From jchris.fillionr at kitware.com Tue Sep 1 11:19:18 2015 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Tue, 1 Sep 2015 11:19:18 -0400 Subject: [ITK-dev] [ITK] compare between MITK.ORG AND 3D SLICER In-Reply-To: References: Message-ID: Hi Marco, Both applications: - follows the best software development practices (See [1] and [2]) - have a thriving community (See [3] and [4]) - are built on top of proven technologies CTK, ITK, OpenCV, Python, QT and VTK, ... - provide an interface to execute Command Line module: http://commontk.org/index.php/Documentation/Command_Line_Interface - .... Reading the following paper from David Punzo could be helpful. While it applies to a different domain, it described some interesting comparison criteria: The role of 3-D interactive visualization in blind surveys of HI in galaxies http://arxiv.org/abs/1505.06976 Looking at the list of modules and functionalities offered by both may also be helpful: http://docs.mitk.org/nightly/PluginListPage.html http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly#Modules_by_name All of that said, if you have any questions regarding 3D Slicer, you are welcome to join the mailing list and join the weekly hangout (Tuesday at 2.30pm EST): http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/StartHere http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Meetings Thanks Jc Disclaimer: I am on the of Slicer core developer. [1] http://cdash.mitk.org/index.php?project=MITK [2] http://slicer.cdash.org/index.php?project=Slicer4 [3] http://mitk.org/wiki/MITK_Users_Meeting_2015_Slides [4] http://www.na-mic.org/Wiki/index.php/2015_Summer_Project_Week On Sat, Aug 29, 2015 at 12:18 PM, Marco Dev wrote: > 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 > > _______________________________________________ > 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 > > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mohammedrashadkm at gmail.com Thu Sep 3 03:17:15 2015 From: mohammedrashadkm at gmail.com (Rashad M) Date: Thu, 3 Sep 2015 09:17:15 +0200 Subject: [ITK-dev] Import and export contents itk::MetaDataDictionary into files Message-ID: Hello all, I would like to check if there is any way in itk to read contents of file into a metadata dictionary. I found this wiki page - http://itk.org/Wiki/ITK/Examples/Broken/SimpleOperations/MetaDataDictionary It says " There are two problems. 1) UNKNOWN_PRINT_CHARACTERISTICS should be replaced with 1.2. 2) The data does not seem to be retrieved from the file. " I dont know if is any update on this or if such thing is planned in next release or so. IMHO, having a format independent way of importing and exporting metadata would be nice. -- Regards, Rashad -------------- next part -------------- An HTML attachment was scrubbed... URL: From mathieu.malaterre at gmail.com Fri Sep 4 03:55:52 2015 From: mathieu.malaterre at gmail.com (Mathieu Malaterre) Date: Fri, 4 Sep 2015 09:55:52 +0200 Subject: [ITK-dev] Module_ITKIOGDCM:INTERNAL=OFF Message-ID: Dear all, My goal is to be able to compile ITK without the GDCM module. Long story short, GDCM toolkit is not being mangled, which means very complex build setup to be able to use GDCM and ITK in an application. So far I have tried setting: Module_ITKIOGDCM:INTERNAL=OFF with no luck I suspect that GDCM is activated by ITK_BUILD_DEFAULT_MODULES, so I tried: $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF this leads to: -- Check if the system is big endian - little endian CMake Error at Examples/CMakeLists.txt:2 (message): BUILD_EXAMPLES requires ITK_BUILD_DEFAULT_MODULES to be ON -- Configuring incomplete, errors occurred! Later I tried: $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF .. which states: -- Enabled ITKIOGDCM, needed by [ITKTestKernel]. and -- Enabled ITKTestKernel, needed by [ITKGroup_Core]. However I do not want to set -DITKGroup_Core:BOOL=OFF (obvisouly). Is there any particular reason to have GDCM be part of the core group ? Thanks, -- Mathieu From blowekamp at mail.nih.gov Fri Sep 4 15:21:36 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 04 Sep 2015 15:21:36 -0400 Subject: [ITK-dev] Module_ITKIOGDCM:INTERNAL=OFF In-Reply-To: References: Message-ID: <883004AB-7E1A-4C95-A3A5-5B7CC274F914@mail.nih.gov> Hello, Have you looking into "ITK_USE_SYSTEM_GDCM", this should allow ITK to use the same version of GDCM that the rest of your application is? For the modular build, have you looked into disabling "BUILD_TESTING"? Also please keep in mind that the a module's status is cached in CMake. So you must start with a fresh directory then configure from the command line which modules are on and off. Many ImageIOs are needed to do testing [1], supporting DICOM and DICOM metadata are of core importance for ITK, so we do test with it in many places.The modularization works really good without the ITK testing enabled. But the interdependency of testing that everything works does enable most modules. HTH, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/TestKernel/itk-module.cmake On Sep 4, 2015, at 3:55 AM, Mathieu Malaterre wrote: > Dear all, > > My goal is to be able to compile ITK without the GDCM module. > > Long story short, GDCM toolkit is not being mangled, which means very > complex build setup to be able to use GDCM and ITK in an application. > > So far I have tried setting: > > Module_ITKIOGDCM:INTERNAL=OFF > > with no luck > > I suspect that GDCM is activated by ITK_BUILD_DEFAULT_MODULES, so I tried: > > $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF > > this leads to: > > -- Check if the system is big endian - little endian > CMake Error at Examples/CMakeLists.txt:2 (message): > BUILD_EXAMPLES requires ITK_BUILD_DEFAULT_MODULES to be ON > > > -- Configuring incomplete, errors occurred! > > > Later I tried: > > $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF .. > > which states: > > -- Enabled ITKIOGDCM, needed by [ITKTestKernel]. > and > -- Enabled ITKTestKernel, needed by [ITKGroup_Core]. > > > However I do not want to set -DITKGroup_Core:BOOL=OFF (obvisouly). > > Is there any particular reason to have GDCM be part of the core group ? > > > > Thanks, > -- > Mathieu > _______________________________________________ > 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 Mon Sep 14 01:17:13 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Mon, 14 Sep 2015 09:47:13 +0430 Subject: [ITK-dev] transparency or opacity Message-ID: Hi, how to opacity on a Dicom image in itk is there any Clear Example Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 14 12:30:29 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 14 Sep 2015 12:30:29 -0400 Subject: [ITK-dev] Fwd: New Defects reported by Coverity Scan for InsightSoftwareConsortium In-Reply-To: <55f3cecd3391e_44883d9334316f6@scan.mail> References: <55f3cecd3391e_44883d9334316f6@scan.mail> Message-ID: Hello, Does the new Coverity defect below ring a bell with anyone? Thanks, Matt ---------- Forwarded message ---------- From: Date: Sat, Sep 12, 2015 at 3:05 AM Subject: New Defects reported by Coverity Scan for InsightSoftwareConsortium To: matt.mccormick at kitware.com Hi, Please find the latest report on new defect(s) introduced to InsightSoftwareConsortium found with Coverity Scan. 1 new defect(s) introduced to InsightSoftwareConsortium found with Coverity Scan. 395 defect(s), reported by Coverity Scan earlier, were marked fixed in the recent build analyzed by Coverity Scan. New defect(s) Reported-by: Coverity Scan Showing 1 of 1 defect(s) ** CID 1323843: Error handling issues (UNCAUGHT_EXCEPT) /home/kitware/Dashboards/Coverity/ITK/Modules/Core/Common/src/itkObject.cxx: 412 in itk::Object::UnRegister() const() ________________________________________________________________________________________________________ *** CID 1323843: Error handling issues (UNCAUGHT_EXCEPT) /home/kitware/Dashboards/Coverity/ITK/Modules/Core/Common/src/itkObject.cxx: 412 in itk::Object::UnRegister() const() 406 407 /** 408 * Decrease the reference count (release by another object). 409 */ 410 void 411 Object >>> CID 1323843: Error handling issues (UNCAUGHT_EXCEPT) >>> An exception of type "itk::ExceptionObject" is thrown but the throw list "throw ()" doesn't allow it to be thrown. This will cause a call to unexpected() which usually calls terminate(). 412 ::UnRegister() const ITK_NOEXCEPT 413 { 414 // call the parent 415 itkDebugMacro( << "UnRegistered, " 416 << "ReferenceCount = " << ( m_ReferenceCount - 1 ) ); 417 ________________________________________________________________________________________________________ To view the defects in Coverity Scan visit, https://scan.coverity.com/projects/insightsoftwareconsortium?tab=overview To manage Coverity Scan email notifications for "matt.mccormick at kitware.com", click https://scan.coverity.com/subscriptions/edit?email=matt.mccormick%40kitware.com&token=d32d0bd32d3dfdd9bc75f2cd636b6067 From blowekamp at mail.nih.gov Mon Sep 14 13:18:50 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 14 Sep 2015 13:18:50 -0400 Subject: [ITK-dev] New Defects reported by Coverity Scan for InsightSoftwareConsortium In-Reply-To: References: <55f3cecd3391e_44883d9334316f6@scan.mail> Message-ID: Matt, This defect looks legitimate. I added the noexept specifier here[1]. My guess is that Coverity has just added this feature for C++11. I'll dig into this and help to ensure out destructors have better exception safety... Brad [1] https://github.com/InsightSoftwareConsortium/ITK/commit/06f8ef0175d901ec5d23197efb4f9044c1b62ab3 On Sep 14, 2015, at 12:30 PM, Matt McCormick wrote: > Hello, > > Does the new Coverity defect below ring a bell with anyone? > > Thanks, > Matt > > > ---------- Forwarded message ---------- > From: > Date: Sat, Sep 12, 2015 at 3:05 AM > Subject: New Defects reported by Coverity Scan for InsightSoftwareConsortium > To: matt.mccormick at kitware.com > > > > Hi, > > Please find the latest report on new defect(s) introduced to > InsightSoftwareConsortium found with Coverity Scan. > > 1 new defect(s) introduced to InsightSoftwareConsortium found with > Coverity Scan. > 395 defect(s), reported by Coverity Scan earlier, were marked fixed in > the recent build analyzed by Coverity Scan. > > New defect(s) Reported-by: Coverity Scan > Showing 1 of 1 defect(s) > > > ** CID 1323843: Error handling issues (UNCAUGHT_EXCEPT) > /home/kitware/Dashboards/Coverity/ITK/Modules/Core/Common/src/itkObject.cxx: > 412 in itk::Object::UnRegister() const() > > > ________________________________________________________________________________________________________ > *** CID 1323843: Error handling issues (UNCAUGHT_EXCEPT) > /home/kitware/Dashboards/Coverity/ITK/Modules/Core/Common/src/itkObject.cxx: > 412 in itk::Object::UnRegister() const() > 406 > 407 /** > 408 * Decrease the reference count (release by another object). > 409 */ > 410 void > 411 Object >>>> CID 1323843: Error handling issues (UNCAUGHT_EXCEPT) >>>> An exception of type "itk::ExceptionObject" is thrown but the throw list "throw ()" doesn't allow it to be thrown. This will cause a call to unexpected() which usually calls terminate(). > 412 ::UnRegister() const ITK_NOEXCEPT > 413 { > 414 // call the parent > 415 itkDebugMacro( << "UnRegistered, " > 416 << "ReferenceCount = " << ( m_ReferenceCount - 1 ) ); > 417 > > > ________________________________________________________________________________________________________ > To view the defects in Coverity Scan visit, > https://scan.coverity.com/projects/insightsoftwareconsortium?tab=overview > > To manage Coverity Scan email notifications for > "matt.mccormick at kitware.com", click > https://scan.coverity.com/subscriptions/edit?email=matt.mccormick%40kitware.com&token=d32d0bd32d3dfdd9bc75f2cd636b6067 > _______________________________________________ > 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 Sep 15 07:15:42 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Tue, 15 Sep 2015 15:45:42 +0430 Subject: [ITK-dev] draw diocom image in vtk window via itk reader Message-ID: Hi, how can to read a dicom image through itk::gdcm reader and show in vtk render window I want to read from itk reader no vtkdicomreader I read dicom images then converted to vtkImageData but the image poistion is not correct in drawing imageViewer->SetInputConnection(reader->GetOutputPort()); Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Tue Sep 15 08:31:12 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Tue, 15 Sep 2015 17:01:12 +0430 Subject: [ITK-dev] PET Cult Message-ID: Hi, Preset for PET Clut in vtkLookupTable format look like such as follow bellow: vtkSmartPointer lut = lut::New(); // hot color map lut->SetRange(x, y); lut->SetHueRange(x,y ); lut->SetValueRange( y, y ); lut->Build(); Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From mathieu.malaterre at gmail.com Tue Sep 15 12:02:35 2015 From: mathieu.malaterre at gmail.com (Mathieu Malaterre) Date: Tue, 15 Sep 2015 18:02:35 +0200 Subject: [ITK-dev] Module_ITKIOGDCM:INTERNAL=OFF In-Reply-To: <883004AB-7E1A-4C95-A3A5-5B7CC274F914@mail.nih.gov> References: <883004AB-7E1A-4C95-A3A5-5B7CC274F914@mail.nih.gov> Message-ID: Hi Brad, ITK_USE_SYSTEM_GDCM is not an option for me. I am given an already compiled ITK version (statically if that matters). I understand now the need for GDCM deep down in the build settings. I think I should be able to tweak `include(${ITK_USE_FILE})` to remove automatic io factory registration and drop "*GDCM*" from ${ITK_LIBRARIES}. Will let you know how it goes. Thanks for your help. -M On Fri, Sep 4, 2015 at 9:21 PM, Bradley Lowekamp wrote: > Hello, > > Have you looking into "ITK_USE_SYSTEM_GDCM", this should allow ITK to use the same version of GDCM that the rest of your application is? > > For the modular build, have you looked into disabling "BUILD_TESTING"? Also please keep in mind that the a module's status is cached in CMake. So you must start with a fresh directory then configure from the command line which modules are on and off. > > Many ImageIOs are needed to do testing [1], supporting DICOM and DICOM metadata are of core importance for ITK, so we do test with it in many places.The modularization works really good without the ITK testing enabled. But the interdependency of testing that everything works does enable most modules. > > HTH, > Brad > > [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/TestKernel/itk-module.cmake > > On Sep 4, 2015, at 3:55 AM, Mathieu Malaterre wrote: > >> Dear all, >> >> My goal is to be able to compile ITK without the GDCM module. >> >> Long story short, GDCM toolkit is not being mangled, which means very >> complex build setup to be able to use GDCM and ITK in an application. >> >> So far I have tried setting: >> >> Module_ITKIOGDCM:INTERNAL=OFF >> >> with no luck >> >> I suspect that GDCM is activated by ITK_BUILD_DEFAULT_MODULES, so I tried: >> >> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF >> >> this leads to: >> >> -- Check if the system is big endian - little endian >> CMake Error at Examples/CMakeLists.txt:2 (message): >> BUILD_EXAMPLES requires ITK_BUILD_DEFAULT_MODULES to be ON >> >> >> -- Configuring incomplete, errors occurred! >> >> >> Later I tried: >> >> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF .. >> >> which states: >> >> -- Enabled ITKIOGDCM, needed by [ITKTestKernel]. >> and >> -- Enabled ITKTestKernel, needed by [ITKGroup_Core]. >> >> >> However I do not want to set -DITKGroup_Core:BOOL=OFF (obvisouly). >> >> Is there any particular reason to have GDCM be part of the core group ? >> >> >> >> Thanks, >> -- >> Mathieu >> _______________________________________________ >> 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 > -- Mathieu From bill.lorensen at gmail.com Tue Sep 15 13:17:26 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 15 Sep 2015 13:17:26 -0400 Subject: [ITK-dev] Module_ITKIOGDCM:INTERNAL=OFF In-Reply-To: References: <883004AB-7E1A-4C95-A3A5-5B7CC274F914@mail.nih.gov> Message-ID: You can specify the specific module you need. For example: set(ITK_IO_MODULES_USED "ITKIONRRD;ITKIOPNG;ITKIONIFTI") find_package(ITK COMPONENTS ITKCommon ITKIOImageBase ITKImageGrid ITKImageStatistics ITKVtkGlue ${ITK_IO_MODULES_USED} ) include(${ITK_USE_FILE}) AND you can find the modules used by your app with ITK/Utilities/Maintenance/WhatModulesITK.py On Tue, Sep 15, 2015 at 12:02 PM, Mathieu Malaterre wrote: > Hi Brad, > > ITK_USE_SYSTEM_GDCM is not an option for me. I am given an already > compiled ITK version (statically if that matters). > > I understand now the need for GDCM deep down in the build settings. I > think I should be able to tweak `include(${ITK_USE_FILE})` to remove > automatic io factory registration and drop "*GDCM*" from > ${ITK_LIBRARIES}. > > Will let you know how it goes. Thanks for your help. > > -M > > On Fri, Sep 4, 2015 at 9:21 PM, Bradley Lowekamp wrote: >> Hello, >> >> Have you looking into "ITK_USE_SYSTEM_GDCM", this should allow ITK to use the same version of GDCM that the rest of your application is? >> >> For the modular build, have you looked into disabling "BUILD_TESTING"? Also please keep in mind that the a module's status is cached in CMake. So you must start with a fresh directory then configure from the command line which modules are on and off. >> >> Many ImageIOs are needed to do testing [1], supporting DICOM and DICOM metadata are of core importance for ITK, so we do test with it in many places.The modularization works really good without the ITK testing enabled. But the interdependency of testing that everything works does enable most modules. >> >> HTH, >> Brad >> >> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/TestKernel/itk-module.cmake >> >> On Sep 4, 2015, at 3:55 AM, Mathieu Malaterre wrote: >> >>> Dear all, >>> >>> My goal is to be able to compile ITK without the GDCM module. >>> >>> Long story short, GDCM toolkit is not being mangled, which means very >>> complex build setup to be able to use GDCM and ITK in an application. >>> >>> So far I have tried setting: >>> >>> Module_ITKIOGDCM:INTERNAL=OFF >>> >>> with no luck >>> >>> I suspect that GDCM is activated by ITK_BUILD_DEFAULT_MODULES, so I tried: >>> >>> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF >>> >>> this leads to: >>> >>> -- Check if the system is big endian - little endian >>> CMake Error at Examples/CMakeLists.txt:2 (message): >>> BUILD_EXAMPLES requires ITK_BUILD_DEFAULT_MODULES to be ON >>> >>> >>> -- Configuring incomplete, errors occurred! >>> >>> >>> Later I tried: >>> >>> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF .. >>> >>> which states: >>> >>> -- Enabled ITKIOGDCM, needed by [ITKTestKernel]. >>> and >>> -- Enabled ITKTestKernel, needed by [ITKGroup_Core]. >>> >>> >>> However I do not want to set -DITKGroup_Core:BOOL=OFF (obvisouly). >>> >>> Is there any particular reason to have GDCM be part of the core group ? >>> >>> >>> >>> Thanks, >>> -- >>> Mathieu >>> _______________________________________________ >>> 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 >> > > > > -- > Mathieu > _______________________________________________ > 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 -- Unpaid intern in BillsBasement at noware dot com From marco.dev.open at gmail.com Wed Sep 16 01:23:04 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Wed, 16 Sep 2015 09:53:04 +0430 Subject: [ITK-dev] Blending dicom images Message-ID: Hi, I try to bending two dicom images via itk reader and visualization by VTK as you know for blending in vtk use this such as line code follow bellow : vtkSmartPointer firstColorMapper = vtkSmartPointer::New(); * firstColorMapper->SetInputConnection( imgReader->GetOutputPort() ); // vtk reader firstColorMapper->SetInputData( image ); // itk reader * firstColorMapper->SetLookupTable( imgFirstColorMap ); vtkSmartPointer imgBlender = vtkSmartPointer::New(); imgBlender->SetOpacity( 0, 0.5 ); imgBlender->SetOpacity( 1, 1.0 ); imgBlender->AddInputConnection( firstColorMapper->GetOutputPort() ); imgBlender->AddInputConnection( secondColorMapper->GetOutputPort() ); But this pipeline for vtk reader (// vtk reader) via *SetInputConnection is correct * But for itk reader no effect Opacity and ... *in totally I want to Blend two dicom images via itk reader* can you give me a guide line Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From mathieu.malaterre at gmail.com Wed Sep 16 03:08:16 2015 From: mathieu.malaterre at gmail.com (Mathieu Malaterre) Date: Wed, 16 Sep 2015 09:08:16 +0200 Subject: [ITK-dev] Module_ITKIOGDCM:INTERNAL=OFF In-Reply-To: References: <883004AB-7E1A-4C95-A3A5-5B7CC274F914@mail.nih.gov> Message-ID: Very elegant solution. Thanks very much Bill ! On Tue, Sep 15, 2015 at 7:17 PM, Bill Lorensen wrote: > You can specify the specific module you need. For example: > > set(ITK_IO_MODULES_USED "ITKIONRRD;ITKIOPNG;ITKIONIFTI") > find_package(ITK COMPONENTS > ITKCommon > ITKIOImageBase > ITKImageGrid > ITKImageStatistics > ITKVtkGlue > ${ITK_IO_MODULES_USED} > ) > include(${ITK_USE_FILE}) > > > AND > you can find the modules used by your app with > ITK/Utilities/Maintenance/WhatModulesITK.py > > On Tue, Sep 15, 2015 at 12:02 PM, Mathieu Malaterre > wrote: >> Hi Brad, >> >> ITK_USE_SYSTEM_GDCM is not an option for me. I am given an already >> compiled ITK version (statically if that matters). >> >> I understand now the need for GDCM deep down in the build settings. I >> think I should be able to tweak `include(${ITK_USE_FILE})` to remove >> automatic io factory registration and drop "*GDCM*" from >> ${ITK_LIBRARIES}. >> >> Will let you know how it goes. Thanks for your help. >> >> -M >> >> On Fri, Sep 4, 2015 at 9:21 PM, Bradley Lowekamp wrote: >>> Hello, >>> >>> Have you looking into "ITK_USE_SYSTEM_GDCM", this should allow ITK to use the same version of GDCM that the rest of your application is? >>> >>> For the modular build, have you looked into disabling "BUILD_TESTING"? Also please keep in mind that the a module's status is cached in CMake. So you must start with a fresh directory then configure from the command line which modules are on and off. >>> >>> Many ImageIOs are needed to do testing [1], supporting DICOM and DICOM metadata are of core importance for ITK, so we do test with it in many places.The modularization works really good without the ITK testing enabled. But the interdependency of testing that everything works does enable most modules. >>> >>> HTH, >>> Brad >>> >>> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/TestKernel/itk-module.cmake >>> >>> On Sep 4, 2015, at 3:55 AM, Mathieu Malaterre wrote: >>> >>>> Dear all, >>>> >>>> My goal is to be able to compile ITK without the GDCM module. >>>> >>>> Long story short, GDCM toolkit is not being mangled, which means very >>>> complex build setup to be able to use GDCM and ITK in an application. >>>> >>>> So far I have tried setting: >>>> >>>> Module_ITKIOGDCM:INTERNAL=OFF >>>> >>>> with no luck >>>> >>>> I suspect that GDCM is activated by ITK_BUILD_DEFAULT_MODULES, so I tried: >>>> >>>> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF >>>> >>>> this leads to: >>>> >>>> -- Check if the system is big endian - little endian >>>> CMake Error at Examples/CMakeLists.txt:2 (message): >>>> BUILD_EXAMPLES requires ITK_BUILD_DEFAULT_MODULES to be ON >>>> >>>> >>>> -- Configuring incomplete, errors occurred! >>>> >>>> >>>> Later I tried: >>>> >>>> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF .. >>>> >>>> which states: >>>> >>>> -- Enabled ITKIOGDCM, needed by [ITKTestKernel]. >>>> and >>>> -- Enabled ITKTestKernel, needed by [ITKGroup_Core]. >>>> >>>> >>>> However I do not want to set -DITKGroup_Core:BOOL=OFF (obvisouly). >>>> >>>> Is there any particular reason to have GDCM be part of the core group ? >>>> >>>> >>>> >>>> Thanks, >>>> -- >>>> Mathieu >>>> _______________________________________________ >>>> 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 >>> >> >> >> >> -- >> Mathieu >> _______________________________________________ >> 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 > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Mathieu From drcjaudet at gmail.com Wed Sep 16 03:16:33 2015 From: drcjaudet at gmail.com (Cyril Jaudet) Date: Wed, 16 Sep 2015 09:16:33 +0200 Subject: [ITK-dev] Divide a label into Nregion of the same volume Message-ID: Hello ITK community, I recently use itk to segment a ring around a tumor on CT images. Is it possible to divide the label (value 0,1) into a label map consiting of N connected region (0-N) each with the same volume? Thank You, Cyril Jaudet; PhD UZbrussel -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.zaffino at yahoo.it Wed Sep 16 04:35:38 2015 From: p.zaffino at yahoo.it (Paolo Zaffino) Date: Wed, 16 Sep 2015 10:35:38 +0200 Subject: [ITK-dev] SimpleITK example, possible typo Message-ID: <55F929DA.7030202@yahoo.it> Dear all, I think I have found a typo into the SimpleITK example "ImageRegistrationMethodBSpline1.py" (in particular see [1]). I think that "maximumNumberOfIterations=100" should be "numberOfIterations=100". Am I wrong? Anyway thank you very much for the outstanding job...simpleITK is amazing! Best. Paolo [1] https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline1.py#L51 From blowekamp at mail.nih.gov Wed Sep 16 10:00:52 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 16 Sep 2015 10:00:52 -0400 Subject: [ITK-dev] [ITK] SimpleITK example, possible typo In-Reply-To: <55F929DA.7030202@yahoo.it> References: <55F929DA.7030202@yahoo.it> Message-ID: Hello, The file you linked is setting the keyword argument "numberOfIterations" and it's tested nightly. Are you getting an error or incorrect results? Patches to fix errors are welcome. Thanks, Brad On Sep 16, 2015, at 4:35 AM, Paolo Zaffino wrote: > Dear all, > I think I have found a typo into the SimpleITK example "ImageRegistrationMethodBSpline1.py" (in particular see [1]). > I think that "maximumNumberOfIterations=100" should be "numberOfIterations=100". > Am I wrong? > > Anyway thank you very much for the outstanding job...simpleITK is amazing! > > Best. > Paolo > > [1] https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline1.py#L51 > _______________________________________________ > 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 p.zaffino at yahoo.it Wed Sep 16 11:42:53 2015 From: p.zaffino at yahoo.it (Paolo Zaffino) Date: Wed, 16 Sep 2015 17:42:53 +0200 Subject: [ITK-dev] [ITK] SimpleITK example, possible typo In-Reply-To: References: <55F929DA.7030202@yahoo.it> Message-ID: <55F98DFD.7000704@yahoo.it> Hi Brad, yes, I get this error: /usr/lib/python3.4/site-packages/SimpleITK-0.9.0-py3.4-linux-x86_64.egg/SimpleITK/SimpleITK.py in SetOptimizerAsLBFGSB(self, *args, **kwargs) 8706 8707 """ -> 8708return _SimpleITK.ImageRegistrationMethod_SetOptimizerAsLBFGSB(self, *args, **kwargs)8709 8710 TypeError: 'numberOfIterations' is an invalid keyword argument for this function "maximumNumberOfIterations" runs without any problem. Regards. Paolo On 16/09/2015 16:00, Bradley Lowekamp wrote: > Hello, > > The file you linked is setting the keyword argument "numberOfIterations" and it's tested nightly. > > Are you getting an error or incorrect results? > > Patches to fix errors are welcome. > > Thanks, > Brad > > On Sep 16, 2015, at 4:35 AM, Paolo Zaffino wrote: > >> Dear all, >> I think I have found a typo into the SimpleITK example "ImageRegistrationMethodBSpline1.py" (in particular see [1]). >> I think that "maximumNumberOfIterations=100" should be "numberOfIterations=100". >> Am I wrong? >> >> Anyway thank you very much for the outstanding job...simpleITK is amazing! >> >> Best. >> Paolo >> >> [1] https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistrationMethodBSpline1.py#L51 >> _______________________________________________ >> 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 Sep 16 12:07:49 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 16 Sep 2015 12:07:49 -0400 Subject: [ITK-dev] Divide a label into Nregion of the same volume In-Reply-To: References: Message-ID: Hi Cyril, Yes, either http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToLabelMapFilter.html can be used to do further computation as a LabelMap or http://www.itk.org/Doxygen/html/classitk_1_1ConnectedComponentImageFilter.html can be used if you want to work with it as an Image. Both with identify the connected components in the segmentation. HTH, Matt On Wed, Sep 16, 2015 at 3:16 AM, Cyril Jaudet wrote: > Hello ITK community, > I recently use itk to segment a ring around a tumor on CT images. Is it > possible to divide the label (value 0,1) into a label map consiting of N > connected region (0-N) each with the same volume? > Thank You, > Cyril Jaudet; PhD > UZbrussel > > > > _______________________________________________ > 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 zivrafael.yaniv at nih.gov Wed Sep 16 12:13:53 2015 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Wed, 16 Sep 2015 16:13:53 +0000 Subject: [ITK-dev] [ITK] SimpleITK example, possible typo In-Reply-To: <55F98DFD.7000704@yahoo.it> References: <55F929DA.7030202@yahoo.it> <55F98DFD.7000704@yahoo.it> Message-ID: Hi Paolo, You are working with the 0.9 release where this variable was indeed named maximumNumberOfIterations (doxygen for 0.9 http://www.itk.org/SimpleITKDoxygen09/html/classitk_1_1simple_1_1ImageRegis trationMethod.html#a371bccf9aa6fd5981e9f616a6ae88296). We changed the variable name to match the other optimizers (https://issues.itk.org/jira/browse/SIMPLEITK-643). This change is in our master and will appear in the next release (doxygen for master http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistr ationMethod.html#abbc7ac9efb6de282513e41a8a8d81db7). sorry for the confusion Ziv On 9/16/15, 11:42 AM, "Paolo Zaffino" wrote: >Hi Brad, >yes, I get this error: > >/usr/lib/python3.4/site-packages/SimpleITK-0.9.0-py3.4-linux-x86_64.egg/Si >mpleITK/SimpleITK.py >in SetOptimizerAsLBFGSB(self, *args, **kwargs) 8706 8707 """ -> >8708return _SimpleITK.ImageRegistrationMethod_SetOptimizerAsLBFGSB(self, >*args, **kwargs)8709 8710 TypeError: 'numberOfIterations' is an invalid >keyword argument for this function > > >"maximumNumberOfIterations" runs without any problem. > >Regards. >Paolo > > >On 16/09/2015 16:00, Bradley Lowekamp wrote: >> Hello, >> >> The file you linked is setting the keyword argument >>"numberOfIterations" and it's tested nightly. >> >> Are you getting an error or incorrect results? >> >> Patches to fix errors are welcome. >> >> Thanks, >> Brad >> >> On Sep 16, 2015, at 4:35 AM, Paolo Zaffino wrote: >> >>> Dear all, >>> I think I have found a typo into the SimpleITK example >>>"ImageRegistrationMethodBSpline1.py" (in particular see [1]). >>> I think that "maximumNumberOfIterations=100" should be >>>"numberOfIterations=100". >>> Am I wrong? >>> >>> Anyway thank you very much for the outstanding job...simpleITK is >>>amazing! >>> >>> Best. >>> Paolo >>> >>> [1] >>>https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistr >>>ationMethodBSpline1.py#L51 >>> _______________________________________________ >>> 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 >> > >_______________________________________________ >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 p.zaffino at yahoo.it Wed Sep 16 12:33:39 2015 From: p.zaffino at yahoo.it (Paolo Zaffino) Date: Wed, 16 Sep 2015 18:33:39 +0200 Subject: [ITK-dev] [ITK] SimpleITK example, possible typo In-Reply-To: References: <55F929DA.7030202@yahoo.it> <55F98DFD.7000704@yahoo.it> Message-ID: <55F999E3.8010502@yahoo.it> Hi Ziv, thank you for the clarification. It was just to point that out, only in case it was a "silent" typo. Thanks! Paolo On 16/09/2015 18:13, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] wrote: > Hi Paolo, > > You are working with the 0.9 release where this variable was indeed named > maximumNumberOfIterations (doxygen for 0.9 > http://www.itk.org/SimpleITKDoxygen09/html/classitk_1_1simple_1_1ImageRegis > trationMethod.html#a371bccf9aa6fd5981e9f616a6ae88296). We changed the > variable name to match the other optimizers > (https://issues.itk.org/jira/browse/SIMPLEITK-643). > > This change is in our master and will appear in the next release (doxygen > for master > http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistr > ationMethod.html#abbc7ac9efb6de282513e41a8a8d81db7). > > sorry for the confusion > > Ziv > > > On 9/16/15, 11:42 AM, "Paolo Zaffino" wrote: > >> Hi Brad, >> yes, I get this error: >> >> /usr/lib/python3.4/site-packages/SimpleITK-0.9.0-py3.4-linux-x86_64.egg/Si >> mpleITK/SimpleITK.py >> in SetOptimizerAsLBFGSB(self, *args, **kwargs) 8706 8707 """ -> >> 8708return _SimpleITK.ImageRegistrationMethod_SetOptimizerAsLBFGSB(self, >> *args, **kwargs)8709 8710 TypeError: 'numberOfIterations' is an invalid >> keyword argument for this function >> >> >> "maximumNumberOfIterations" runs without any problem. >> >> Regards. >> Paolo >> >> >> On 16/09/2015 16:00, Bradley Lowekamp wrote: >>> Hello, >>> >>> The file you linked is setting the keyword argument >>> "numberOfIterations" and it's tested nightly. >>> >>> Are you getting an error or incorrect results? >>> >>> Patches to fix errors are welcome. >>> >>> Thanks, >>> Brad >>> >>> On Sep 16, 2015, at 4:35 AM, Paolo Zaffino wrote: >>> >>>> Dear all, >>>> I think I have found a typo into the SimpleITK example >>>> "ImageRegistrationMethodBSpline1.py" (in particular see [1]). >>>> I think that "maximumNumberOfIterations=100" should be >>>> "numberOfIterations=100". >>>> Am I wrong? >>>> >>>> Anyway thank you very much for the outstanding job...simpleITK is >>>> amazing! >>>> >>>> Best. >>>> Paolo >>>> >>>> [1] >>>> https://github.com/SimpleITK/SimpleITK/blob/master/Examples/ImageRegistr >>>> ationMethodBSpline1.py#L51 >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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 marco.dev.open at gmail.com Thu Sep 17 08:12:26 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Thu, 17 Sep 2015 16:42:26 +0430 Subject: [ITK-dev] overlay a color-mapped Message-ID: Hi, how to overlay a color-mapped PET image onto an image can you give a guide line Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Thu Sep 17 10:43:58 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Thu, 17 Sep 2015 19:13:58 +0430 Subject: [ITK-dev] nrrd to dicom series Message-ID: Hi, How to generate a DICOM series from .nrrd file do you have any way for compound the pipeline itk and vtk Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Thu Sep 17 11:01:19 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Thu, 17 Sep 2015 19:31:19 +0430 Subject: [ITK-dev] nrrd to dicom series In-Reply-To: References: Message-ID: Hi, 3D Slicer has a module "Create a Dicom Series" for doing this option Thanks On Thu, Sep 17, 2015 at 7:13 PM, Marco Dev wrote: > Hi, > How to generate a DICOM series from .nrrd file do you have any way for > compound the pipeline itk and vtk > Thanks > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Thu Sep 17 12:25:51 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Thu, 17 Sep 2015 20:55:51 +0430 Subject: [ITK-dev] PET/CT DICOM SERIES Message-ID: Hi, Can you help me I need to the same PET/CT dicom series patient there is a create dicom series module in 3d slicer for convert .nrrd to dicom series But there is not (float) pixel type for converting That .nrrd PET is float so Ii can not convert with correct pixel type Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Sep 18 11:06:40 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 18 Sep 2015 11:06:40 -0400 Subject: [ITK-dev] Test failures on Mac10.6-gcc-rel-x86_64-static Message-ID: Hi Alex, Sean, Hans, I know we made some good progress on the Mac10.6-gcc-rel-x86_64-static build failures, but I lost track of where we are at. It looks like there are still five failing tests on the dashboard: https://open.cdash.org/viewTest.php?onlyfailed&buildid=4016692 is the source of the issue known? Is there a patch in the works? Thanks, Matt From hans-johnson at uiowa.edu Fri Sep 18 11:21:00 2015 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Fri, 18 Sep 2015 15:21:00 +0000 Subject: [ITK-dev] Test failures on Mac10.6-gcc-rel-x86_64-static In-Reply-To: References: Message-ID: Matt, We have not been able to reproduce the errors. We tried installing the oldest verions of OS X that we could find, and compiled with gcc, but could not replicate the errors. Mac10.6-gcc-rel-x86_64-static It is exceptionally difficult to track down the problem when we can?t replicate it. Do you have any suggestions? Hans On 9/18/15, 10:06 AM, "Insight-developers on behalf of Matt McCormick" wrote: >Hi Alex, Sean, Hans, > >I know we made some good progress on the Mac10.6-gcc-rel-x86_64-static >build failures, but I lost track of where we are at. It looks like >there are still five failing tests on the dashboard: > > https://open.cdash.org/viewTest.php?onlyfailed&buildid=4016692 > >is the source of the issue known? Is there a patch in the works? > >Thanks, >Matt >_______________________________________________ >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 ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ From marco.dev.open at gmail.com Sat Sep 19 02:53:54 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Sat, 19 Sep 2015 11:23:54 +0430 Subject: [ITK-dev] color overlay Message-ID: Hi, Are there notices about color overlay for setting (threshold and window level ) in two dicom images For Example range of between in two issue Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Sat Sep 19 16:47:22 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 19 Sep 2015 16:47:22 -0400 Subject: [ITK-dev] Test failures on Mac10.6-gcc-rel-x86_64-static In-Reply-To: References: Message-ID: Hi Sean, Do you have any insights on why the tests are failing or suggestions to reproduce the failures? Thanks, Matt On Fri, Sep 18, 2015 at 11:21 AM, Johnson, Hans J wrote: > Matt, > > We have not been able to reproduce the errors. We tried installing the oldest verions of OS X that we could find, and compiled with gcc, but could not replicate the errors. > > Mac10.6-gcc-rel-x86_64-static > > > It is exceptionally difficult to track down the problem when we can?t replicate it. > > Do you have any suggestions? > > Hans > > > > > On 9/18/15, 10:06 AM, "Insight-developers on behalf of Matt McCormick" wrote: > >>Hi Alex, Sean, Hans, >> >>I know we made some good progress on the Mac10.6-gcc-rel-x86_64-static >>build failures, but I lost track of where we are at. It looks like >>there are still five failing tests on the dashboard: >> >> https://open.cdash.org/viewTest.php?onlyfailed&buildid=4016692 >> >>is the source of the issue known? Is there a patch in the works? >> >>Thanks, >>Matt >>_______________________________________________ >>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 > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > ________________________________ From micahliu2012 at gmail.com Sun Sep 20 05:32:18 2015 From: micahliu2012 at gmail.com (Micah Liu) Date: Sun, 20 Sep 2015 17:32:18 +0800 Subject: [ITK-dev] there are some confusing memory leaks in ITK Message-ID: Dear All, Yesterday I build ITK project by using MFC frist time. It is weird. I only try to do such as: std::string szPathName = "... ...";//get Dicom files Directory GDCMSeriesFileNames::Pointer spNamesGenerator = GDCMSeriesFileNames::New(); spNamesGenerator->SetInputDirectory(szPathName); then end my program, which not any other operations. But the _CrtDumpMemoryLeaks dump so much blocks reporting memory leaks. I check ITK source code carefully. find it happen in following functions: ____________________________________________________________________ void GDCMSeriesFileNames::SetInputDirectory (std::string const &name) , then into void SerieHelper::SetDirectory(std::string const &dir, bool recursive) ,then into void SerieHelper::AddFileName(std::string const &filename), then into bool File::Load( ) , then into bool Document::Load( ), then into bool Document::DoTheLoadingDocumentJob( ) then into ... ... ... ... SeqEntry* DocEntrySet::NewSeqEntry(uint16_t group, uint16_t elem) finally, check NewSeqEntry function: SeqEntry* DocEntrySet::NewSeqEntry(uint16_t group, uint16_t elem) { DictEntry *dictEntry = GetDictEntry(group, elem, "SQ"); gdcmAssertMacro(dictEntry); SeqEntry *newEntry = new SeqEntry( dictEntry ); if (!newEntry) { gdcmWarningMacro( "Failed to allocate SeqEntry"); return 0; } return newEntry; } _CrtDumpMemoryLeak tell me "SeqEntry *newEntry = new SeqEntry( dictEntry );" make these leaks happen. but I check every relevant ITK code ,ITK don't do anything wrong , they release all that objects they need to release before _CrtDumpMemoryLeak is called when program exit. So I confused. There is any chance that _CrtDumpMemoryLeak make a mistake ? At last, I use Visual Leak Detector check it again. VLD give me something maybe valueable: ___________________________________________________________________ Leak Hash: 0x05D5522E, Count: 1, Total 16 bytes Call Stack (TID 46040): e:\program files (x86)\microsoft visual studio 11.0\vc\include\xmemory0 (592): nodeItkLib.dll!std::allocator::allocate e:\program files (x86)\microsoft visual studio 11.0\vc\include\xstring (671): nodeItkLib.dll!std::_String_alloc<0,std::_String_base_types > >::_Alloc_proxy + 0xF bytes e:\program files (x86)\microsoft visual studio 11.0\vc\include\xstring (650): nodeItkLib.dll!std::_String_alloc<0,std::_String_base_types > >::_String_alloc<0,std::_String_base_types > > + 0xA bytes e:\program files (x86)\microsoft visual studio 11.0\vc\include\xstring (749): nodeItkLib.dll!std::basic_string,std::allocator >::basic_string,std::allocator > + 0x3E bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocentry.cxx (39): nodeItkLib.dll!gdcm::DocEntry::DocEntry + 0x57 bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmseqentry.cxx (40): nodeItkLib.dll!gdcm::SeqEntry::SeqEntry + 0x3B bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocentryset.cxx (526): nodeItkLib.dll!gdcm::DocEntrySet::NewSeqEntry + 0x2F bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx (2404): nodeItkLib.dll!gdcm::Document::ReadNextDocEntry + 0x18 bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx (1013): nodeItkLib.dll!gdcm::Document::ParseDES + 0xD bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx (186): nodeItkLib.dll!gdcm::Document::DoTheLoadingDocumentJob e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx (123): nodeItkLib.dll!gdcm::Document::Load e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmfile.cxx (151): nodeItkLib.dll!gdcm::File::Load + 0xA bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmseriehelper.cxx (99): nodeItkLib.dll!gdcm::SerieHelper::AddFileName e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmseriehelper.cxx (249): nodeItkLib.dll!gdcm::SerieHelper::SetDirectory + 0x1D bytes e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\code\io\itkgdcmseriesfilenames.cxx (82): nodeItkLib.dll!itk::GDCMSeriesFileNames::SetInputDirectory ... ... ... ... Data: 00 89 82 04 00 00 00 00 00 00 00 00 00 00 00 00 ........ ........ ______________________________________________________ above mensioned segment is one of VLD dumped. it is look like some leaks happen in SeqEntry's base class DocEntry,some STL string or list container. It's any possible that STL inside problem lead to these upper leaks??? I guess... ... Anyway , I can't enough time to find the answer out by time limit for a project. If anybody understand what exactly happen here. pls kindly share with me. Thank a lot. Thanks & Bast Regards, Micah Liu -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Sun Sep 20 06:58:48 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Sun, 20 Sep 2015 15:28:48 +0430 Subject: [ITK-dev] Automated Threshold-Finding Methods Message-ID: Hi , is there any method in itk vtk or 3d slicer or any image proceeding field about this subject "Automated Threshold-Finding Methods " Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Sun Sep 20 15:41:17 2015 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Sun, 20 Sep 2015 21:41:17 +0200 Subject: [ITK-dev] [slicer-devel] Automated Threshold-Finding Methods In-Reply-To: <1ba272cc4be04cabbce057be510b0ad4@PHSX10HT3.partners.org> References: <1ba272cc4be04cabbce057be510b0ad4@PHSX10HT3.partners.org> Message-ID: Dear Marco, you may find useful the OtsuThresholdImageFilter [1] provided by ITK. HTH, JON HAITZ [1] http://www.itk.org/Doxygen/html/classitk_1_1OtsuThresholdImageFilter.html On 20 September 2015 at 12:58, Marco Dev wrote: > Hi , > is there any method in itk vtk or 3d slicer or any image proceeding field > about this subject " Automated Threshold-Finding Methods " > > Thanks > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with > unsubscribe as the subject > > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From steve at sumost.ca Sun Sep 20 23:03:20 2015 From: steve at sumost.ca (Steve M. Robbins) Date: Sun, 20 Sep 2015 22:03:20 -0500 Subject: [ITK-dev] ITK 4.8, castxml, and 32-bits Debian/gcc Message-ID: <2555189.VASa47qrgP@riemann> Hi, Just began looking at a build failure for Debian 32-bits that shows up when wrapping is enabled [1]. The failure shows in the build log as: [ 13%] Building C object Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeFiles/itkopenjpeg.dir/raw.c.o cd /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/BUILD/Modules/ThirdParty/OpenJPEG/src/openjpeg && /usr/bin/cc -Ditkopenjpeg_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wno-uninitialized -Wno-unused-parameter -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 -w -fPIC -I/usr/include/gdcm-2.4 -I/home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/BUILD/Modules/ThirdParty/OpenJPEG/src/openjpeg -I/home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/ThirdParty/OpenJPEG/src/openjpeg -o CMakeFiles/itkopenjpeg.dir/raw.c.o -c /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/ThirdParty/OpenJPEG/src/openjpeg/raw.c In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/BUILD/Wrapping/Modules/ITKCommon/vcl_complex.cxx:5: In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkContinuousIndex.h:22: In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkIndex.h:23: In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkMath.h:32: In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkMathDetail.h:43: /usr/share/castxml/clang/include/emmintrin.h:28:2: error: "SSE2 instruction set not enabled" #error "SSE2 instruction set not enabled" ^ The lines in emmintrin.h tests CPP symbol __SSE2__, which is not defined for 32-bit compiler in Debian. Interestingly, the content of itkMathDetail.h near line 43 is: 42 #if defined( ITK_HAVE_EMMINTRIN_H ) && !defined( __GCCXML__ ) 43 #include // sse 2 intrinsics 44 #endif /* ITK_HAVE_EMMINTRIN_H && ! __GCCXML__ */ First observation: prior to ITK 4.8, we used gccxml which defines __GCCXML__ and thus avoids including emmintrin.h. Now we are using castxml, which does not define this symbol. For compatibility, maybe it should? Brad? Secondly, I am slightly surprised that ITK should even need to guard against including things when __GCCXML __ is defined. I had naively assumed that gccxml should be seeing the same code as the regular parser. Is this a work-around for some gccxml issues of the past or is it still needed? Thirdly, the emmintrin.h file that castxml uses presumably comes from clang and clearly depends on the symbol __SSE2__ being defined. However, the emmintrin.h shipped with GCC does not; does this represent an incompatibility between castxml and gcc? steve at riemann{insighttoolkit4-4.8.0}g++ -E /usr/lib/gcc/i586-linux-gnu/5/include/emmintrin.h >/dev/null steve at riemann{insighttoolkit4-4.8.0}g++ -E /usr/share/castxml/clang/include/emmintrin.h >/dev/null /usr/share/castxml/clang/include/emmintrin.h:28:2: error: #error "SSE2 instruction set not enabled" #error "SSE2 instruction set not enabled" ^ steve at riemann{insighttoolkit4-4.8.0} Thanks, -Steve [1] https://buildd.debian.org/status/fetch.php?pkg=insighttoolkit4&arch=i386&ver=4.8.0-1&stamp=1440593857 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 811 bytes Desc: This is a digitally signed message part. URL: From mathieu.malaterre at gmail.com Mon Sep 21 10:05:38 2015 From: mathieu.malaterre at gmail.com (Mathieu Malaterre) Date: Mon, 21 Sep 2015 16:05:38 +0200 Subject: [ITK-dev] Module_ITKIOGDCM:INTERNAL=OFF In-Reply-To: References: <883004AB-7E1A-4C95-A3A5-5B7CC274F914@mail.nih.gov> Message-ID: For anyone reading this thread later on. This only differ the issue to the next level up. On Wed, Sep 16, 2015 at 9:08 AM, Mathieu Malaterre wrote: > Very elegant solution. Thanks very much Bill ! > > On Tue, Sep 15, 2015 at 7:17 PM, Bill Lorensen wrote: >> You can specify the specific module you need. For example: >> >> set(ITK_IO_MODULES_USED "ITKIONRRD;ITKIOPNG;ITKIONIFTI") >> find_package(ITK COMPONENTS >> ITKCommon >> ITKIOImageBase >> ITKImageGrid >> ITKImageStatistics >> ITKVtkGlue >> ${ITK_IO_MODULES_USED} >> ) >> include(${ITK_USE_FILE}) >> >> >> AND >> you can find the modules used by your app with >> ITK/Utilities/Maintenance/WhatModulesITK.py >> >> On Tue, Sep 15, 2015 at 12:02 PM, Mathieu Malaterre >> wrote: >>> Hi Brad, >>> >>> ITK_USE_SYSTEM_GDCM is not an option for me. I am given an already >>> compiled ITK version (statically if that matters). >>> >>> I understand now the need for GDCM deep down in the build settings. I >>> think I should be able to tweak `include(${ITK_USE_FILE})` to remove >>> automatic io factory registration and drop "*GDCM*" from >>> ${ITK_LIBRARIES}. >>> >>> Will let you know how it goes. Thanks for your help. >>> >>> -M >>> >>> On Fri, Sep 4, 2015 at 9:21 PM, Bradley Lowekamp wrote: >>>> Hello, >>>> >>>> Have you looking into "ITK_USE_SYSTEM_GDCM", this should allow ITK to use the same version of GDCM that the rest of your application is? >>>> >>>> For the modular build, have you looked into disabling "BUILD_TESTING"? Also please keep in mind that the a module's status is cached in CMake. So you must start with a fresh directory then configure from the command line which modules are on and off. >>>> >>>> Many ImageIOs are needed to do testing [1], supporting DICOM and DICOM metadata are of core importance for ITK, so we do test with it in many places.The modularization works really good without the ITK testing enabled. But the interdependency of testing that everything works does enable most modules. >>>> >>>> HTH, >>>> Brad >>>> >>>> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/TestKernel/itk-module.cmake >>>> >>>> On Sep 4, 2015, at 3:55 AM, Mathieu Malaterre wrote: >>>> >>>>> Dear all, >>>>> >>>>> My goal is to be able to compile ITK without the GDCM module. >>>>> >>>>> Long story short, GDCM toolkit is not being mangled, which means very >>>>> complex build setup to be able to use GDCM and ITK in an application. >>>>> >>>>> So far I have tried setting: >>>>> >>>>> Module_ITKIOGDCM:INTERNAL=OFF >>>>> >>>>> with no luck >>>>> >>>>> I suspect that GDCM is activated by ITK_BUILD_DEFAULT_MODULES, so I tried: >>>>> >>>>> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF >>>>> >>>>> this leads to: >>>>> >>>>> -- Check if the system is big endian - little endian >>>>> CMake Error at Examples/CMakeLists.txt:2 (message): >>>>> BUILD_EXAMPLES requires ITK_BUILD_DEFAULT_MODULES to be ON >>>>> >>>>> >>>>> -- Configuring incomplete, errors occurred! >>>>> >>>>> >>>>> Later I tried: >>>>> >>>>> $ cmake -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF .. >>>>> >>>>> which states: >>>>> >>>>> -- Enabled ITKIOGDCM, needed by [ITKTestKernel]. >>>>> and >>>>> -- Enabled ITKTestKernel, needed by [ITKGroup_Core]. >>>>> >>>>> >>>>> However I do not want to set -DITKGroup_Core:BOOL=OFF (obvisouly). >>>>> >>>>> Is there any particular reason to have GDCM be part of the core group ? >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> -- >>>>> Mathieu >>>>> _______________________________________________ >>>>> 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 >>>> >>> >>> >>> >>> -- >>> Mathieu >>> _______________________________________________ >>> 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 >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com > > > > -- > Mathieu -- Mathieu From brad.king at kitware.com Mon Sep 21 11:42:20 2015 From: brad.king at kitware.com (Brad King) Date: Mon, 21 Sep 2015 11:42:20 -0400 Subject: [ITK-dev] ITK 4.8, castxml, and 32-bits Debian/gcc In-Reply-To: <2555189.VASa47qrgP@riemann> References: <2555189.VASa47qrgP@riemann> Message-ID: <5600255C.4040804@kitware.com> On 09/20/2015 11:03 PM, Steve M. Robbins wrote: > /usr/share/castxml/clang/include/emmintrin.h:28:2: error: "SSE2 instruction set not enabled" > #error "SSE2 instruction set not enabled" CastXML (currently) needs to be invoked with a flag to enable these instructions. See below. > The lines in emmintrin.h tests CPP symbol __SSE2__, which is not defined for 32-bit compiler in Debian. Interestingly, the content of itkMathDetail.h near line 43 is: > > 42 #if defined( ITK_HAVE_EMMINTRIN_H ) && !defined( __GCCXML__ ) > 43 #include // sse 2 intrinsics > 44 #endif /* ITK_HAVE_EMMINTRIN_H && ! __GCCXML__ */ > > First observation: prior to ITK 4.8, we used gccxml which > defines __GCCXML__ and thus avoids including emmintrin.h. > Now we are using castxml, which does not define this symbol. > For compatibility, maybe it should? Brad? CastXML is not intended to be a 100% drop-in replacement for gccxml but merely to make explicit porting relatively easy. I do not think CastXML should pretend to be __GCCXML__ at preprocessing time. The above-quoted block in ITK could be ported to work with CastXML. > Secondly, I am slightly surprised that ITK should even need to > guard against including things when __GCCXML __ is defined. > I had naively assumed that gccxml should be seeing the same > code as the regular parser. Is this a work-around for some > gccxml issues of the past or is it still needed? It was a workaround for gccxml because its parser was hard-coded to a specific architecture and had no way to simulate the intrinsics of other architectures. This should not be necessary for CastXML because it really invokes its Clang compiler with the proper target architecture. > Thirdly, the emmintrin.h file that castxml uses presumably > comes from clang and clearly depends on the symbol __SSE2__ > being defined. However, the emmintrin.h shipped with GCC > does not; does this represent an incompatibility between > castxml and gcc? I don't think so. The emmintrin.h and similar headers are part of the compiler's implementation details. Such intrinsic headers need to match the actual compiler, which within CastXML is actually Clang regardless of what compiler is simulated. That is why CastXML comes with copies of these headers from the Clang against which it was built. ----------------------------------------------------------------- I think the problem here is that CastXML needs to know when to enable SSE as part of its target architecture configuration. One could do that explicitly by adding '-msse' to the castxml command-line right now. That may get your build going. It may also be possible for CastXML to configure itself when given '--castxml-cc-gnu "(" gcc -msse ")"'. For example, the '-msse' flag causes gcc to add some predefined macros: #define __MMX__ 1 #define __pentium_mmx__ 1 #define __SSE__ 1 CastXML could recognize these to enable SSE internally. One challenge is that there are actually many variations of -msse and we would need to figure out which one to use. -Brad From blowekamp at mail.nih.gov Mon Sep 21 11:50:43 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 21 Sep 2015 11:50:43 -0400 Subject: [ITK-dev] ITK 4.8, castxml, and 32-bits Debian/gcc In-Reply-To: <2555189.VASa47qrgP@riemann> References: <2555189.VASa47qrgP@riemann> Message-ID: <029F2DAF-488C-4B79-A617-EAEBED3C5FD8@mail.nih.gov> Looking at this command closely: On Sep 20, 2015, at 11:03 PM, Steve M. Robbins wrote: > [ 13%] Building C object Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeFiles/itkopenjpeg.dir/raw.c.o > cd /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/BUILD/Modules/ThirdParty/OpenJPEG/src/openjpeg && /usr/bin/cc -Ditkopenjpeg_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wno-uninitialized -Wno-unused-parameter -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 -w -fPIC -I/usr/include/gdcm-2.4 -I/home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/BUILD/Modules/ThirdParty/OpenJPEG/src/openjpeg -I/home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/ThirdParty/OpenJPEG/src/openjpeg -o CMakeFiles/itkopenjpeg.dir/raw.c.o -c /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/ThirdParty/OpenJPEG/src/openjpeg/raw.c > In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/BUILD/Wrapping/Modules/ITKCommon/vcl_complex.cxx:5: > In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkContinuousIndex.h:22: > In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkIndex.h:23: > In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkMath.h:32: > In file included from /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkMathDetail.h:43: > /usr/share/castxml/clang/include/emmintrin.h:28:2: error: "SSE2 instruction set not enabled" > #error "SSE2 instruction set not enabled" > ^ Why is "/usr/bin/cc" including ".../castxml/clang/include/emmintrin.h"? It doesn't look like castxml is being run here? HTH, Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Mon Sep 21 12:43:38 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Mon, 21 Sep 2015 21:13:38 +0430 Subject: [ITK-dev] pet/ct threshold segmentation Message-ID: Hi , How about ConnectedThresholdSegmentatio for (PET / CT ) ?? Full body I want to after give specific CLUT for pet rainbow and for ct grey .... this filter should remove the RED color from rainbow to boundary shape means (OUTSIDE - INSIDE ) can you give me a guide line Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From nexnaru at gmail.com Mon Sep 21 14:54:37 2015 From: nexnaru at gmail.com (Maryana) Date: Mon, 21 Sep 2015 11:54:37 -0700 Subject: [ITK-dev] Streamed Read/Write Truncating Data Message-ID: Hi ITK Users/Devs, I'm new to ITK and I need to write a small program to convert Nifti images to MetaIO. However, I need to use the streamed reader/writer because my image volumes can have several gigabytes. I was doing some tests with the following code but I've realized that whenever I use the stream I end up with a truncated volume. I'm using ITK 4.8. I'm sure my volume is of unsigned char type. Also, when I comment out the writer->SetNumberOfStreamDivisions(20); line I works fine. Does anyone knows what is wrong? Thank you! #include #include #include #include "itkImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkImageRegionIterator.h" #include "itkNiftiImageIO.h" #include "itkMetaImageIO.h" int main(int argc, char const *argv[]){ std::string fileIn = "brain_8bit.nii"; std::string fileOut = "mri2_stream.mha"; typedef itk::Image Image3D; //Reader typedef itk::ImageFileReader ReaderType; ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(fileIn); //Writer typedef itk::ImageFileWriter WriterType; WriterType::Pointer writer = WriterType::New(); writer->SetFileName(fileOut); writer->SetNumberOfStreamDivisions(20); writer->SetInput(reader->GetOutput()); std::cout << "Input: " << fileIn << std::endl; std::cout << "Output: " << fileOut << std::endl; std::cout << "Writing..." << std::endl; try { writer->Update(); } catch( itk::ExceptionObject & err ) { std::cerr << "ExceptionObject caught !" << std::endl; std::cerr << err << std::endl; return EXIT_FAILURE; } std::cout << "Finished." << std::endl; return EXIT_SUCCESS; } -- "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra mol?cula e nasceu a vida" - Clarice Lispector -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Mon Sep 21 14:55:53 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 21 Sep 2015 14:55:53 -0400 Subject: [ITK-dev] Streamed Read/Write Truncating Data In-Reply-To: References: Message-ID: <191044B9-EE73-479F-89C4-BA7FEA977740@mail.nih.gov> Hello Maryana, What compiler, platform and architecture are you compiling for? Brad On Sep 21, 2015, at 2:54 PM, Maryana wrote: > > Hi ITK Users/Devs, > > I'm new to ITK and I need to write a small program to convert Nifti images to MetaIO. However, I need to use the streamed reader/writer because my image volumes can have several gigabytes. I was doing some tests with the following code but I've realized that whenever I use the stream I end up with a truncated volume. I'm using ITK 4.8. I'm sure my volume is of unsigned char type. Also, when I comment out the writer->SetNumberOfStreamDivisions(20); line I works fine. Does anyone knows what is wrong? > > Thank you! > > #include > #include > #include > > #include "itkImage.h" > #include "itkImageFileReader.h" > #include "itkImageFileWriter.h" > #include "itkImageRegionIterator.h" > #include "itkNiftiImageIO.h" > #include "itkMetaImageIO.h" > > > int main(int argc, char const *argv[]){ > > std::string fileIn = "brain_8bit.nii"; > std::string fileOut = "mri2_stream.mha"; > > typedef itk::Image Image3D; > > //Reader > typedef itk::ImageFileReader ReaderType; > ReaderType::Pointer reader = ReaderType::New(); > reader->SetFileName(fileIn); > > //Writer > typedef itk::ImageFileWriter WriterType; > WriterType::Pointer writer = WriterType::New(); > writer->SetFileName(fileOut); > writer->SetNumberOfStreamDivisions(20); > writer->SetInput(reader->GetOutput()); > > > std::cout << "Input: " << fileIn << std::endl; > std::cout << "Output: " << fileOut << std::endl; > > std::cout << "Writing..." << std::endl; > try > { > writer->Update(); > } > catch( itk::ExceptionObject & err ) > { > std::cerr << "ExceptionObject caught !" << std::endl; > std::cerr << err << std::endl; > return EXIT_FAILURE; > } > std::cout << "Finished." << std::endl; > > > return EXIT_SUCCESS; > } > > > > > > -- > "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra mol?cula e nasceu a vida" - Clarice Lispector > _______________________________________________ > 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 nexnaru at gmail.com Mon Sep 21 15:07:42 2015 From: nexnaru at gmail.com (Maryana) Date: Mon, 21 Sep 2015 12:07:42 -0700 Subject: [ITK-dev] Streamed Read/Write Truncating Data In-Reply-To: <191044B9-EE73-479F-89C4-BA7FEA977740@mail.nih.gov> References: <191044B9-EE73-479F-89C4-BA7FEA977740@mail.nih.gov> Message-ID: Hi, I use Linux Mint 64bits, GCC 4.8, Cmake 2.8. I'm compiling to this platform. Thank you! On Mon, Sep 21, 2015 at 11:55 AM, Bradley Lowekamp wrote: > Hello Maryana, > > What compiler, platform and architecture are you compiling for? > > Brad > > On Sep 21, 2015, at 2:54 PM, Maryana wrote: > > > > > Hi ITK Users/Devs, > > > > I'm new to ITK and I need to write a small program to convert Nifti > images to MetaIO. However, I need to use the streamed reader/writer because > my image volumes can have several gigabytes. I was doing some tests with > the following code but I've realized that whenever I use the stream I end > up with a truncated volume. I'm using ITK 4.8. I'm sure my volume is of > unsigned char type. Also, when I comment out the > writer->SetNumberOfStreamDivisions(20); line I works fine. Does anyone > knows what is wrong? > > > > Thank you! > > > > #include > > #include > > #include > > > > #include "itkImage.h" > > #include "itkImageFileReader.h" > > #include "itkImageFileWriter.h" > > #include "itkImageRegionIterator.h" > > #include "itkNiftiImageIO.h" > > #include "itkMetaImageIO.h" > > > > > > int main(int argc, char const *argv[]){ > > > > std::string fileIn = "brain_8bit.nii"; > > std::string fileOut = "mri2_stream.mha"; > > > > typedef itk::Image Image3D; > > > > //Reader > > typedef itk::ImageFileReader ReaderType; > > ReaderType::Pointer reader = ReaderType::New(); > > reader->SetFileName(fileIn); > > > > //Writer > > typedef itk::ImageFileWriter WriterType; > > WriterType::Pointer writer = WriterType::New(); > > writer->SetFileName(fileOut); > > writer->SetNumberOfStreamDivisions(20); > > writer->SetInput(reader->GetOutput()); > > > > > > std::cout << "Input: " << fileIn << std::endl; > > std::cout << "Output: " << fileOut << std::endl; > > > > std::cout << "Writing..." << std::endl; > > try > > { > > writer->Update(); > > } > > catch( itk::ExceptionObject & err ) > > { > > std::cerr << "ExceptionObject caught !" << std::endl; > > std::cerr << err << std::endl; > > return EXIT_FAILURE; > > } > > std::cout << "Finished." << std::endl; > > > > > > return EXIT_SUCCESS; > > } > > > > > > > > > > > > -- > > "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra > mol?cula e nasceu a vida" - Clarice Lispector > > _______________________________________________ > > 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 > > -- "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra mol?cula e nasceu a vida" - Clarice Lispector -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 21 17:40:33 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 21 Sep 2015 17:40:33 -0400 Subject: [ITK-dev] ITK 4.8, castxml, and 32-bits Debian/gcc In-Reply-To: <029F2DAF-488C-4B79-A617-EAEBED3C5FD8@mail.nih.gov> References: <2555189.VASa47qrgP@riemann> <029F2DAF-488C-4B79-A617-EAEBED3C5FD8@mail.nih.gov> Message-ID: FYI, I have pushed a few patches related to this thread: This one http://review.source.kitware.com/#/c/20209/ passes the compiler flags to CastXML. This one: http://review.source.kitware.com/#/c/20218/ should address the reported issue (although further improvements that remove the need for the pre-processor macro would be welcome). These: http://review.source.kitware.com/#/c/20220 improve naming. Thanks, Matt From nexnaru at gmail.com Mon Sep 21 18:32:08 2015 From: nexnaru at gmail.com (Maryana) Date: Mon, 21 Sep 2015 15:32:08 -0700 Subject: [ITK-dev] Fwd: Streamed Read/Write Truncating Data In-Reply-To: References: <191044B9-EE73-479F-89C4-BA7FEA977740@mail.nih.gov> Message-ID: Hi! If anyone would like to repeat the test, this is my test file: https://www.dropbox.com/s/7hpen46znk1h58l/brain_8bit.nii?dl=0 If I convert that file to MetaIO without streams, and use ExtractImageFilter to read one file perpendicular to Y (as in the code I'm sending bellow) it works fine. However if I convert it to MetaIO using streams and use the same code to read the same slice, I end up with a truncated image. I have the same result when I use Paraview for visualization. By the way, for what I've read from ITK documentation NIfti supposedly supports streamed reading. So I'm guessing that using Nifti in this case would be ok. Is this correct? Would anyone have an idea on what's wrong? Thank you! Code for reading slice: #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkExtractImageFilter.h" #include "itkImage.h" int main( int argc, char ** argv ) { typedef unsigned char InputPixelType; typedef unsigned char OutputPixelType; typedef itk::Image< InputPixelType, 3 > InputImageType; typedef itk::Image< OutputPixelType, 2 > OutputImageType; typedef itk::ImageFileReader< InputImageType > ReaderType; typedef itk::ImageFileWriter< OutputImageType > WriterType; std::string fileIn = "mri2_stream.mha"; std::string fileOut = "slice.tif"; const char * inputFilename = fileIn.c_str(); const char * outputFilename = fileOut.c_str(); ReaderType::Pointer reader = ReaderType::New(); WriterType::Pointer writer = WriterType::New(); reader->SetFileName( inputFilename ); writer->SetFileName( outputFilename ); typedef itk::ExtractImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New(); filter->InPlaceOn(); filter->SetDirectionCollapseToSubmatrix(); reader->UpdateOutputInformation(); InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion(); InputImageType::SizeType size = inputRegion.GetSize(); std::cout << "Size: " << std::endl; std::cout << size[0] << std::endl; std::cout << size[1] << std::endl; std::cout << size[2] << std::endl; InputImageType::IndexType start = inputRegion.GetIndex(); const unsigned int sliceNumber = 800; std::cout << "Start: " << std::endl; std::cout << start[0] << std::endl; std::cout << start[1] << std::endl; std::cout << start[2] << std::endl; size[1] = 0; start[1] = sliceNumber; InputImageType::RegionType desiredRegion; desiredRegion.SetSize( size ); desiredRegion.SetIndex( start ); filter->SetExtractionRegion( desiredRegion ); filter->SetInput( reader->GetOutput() ); writer->SetInput( filter->GetOutput() ); try { writer->Update(); } catch( itk::ExceptionObject & err ) { std::cerr << "ExceptionObject caught !" << std::endl; std::cerr << err << std::endl; return EXIT_FAILURE; } return EXIT_SUCCESS; } On Mon, Sep 21, 2015 at 12:07 PM, Maryana wrote: > Hi, > > I use Linux Mint 64bits, GCC 4.8, Cmake 2.8. I'm compiling to this > platform. > > Thank you! > > On Mon, Sep 21, 2015 at 11:55 AM, Bradley Lowekamp > wrote: > >> Hello Maryana, >> >> What compiler, platform and architecture are you compiling for? >> >> Brad >> >> On Sep 21, 2015, at 2:54 PM, Maryana wrote: >> >> > >> > Hi ITK Users/Devs, >> > >> > I'm new to ITK and I need to write a small program to convert Nifti >> images to MetaIO. However, I need to use the streamed reader/writer because >> my image volumes can have several gigabytes. I was doing some tests with >> the following code but I've realized that whenever I use the stream I end >> up with a truncated volume. I'm using ITK 4.8. I'm sure my volume is of >> unsigned char type. Also, when I comment out the >> writer->SetNumberOfStreamDivisions(20); line I works fine. Does anyone >> knows what is wrong? >> > >> > Thank you! >> > >> > #include >> > #include >> > #include >> > >> > #include "itkImage.h" >> > #include "itkImageFileReader.h" >> > #include "itkImageFileWriter.h" >> > #include "itkImageRegionIterator.h" >> > #include "itkNiftiImageIO.h" >> > #include "itkMetaImageIO.h" >> > >> > >> > int main(int argc, char const *argv[]){ >> > >> > std::string fileIn = "brain_8bit.nii"; >> > std::string fileOut = "mri2_stream.mha"; >> > >> > typedef itk::Image Image3D; >> > >> > //Reader >> > typedef itk::ImageFileReader ReaderType; >> > ReaderType::Pointer reader = ReaderType::New(); >> > reader->SetFileName(fileIn); >> > >> > //Writer >> > typedef itk::ImageFileWriter WriterType; >> > WriterType::Pointer writer = WriterType::New(); >> > writer->SetFileName(fileOut); >> > writer->SetNumberOfStreamDivisions(20); >> > writer->SetInput(reader->GetOutput()); >> > >> > >> > std::cout << "Input: " << fileIn << std::endl; >> > std::cout << "Output: " << fileOut << std::endl; >> > >> > std::cout << "Writing..." << std::endl; >> > try >> > { >> > writer->Update(); >> > } >> > catch( itk::ExceptionObject & err ) >> > { >> > std::cerr << "ExceptionObject caught !" << std::endl; >> > std::cerr << err << std::endl; >> > return EXIT_FAILURE; >> > } >> > std::cout << "Finished." << std::endl; >> > >> > >> > return EXIT_SUCCESS; >> > } >> > >> > >> > >> > >> > >> > -- >> > "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra >> mol?cula e nasceu a vida" - Clarice Lispector >> > _______________________________________________ >> > 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 steve at sumost.ca Mon Sep 21 21:17:05 2015 From: steve at sumost.ca (Steve M. Robbins) Date: Mon, 21 Sep 2015 20:17:05 -0500 Subject: [ITK-dev] ITK 4.8, castxml, and 32-bits Debian/gcc In-Reply-To: <5600255C.4040804@kitware.com> References: <2555189.VASa47qrgP@riemann> <5600255C.4040804@kitware.com> Message-ID: <2633632.jgyLRj10zY@riemann> Thanks, Brad! On Monday, September 21, 2015 11:42:20 AM Brad King wrote: > On 09/20/2015 11:03 PM, Steve M. Robbins wrote: > > Secondly, I am slightly surprised that ITK should even need to > > guard against including things when __GCCXML __ is defined. > > I had naively assumed that gccxml should be seeing the same > > code as the regular parser. Is this a work-around for some > > gccxml issues of the past or is it still needed? > > It was a workaround for gccxml because its parser was hard-coded > to a specific architecture and had no way to simulate the > intrinsics of other architectures. This should not be necessary > for CastXML because it really invokes its Clang compiler with > the proper target architecture. OK. But later Matt McCormick replied with a patch that essentially changes __GCCXML__ to CABLE_CONFIGURATION which is defined during the build. That change seems to imply that the workaround is still required. (?) > I think the problem here is that CastXML needs to know when > to enable SSE as part of its target architecture configuration. > One could do that explicitly by adding '-msse' to the castxml > command-line right now. That may get your build going. OK. So I'm well out of my depth with SSE, but: since the build is targeting i386, I think there would not be SSE support. Another data point is that the cmake configuration step outputs: -- Performing Test VXL_HAS_SSE2_HARDWARE_SUPPORT -- Performing Try-Run Test VXL_HAS_SSE2_HARDWARE_SUPPORT - Test Compilation Failed -- Performing Test VXL_SSE2_HARDWARE_SUPPORT_POSSIBLE -- Performing Test VXL_SSE2_HARDWARE_SUPPORT_POSSIBLE - Success ... and ... -- Performing Test ITK_COMPILER_SUPPORTS_SSE2_64 -- Performing Test ITK_COMPILER_SUPPORTS_SSE2_64 - Failed -- Performing Test ITK_COMPILER_SUPPORTS_SSE2_32 -- Performing Test ITK_COMPILER_SUPPORTS_SSE2_32 - Failed -- Performing Test ITK_COMPILER_DOES_NOT_NEED_MSSE2_FLAG -- Performing Test ITK_COMPILER_DOES_NOT_NEED_MSSE2_FLAG - Failed I'll take a closer look at these tonight. -Steve -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 811 bytes Desc: This is a digitally signed message part. URL: From steve at sumost.ca Tue Sep 22 00:03:24 2015 From: steve at sumost.ca (Steve M. Robbins) Date: Mon, 21 Sep 2015 23:03:24 -0500 Subject: [ITK-dev] ITK 4.8, castxml, and 32-bits Debian/gcc In-Reply-To: <029F2DAF-488C-4B79-A617-EAEBED3C5FD8@mail.nih.gov> References: <2555189.VASa47qrgP@riemann> <029F2DAF-488C-4B79-A617-EAEBED3C5FD8@mail.nih.gov> Message-ID: <1884343.KZoiOaJPAm@riemann> Hi Brad, On September 21, 2015 11:50:43 AM Bradley Lowekamp wrote: > Looking at this command closely: > > On Sep 20, 2015, at 11:03 PM, Steve M. Robbins wrote: > > [ 13%] Building C object > > Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeFiles/itkopenjpeg.dir/raw.c > > .o cd > > /home/steve/Packages/insighttoolkit/build-area/insighttoolkit4-4.8.0/BUIL > > D/Modules/ThirdParty/OpenJPEG/src/openjpeg && /usr/bin/cc [...] > It doesn't look like castxml is being run here? Sharp eyes! I hadn't noticed that. It turns out to be an artifact of parallel building: the output is interleaved. The actual command that failed was above this one; it was indeed castxml: steve at riemann{insighttoolkit4-4.8.0}cd /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/BUILD/Wrapping/Modules/ITKCommon && /usr/bin/castxml -o /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/BUILD/Wrapping/Modules/ITKCommon/vcl_complex.xml -- castxml-gccxml --castxml-start _cable_ --castxml-cc-gnu /usr/bin/c++ -w -c @/home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/BUILD/Wrapping/Modules/ITKCommon/castxml.inc /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/BUILD/Wrapping/Modules/ITKCommon/vcl_complex.cxx In file included from /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/BUILD/Wrapping/Modules/ITKCommon/vcl_complex.cxx:5: In file included from /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkContinuousIndex.h:22: In file included from /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkIndex.h:23: In file included from /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkMath.h:32: In file included from /home/steve/Packages/insighttoolkit/build- area/insighttoolkit4-4.8.0/Modules/Core/Common/include/itkMathDetail.h:43: /usr/share/castxml/clang/include/emmintrin.h:28:2: error: "SSE2 instruction set not enabled" #error "SSE2 instruction set not enabled" ^ 1 error generated. -Steve -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 811 bytes Desc: This is a digitally signed message part. URL: From matt.mccormick at kitware.com Tue Sep 22 10:24:05 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 22 Sep 2015 10:24:05 -0400 Subject: [ITK-dev] there are some confusing memory leaks in ITK In-Reply-To: References: Message-ID: Hello Micah, Thank you for the report. Please use and report on the latest ITK 4.X, since this is the focus of development efforts. Thanks, Matt On Sun, Sep 20, 2015 at 5:32 AM, Micah Liu wrote: > Dear All, > > Yesterday I build ITK project by using MFC frist time. > > It is weird. > > I only try to do such as: > > std::string szPathName = "... ...";//get Dicom files Directory > GDCMSeriesFileNames::Pointer spNamesGenerator = GDCMSeriesFileNames::New(); > spNamesGenerator->SetInputDirectory(szPathName); > > then end my program, which not any other operations. But the > _CrtDumpMemoryLeaks dump so much blocks reporting memory leaks. > > I check ITK source code carefully. find it happen in following functions: > ____________________________________________________________________ > void GDCMSeriesFileNames::SetInputDirectory (std::string const &name) , then > into > void SerieHelper::SetDirectory(std::string const &dir, bool recursive) ,then > into > void SerieHelper::AddFileName(std::string const &filename), then into > bool File::Load( ) , then into > bool Document::Load( ), then into > bool Document::DoTheLoadingDocumentJob( ) then into > ... ... ... ... > SeqEntry* DocEntrySet::NewSeqEntry(uint16_t group, uint16_t elem) > > finally, check NewSeqEntry function: > > SeqEntry* DocEntrySet::NewSeqEntry(uint16_t group, uint16_t elem) > { > DictEntry *dictEntry = GetDictEntry(group, elem, "SQ"); > gdcmAssertMacro(dictEntry); > > SeqEntry *newEntry = new SeqEntry( dictEntry ); > if (!newEntry) > { > gdcmWarningMacro( "Failed to allocate SeqEntry"); > return 0; > } > return newEntry; > } > > > _CrtDumpMemoryLeak tell me "SeqEntry *newEntry = new SeqEntry( dictEntry > );" make these leaks happen. > > but I check every relevant ITK code ,ITK don't do anything wrong , they > release all that objects they need to release before _CrtDumpMemoryLeak is > called when program exit. > > So I confused. There is any chance that _CrtDumpMemoryLeak make a mistake > ? > > At last, I use Visual Leak Detector check it again. VLD give me something > maybe valueable: > ___________________________________________________________________ > Leak Hash: 0x05D5522E, Count: 1, Total 16 bytes > Call Stack (TID 46040): > e:\program files (x86)\microsoft visual studio 11.0\vc\include\xmemory0 > (592): nodeItkLib.dll!std::allocator::allocate > e:\program files (x86)\microsoft visual studio 11.0\vc\include\xstring > (671): > nodeItkLib.dll!std::_String_alloc<0,std::_String_base_types >> >::_Alloc_proxy + 0xF bytes > e:\program files (x86)\microsoft visual studio 11.0\vc\include\xstring > (650): > nodeItkLib.dll!std::_String_alloc<0,std::_String_base_types >> >::_String_alloc<0,std::_String_base_types > > + > 0xA bytes > e:\program files (x86)\microsoft visual studio 11.0\vc\include\xstring > (749): > nodeItkLib.dll!std::basic_string,std::allocator >>::basic_string,std::allocator > + 0x3E > bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocentry.cxx > (39): nodeItkLib.dll!gdcm::DocEntry::DocEntry + 0x57 bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmseqentry.cxx > (40): nodeItkLib.dll!gdcm::SeqEntry::SeqEntry + 0x3B bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocentryset.cxx > (526): nodeItkLib.dll!gdcm::DocEntrySet::NewSeqEntry + 0x2F bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx > (2404): nodeItkLib.dll!gdcm::Document::ReadNextDocEntry + 0x18 bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx > (1013): nodeItkLib.dll!gdcm::Document::ParseDES + 0xD bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx > (186): nodeItkLib.dll!gdcm::Document::DoTheLoadingDocumentJob > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmdocument.cxx > (123): nodeItkLib.dll!gdcm::Document::Load > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmfile.cxx > (151): nodeItkLib.dll!gdcm::File::Load + 0xA bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmseriehelper.cxx > (99): nodeItkLib.dll!gdcm::SerieHelper::AddFileName > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\utilities\gdcm\src\gdcmseriehelper.cxx > (249): nodeItkLib.dll!gdcm::SerieHelper::SetDirectory + 0x1D bytes > > e:\itk_vtk_dicom\i_vtk\itk320\insighttoolkit-3.20.1\code\io\itkgdcmseriesfilenames.cxx > (82): nodeItkLib.dll!itk::GDCMSeriesFileNames::SetInputDirectory > ... ... ... ... > > Data: > 00 89 82 04 00 00 00 00 00 00 00 00 00 00 00 00 ........ > ........ > > ______________________________________________________ > > above mensioned segment is one of VLD dumped. it is look like some leaks > happen in SeqEntry's base class DocEntry,some STL string or list container. > It's any possible that STL inside problem lead to these upper leaks??? I > guess... ... > > Anyway , I can't enough time to find the answer out by time limit for a > project. If anybody understand what exactly happen here. pls kindly share > with me. Thank a lot. > > > Thanks & Bast Regards, > Micah Liu > > > _______________________________________________ > 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 Tue Sep 22 12:32:51 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 22 Sep 2015 12:32:51 -0400 Subject: [ITK-dev] Code Review Site Upgrade Downtime Message-ID: Hi, We will be upgrading the code review site tomorrow at 2 PM and anticipate approximately half an hour of downtime. Thanks, Matt From marco.dev.open at gmail.com Tue Sep 22 12:39:01 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Tue, 22 Sep 2015 20:09:01 +0330 Subject: [ITK-dev] Threshold setting Message-ID: HI, I use double scaler type from input but work with (Black or white ) threshold setting My code is follow bellow int apply = 0; imageThreshold->SetInputConnection(firstColorMapper->GetOutputPort()); imageThreshold->ReplaceInOn(); imageThreshold->SetInValue(255); imageThreshold->ReplaceOutOn(); imageThreshold->SetOutValue(255); imageThreshold->SetOutputScalarType(fixedConnector->GetOutput()->GetScalarType()); //double imageThreshold->ThresholdBetween(VTK_SHORT_MIN, VTK_SHORT_MAX); imageThreshold->ThresholdBetween( -3495, 2161 ); imageThreshold->SetOutValue(apply ? 0 : 255); imageThreshold->Update(); double low = (!enableThreshold) ? range[0] : lowThreshold; double upper = (!enableThreshold) ? range[1] : upperThreshold; vtkSmartPointer imageThreshold2 = vtkSmartPointer::New(); // imageThreshold2->SetInputData(mImage); imageThreshold2->SetInputConnection(secondColorMapper->GetOutputPort()); imageThreshold2->ReplaceInOn(); imageThreshold2->SetInValue(255); imageThreshold2->ReplaceOutOn(); imageThreshold2->SetOutValue(255); imageThreshold2->SetOutputScalarType(fixedConnector->GetOutput()->GetScalarType()); //double imageThreshold2->ThresholdBetween(VTK_SHORT_MIN, VTK_SHORT_MAX); imageThreshold2->ThresholdBetween( 160, 6088 ); imageThreshold2->SetOutValue(apply ? 0 : 255); imageThreshold2->Update(); Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Sep 22 18:04:21 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 22 Sep 2015 18:04:21 -0400 Subject: [ITK-dev] Patches for 4.8.1 Message-ID: Hello, We are due for a the 4.8.1 bugfix release. Currently, on the "release" Git branch we have Abhishek Tiwari (1): BUG: "tmpImageIndex" not initialized to 0. Davis Vigneault (1): DOC: Expanded TreeContainer Example Matthew McCormick (9): BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. BUG: Initialize mutex for 32 bit AtomicInt. COMP: Disable the gold linker for static builds on Ubuntu 14.04. BUG: Build BridgeNumPy with Visual Studio. BUG: Support Python 3 wrapping module initialization. BUG: Update itkTemplate.py for Python 3. BUG: Update itkExtras.py for Python 3. BUG: Prevent Python callback addition recursion. BUG: Fix test scripts for Python 3. Michka Popoff (1): ENH: Do not link against specific Python library on OS X Shawn Waldon (1): COMP: Set target OS X version in environment for tools using compiler Tobias Wood (2): BUG: LBFGSB was printing messages even with debug switched off. BUG: Removed an unguarded print statement. Vladimir S. FONOV (2): BUG: Missing ITKIOMINC_EXPORT on __Private() COMP: Changing the order of HDF5 library components Are there any other patches to be added for 4.8.1? Thanks, Matt From jchris.fillionr at kitware.com Wed Sep 23 00:44:22 2015 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Wed, 23 Sep 2015 00:44:22 -0400 Subject: [ITK-dev] [slicer-devel] Threshold setting In-Reply-To: <631fd687330741468305e9159d6208c6@PHSX10HT3.partners.org> References: <631fd687330741468305e9159d6208c6@PHSX10HT3.partners.org> Message-ID: Hi Marco, Great to see you are making progress. While the members of the ITK, VTK and Slicer communities would be more than happy to help you, I think sending an email to all of them will have the opposite effect. Instead, to get meaningful help, before sending an email I would suggest you consider the following checklist. I use it myself everyday. [ ] Did I check the documentation, examples or existing tests of the related projects ? [ ] Did I search the existing mailing archives and/or stack overflow for similar question ? It is not uncommon that other users asked a similar question. Using a search engine should be helpful here. [ ] Did I check FAQ (Frequently Asked Questions) sections of the projects ? For example, on the Slicer wiki there are a user and developer FAQs. [ ] Am I providing enough context for others to understand and reproduce the problem. Reading the SSCCE guidlines [Short, Self Contained, Correct (Compilable), Example] available on http://sscce.org/ is always a good thing. [ ] Is my question specific to a given library (ITK, VTK) or application (Slicer). For example, if the question is about the use of vtkImageThreshold filter, the VTK user list is probably a good place to ask questions. [ ] Did I re-read my email before sending it. Considering your email will be read by hundreds (or may be thousands) of individuals, re-reading before sending is always good. That said, let us know if you have any questions, Thanks, Jc On Tue, Sep 22, 2015 at 12:39 PM, Marco Dev wrote: > HI, > I use double scaler type from input but work with (Black or white ) > threshold setting My code is follow bellow > int apply = 0; > imageThreshold->SetInputConnection(firstColorMapper->GetOutputPort()); > imageThreshold->ReplaceInOn(); > imageThreshold->SetInValue(255); > imageThreshold->ReplaceOutOn(); > imageThreshold->SetOutValue(255); > > imageThreshold->SetOutputScalarType(fixedConnector->GetOutput()->GetScalarType()); > //double > imageThreshold->ThresholdBetween(VTK_SHORT_MIN, VTK_SHORT_MAX); > imageThreshold->ThresholdBetween( -3495, 2161 ); > imageThreshold->SetOutValue(apply ? 0 : 255); > imageThreshold->Update(); > > > > double low = (!enableThreshold) ? range[0] : lowThreshold; > double upper = (!enableThreshold) ? range[1] : upperThreshold; > > > vtkSmartPointer imageThreshold2 = > vtkSmartPointer::New(); > // imageThreshold2->SetInputData(mImage); > > imageThreshold2->SetInputConnection(secondColorMapper->GetOutputPort()); > imageThreshold2->ReplaceInOn(); > imageThreshold2->SetInValue(255); > imageThreshold2->ReplaceOutOn(); > imageThreshold2->SetOutValue(255); > imageThreshold2->SetOutputScalarType(fixedConnector->GetOutput()->GetScalarType()); > //double > imageThreshold2->ThresholdBetween(VTK_SHORT_MIN, VTK_SHORT_MAX); > imageThreshold2->ThresholdBetween( 160, 6088 ); > imageThreshold2->SetOutValue(apply ? 0 : 255); > imageThreshold2->Update(); > > > Thanks > > > > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with > unsubscribe as the subject > > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Sep 23 14:08:16 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 23 Sep 2015 14:08:16 -0400 Subject: [ITK-dev] Patches for 4.8.1 In-Reply-To: References: Message-ID: Hi Matt, I reviewed my patches, and none seem appropriate for the patch release. I am working towards a SimpleITK 0.9.1 patch release too, so hopefully this tag can be made soon. Any idea when? Thanks, Brad On Sep 22, 2015, at 6:04 PM, Matt McCormick wrote: > Hello, > > We are due for a the 4.8.1 bugfix release. Currently, on the > "release" Git branch we have > > Abhishek Tiwari (1): > BUG: "tmpImageIndex" not initialized to 0. > > Davis Vigneault (1): > DOC: Expanded TreeContainer Example > > Matthew McCormick (9): > BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. > BUG: Initialize mutex for 32 bit AtomicInt. > COMP: Disable the gold linker for static builds on Ubuntu 14.04. > BUG: Build BridgeNumPy with Visual Studio. > BUG: Support Python 3 wrapping module initialization. > BUG: Update itkTemplate.py for Python 3. > BUG: Update itkExtras.py for Python 3. > BUG: Prevent Python callback addition recursion. > BUG: Fix test scripts for Python 3. > > Michka Popoff (1): > ENH: Do not link against specific Python library on OS X > > Shawn Waldon (1): > COMP: Set target OS X version in environment for tools using compiler > > Tobias Wood (2): > BUG: LBFGSB was printing messages even with debug switched off. > BUG: Removed an unguarded print statement. > > Vladimir S. FONOV (2): > BUG: Missing ITKIOMINC_EXPORT on __Private() > COMP: Changing the order of HDF5 library components > > > Are there any other patches to be added for 4.8.1? > > Thanks, > Matt > _______________________________________________ > 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 Wed Sep 23 15:47:53 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 23 Sep 2015 15:47:53 -0400 Subject: [ITK-dev] Patches for 4.8.1 In-Reply-To: References: Message-ID: Hi Brad, Thanks for the feedback and checking. It is excellent that this will coincide nicely with SimpleITK 0.9.1. The release announcement is targeted for Monday, but let's tag tomorrow if the dashboard looks fine. I also added this patch: http://review.source.kitware.com/#/c/20218/ for 32-bit wrapping in Debian. Thanks, Matt On Wed, Sep 23, 2015 at 2:08 PM, Bradley Lowekamp wrote: > Hi Matt, > > I reviewed my patches, and none seem appropriate for the patch release. > > I am working towards a SimpleITK 0.9.1 patch release too, so hopefully this tag can be made soon. Any idea when? > > Thanks, > Brad > > On Sep 22, 2015, at 6:04 PM, Matt McCormick wrote: > >> Hello, >> >> We are due for a the 4.8.1 bugfix release. Currently, on the >> "release" Git branch we have >> >> Abhishek Tiwari (1): >> BUG: "tmpImageIndex" not initialized to 0. >> >> Davis Vigneault (1): >> DOC: Expanded TreeContainer Example >> >> Matthew McCormick (9): >> BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. >> BUG: Initialize mutex for 32 bit AtomicInt. >> COMP: Disable the gold linker for static builds on Ubuntu 14.04. >> BUG: Build BridgeNumPy with Visual Studio. >> BUG: Support Python 3 wrapping module initialization. >> BUG: Update itkTemplate.py for Python 3. >> BUG: Update itkExtras.py for Python 3. >> BUG: Prevent Python callback addition recursion. >> BUG: Fix test scripts for Python 3. >> >> Michka Popoff (1): >> ENH: Do not link against specific Python library on OS X >> >> Shawn Waldon (1): >> COMP: Set target OS X version in environment for tools using compiler >> >> Tobias Wood (2): >> BUG: LBFGSB was printing messages even with debug switched off. >> BUG: Removed an unguarded print statement. >> >> Vladimir S. FONOV (2): >> BUG: Missing ITKIOMINC_EXPORT on __Private() >> COMP: Changing the order of HDF5 library components >> >> >> Are there any other patches to be added for 4.8.1? >> >> Thanks, >> Matt >> _______________________________________________ >> 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 Wed Sep 23 16:15:24 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 23 Sep 2015 16:15:24 -0400 Subject: [ITK-dev] Gerrit Code Review upgraded to 2.11.3! Message-ID: Hi folks, Our code review instance has been upgraded to the latest currently released upstream version, Gerrit 2.11.3: http://review.source.kitware.com/ This upgrade brings many exciting enhancements. Most importantly: 1) The new user interface is now the default. Support for the (maligned) old interface has been removed. 2) It is now possible to fully edit patch sets through the web interface! In 2.10, it was possible to edit the commit message. Now, it is also possible to generate new patch sets entirely in the browser, which can be very convenient. Usage is documented here: http://review.source.kitware.com/Documentation/user-inline-edit.html 3) We added the reviewers-by-blame plugin. This plugin attempts to automatically add reviewers based on authorship found via 'git blame' for modified files. As always, reviews from everyone are appreciated. This ensures we maintain high-quality code and communicate knowledge in a scalable and sustainable contribution way. Thanks, Matt From blowekamp at mail.nih.gov Thu Sep 24 10:53:29 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 24 Sep 2015 10:53:29 -0400 Subject: [ITK-dev] [ITK-users] Streamed Read/Write Truncating Data In-Reply-To: References: <191044B9-EE73-479F-89C4-BA7FEA977740@mail.nih.gov> Message-ID: <39B1F2E5-9445-473B-95BE-AC2647B8AB51@mail.nih.gov> Hello, I was able to reproduced a truncated volume with clang on OSX. This looks like a 32-bit truncation issue. I also created the following pipeline: ImageFilterReader->StreamingImageFilter->ImageFileWriter I set the NumberofStreamDivisions to 20 on the StreamingImageFIlter, to make the reader stream, but I didn't use streaming in the writer. The volume still appears truncated. This narrows the problem to the Nifti reading. Hopefully, there is a problem in the itk ImageIO[1], and not in the Nifti library. Contributions to fix the problem are welcome. Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx On Sep 21, 2015, at 6:32 PM, Maryana wrote: > > > > Hi! > > If anyone would like to repeat the test, this is my test file: https://www.dropbox.com/s/7hpen46znk1h58l/brain_8bit.nii?dl=0 > If I convert that file to MetaIO without streams, and use ExtractImageFilter to read one file perpendicular to Y (as in the code I'm sending bellow) it works fine. However if I convert it to MetaIO using streams and use the same code to read the same slice, I end up with a truncated image. I have the same result when I use Paraview for visualization. By the way, for what I've read from ITK documentation NIfti supposedly supports streamed reading. So I'm guessing that using Nifti in this case would be ok. Is this correct? Would anyone have an idea on what's wrong? > > Thank you! > > > > Code for reading slice: > > > > #include "itkImageFileReader.h" > #include "itkImageFileWriter.h" > #include "itkExtractImageFilter.h" > #include "itkImage.h" > > > int main( int argc, char ** argv ) > { > > typedef unsigned char InputPixelType; > typedef unsigned char OutputPixelType; > > typedef itk::Image< InputPixelType, 3 > InputImageType; > typedef itk::Image< OutputPixelType, 2 > OutputImageType; > > typedef itk::ImageFileReader< InputImageType > ReaderType; > typedef itk::ImageFileWriter< OutputImageType > WriterType; > > std::string fileIn = "mri2_stream.mha"; > std::string fileOut = "slice.tif"; > const char * inputFilename = fileIn.c_str(); > const char * outputFilename = fileOut.c_str(); > > ReaderType::Pointer reader = ReaderType::New(); > WriterType::Pointer writer = WriterType::New(); > > reader->SetFileName( inputFilename ); > writer->SetFileName( outputFilename ); > > typedef itk::ExtractImageFilter< InputImageType, OutputImageType > FilterType; > FilterType::Pointer filter = FilterType::New(); > filter->InPlaceOn(); > filter->SetDirectionCollapseToSubmatrix(); > > reader->UpdateOutputInformation(); > InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion(); > > InputImageType::SizeType size = inputRegion.GetSize(); > > std::cout << "Size: " << std::endl; > std::cout << size[0] << std::endl; > std::cout << size[1] << std::endl; > std::cout << size[2] << std::endl; > > > InputImageType::IndexType start = inputRegion.GetIndex(); > const unsigned int sliceNumber = 800; > > std::cout << "Start: " << std::endl; > std::cout << start[0] << std::endl; > std::cout << start[1] << std::endl; > std::cout << start[2] << std::endl; > > size[1] = 0; > start[1] = sliceNumber; > > InputImageType::RegionType desiredRegion; > desiredRegion.SetSize( size ); > desiredRegion.SetIndex( start ); > > filter->SetExtractionRegion( desiredRegion ); > > filter->SetInput( reader->GetOutput() ); > writer->SetInput( filter->GetOutput() ); > > try > { > writer->Update(); > } > catch( itk::ExceptionObject & err ) > { > std::cerr << "ExceptionObject caught !" << std::endl; > std::cerr << err << std::endl; > return EXIT_FAILURE; > } > > > return EXIT_SUCCESS; > } > > > > On Mon, Sep 21, 2015 at 12:07 PM, Maryana wrote: > Hi, > > I use Linux Mint 64bits, GCC 4.8, Cmake 2.8. I'm compiling to this platform. > > Thank you! > > On Mon, Sep 21, 2015 at 11:55 AM, Bradley Lowekamp wrote: > Hello Maryana, > > What compiler, platform and architecture are you compiling for? > > Brad > > On Sep 21, 2015, at 2:54 PM, Maryana wrote: > > > > > Hi ITK Users/Devs, > > > > I'm new to ITK and I need to write a small program to convert Nifti images to MetaIO. However, I need to use the streamed reader/writer because my image volumes can have several gigabytes. I was doing some tests with the following code but I've realized that whenever I use the stream I end up with a truncated volume. I'm using ITK 4.8. I'm sure my volume is of unsigned char type. Also, when I comment out the writer->SetNumberOfStreamDivisions(20); line I works fine. Does anyone knows what is wrong? > > > > Thank you! > > > > #include > > #include > > #include > > > > #include "itkImage.h" > > #include "itkImageFileReader.h" > > #include "itkImageFileWriter.h" > > #include "itkImageRegionIterator.h" > > #include "itkNiftiImageIO.h" > > #include "itkMetaImageIO.h" > > > > > > int main(int argc, char const *argv[]){ > > > > std::string fileIn = "brain_8bit.nii"; > > std::string fileOut = "mri2_stream.mha"; > > > > typedef itk::Image Image3D; > > > > //Reader > > typedef itk::ImageFileReader ReaderType; > > ReaderType::Pointer reader = ReaderType::New(); > > reader->SetFileName(fileIn); > > > > //Writer > > typedef itk::ImageFileWriter WriterType; > > WriterType::Pointer writer = WriterType::New(); > > writer->SetFileName(fileOut); > > writer->SetNumberOfStreamDivisions(20); > > writer->SetInput(reader->GetOutput()); > > > > > > std::cout << "Input: " << fileIn << std::endl; > > std::cout << "Output: " << fileOut << std::endl; > > > > std::cout << "Writing..." << std::endl; > > try > > { > > writer->Update(); > > } > > catch( itk::ExceptionObject & err ) > > { > > std::cerr << "ExceptionObject caught !" << std::endl; > > std::cerr << err << std::endl; > > return EXIT_FAILURE; > > } > > std::cout << "Finished." << std::endl; > > > > > > return EXIT_SUCCESS; > > } > > > > > > > > > > > > -- > > "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra mol?cula e nasceu a vida" - Clarice Lispector > > _______________________________________________ > > 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 > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Sep 24 16:53:04 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 24 Sep 2015 16:53:04 -0400 Subject: [ITK-dev] Patches for 4.8.1 In-Reply-To: References: Message-ID: The v4.8.1 tag has been pushed. On Wed, Sep 23, 2015 at 3:47 PM, Matt McCormick wrote: > Hi Brad, > > Thanks for the feedback and checking. > > It is excellent that this will coincide nicely with SimpleITK 0.9.1. > The release announcement is targeted for Monday, but let's tag > tomorrow if the dashboard looks fine. > > I also added this patch: > > http://review.source.kitware.com/#/c/20218/ > > for 32-bit wrapping in Debian. > > Thanks, > Matt > > On Wed, Sep 23, 2015 at 2:08 PM, Bradley Lowekamp > wrote: >> Hi Matt, >> >> I reviewed my patches, and none seem appropriate for the patch release. >> >> I am working towards a SimpleITK 0.9.1 patch release too, so hopefully this tag can be made soon. Any idea when? >> >> Thanks, >> Brad >> >> On Sep 22, 2015, at 6:04 PM, Matt McCormick wrote: >> >>> Hello, >>> >>> We are due for a the 4.8.1 bugfix release. Currently, on the >>> "release" Git branch we have >>> >>> Abhishek Tiwari (1): >>> BUG: "tmpImageIndex" not initialized to 0. >>> >>> Davis Vigneault (1): >>> DOC: Expanded TreeContainer Example >>> >>> Matthew McCormick (9): >>> BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. >>> BUG: Initialize mutex for 32 bit AtomicInt. >>> COMP: Disable the gold linker for static builds on Ubuntu 14.04. >>> BUG: Build BridgeNumPy with Visual Studio. >>> BUG: Support Python 3 wrapping module initialization. >>> BUG: Update itkTemplate.py for Python 3. >>> BUG: Update itkExtras.py for Python 3. >>> BUG: Prevent Python callback addition recursion. >>> BUG: Fix test scripts for Python 3. >>> >>> Michka Popoff (1): >>> ENH: Do not link against specific Python library on OS X >>> >>> Shawn Waldon (1): >>> COMP: Set target OS X version in environment for tools using compiler >>> >>> Tobias Wood (2): >>> BUG: LBFGSB was printing messages even with debug switched off. >>> BUG: Removed an unguarded print statement. >>> >>> Vladimir S. FONOV (2): >>> BUG: Missing ITKIOMINC_EXPORT on __Private() >>> COMP: Changing the order of HDF5 library components >>> >>> >>> Are there any other patches to be added for 4.8.1? >>> >>> Thanks, >>> Matt >>> _______________________________________________ >>> 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 Sep 25 09:13:37 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 25 Sep 2015 15:13:37 +0200 Subject: [ITK-dev] itk::ThreadedIteratorRangePartitioner and itk::PointSet (i.e. itk::VectorContainer and itk::MapContainer of points) Message-ID: Hi Matt, I would like to use *itk::ThreadedIteratorRangePartitioner *with itk::PointSet which is a itk::VectorContainer or itk::MapContainer of points... I have been trying to add one test of itk::ThreadedIteratorRangePartitioner along with itk::VectorContainer here, but got stucked. Can you have a quick look, since you first wrote the ThreadedIteratorRangePartitioner class, please? http://review.source.kitware.com/#/c/20079/1 Thanks, Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Sep 25 23:26:07 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 25 Sep 2015 23:26:07 -0400 Subject: [ITK-dev] itk::ThreadedIteratorRangePartitioner and itk::PointSet (i.e. itk::VectorContainer and itk::MapContainer of points) In-Reply-To: References: Message-ID: Hi Arnaud, I pushed a new patch set where itk::VectorContainer compiles. HTH, Matt On Fri, Sep 25, 2015 at 9:13 AM, Arnaud Gelas wrote: > Hi Matt, > > I would like to use itk::ThreadedIteratorRangePartitioner with itk::PointSet > which is a itk::VectorContainer or itk::MapContainer of points... > > I have been trying to add one test of itk::ThreadedIteratorRangePartitioner > along with itk::VectorContainer here, but got stucked. Can you have a quick > look, since you first wrote the ThreadedIteratorRangePartitioner class, > please? > > http://review.source.kitware.com/#/c/20079/1 > > Thanks, > Arnaud From marco.dev.open at gmail.com Sat Sep 26 09:06:39 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Sat, 26 Sep 2015 16:36:39 +0330 Subject: [ITK-dev] Fusion in general In-Reply-To: References: Message-ID: Hi, I found the notice Thanks should drag two series into panel and Only series from the same study can be fused Thanks On Sat, Sep 26, 2015 at 4:19 PM, Marco Dev wrote: > HI, > I have two DICOM images (PET/CT) and these images are related to the same > patient for testing > these images in FUSION action I used radiant application But it does not > enable FUSION feature > In general for fusion two images what do we need for understanding which > DICOM parameters we should regarding these dicom images attached with this > mail > Thanks > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Mon Sep 28 03:48:13 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Mon, 28 Sep 2015 09:48:13 +0200 Subject: [ITK-dev] itk::ThreadedIteratorRangePartitioner and itk::PointSet (i.e. itk::VectorContainer and itk::MapContainer of points) In-Reply-To: References: Message-ID: Hi Matt, Awesome, indeed it now compiles!! Working now on fixing test failure! Thank you very much Best, Arnaud On Sat, Sep 26, 2015 at 5:26 AM, Matt McCormick wrote: > Hi Arnaud, > > I pushed a new patch set where itk::VectorContainer compiles. > > HTH, > Matt > > On Fri, Sep 25, 2015 at 9:13 AM, Arnaud Gelas > wrote: > > Hi Matt, > > > > I would like to use itk::ThreadedIteratorRangePartitioner with > itk::PointSet > > which is a itk::VectorContainer or itk::MapContainer of points... > > > > I have been trying to add one test of > itk::ThreadedIteratorRangePartitioner > > along with itk::VectorContainer here, but got stucked. Can you have a > quick > > look, since you first wrote the ThreadedIteratorRangePartitioner class, > > please? > > > > http://review.source.kitware.com/#/c/20079/1 > > > > Thanks, > > Arnaud > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jerome.velut at kitware.com Mon Sep 28 15:07:20 2015 From: jerome.velut at kitware.com (Jerome Velut) Date: Mon, 28 Sep 2015 21:07:20 +0200 Subject: [ITK-dev] ANN: ITK Training Courses in Lyon, France, November 5, 2015 Message-ID: Kitware will be holding an ITK course on November 5, 2015 in Lyon, France. Please visit our web site for more information and registration details at either: http://training.kitware.fr/browse/98 or in French: http://formations.kitware.fr/browse/98 Note that the course could be taught in English. If you have any question, please contact us at formations at http://www.kitware.fr Thank you, -- J?r?me Velut Research and Development Kitware SAS 26 rue Louis Gu?rin 69100 Villeurbanne, France F: +33 (0)4.37.45.04.15 http://www.kitware.fr http://www.kitware.com/company/team/velut.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Sep 29 10:21:27 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 29 Sep 2015 10:21:27 -0400 Subject: [ITK-dev] ITK 4.8.1 has been released! Message-ID: On behalf of the Insight Toolkit Community, we are happy to announce the release of ITK 4.8.1! Release files can be downloaded from: http://itk.org/ITK/resources/software.html This is a patch release that fixes critical issues, regressions, important documentation, and compiler support. Most importantly, the 4.8.1 release completes fixes for Python 3 wrapping! A number of other Python-related fixes are included, such as NumPy bridge support for Visual Studio, and Python library binary compatibility improvements for system / HomeBrew / Anaconda Python on Mac OSX. There are also a number of other various fixes, described in the log below. The next feature release, 4.9.0, is scheduled for December, and it will feature many exciting enhancements! Enjoy ITK! Changes from v4.8.0 to v4.8.1: Abhishek Tiwari (1): BUG: "tmpImageIndex" not initialized to 0. Davis Vigneault (1): DOC: Expanded TreeContainer Example Matthew McCormick (11): BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. BUG: Initialize mutex for 32 bit AtomicInt. COMP: Disable the gold linker for static builds on Ubuntu 14.04. BUG: Build BridgeNumPy with Visual Studio. BUG: Support Python 3 wrapping module initialization. BUG: Update itkTemplate.py for Python 3. BUG: Update itkExtras.py for Python 3. BUG: Prevent Python callback addition recursion. BUG: Fix test scripts for Python 3. BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. ENH: Bump CMakeLists.txt version to 4.8.1. Michka Popoff (1): ENH: Do not link against specific Python library on OS X Shawn Waldon (1): COMP: Set target OS X version in environment for tools using compiler Tobias Wood (2): BUG: LBFGSB was printing messages even with debug switched off. BUG: Removed an unguarded print statement. Vladimir S. FONOV (2): BUG: Missing ITKIOMINC_EXPORT on __Private() COMP: Changing the order of HDF5 library components From nexnaru at gmail.com Mon Sep 21 16:27:10 2015 From: nexnaru at gmail.com (Maryana) Date: Mon, 21 Sep 2015 20:27:10 -0000 Subject: [ITK-dev] Streamed Read/Write Truncating Data In-Reply-To: References: <191044B9-EE73-479F-89C4-BA7FEA977740@mail.nih.gov> Message-ID: Hi! If anyone would like to repeat the test, this is my test file: https://www.dropbox.com/s/7hpen46znk1h58l/brain_8bit.nii?dl=0 If I convert that file to MetaIO without streams, and use ExtractImageFilter to read one file perpendicular to Y (as in the code I'm sending bellow) it works fine (see slice.tif). However if I convert it to MetaIO using streams and use the same code to read the same slice, I end up with a truncated image (file slice_stream.tif). I have the same result when I use Paraview for visualization. By the way, for what I've read from ITK documentation NIfti supposedly supports streamed reading. So I'm guessing that using Nifti in this case would be ok. Is this correct? Would anyone have an idea on what's wrong? Thank you! Code for reading slice: #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkExtractImageFilter.h" #include "itkImage.h" int main( int argc, char ** argv ) { typedef unsigned char InputPixelType; typedef unsigned char OutputPixelType; typedef itk::Image< InputPixelType, 3 > InputImageType; typedef itk::Image< OutputPixelType, 2 > OutputImageType; typedef itk::ImageFileReader< InputImageType > ReaderType; typedef itk::ImageFileWriter< OutputImageType > WriterType; std::string fileIn = "mri2_stream.mha"; std::string fileOut = "slice.tif"; const char * inputFilename = fileIn.c_str(); const char * outputFilename = fileOut.c_str(); ReaderType::Pointer reader = ReaderType::New(); WriterType::Pointer writer = WriterType::New(); reader->SetFileName( inputFilename ); writer->SetFileName( outputFilename ); typedef itk::ExtractImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New(); filter->InPlaceOn(); filter->SetDirectionCollapseToSubmatrix(); reader->UpdateOutputInformation(); InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion(); InputImageType::SizeType size = inputRegion.GetSize(); std::cout << "Size: " << std::endl; std::cout << size[0] << std::endl; std::cout << size[1] << std::endl; std::cout << size[2] << std::endl; InputImageType::IndexType start = inputRegion.GetIndex(); const unsigned int sliceNumber = 800; std::cout << "Start: " << std::endl; std::cout << start[0] << std::endl; std::cout << start[1] << std::endl; std::cout << start[2] << std::endl; size[1] = 0; start[1] = sliceNumber; InputImageType::RegionType desiredRegion; desiredRegion.SetSize( size ); desiredRegion.SetIndex( start ); filter->SetExtractionRegion( desiredRegion ); filter->SetInput( reader->GetOutput() ); writer->SetInput( filter->GetOutput() ); try { writer->Update(); } catch( itk::ExceptionObject & err ) { std::cerr << "ExceptionObject caught !" << std::endl; std::cerr << err << std::endl; return EXIT_FAILURE; } return EXIT_SUCCESS; } On Mon, Sep 21, 2015 at 12:07 PM, Maryana wrote: > Hi, > > I use Linux Mint 64bits, GCC 4.8, Cmake 2.8. I'm compiling to this > platform. > > Thank you! > > On Mon, Sep 21, 2015 at 11:55 AM, Bradley Lowekamp > wrote: > >> Hello Maryana, >> >> What compiler, platform and architecture are you compiling for? >> >> Brad >> >> On Sep 21, 2015, at 2:54 PM, Maryana wrote: >> >> > >> > Hi ITK Users/Devs, >> > >> > I'm new to ITK and I need to write a small program to convert Nifti >> images to MetaIO. However, I need to use the streamed reader/writer because >> my image volumes can have several gigabytes. I was doing some tests with >> the following code but I've realized that whenever I use the stream I end >> up with a truncated volume. I'm using ITK 4.8. I'm sure my volume is of >> unsigned char type. Also, when I comment out the >> writer->SetNumberOfStreamDivisions(20); line I works fine. Does anyone >> knows what is wrong? >> > >> > Thank you! >> > >> > #include >> > #include >> > #include >> > >> > #include "itkImage.h" >> > #include "itkImageFileReader.h" >> > #include "itkImageFileWriter.h" >> > #include "itkImageRegionIterator.h" >> > #include "itkNiftiImageIO.h" >> > #include "itkMetaImageIO.h" >> > >> > >> > int main(int argc, char const *argv[]){ >> > >> > std::string fileIn = "brain_8bit.nii"; >> > std::string fileOut = "mri2_stream.mha"; >> > >> > typedef itk::Image Image3D; >> > >> > //Reader >> > typedef itk::ImageFileReader ReaderType; >> > ReaderType::Pointer reader = ReaderType::New(); >> > reader->SetFileName(fileIn); >> > >> > //Writer >> > typedef itk::ImageFileWriter WriterType; >> > WriterType::Pointer writer = WriterType::New(); >> > writer->SetFileName(fileOut); >> > writer->SetNumberOfStreamDivisions(20); >> > writer->SetInput(reader->GetOutput()); >> > >> > >> > std::cout << "Input: " << fileIn << std::endl; >> > std::cout << "Output: " << fileOut << std::endl; >> > >> > std::cout << "Writing..." << std::endl; >> > try >> > { >> > writer->Update(); >> > } >> > catch( itk::ExceptionObject & err ) >> > { >> > std::cerr << "ExceptionObject caught !" << std::endl; >> > std::cerr << err << std::endl; >> > return EXIT_FAILURE; >> > } >> > std::cout << "Finished." << std::endl; >> > >> > >> > return EXIT_SUCCESS; >> > } >> > >> > >> > >> > >> > >> > -- >> > "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra >> mol?cula e nasceu a vida" - Clarice Lispector >> > _______________________________________________ >> > 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 >> >> > > > -- > "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra mol?cula > e nasceu a vida" - Clarice Lispector > -- "Tudo no mundo come?ou com um sim. Uma mol?cula disse sim a outra mol?cula e nasceu a vida" - Clarice Lispector -------------- next part -------------- An HTML attachment was scrubbed... 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