks, Arnaud On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick wrote: > Hi Arnaud, > > Is this with building the examples with the superbuild? I think I was > getting this error, too. Here is a patch that should address it: > > http://review.source.kitware.com/#/c/20077/ > > Thanks, > Matt > > On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas > wrote: > > Hi all, > > > > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I > get > > the following link error > > > > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 > > > > [...] > > > > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > > 'itk::VideoIOBase::VideoIOBase()' > > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > > 'itk::VideoIOBase::~VideoIOBase()' > > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' > > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > > 'typeinfo for itk::VideoIOBase' > > collect2: error: ld returned 1 exit status > > > > I have checked these methods are implemented in itkVideoIOBase.cxx... > > > > Any idea? > > > > Thanks > > Arnaud > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://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 arnaudgelas at gmail.com Fri Aug 14 03:48:22 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 14 Aug 2015 09:48:22 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: I have restarted from scratch... So instead of using gold linker, it is using the default linker, the header test is now ok, but I still have linking errors: $ ninja ITKVideoBridgeOpenCV-all [1/1] Linking CXX executable bin/ITKVideoBridgeOpenCVTestDriver FAILED: : && /usr/lib/ccache/c++ -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -Wno-array-bounds -msse2 -g Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/ITKVideoBridgeOpenCVTestDriver.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeGrayScaleTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeRGBTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOFactoryTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVBasicTypeBridgeTest.cxx.o -o bin/ITKVideoBridgeOpenCVTestDriver -rdynamic lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1 lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1 lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1 lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1 lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1 lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1 lib/libITKVideoBridgeOpenCV-4.9.so.1 /home/arnaud/install/lib/libopencv_videostab.so.2.4.9 /home/arnaud/install/lib/libopencv_video.so.2.4.9 /home/arnaud/install/lib/libopencv_ts.a /home/arnaud/install/lib/libopencv_superres.so.2.4.9 /home/arnaud/install/lib/libopencv_stitching.so.2.4.9 /home/arnaud/install/lib/libopencv_photo.so.2.4.9 /home/arnaud/install/lib/libopencv_ocl.so.2.4.9 /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9 /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9 /home/arnaud/install/lib/libopencv_ml.so.2.4.9 /home/arnaud/install/lib/libopencv_legacy.so.2.4.9 /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9 /home/arnaud/install/lib/libopencv_highgui.so.2.4.9 /home/arnaud/install/lib/libopencv_gpu.so.2.4.9 /home/arnaud/install/lib/libopencv_flann.so.2.4.9 /home/arnaud/install/lib/libopencv_features2d.so.2.4.9 /home/arnaud/install/lib/libopencv_core.so.2.4.9 /home/arnaud/install/lib/libopencv_contrib.so.2.4.9 /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9 lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1 lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1 lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1 lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1 lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1 lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1 -lm -lpthread -lrt -ltbb /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9 /home/arnaud/install/lib/libopencv_ocl.so.2.4.9 /home/arnaud/install/lib/libopencv_gpu.so.2.4.9 /home/arnaud/install/lib/libopencv_photo.so.2.4.9 /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9 /home/arnaud/install/lib/libopencv_legacy.so.2.4.9 /home/arnaud/install/lib/libopencv_video.so.2.4.9 /home/arnaud/install/lib/libopencv_ml.so.2.4.9 /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9 /home/arnaud/install/lib/libopencv_features2d.so.2.4.9 /home/arnaud/install/lib/libopencv_highgui.so.2.4.9 /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9 /home/arnaud/install/lib/libopencv_flann.so.2.4.9 /home/arnaud/install/lib/libopencv_core.so.2.4.9 lib/libITKVideoIO-4.9.so.1 lib/libITKIOImageBase-4.9.so.1 lib/libITKVideoCore-4.9.so.1 lib/libITKCommon-4.9.so.1 lib/libitkdouble-conversion-4.9.so.1 lib/libitksys-4.9.so.1 lib/libITKVNLInstantiation-4.9.so.1 -lvnl_algo -lvnl -lv3p_netlib -lnetlib -lvcl -lpthread -lm -ldl -Wl,-rpath,/home/arnaud/source/build-itk/lib:/home/arnaud/install/lib -Wl,-rpath-link,/home/arnaud/source/build-itk/lib && : Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o: In function `itk::OpenCVVideoIOFactory::New()': /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIOFactory.h:46: undefined reference to `itk::OpenCVVideoIOFactory::OpenCVVideoIOFactory()' Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o: In function `itk::OpenCVVideoIO::New()': /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIO.h:48: undefined reference to `itk::OpenCVVideoIO::OpenCVVideoIO()' Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o: In function `itk::ObjectFactory::Create()': /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:60: undefined reference to `typeinfo for itk::OpenCVVideoIO' /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:62: undefined reference to `typeinfo for itk::OpenCVVideoIO' collect2: error: ld returned 1 exit status ninja: build stopped: subcommand failed. On Fri, Aug 14, 2015 at 8:21 AM, Arnaud Gelas wrote: > Hi Matt, > > It happened while directly building ITK with OpenCV 2.4.9, without any > superbuild... > Thanks for the patch, but that does not solve it... > > I wonder if it could have something to do with the new linking system > (note it uses COMPILE_DEPENDS) ? > > Thanks, > Arnaud > > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi Arnaud, >> >> Is this with building the examples with the superbuild? I think I was >> getting this error, too. Here is a patch that should address it: >> >> http://review.source.kitware.com/#/c/20077/ >> >> Thanks, >> Matt >> >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas >> wrote: >> > Hi all, >> > >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I >> get >> > the following link error >> > >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 >> > >> > [...] >> > >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'itk::VideoIOBase::VideoIOBase()' >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'itk::VideoIOBase::~VideoIOBase()' >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'typeinfo for itk::VideoIOBase' >> > collect2: error: ld returned 1 exit status >> > >> > I have checked these methods are implemented in itkVideoIOBase.cxx... >> > >> > Any idea? >> > >> > Thanks >> > Arnaud >> > >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://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 arnaudgelas at gmail.com Fri Aug 14 05:30:07 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 14 Aug 2015 11:30:07 +0200 Subject: [ITK-dev] use ThreadedIteratorRangePartitioner with itk Container ? Message-ID: Hi Matt, I would like to use itk::ThreadedIteratorRangePartitioner with itk::Mesh::PointsContainer or itk::Mesh::CellsContainer (i.e. itk::VectorContainer or itk::MapContainer). At first, I am trying to add one test which basically duplicates itkThreadedIteratorRangePartitionerTest for the case of itk::VectorContainer, you can find a patch here: http://review.source.kitware.com/#/c/20079/ I have compilation errors, due to the fact that internally itk::ThreadedIteratorRangePartitioner uses std::distance and std::advance which requires some typedefs which are not available for itk::VectorContainer iterators... Should I keep on working in that direction? I mean to try to fix these classes for itk container's iterator (adapt it for these cases)? Make specialization? Thanks, Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Fri Aug 14 09:21:05 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 14 Aug 2015 09:21:05 -0400 Subject: [ITK-dev] [ITK] use ThreadedIteratorRangePartitioner with itk Container ? In-Reply-To: References: Message-ID: <7407F7E9-F13B-4AA4-9116-625F5DD09FDF@mail.nih.gov> Arnaund, I would recommend using an index based partitioner as opposed to the iterator based algorithm due to on big O performance of the partitioning algorithms. Brad On Aug 14, 2015, at 5:30 AM, Arnaud Gelas wrote: > Hi Matt, > > I would like to use itk::ThreadedIteratorRangePartitioner with itk::Mesh::PointsContainer or itk::Mesh::CellsContainer (i.e. itk::VectorContainer or itk::MapContainer). > > At first, I am trying to add one test which basically duplicates itkThreadedIteratorRangePartitionerTest for the case of itk::VectorContainer, you can find a patch here: > > http://review.source.kitware.com/#/c/20079/ > > I have compilation errors, due to the fact that internally itk::ThreadedIteratorRangePartitioner uses std::distance and std::advance which requires some typedefs which are not available for itk::VectorContainer iterators... > > Should I keep on working in that direction? I mean to try to fix these classes for itk container's iterator (adapt it for these cases)? Make specialization? > > Thanks, > Arnaud > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://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 matt.mccormick at kitware.com Fri Aug 14 12:11:48 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 14 Aug 2015 12:11:48 -0400 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Hi Arnaud, Yes, you are probably right. The suggestion by Zach in this patch (to use DEPENDS) is promising: http://review.source.kitware.com/#/c/20078/ Thanks, Matt On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas wrote: > Hi Matt, > > It happened while directly building ITK with OpenCV 2.4.9, without any > superbuild... > Thanks for the patch, but that does not solve it... > > I wonder if it could have something to do with the new linking system (note > it uses COMPILE_DEPENDS) ? > > Thanks, > Arnaud > > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick > wrote: >> >> Hi Arnaud, >> >> Is this with building the examples with the superbuild? I think I was >> getting this error, too. Here is a patch that should address it: >> >> http://review.source.kitware.com/#/c/20077/ >> >> Thanks, >> Matt >> >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas >> wrote: >> > Hi all, >> > >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I >> > get >> > the following link error >> > >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 >> > >> > [...] >> > >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'itk::VideoIOBase::VideoIOBase()' >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'itk::VideoIOBase::~VideoIOBase()' >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> > 'typeinfo for itk::VideoIOBase' >> > collect2: error: ld returned 1 exit status >> > >> > I have checked these methods are implemented in itkVideoIOBase.cxx... >> > >> > Any idea? >> > >> > Thanks >> > Arnaud >> > >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://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 arnaudgelas at gmail.com Fri Aug 14 12:24:59 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 14 Aug 2015 18:24:59 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: I have already tried it, does not solve it... I will retry it with a fresh build once again... On Fri, Aug 14, 2015 at 6:11 PM, Matt McCormick wrote: > Hi Arnaud, > > Yes, you are probably right. The suggestion by Zach in this patch (to > use DEPENDS) is promising: > > http://review.source.kitware.com/#/c/20078/ > > Thanks, > Matt > > On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas > wrote: > > Hi Matt, > > > > It happened while directly building ITK with OpenCV 2.4.9, without any > > superbuild... > > Thanks for the patch, but that does not solve it... > > > > I wonder if it could have something to do with the new linking system > (note > > it uses COMPILE_DEPENDS) ? > > > > Thanks, > > Arnaud > > > > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick < > matt.mccormick at kitware.com> > > wrote: > >> > >> Hi Arnaud, > >> > >> Is this with building the examples with the superbuild? I think I was > >> getting this error, too. Here is a patch that should address it: > >> > >> http://review.source.kitware.com/#/c/20077/ > >> > >> Thanks, > >> Matt > >> > >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas > >> wrote: > >> > Hi all, > >> > > >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and I > >> > get > >> > the following link error > >> > > >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 > >> > > >> > [...] > >> > > >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > >> > 'itk::VideoIOBase::VideoIOBase()' > >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > >> > 'itk::VideoIOBase::~VideoIOBase()' > >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' > >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to > >> > 'typeinfo for itk::VideoIOBase' > >> > collect2: error: ld returned 1 exit status > >> > > >> > I have checked these methods are implemented in itkVideoIOBase.cxx... > >> > > >> > Any idea? > >> > > >> > Thanks > >> > Arnaud > >> > > >> > _______________________________________________ > >> > Powered by www.kitware.com > >> > > >> > Visit other Kitware open-source projects at > >> > http://www.kitware.com/opensource/opensource.html > >> > > >> > Kitware offers ITK Training Courses, for more information visit: > >> > http://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 arnaudgelas at gmail.com Fri Aug 14 12:34:46 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 14 Aug 2015 18:34:46 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Here is the resulting link error: [1563/1563] Linking CXX executable bin/ITKVideoBridgeOpenCVTestDriver FAILED: : && /usr/lib/ccache/c++ -Wall -Wextra -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -Wno-array-bounds -msse2 -g Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/ITKVideoBridgeOpenCVTestDriver.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeGrayScaleTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeRGBTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOFactoryTest.cxx.o Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVBasicTypeBridgeTest.cxx.o -o bin/ITKVideoBridgeOpenCVTestDriver -rdynamic lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1 lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1 lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1 lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1 lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1 lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1 lib/libITKVideoBridgeOpenCV-4.9.so.1 /home/arnaud/install/lib/libopencv_videostab.so.2.4.9 /home/arnaud/install/lib/libopencv_video.so.2.4.9 /home/arnaud/install/lib/libopencv_ts.a /home/arnaud/install/lib/libopencv_superres.so.2.4.9 /home/arnaud/install/lib/libopencv_stitching.so.2.4.9 /home/arnaud/install/lib/libopencv_photo.so.2.4.9 /home/arnaud/install/lib/libopencv_ocl.so.2.4.9 /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9 /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9 /home/arnaud/install/lib/libopencv_ml.so.2.4.9 /home/arnaud/install/lib/libopencv_legacy.so.2.4.9 /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9 /home/arnaud/install/lib/libopencv_highgui.so.2.4.9 /home/arnaud/install/lib/libopencv_gpu.so.2.4.9 /home/arnaud/install/lib/libopencv_flann.so.2.4.9 /home/arnaud/install/lib/libopencv_features2d.so.2.4.9 /home/arnaud/install/lib/libopencv_core.so.2.4.9 /home/arnaud/install/lib/libopencv_contrib.so.2.4.9 /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9 lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1 lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1 lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1 lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1 lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1 lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1 -lpthread -lrt -ltbb /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9 /home/arnaud/install/lib/libopencv_ocl.so.2.4.9 /home/arnaud/install/lib/libopencv_gpu.so.2.4.9 /home/arnaud/install/lib/libopencv_photo.so.2.4.9 /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9 /home/arnaud/install/lib/libopencv_legacy.so.2.4.9 /home/arnaud/install/lib/libopencv_video.so.2.4.9 /home/arnaud/install/lib/libopencv_ml.so.2.4.9 /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9 /home/arnaud/install/lib/libopencv_features2d.so.2.4.9 /home/arnaud/install/lib/libopencv_highgui.so.2.4.9 /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9 /home/arnaud/install/lib/libopencv_flann.so.2.4.9 /home/arnaud/install/lib/libopencv_core.so.2.4.9 lib/libITKVideoIO-4.9.so.1 lib/libITKIOImageBase-4.9.so.1 lib/libITKVideoCore-4.9.so.1 lib/libITKCommon-4.9.so.1 lib/libitkdouble-conversion-4.9.so.1 lib/libitksys-4.9.so.1 lib/libITKVNLInstantiation-4.9.so.1 lib/libitkvnl_algo-4.9.so.1 lib/libitkv3p_lsqr-4.9.so.1 lib/libitkvnl-4.9.so.1 lib/libitkvcl-4.9.so.1 lib/libitkv3p_netlib-4.9.so.1 -lm -lpthread -lm -ldl -Wl,-rpath,/home/arnaud/source/build-itk/lib:/home/arnaud/install/lib -Wl,-rpath-link,/home/arnaud/source/build-itk/lib && : Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o: In function `itk::OpenCVVideoIOFactory::New()': /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIOFactory.h:46: undefined reference to `itk::OpenCVVideoIOFactory::OpenCVVideoIOFactory()' Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o: In function `itk::OpenCVVideoIO::New()': /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIO.h:48: undefined reference to `itk::OpenCVVideoIO::OpenCVVideoIO()' Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o: In function `itk::ObjectFactory::Create()': /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:60: undefined reference to `typeinfo for itk::OpenCVVideoIO' /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:62: undefined reference to `typeinfo for itk::OpenCVVideoIO' collect2: error: ld returned 1 exit status ninja: build stopped: subcommand failed. On Fri, Aug 14, 2015 at 6:24 PM, Arnaud Gelas wrote: > I have already tried it, does not solve it... I will retry it with a fresh > build once again... > > On Fri, Aug 14, 2015 at 6:11 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi Arnaud, >> >> Yes, you are probably right. The suggestion by Zach in this patch (to >> use DEPENDS) is promising: >> >> http://review.source.kitware.com/#/c/20078/ >> >> Thanks, >> Matt >> >> On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas >> wrote: >> > Hi Matt, >> > >> > It happened while directly building ITK with OpenCV 2.4.9, without any >> > superbuild... >> > Thanks for the patch, but that does not solve it... >> > >> > I wonder if it could have something to do with the new linking system >> (note >> > it uses COMPILE_DEPENDS) ? >> > >> > Thanks, >> > Arnaud >> > >> > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick < >> matt.mccormick at kitware.com> >> > wrote: >> >> >> >> Hi Arnaud, >> >> >> >> Is this with building the examples with the superbuild? I think I was >> >> getting this error, too. Here is a patch that should address it: >> >> >> >> http://review.source.kitware.com/#/c/20077/ >> >> >> >> Thanks, >> >> Matt >> >> >> >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas >> >> wrote: >> >> > Hi all, >> >> > >> >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 and >> I >> >> > get >> >> > the following link error >> >> > >> >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 >> >> > >> >> > [...] >> >> > >> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> >> > 'itk::VideoIOBase::VideoIOBase()' >> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> >> > 'itk::VideoIOBase::~VideoIOBase()' >> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' >> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >> >> > 'typeinfo for itk::VideoIOBase' >> >> > collect2: error: ld returned 1 exit status >> >> > >> >> > I have checked these methods are implemented in itkVideoIOBase.cxx... >> >> > >> >> > Any idea? >> >> > >> >> > Thanks >> >> > Arnaud >> >> > >> >> > _______________________________________________ >> >> > Powered by www.kitware.com >> >> > >> >> > Visit other Kitware open-source projects at >> >> > http://www.kitware.com/opensource/opensource.html >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > http://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 arnaudgelas at gmail.com Fri Aug 14 13:31:39 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 14 Aug 2015 19:31:39 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make much sense to me?), same link error... If it helps, I can prepare a docker build file to track this error (for anyone willing to help)? Thanks On Fri, Aug 14, 2015 at 6:59 PM, Williamson, Zachary E < zachary-williamson at uiowa.edu> wrote: > It's the test driver that is failing here, make sure that all of the > modules needed for the tests are included under TEST_DEPENDS. > > > ------------------------------ > *From:* Arnaud Gelas > *Sent:* Friday, August 14, 2015 11:34 AM > *To:* Matt McCormick > *Cc:* insight-developers at itk.org; Williamson, Zachary E > *Subject:* Re: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on > Ubuntu 14.04 > > Here is the resulting link error: > > [1563/1563] Linking CXX executable bin/ITKVideoBridgeOpenCVTestDriver > FAILED: : && /usr/lib/ccache/c++ -Wall -Wextra -Wall -Wcast-align > -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch > -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings > -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof > -Woverloaded-virtual -Wstrict-null-sentinel -Wno-array-bounds -msse2 -g > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/ITKVideoBridgeOpenCVTestDriver.cxx.o > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeGrayScaleTest.cxx.o > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVImageBridgeRGBTest.cxx.o > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOFactoryTest.cxx.o > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVBasicTypeBridgeTest.cxx.o > -o bin/ITKVideoBridgeOpenCVTestDriver -rdynamic > lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1 > lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1 > lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1 > lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1 > lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1 > lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1 > lib/libITKVideoBridgeOpenCV-4.9.so.1 > /home/arnaud/install/lib/libopencv_videostab.so.2.4.9 > /home/arnaud/install/lib/libopencv_video.so.2.4.9 > /home/arnaud/install/lib/libopencv_ts.a > /home/arnaud/install/lib/libopencv_superres.so.2.4.9 > /home/arnaud/install/lib/libopencv_stitching.so.2.4.9 > /home/arnaud/install/lib/libopencv_photo.so.2.4.9 > /home/arnaud/install/lib/libopencv_ocl.so.2.4.9 > /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9 > /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9 > /home/arnaud/install/lib/libopencv_ml.so.2.4.9 > /home/arnaud/install/lib/libopencv_legacy.so.2.4.9 > /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9 > /home/arnaud/install/lib/libopencv_highgui.so.2.4.9 > /home/arnaud/install/lib/libopencv_gpu.so.2.4.9 > /home/arnaud/install/lib/libopencv_flann.so.2.4.9 > /home/arnaud/install/lib/libopencv_features2d.so.2.4.9 > /home/arnaud/install/lib/libopencv_core.so.2.4.9 > /home/arnaud/install/lib/libopencv_contrib.so.2.4.9 > /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9 > lib/libitkdouble-conversion-4.9.so.1 lib/libITKIOBMP-4.9.so.1 > lib/libITKIOGDCM-4.9.so.1 lib/libITKIOGIPL-4.9.so.1 > lib/libITKIOImageBase-4.9.so.1 lib/libITKIOJPEG-4.9.so.1 > lib/libITKIOMeta-4.9.so.1 lib/libITKIONIFTI-4.9.so.1 > lib/libITKIONRRD-4.9.so.1 lib/libITKIOPNG-4.9.so.1 > lib/libITKIOTIFF-4.9.so.1 lib/libITKIOVTK-4.9.so.1 lib/libitksys-4.9.so.1 > -lpthread -lrt -ltbb /home/arnaud/install/lib/libopencv_nonfree.so.2.4.9 > /home/arnaud/install/lib/libopencv_ocl.so.2.4.9 > /home/arnaud/install/lib/libopencv_gpu.so.2.4.9 > /home/arnaud/install/lib/libopencv_photo.so.2.4.9 > /home/arnaud/install/lib/libopencv_objdetect.so.2.4.9 > /home/arnaud/install/lib/libopencv_legacy.so.2.4.9 > /home/arnaud/install/lib/libopencv_video.so.2.4.9 > /home/arnaud/install/lib/libopencv_ml.so.2.4.9 > /home/arnaud/install/lib/libopencv_calib3d.so.2.4.9 > /home/arnaud/install/lib/libopencv_features2d.so.2.4.9 > /home/arnaud/install/lib/libopencv_highgui.so.2.4.9 > /home/arnaud/install/lib/libopencv_imgproc.so.2.4.9 > /home/arnaud/install/lib/libopencv_flann.so.2.4.9 > /home/arnaud/install/lib/libopencv_core.so.2.4.9 lib/libITKVideoIO-4.9.so.1 > lib/libITKIOImageBase-4.9.so.1 lib/libITKVideoCore-4.9.so.1 > lib/libITKCommon-4.9.so.1 lib/libitkdouble-conversion-4.9.so.1 > lib/libitksys-4.9.so.1 lib/libITKVNLInstantiation-4.9.so.1 > lib/libitkvnl_algo-4.9.so.1 lib/libitkv3p_lsqr-4.9.so.1 > lib/libitkvnl-4.9.so.1 lib/libitkvcl-4.9.so.1 lib/libitkv3p_netlib-4.9.so.1 > -lm -lpthread -lm -ldl > -Wl,-rpath,/home/arnaud/source/build-itk/lib:/home/arnaud/install/lib > -Wl,-rpath-link,/home/arnaud/source/build-itk/lib && : > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoCaptureTest.cxx.o: > In function `itk::OpenCVVideoIOFactory::New()': > /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIOFactory.h:46: > undefined reference to `itk::OpenCVVideoIOFactory::OpenCVVideoIOFactory()' > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o: > In function `itk::OpenCVVideoIO::New()': > /home/arnaud/source/itk/Modules/Video/BridgeOpenCV/include/itkOpenCVVideoIO.h:48: > undefined reference to `itk::OpenCVVideoIO::OpenCVVideoIO()' > Modules/Video/BridgeOpenCV/test/CMakeFiles/ITKVideoBridgeOpenCVTestDriver.dir/itkOpenCVVideoIOTest.cxx.o: > In function `itk::ObjectFactory::Create()': > /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:60: > undefined reference to `typeinfo for itk::OpenCVVideoIO' > /home/arnaud/source/itk/Modules/Core/Common/include/itkObjectFactory.h:62: > undefined reference to `typeinfo for itk::OpenCVVideoIO' > collect2: error: ld returned 1 exit status > ninja: build stopped: subcommand failed. > > > On Fri, Aug 14, 2015 at 6:24 PM, Arnaud Gelas > wrote: > >> I have already tried it, does not solve it... I will retry it with a >> fresh build once again... >> >> On Fri, Aug 14, 2015 at 6:11 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >>> Hi Arnaud, >>> >>> Yes, you are probably right. The suggestion by Zach in this patch (to >>> use DEPENDS) is promising: >>> >>> http://review.source.kitware.com/#/c/20078/ >>> >>> Thanks, >>> Matt >>> >>> On Fri, Aug 14, 2015 at 2:21 AM, Arnaud Gelas >>> wrote: >>> > Hi Matt, >>> > >>> > It happened while directly building ITK with OpenCV 2.4.9, without any >>> > superbuild... >>> > Thanks for the patch, but that does not solve it... >>> > >>> > I wonder if it could have something to do with the new linking system >>> (note >>> > it uses COMPILE_DEPENDS) ? >>> > >>> > Thanks, >>> > Arnaud >>> > >>> > On Thu, Aug 13, 2015 at 6:41 PM, Matt McCormick < >>> matt.mccormick at kitware.com> >>> > wrote: >>> >> >>> >> Hi Arnaud, >>> >> >>> >> Is this with building the examples with the superbuild? I think I was >>> >> getting this error, too. Here is a patch that should address it: >>> >> >>> >> http://review.source.kitware.com/#/c/20077/ >>> >> >>> >> Thanks, >>> >> Matt >>> >> >>> >> On Thu, Aug 13, 2015 at 11:40 AM, Arnaud Gelas >> > >>> >> wrote: >>> >> > Hi all, >>> >> > >>> >> > I have just tried building ITK with BridgeOpenCV on Ubuntu 14.04 >>> and I >>> >> > get >>> >> > the following link error >>> >> > >>> >> > [2/2] Linking CXX executable bin/ITKVideoBridgeOpenCVHeaderTest1 >>> >> > >>> >> > [...] >>> >> > >>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >>> >> > 'itk::VideoIOBase::VideoIOBase()' >>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >>> >> > 'itk::VideoIOBase::~VideoIOBase()' >>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >>> >> > 'itk::VideoIOBase::PrintSelf(std::ostream&, itk::Indent) const' >>> >> > lib/libITKVideoBridgeOpenCV-4.9.so.1: error: undefined reference to >>> >> > 'typeinfo for itk::VideoIOBase' >>> >> > collect2: error: ld returned 1 exit status >>> >> > >>> >> > I have checked these methods are implemented in >>> itkVideoIOBase.cxx... >>> >> > >>> >> > Any idea? >>> >> > >>> >> > Thanks >>> >> > Arnaud >>> >> > >>> >> > _______________________________________________ >>> >> > Powered by www.kitware.com >>> >> > >>> >> > Visit other Kitware open-source projects at >>> >> > http://www.kitware.com/opensource/opensource.html >>> >> > >>> >> > Kitware offers ITK Training Courses, for more information visit: >>> >> > http://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 Fri Aug 14 15:54:14 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 14 Aug 2015 15:54:14 -0400 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas wrote: > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make > much sense to me?), same link error... > > If it helps, I can prepare a docker build file to track this error (for > anyone willing to help)? That would be awesome :-) Thanks, Matt From bill.lorensen at gmail.com Sat Aug 15 15:09:46 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Sat, 15 Aug 2015 15:09:46 -0400 Subject: [ITK-dev] Link error after recent commit Message-ID: I get link errors resembling this: Linking CXX executable ../../../../bin/ITKLevelSetsv4VisualizationTestDriver /usr/bin/ld: CMakeFiles/ITKLevelSetsv4VisualizationTestDriver.dir/itkVTKVisualizeLevelSetsInteractivePauseTest.cxx.o: undefined reference to symbol '_ZNK3itk18VTKImageExportBase32GetPropagateUpdateExtentCallbackEv' /usr/bin/ld: note: '_ZNK3itk18VTKImageExportBase32GetPropagateUpdateExtentCallbackEv' is defined in DSO /home/lorensen/ProjectsGIT/ITKGerrit-linux/lib/libITKVTK-4.9.so.1 so try adding it to the linker command line /home/lorensen/ProjectsGIT/ITKGerrit-linux/lib/libITKVTK-4.9.so.1: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status make[2]: *** [bin/ITKLevelSetsv4VisualizationTestDriver] Error 1 make[1]: *** [Modules/Segmentation/LevelSetsv4Visualization/test/CMakeFiles/ITKLevelSetsv4VisualizationTestDriver.dir/all] Error 2 ---------------------------------- git bisect commit identified this commit: Author: Zach Williamson Date: Wed Jul 15 10:39:04 2015 -0500 ENH: Use new linking system macros This is a work-in-progress to demonstrate using the new linking system (DEPENDS, COMPILE_DEPENDS, PRIVATE_DEPENDS etc.) Most changes so far are using private_depends where applicable to reduce the total number of links being created (since public dependencies are linked recursively while private dependencies are not) Change-Id: I41bed74b8d6ed508f2014163854799ed0ef17919 This build has: Module_ITKLevelSetsv4Visualization:BOOL=ON From arnaudgelas at gmail.com Mon Aug 17 10:03:26 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Mon, 17 Aug 2015 16:03:26 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Matt, Here you go Thanks, Arnaud On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick wrote: > On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas > wrote: > > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make > > much sense to me?), same link error... > > > > If it helps, I can prepare a docker build file to track this error (for > > anyone willing to help)? > > That would be awesome :-) > > Thanks, > Matt > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Dockerfile Type: application/octet-stream Size: 1994 bytes Desc: not available URL: From marco.dev.open at gmail.com Mon Aug 17 10:14:56 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Mon, 17 Aug 2015 07:14:56 -0700 Subject: [ITK-dev] vtk transform filter on .RAW Message-ID: Hi, why does not work vtk transform filter correctly on .RAW file I read the .raw file through ifstream then create a image type from this buffer as follow bellow: ifstream fin(filePath[0], ios::in | ios::binary); signed short iSample; cout << "Samples Output" << endl; while (fin.read((char *)&iSample, sizeof(signed short))) { m_Short.push_back(iSample); } cout << " size of short vector " << m_Short.size(); m_Aloc = (signed short*)malloc(m_Short.size() * 2); int counter = 0; for (std::vector::iterator it = m_Short.begin(); it != m_Short.end(); ++it, counter++){ m_Aloc[counter] = (*it); } . . // set nidex size orientation spacing ,,,,, to itk filter . . importFilter->SetImportPointer(m_Aloc,sizeX*sizeY*sizeZ, true); try { importFilter->Update(); pVol = importFilter->GetOutput(); } catch (itk::ExceptionObject & err) { return false; } pVol->Register(); typedef itk::ImageToVTKImageFilter itkVtkConverter; itkVtkConverter::Pointer conv = itkVtkConverter::New(); conv->SetInput(pVol); conv->Update(); vtkSmartPointer vtkImage = vtkSmartPointer::New(); vtkImage->ShallowCopy(conv->GetOutput()); //shallow copy is vtk's equivalent of disconnect pipeline volumeRayCatMapper = vtkSmartPointer::New(); volumeRayCatMapper->SetInputData(vtkImage); . . . . //Skin color->AddRGBPoint(-3024, 0, 0, 0, 0.5, 0.0); color->AddRGBPoint(-1000, .62, .36, .18, 0.5, 0.0); color->AddRGBPoint(-500, .88, .60, .29, 0.33, 0.45); color->AddRGBPoint(3071, .83, .66, 1, 0.5, 0.0); compositeOpacity->AddPoint(-3024, 0, 0.5, 0.0); compositeOpacity->AddPoint(-1000, 0, 0.5, 0.0); compositeOpacity->AddPoint(-500, 1.0, 0.33, 0.45); compositeOpacity->AddPoint(3071, 1.0, 0.5, 0.0); volumeRayCatMapper->SetBlendModeToComposite(); volumeProperty->ShadeOn(); volumeProperty->SetAmbient(0.1); volumeProperty->SetDiffuse(0.9); volumeProperty->SetSpecular(0.2); volumeProperty->SetSpecularPower(10.0); volumeProperty->SetScalarOpacityUnitDistance(0.8919); why does not work correctly on volume ? if I read the dicom series from itk reader it does work correctly Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Aug 18 09:00:29 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 18 Aug 2015 09:00:29 -0400 Subject: [ITK-dev] Sphinx and ITK WIki example regression Message-ID: Folks, The addition of the new math equality checks caused Sphinx and Wiki examples using itkCustomColormapFunction to segfault. I submitted a patch to fix this. However, this brings up an issue. I'm sorry now that I did not review the math equality check changes. I see the need for fuzzy math comparison for real types, but why for integral types? What is the justification for replacing int i; int j; if (i == j) ? with if (Math::AlmostEquals(i,j)) ? of if(Math::AlmostEquals(i,j))... -- Unpaid intern in BillsBasement at noware dot com From arnaudgelas at gmail.com Tue Aug 18 11:36:30 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Tue, 18 Aug 2015 17:36:30 +0200 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Matt, Do you have any idea on that matter? Thanks Arnaud On Mon, Aug 17, 2015 at 4:03 PM, Arnaud Gelas wrote: > Matt, > > Here you go > > Thanks, > Arnaud > > On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas >> wrote: >> > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not make >> > much sense to me?), same link error... >> > >> > If it helps, I can prepare a docker build file to track this error (for >> > anyone willing to help)? >> >> That would be awesome :-) >> >> Thanks, >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Aug 18 11:42:46 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 18 Aug 2015 11:42:46 -0400 Subject: [ITK-dev] New math comparison methods Message-ID: Folks, It is hard for me see see why the new math comparison operators are used for statements like this one in Core/Common/test/ itkDerivativeOperatorTest if( itk::Math::NotAlmostEquals( expected.size(), coefficients.size() ) ) instead of the original: if( expected.size() != coefficients.size() ) Can we revisit this topic? Bill From matt.mccormick at kitware.com Tue Aug 18 11:43:50 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 18 Aug 2015 11:43:50 -0400 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Hi Arnaud, With the excellent Dockerfile, I have been able to reproduce the error :-), but I have not had a chance to dive in further. I will do soon. Thanks, Matt On Tue, Aug 18, 2015 at 11:36 AM, Arnaud Gelas wrote: > Matt, > > Do you have any idea on that matter? > > Thanks > Arnaud > > On Mon, Aug 17, 2015 at 4:03 PM, Arnaud Gelas wrote: >> >> Matt, >> >> Here you go >> >> Thanks, >> Arnaud >> >> On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick >> wrote: >>> >>> On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas >>> wrote: >>> > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not >>> > make >>> > much sense to me?), same link error... >>> > >>> > If it helps, I can prepare a docker build file to track this error (for >>> > anyone willing to help)? >>> >>> That would be awesome :-) >>> >>> Thanks, >>> Matt >> >> > From bill.lorensen at gmail.com Tue Aug 18 12:07:21 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 18 Aug 2015 12:07:21 -0400 Subject: [ITK-dev] New math comparison methods In-Reply-To: References: Message-ID: If there are no objections, I'll take a pass on changing new math comparison operators back to vanilla comparisons for cases where two integral types of the same type are compared for example in Modules/Segmentation/Classifiers/include/itkImageGaussianModelEstimator.hxx: if ( Math::NotAlmostEquals( ( m_NumberOfSamples[classIndex][0] - 1 ), 0.0 ) ) I think there may be other cases that can be reverted but I won't know until I do a line by line inspection./ On Tue, Aug 18, 2015 at 11:42 AM, Bill Lorensen wrote: > Folks, > > It is hard for me see see why the new math comparison operators are > used for statements like this one in Core/Common/test/ > itkDerivativeOperatorTest > > if( itk::Math::NotAlmostEquals( expected.size(), coefficients.size() ) ) > instead of the original: > if( expected.size() != coefficients.size() ) > > Can we revisit this topic? > > Bill -- Unpaid intern in BillsBasement at noware dot com From matt.mccormick at kitware.com Tue Aug 18 12:12:34 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 18 Aug 2015 12:12:34 -0400 Subject: [ITK-dev] [ITK] New math comparison methods In-Reply-To: References: Message-ID: Hi Bill, Thanks for taking a look at this, and trying to improve the result. Yes, we should probably only use the operator in situations where templates generate comparisons in a hybrid of floating point and integer situations -- integer only could use operator==. Thanks, Matt On Tue, Aug 18, 2015 at 12:07 PM, Bill Lorensen wrote: > If there are no objections, I'll take a pass on changing new math > comparison operators back to vanilla comparisons for cases where > > two integral types of the same type are compared > for example in > Modules/Segmentation/Classifiers/include/itkImageGaussianModelEstimator.hxx: > if ( Math::NotAlmostEquals( ( m_NumberOfSamples[classIndex][0] - 1 ), 0.0 ) ) > > I think there may be other cases that can be reverted but I won't know > until I do a line by line inspection./ > > > > > On Tue, Aug 18, 2015 at 11:42 AM, Bill Lorensen wrote: >> Folks, >> >> It is hard for me see see why the new math comparison operators are >> used for statements like this one in Core/Common/test/ >> itkDerivativeOperatorTest >> >> if( itk::Math::NotAlmostEquals( expected.size(), coefficients.size() ) ) >> instead of the original: >> if( expected.size() != coefficients.size() ) >> >> Can we revisit this topic? >> >> Bill > > > > -- > Unpaid intern in BillsBasement at noware dot com > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://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 From mohammedrashadkm at gmail.com Tue Aug 18 14:26:15 2015 From: mohammedrashadkm at gmail.com (Rashad M) Date: Tue, 18 Aug 2015 20:26:15 +0200 Subject: [ITK-dev] regarding ImageFileReader::GenerateOutputInformation() In-Reply-To: <3284837D-9DD6-48A1-A65D-5ED81EC1A95B@mail.nih.gov> References: <3284837D-9DD6-48A1-A65D-5ED81EC1A95B@mail.nih.gov> Message-ID: Hello Brad, Thanks for your reply. I had check the UpdateOutputInformation() with a seperate test code and there was no problem. I found that there are multiple instances of Reader created in every execution of the my code which was the cause of the error/behaviour I was having. On Thu, Aug 13, 2015 at 9:11 PM, Bradley Lowekamp wrote: > Hello Rashad, > > If you call ImageFileReader::UpdateOutputInformation() 2 times is "should" > only call GenerateOutputInformation once. > > The key to this behavior is the management of the timestamps in the > process object classes done here [1]. > > What is required for this to work correctly is that the only the correct > object get modified in these pipeline methods. When an object is modified > the timestamp should be updated, and downstream processes get marked as out > of date. > > The best way to make sure your ImageSource does not get call twice is to > write a test, that makes sure the process object's MTime does not change in > GenerateOutputInformation call. > > HTH, > Brad > > [1] > https://github.com/InsightSoftwareConsortium/ITK/blob/9f88e4e3b388ee2f1c1c006ae36de0613d305284/Modules/Core/Common/src/itkProcessObject.cxx#L1431-L1542 > > On Aug 13, 2015, at 2:55 PM, Rashad M wrote: > > Hello all, > > The documentation of itk::ProcessObject::GenerateOutputInformation( ) > says > Generate the information describing the output data. [1]. The GenerateOutputInformation() > in itkImageFileReader first create all instances of ImageIO and setup > direction, spacing, etc.. > > If I understand correctly, the GenerateOutputInformation in the image file > reader is called by UpdateOutputInformation( ) > > To my question, > If I call reader->UpdateOutputInformation() for first time it calls > reader->GenerateOutputInformation() as described in docs[2]. > > Now If I have a second call to reader->UpdateOutputInformation( ) ? > > Will it again go to GenerateOutputInformation() and createAllInstances of > imageio , do the same thing again! > > In itkProcessObject.cxx, there is the below documentation > > * Call GenerateOutputInformation for subclass specific information. > * Since UpdateOutputInformation propagates all the way up the pipeline, > * we need to be careful here to call GenerateOutputInformation only if > * necessary. Otherwise, we may cause this source to be modified which > * will cause it to execute again on the next update. > > How can I prevent it from calling it again in class sub class of > itk::ImageSource? > > [1] > http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#abe61fb6b7de8c443e7af1561bd722736 > > > -- > Regards, > Rashad > _______________________________________________ > 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 > > > -- Regards, Rashad -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Aug 19 00:20:27 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 19 Aug 2015 00:20:27 -0400 Subject: [ITK-dev] link failure ITKVideoBridgeOpenCVHeaderTest1 on Ubuntu 14.04 In-Reply-To: References: Message-ID: Hi Arnaud, It looks like there are some missing export macros -- I uploaded a new patch set to your change. Thanks, Matt On Tue, Aug 18, 2015 at 11:43 AM, Matt McCormick wrote: > Hi Arnaud, > > With the excellent Dockerfile, I have been able to reproduce the error > :-), but I have not had a chance to dive in further. I will do soon. > > Thanks, > Matt > > On Tue, Aug 18, 2015 at 11:36 AM, Arnaud Gelas wrote: >> Matt, >> >> Do you have any idea on that matter? >> >> Thanks >> Arnaud >> >> On Mon, Aug 17, 2015 at 4:03 PM, Arnaud Gelas wrote: >>> >>> Matt, >>> >>> Here you go >>> >>> Thanks, >>> Arnaud >>> >>> On Fri, Aug 14, 2015 at 9:54 PM, Matt McCormick >>> wrote: >>>> >>>> On Fri, Aug 14, 2015 at 1:31 PM, Arnaud Gelas >>>> wrote: >>>> > I have also tried adding ITKVideoIO in TEST_DEPENDS (which does not >>>> > make >>>> > much sense to me?), same link error... >>>> > >>>> > If it helps, I can prepare a docker build file to track this error (for >>>> > anyone willing to help)? >>>> >>>> That would be awesome :-) >>>> >>>> Thanks, >>>> Matt >>> >>> >> From bill.lorensen at gmail.com Wed Aug 19 10:45:47 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 19 Aug 2015 10:45:47 -0400 Subject: [ITK-dev] Recent changes have introduced valgrind defects Message-ID: Folks, Recent changes have caused valgrid defects: https://open.cdash.org/viewDynamicAnalysis.php?buildid=3962722 Bill -- Unpaid intern in BillsBasement at noware dot com From matt.mccormick at kitware.com Wed Aug 19 11:41:14 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 19 Aug 2015 11:41:14 -0400 Subject: [ITK-dev] [ITK] Recent changes have introduced valgrind defects In-Reply-To: References: Message-ID: Hi Luc, These are probably related to this change: http://review.source.kitware.com/#/c/19962/ Could you please take a look? Thanks, Matt On Wed, Aug 19, 2015 at 10:45 AM, Bill Lorensen wrote: > Folks, > > Recent changes have caused valgrid defects: > https://open.cdash.org/viewDynamicAnalysis.php?buildid=3962722 > > Bill > > -- > Unpaid intern in BillsBasement at noware dot com > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://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 From matt.mccormick at kitware.com Wed Aug 19 12:55:38 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 19 Aug 2015 12:55:38 -0400 Subject: [ITK-dev] [ITK] Recent changes have introduced valgrind defects In-Reply-To: <55D4A74C.2020506@c-s.fr> References: <55D4A74C.2020506@c-s.fr> Message-ID: On Wed, Aug 19, 2015 at 11:57 AM, Luc Hermitte wrote: >>> Recent changes have caused valgrid defects: >>> https://open.cdash.org/viewDynamicAnalysis.php?buildid=3962722 >> These are probably related to this change: >> >> http://review.source.kitware.com/#/c/19962/ >> > The tests on lines 160, 166, and 172 are incorrect. After the SetSize, > the value x[0] is left uninitialized on purpose. It could be equal to > ref[0]. > Instead, we should test that x[0] is uninitialized. But I don't know any > way to do it. In that case, please remove them. > I'll comment these lines for my next commit (on C++ rvalue references) > if it's OK with you. Please keep the patches divided by subject if possible. Is there a different issue causing the defect in itkImageToVectorImageFilterTest? Thanks, Matt From matt.mccormick at kitware.com Thu Aug 20 15:01:02 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 20 Aug 2015 15:01:02 -0400 Subject: [ITK-dev] CDash Downtime Wednesday 8/26 Message-ID: Hello, There is planned CDash downtime effecting ITK / SimpleITK: Wednesday 8/26, 4:30 - 6:30 PM Eastern US Time Matt From matt.mccormick at kitware.com Thu Aug 20 22:37:43 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 20 Aug 2015 22:37:43 -0400 Subject: [ITK-dev] Failing tests related to eigen analysis change Message-ID: Hi Olivier, Since it requires Module_ITKReview to be ON, we missed some failing tests that result from the eigen analysis update: https://open.cdash.org/viewTest.php?onlyfailed&buildid=3965258 Git bisect confirms they follow from this patch: http://review.source.kitware.com/#/c/20092/ If the result is more correct, we should just update the baseline images, agreed? Thanks, Matt From marco.dev.open at gmail.com Fri Aug 21 12:16:00 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Fri, 21 Aug 2015 20:46:00 +0430 Subject: [ITK-dev] gdcm2.x dicom parse Message-ID: Hi , As you know gdcm used by ITK for parsing dicom images how many kind of dicom images can read with the GDCM 2.X I also read some feature about reding Compress dicom images ..... It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE ...... for all of kind of DICOM images ? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Aug 21 17:28:05 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 21 Aug 2015 17:28:05 -0400 Subject: [ITK-dev] gdcm2.x dicom parse In-Reply-To: References: Message-ID: Hi Marco, A list of supported formats can be found here: http://gdcm.sourceforge.net/wiki/index.php/Main_Page ITK does build with JPEG 2000 support. HTH, Matt On Fri, Aug 21, 2015 at 12:16 PM, Marco Dev wrote: > Hi , > As you know gdcm used by ITK for parsing dicom images how many kind of dicom > images can read with the GDCM 2.X I also read some feature about reding > Compress dicom images ..... > It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE ...... > for all of kind of DICOM images ? > Thanks > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://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 marco.dev.open at gmail.com Tue Aug 25 10:41:32 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Tue, 25 Aug 2015 19:11:32 +0430 Subject: [ITK-dev] Fusion in action Message-ID: Hi, As you knew there some Examples in itk for registration RIGID - DEFORMABLE .... in other hand We have Fusion issue in registration which algorithm should be used for doing the FUSION can you give me a guide line whole this subject Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Aug 26 08:36:39 2015 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 26 Aug 2015 12:36:39 +0000 Subject: [ITK-dev] NLM RFP: ITK Algorithms, Extensibility, Integration, & Outreach for SimpleITK 2015 Message-ID: The National Institutes of Health (NIH), National Library of Medicine (NLM) is solicitation proposals for improvements to SimpleITK/ITK. The FedBizOpps has complete information: https://www.fbo.gov/spg/HHS/NIH/OAM/RFP_NIHLM2015597KB/listing.html The response date is Sep 08, 2015 12:00pm Eastern. Bradley Lowekamp MSC Contractor NIH/NLM/LHC/OHPCC From blowekamp at mail.nih.gov Thu Aug 27 11:16:52 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 27 Aug 2015 11:16:52 -0400 Subject: [ITK-dev] libpng valgrind issue Message-ID: <83129BAA-6BB0-4DAF-AA63-77469C4FB818@mail.nih.gov> Hello, I narrowed down a couple valgrind [1] defects to a recent change to fix a warning. I am surprised to see how active the libpng library is. It looks like we are a good bit out of date. I was thinking of working on a ThirdParty update script with the subtree to update the library. Wondering if there is any prior work or experience with updating libpng? Thanks, Brad [1] https://open.cdash.org/viewDynamicAnalysisFile.php?id=3530475 From matt.mccormick at kitware.com Thu Aug 27 12:05:30 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 27 Aug 2015 12:05:30 -0400 Subject: [ITK-dev] libpng valgrind issue In-Reply-To: <83129BAA-6BB0-4DAF-AA63-77469C4FB818@mail.nih.gov> References: <83129BAA-6BB0-4DAF-AA63-77469C4FB818@mail.nih.gov> Message-ID: Hi Brad, Updating libpng with the ThirdParty update script is a great idea! As a reminder, there are some methods detailed in itk_tiff_mangle.h [1] that may be helpful for the name mangling process. [1] HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/TIFF/src/itktiff/itk_tiff_mangle.h;h=e65dadec55cf9d03d68580a39fa986c1147b3520;hb=HEAD On Thu, Aug 27, 2015 at 11:16 AM, Bradley Lowekamp wrote: > Hello, > > I narrowed down a couple valgrind [1] defects to a recent change to fix a warning. > > I am surprised to see how active the libpng library is. It looks like we are a good bit out of date. I was thinking of working on a ThirdParty update script with the subtree to update the library. > > Wondering if there is any prior work or experience with updating libpng? > > Thanks, > Brad > > [1] https://open.cdash.org/viewDynamicAnalysisFile.php?id=3530475 > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Fri Aug 28 11:16:53 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 28 Aug 2015 11:16:53 -0400 Subject: [ITK-dev] =?utf-8?q?Test_failures_on_RogueResearch9_=EF=BF=BCMac1?= =?utf-8?q?0=2E6-gcc-rel-x86=5F64-static?= Message-ID: Hi Sean, In checking up on the dashboard, we recently have acquired 8 failing tests on RogueResearch9 ?Mac10.6-gcc-rel-x86_64-static: https://open.cdash.org/viewTest.php?onlyfailed&buildid=3973444 They started on August 18th, but there were many changes that day: https://open.cdash.org/index.php?project=Insight&date=20150818 and it is difficult to know the source of the problem. Could git bisect please be run on that box or is there any other information to help find the source of the issue? Thanks, Matt From marco.dev.open at gmail.com Sat Aug 29 12:18:52 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Sat, 29 Aug 2015 20:48:52 +0430 Subject: [ITK-dev] compare between MITK.ORG AND 3D SLICER Message-ID: Hi, I want to choice between MITK and 3d slicer for working in medical features which one is powerful and going to improving in aspect code and example ... Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Sat Aug 29 19:56:44 2015 From: sean at rogue-research.com (Sean McBride) Date: Sat, 29 Aug 2015 19:56:44 -0400 Subject: [ITK-dev] Test failures on RogueResearch9 ?Mac10.6-gcc-rel-x86_64-static In-Reply-To: References: Message-ID: <20150829235644.614532161@mail.rogue-research.com> On Fri, 28 Aug 2015 11:16:53 -0400, Matt McCormick said: >Hi Sean, > >In checking up on the dashboard, we recently have acquired 8 failing >tests on RogueResearch9 ?Mac10.6-gcc-rel-x86_64-static: > > https://open.cdash.org/viewTest.php?onlyfailed&buildid=3973444 > > >They started on August 18th, but there were many changes that day: > > https://open.cdash.org/index.php?project=Insight&date=20150818 > >and it is difficult to know the source of the problem. Could git >bisect please be run on that box or is there any other information to >help find the source of the issue? Took a while to run, but: git bisect start git bisect good 27e871d35c12ff85c798359c87b1828ee6d55d48 git bisect bad 0d769889367c013836d43691d13091326d6a998d 9ea5521e0fd2ed30404a72c53b1bdb15ab51a057 is the first bad commit commit 9ea5521e0fd2ed30404a72c53b1bdb15ab51a057 Author: Alexander Leinoff Date: Fri Aug 14 09:11:46 2015 -0500 COMP: Removes floating-point equality checks Equality checks between floating point values and other types are sometimes required to be exact and other times need only be approximate. Here direct equality checks are replaced with functions calls to either an exact or approximate comparison. Using these functions explicitly stating which kind of comparison is being requested improves clarity and readability of code, and removes compiler warnings ie. Wfloat-equal. Change-Id: I93241acc40178b50ab04158acfdbce5a93242890 :040000 040000 0875e6abbbbe9ae31f0e5992a25b8f17ef72ea8c 3bb3c0776a4e65c2a5dc35624b67f7a8e836c5fb M Examples :040000 040000 d8cbeb4d22f289a1c590b8cb43e4f05826e2c476 4e62bf45576ef2ff5b42326330b5eced60c4e367 M Modules Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From bill.hoffman at kitware.com Mon Aug 31 17:10:32 2015 From: bill.hoffman at kitware.com (Bill Hoffman) Date: Mon, 31 Aug 2015 17:10:32 -0400 Subject: [ITK-dev] Happy Birthday CMake! Message-ID: <55E4C2C8.1040501@kitware.com> Today is the 15th birthday of CMake: http://www.kitware.com/blog/home/post/959 Thanks to everyone that has used and contributed to CMake over the years! -Bill