[Insight-users] now my dicom series reader seg faults with the changes
Bill Lorensen
bill.lorensen at gmail.com
Thu Dec 3 23:43:53 EST 2009
Fantastic!
On Thu, Dec 3, 2009 at 11:41 PM, John Drozd <john.drozd at gmail.com> wrote:
> Hi Bill,
>
> You don't have to test my code anymore. Everything is fine now.
> There was an error in my CMakeLists.txt file that was causing the seg fault.
> I updated my 3DSlicer which updated its ITK and now both my dicom series
> reader code and my segmentation code works.
>
> Thanks,
> john
>
> On Thu, Dec 3, 2009 at 6:54 PM, John Drozd <john.drozd at gmail.com> wrote:
>>
>> Hi Bill,
>>
>> Thanks. Of course, try this when you find time. That's fine.
>>
>> BUT BEFORE YOU DO ANYTHING, give me a day to download the latest Slicer
>> and CVS and 3.16 to retest my code.
>>
>> The ITK that my dicom series reader code worked with was ITK 3.14 that
>> came with Slicer 3.4.
>>
>> The ITK that my dicom series reader code seg faults with is the ITK that
>> came with the 3D Slicer 3.5 alpha download that I downloaded on 2009-12-02
>> 15:43. I believe that this version of Slicer that I downloaded has ITK 3.16
>> with the fix that you did to establish the correct orientation, because with
>> this version of ITK, I get the correct orientation from my segmentation code
>> that I sent a few days ago.
>>
>> I've also tested the CVS that I downloaded on 2009-12-01 12:07 and my
>> dicom series reader code seg faults as well.
>>
>> Thanks,
>> john
>>
>>
>> On Thu, Dec 3, 2009 at 4:46 PM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>>>
>>> I'll take a look, but it won't be for a few days... Can you clarify
>>> what version of itk you are referring to? Is it 3.16? If not, is it
>>> the current cvs? There was a bug introduced in the current cvs
>>> yesterday. It has been removed. That's why we must know clearly which
>>> version you are talking about.
>>>
>>> Bill
>>>
>>> On Thu, Dec 3, 2009 at 3:35 PM, John Drozd <john.drozd at gmail.com> wrote:
>>> > Hi Bill,
>>> >
>>> > Sorry, but it's getting more complicated with itkGDCMIMageIO.cxx.
>>> >
>>> > With the previous ITK (the version prior to the rev 1.162 change that
>>> > you
>>> > did to itkGDCMIMageIO.cxx so my outputted 3d dicom volume would be in
>>> > the
>>> > correct orientation):
>>> >
>>> > With this previous ITK, I had code working that read two dicom series
>>> > and
>>> > wrote them to a 3d dicom single file volume.
>>> >
>>> > Now with the revised ITK (the version with the re 1.162 change that you
>>> > did
>>> > to itkGDCMIMageIO.cxx so my outputted 3d dicom volume would be in the
>>> > correct orientation):
>>> >
>>> > With this revised ITK, my code that reads two dicom series and writes
>>> > them
>>> > to a 3d dicom single file volume.
>>> > seg faults.
>>> >
>>> > Could you check this for me please.
>>> >
>>> > Ideally, I would like my previous segmentation code to output the
>>> > correct
>>> > dicom orientation, and my code that reads dicom series to both work
>>> > with the
>>> > same version of ITK.
>>> >
>>> > Thanks,
>>> > john
>>> >
>>> > You can download my dicom series data as compressed tar.gz from the
>>> > following links:
>>> >
>>> > http://www.apmaths.uwo.ca/~jdrozd/datasubject.tar.gz
>>> >
>>> > and
>>> >
>>> > http://www.apmaths.uwo.ca/~jdrozd/datasubject4.tar.gz
>>> >
>>> > (Prior to running the below code, untar and unzip these two compressed
>>> > files
>>> > and have them in the same directory as the code executable)
>>> >
>>> > Below is my code:
>>> >
>>> > /* to run ReadAtlasDicomSeriesAndReadSubjectDicomSeries.cxx, compile
>>> > and
>>> > type:
>>> > ./ReadAtlasDicomSeriesAndReadSubjectDicomSeries "datasubject"
>>> >
>>> > "datasubject4/136_S_0429/MPR__GradWarp__B1_Correction__N3__Scaled/2007-06-18_13_28_06.0/S33724/70809234826766_S33724_I66806_Dicom"
>>> > */
>>> >
>>> > #if defined(_MSC_VER)
>>> > #pragma warning ( disable : 4786 )
>>> > #endif
>>> >
>>> > #include "itkImageFileReader.h"
>>> > #include "itkImageFileWriter.h"
>>> > #include "itkOrientedImage.h"
>>> > #include "itkGDCMImageIO.h"
>>> > #include "itkGDCMSeriesFileNames.h"
>>> > #include "itkImageSeriesReader.h"
>>> >
>>> > int main(int argc, char *argv[])
>>> > {
>>> >
>>> > typedef short InputPixelType;
>>> > const unsigned int InputDimension = 3;
>>> >
>>> > typedef itk::Image< InputPixelType, InputDimension > InputImageType;
>>> >
>>> > typedef itk::ImageSeriesReader< InputImageType >
>>> > AtlasReaderSeriesType;
>>> >
>>> > typedef itk::ImageSeriesReader< InputImageType >
>>> > SubjectReaderSeriesType;
>>> >
>>> > AtlasReaderSeriesType::Pointer movingatlasfilter =
>>> > AtlasReaderSeriesType::New();
>>> >
>>> > SubjectReaderSeriesType::Pointer fixedsubjectfilter =
>>> > SubjectReaderSeriesType::New();
>>> >
>>> > typedef itk::GDCMImageIO ImageIOType;
>>> >
>>> > ImageIOType::Pointer gdcmImageIOAtlas = ImageIOType::New();
>>> >
>>> > ImageIOType::Pointer gdcmImageIOSubject = ImageIOType::New();
>>> >
>>> > fixedsubjectfilter->SetImageIO( gdcmImageIOSubject );
>>> >
>>> > movingatlasfilter->SetImageIO( gdcmImageIOAtlas );
>>> >
>>> > typedef itk::GDCMSeriesFileNames AtlasNamesGeneratorType;
>>> > AtlasNamesGeneratorType::Pointer AtlasnameGenerator =
>>> > AtlasNamesGeneratorType::New();
>>> >
>>> > typedef itk::GDCMSeriesFileNames SubjectNamesGeneratorType;
>>> > SubjectNamesGeneratorType::Pointer SubjectnameGenerator =
>>> > SubjectNamesGeneratorType::New();
>>> >
>>> > SubjectnameGenerator->SetUseSeriesDetails( true );
>>> > SubjectnameGenerator->AddSeriesRestriction("0008|0021" );
>>> >
>>> > SubjectnameGenerator->SetDirectory( argv[2] );
>>> >
>>> > AtlasnameGenerator->SetUseSeriesDetails( true );
>>> > AtlasnameGenerator->AddSeriesRestriction("0008|0021" );
>>> >
>>> > AtlasnameGenerator->SetDirectory( argv[1] );
>>> >
>>> > try
>>> > {
>>> > std::cout << std::endl << "The directory: " << std::endl;
>>> > std::cout << std::endl << argv[1] << std::endl << std::endl;
>>> > std::cout << "Contains the following Atlas DICOM Series: ";
>>> > std::cout << std::endl << std::endl;
>>> >
>>> > typedef std::vector< std::string > AtlasSeriesIdContainer;
>>> >
>>> > const AtlasSeriesIdContainer & AtlasseriesUID =
>>> > AtlasnameGenerator->GetSeriesUIDs();
>>> >
>>> > AtlasSeriesIdContainer::const_iterator AtlasseriesItr =
>>> > AtlasseriesUID.begin();
>>> > AtlasSeriesIdContainer::const_iterator AtlasseriesEnd =
>>> > AtlasseriesUID.end();
>>> > while( AtlasseriesItr != AtlasseriesEnd )
>>> > {
>>> > std::cout << AtlasseriesItr->c_str() << std::endl;
>>> > AtlasseriesItr++;
>>> > }
>>> >
>>> > std::string AtlasseriesIdentifier;
>>> >
>>> > if( argc > 4 ) // If no optional series identifier
>>> > {
>>> > AtlasseriesIdentifier = argv[3];
>>> > }
>>> > else
>>> > {
>>> > AtlasseriesIdentifier = AtlasseriesUID.begin()->c_str();
>>> > }
>>> >
>>> > std::cout << std::endl << std::endl;
>>> > std::cout << "Now reading Atlas series: " << std::endl <<
>>> > std::endl;
>>> > std::cout << AtlasseriesIdentifier << std::endl;
>>> > std::cout << std::endl << std::endl;
>>> >
>>> > typedef std::vector< std::string > AtlasFileNamesContainer;
>>> > AtlasFileNamesContainer AtlasfileNames;
>>> >
>>> > AtlasfileNames = AtlasnameGenerator->GetFileNames(
>>> > AtlasseriesIdentifier
>>> > );
>>> >
>>> > movingatlasfilter->SetFileNames( AtlasfileNames );
>>> >
>>> >
>>> > try
>>> > {
>>> > movingatlasfilter->Update();
>>> > std::cout << "Atlas read successfully" << std::endl;
>>> > }
>>> > catch (itk::ExceptionObject &ex)
>>> > {
>>> > std::cout << ex << std::endl;
>>> > return EXIT_FAILURE;
>>> > }
>>> >
>>> > typedef itk::ImageFileWriter< InputImageType >
>>> > AtlasWriterSubjectType;
>>> >
>>> > AtlasWriterSubjectType::Pointer movingatlasfilterwriter =
>>> > AtlasWriterSubjectType::New();
>>> >
>>> >
>>> > movingatlasfilterwriter->UseInputMetaDataDictionaryOff();
>>> > movingatlasfilterwriter->SetImageIO( gdcmImageIOAtlas );
>>> >
>>> >
>>> > movingatlasfilterwriter->SetFileName( "atlasout.dcm" );
>>> >
>>> > movingatlasfilterwriter->SetInput( movingatlasfilter->GetOutput() );
>>> >
>>> >
>>> > try
>>> > {
>>> > movingatlasfilterwriter->Update();
>>> > }
>>> > catch (itk::ExceptionObject &ex)
>>> > {
>>> > std::cout << ex << std::endl;
>>> > return EXIT_FAILURE;
>>> > }
>>> > }
>>> > catch (itk::ExceptionObject &ex)
>>> > {
>>> > std::cout << ex << std::endl;
>>> > return EXIT_FAILURE;
>>> > }
>>> >
>>> > try
>>> > {
>>> > std::cout << std::endl << "The directory: " << std::endl;
>>> > std::cout << std::endl << argv[2] << std::endl << std::endl;
>>> > std::cout << "Contains the following Subject DICOM Series: ";
>>> > std::cout << std::endl << std::endl;
>>> >
>>> > typedef std::vector< std::string > SubjectSeriesIdContainer;
>>> >
>>> > const SubjectSeriesIdContainer & SubjectseriesUID =
>>> > SubjectnameGenerator->GetSeriesUIDs();
>>> >
>>> > SubjectSeriesIdContainer::const_iterator SubjectseriesItr =
>>> > SubjectseriesUID.begin();
>>> > SubjectSeriesIdContainer::const_iterator SubjectseriesEnd =
>>> > SubjectseriesUID.end();
>>> > while( SubjectseriesItr != SubjectseriesEnd )
>>> > {
>>> > std::cout << SubjectseriesItr->c_str() << std::endl;
>>> > SubjectseriesItr++;
>>> > }
>>> >
>>> > std::string SubjectseriesIdentifier;
>>> >
>>> > if( argc > 4 ) // If no optional series identifier
>>> > {
>>> > SubjectseriesIdentifier = argv[2];
>>> > }
>>> > else
>>> > {
>>> > SubjectseriesIdentifier = SubjectseriesUID.begin()->c_str();
>>> > }
>>> >
>>> > std::cout << std::endl << std::endl;
>>> > std::cout << "Now reading Subject series: " << std::endl <<
>>> > std::endl;
>>> > std::cout << SubjectseriesIdentifier << std::endl;
>>> > std::cout << std::endl << std::endl;
>>> >
>>> > typedef std::vector< std::string > SubjectFileNamesContainer;
>>> > SubjectFileNamesContainer SubjectfileNames;
>>> >
>>> > SubjectfileNames = SubjectnameGenerator->GetFileNames(
>>> > SubjectseriesIdentifier );
>>> >
>>> > fixedsubjectfilter->SetFileNames( SubjectfileNames );
>>> >
>>> > try
>>> > {
>>> > fixedsubjectfilter->Update();
>>> > std::cout << "Subject read successfully" << std::endl;
>>> > }
>>> > catch (itk::ExceptionObject &ex)
>>> > {
>>> > std::cout << ex << std::endl;
>>> > return EXIT_FAILURE;
>>> > }
>>> >
>>> > typedef itk::ImageFileWriter< InputImageType >
>>> > SubjectWriterSubjectType;
>>> >
>>> > SubjectWriterSubjectType::Pointer fixedsubjectfilterwriter =
>>> > SubjectWriterSubjectType::New();
>>> >
>>> > fixedsubjectfilterwriter->UseInputMetaDataDictionaryOff();
>>> > fixedsubjectfilterwriter->SetImageIO( gdcmImageIOSubject );
>>> >
>>> > fixedsubjectfilterwriter->SetFileName( "subjectout.dcm" );
>>> >
>>> > fixedsubjectfilterwriter->SetInput( fixedsubjectfilter->GetOutput()
>>> > );
>>> >
>>> >
>>> > try
>>> > {
>>> > fixedsubjectfilterwriter->Update();
>>> > }
>>> > catch (itk::ExceptionObject &ex)
>>> > {
>>> > std::cout << ex << std::endl;
>>> > return EXIT_FAILURE;
>>> > }
>>> > }
>>> > catch (itk::ExceptionObject &ex)
>>> > {
>>> > std::cout << ex << std::endl;
>>> > return EXIT_FAILURE;
>>> > }
>>> >
>>> >
>>> >
>>> > return EXIT_SUCCESS;
>>> > }
>>> >
>>> >
>>
>
>
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