[Insight-users] Fwd: Re: Problem ITK and GDCM in the same script
Lars Friedrich Lars
lars-friedrich at gmx.net
Sun Mar 21 10:49:32 EDT 2010
-------- Original-Nachricht --------
Datum: Sun, 21 Mar 2010 15:46:53 +0100
Von: "Lars Friedrich Lars" <lars-friedrich at gmx.net>
An: edoardo.belletti at alice.it
Betreff: Re: [Insight-users] Problem ITK and GDCM in the same script
Hello Eduardo,
without exactly knowing what you expect your DICOM application to do ...
Did you compile the ITK with ITK_USE_SYSTEM_GDCM (CMake-option of ITK)? If you did not, you should. This causes the ITK to take the system-installed GDCM (usually 2.++) instead of the one shipped with the ITK. If you did that you do no longer have to enter the GDCM-specific CMakeLists-entries (FIND_PACKAGE(GDCM) and so on), it should normally be sufficient to do the FIND_PACKAGE(ITK) stuff.
I had similar problems with a mixed-up ITK/VTK/GDCM2.0 application at the very beginning (the error messages were partially funny and not really trackable).
HTH,
lars
-------- Original-Nachricht --------
> Datum: Sun, 21 Mar 2010 12:21:26 +0100
> Von: edoardo.belletti at alice.it
> An: "ITK_forum " <insight-users at itk.org>
> Betreff: [Insight-users] Problem ITK and GDCM in the same script
> Hi
> I have a problem with configuring ITK with GDCM 2.0
> I have wrote this script which use the gdcm library for extract some tag
> from the header dicom and it works, but when in the same script I try to use
> also the itk's library the output is: Segmentation Fault (wherever I call
> Update() or I create a new smartpointer with New)
> I don't know if it is a problem of CMakeLists and so I have put in this
> email also my CMakeLists.txt.
>
> Thank you very much
>
> Edoardo Belletti
>
> CMakeLists.txt:
>
> CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
>
> PROJECT(ImageIO)
>
> # Find ITK.
> FIND_PACKAGE(ITK REQUIRED)
> IF(ITK_FOUND)
> INCLUDE(${ITK_USE_FILE})
> ENDIF(ITK_FOUND)
>
> # Find GDCM
> FIND_PACKAGE(GDCM)
> IF(GDCM_FOUND)
> INCLUDE(${GDCM_USE_FILE})
> IF( "${GDCM_MAJOR_VERSION}" LESS 2.0 )
> SET(MITK_GDCM_LIBRARIES gdcm)
> ELSE( "${GDCM_MAJOR_VERSION}" LESS 2.0 )
> SET(MITK_GDCM_LIBRARIES gdcmMSFF)
> ENDIF( "${GDCM_MAJOR_VERSION}" LESS 2.0 )
> ELSE(GDCM_FOUND)
> MESSAGE(FATAL_ERROR "Must set GDCM_DIR for MITK_USE_SYSTEM_GDCM.")
> ENDIF(GDCM_FOUND)
>
>
>
> ADD_EXECUTABLE(ReadAndDumpDICOMDIR ReadAndDumpDICOMDIR.cxx )
> TARGET_LINK_LIBRARIES(ReadAndDumpDICOMDIR ITKCommon ITKIO gdcmMSFF)
>
>
> //==========================================================
>
>
> // Librerie ITK
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkSobelEdgeDetectionImageFilter.h"
> #include "itkCastImageFilter.h"
> #include "itkRescaleIntensityImageFilter.h"
> #include "itkGDCMImageIO.h"
> #include "itkRegionOfInterestImageFilter.h"
> // Librerie GDCM
> #include "gdcmReader.h"
> #include "gdcmMediaStorage.h"
> #include "gdcmAttribute.h"
> #include "gdcmApplicationEntity.h"
> #include "gdcmElement.h"
> #include "gdcmSequenceOfItems.h"
>
> bool Region ( char* nomefile, unsigned int X_min, unsigned int Y_min,
> unsigned int X_max, unsigned int Y_max );
>
>
> int main(int argc, char* argv[] )
> {
> // Controllo del numero di argomenti introdotti da riga di comando
> if( argc < 3 )
> {
> std::cerr << "Usage: " << std::endl;
> std::cerr << argv[0] << " inputImageFile outputImageFile " <<
> std::endl;
> return EXIT_FAILURE;
> }
> // Settaggio delle variabili in input
> const char * InputImageFilename = argv[1];
> const char * OutputImageFilename = argv[2];
>
> // Dichiarazione dei tipi
> const unsigned int Dimension = 2;
> typedef unsigned char PixelType;
> typedef itk::Image< PixelType, Dimension > ImageType;
>
> typedef itk::ImageFileReader< ImageType > ReaderType;
> typedef itk::ImageFileWriter< ImageType > WriterType;
>
> typedef itk::GDCMImageIO ImageIOType;
> ImageIOType::Pointer dicomIO = ImageIOType::New();
>
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName( InputImageFilename );
> reader->SetImageIO( dicomIO );
>
> WriterType::Pointer writer = WriterType::New();
> writer->SetFileName( OutputImageFilename );
> writer->SetInput( reader->GetOutput() );
> writer->Update();
>
> unsigned int x_min = 1;
> unsigned int y_min = 1;
> unsigned int x_max = 1;
> unsigned int y_max = 1;
>
> if( Region ( argv[1], x_min, y_min, x_max, y_max ) )
> std::cout << "ok\n";
>
> else
> {
> std::cout << "no\n";
>
> }
>
>
> }
>
> bool Region ( char* nomefile, unsigned int X_min, unsigned int Y_min,
> unsigned int X_max, unsigned int Y_max )
> {
> gdcm::Reader reader;
> reader.SetFileName( nomefile );
> if( !reader.Read() )
> {
> std::cerr << "Could not read: " << nomefile << std::endl;
> return false;
> }
>
> gdcm::File &file = reader.GetFile();
> gdcm::DataSet &ds = file.GetDataSet();
>
> gdcm::Tag tsqur(0x0018,0x6011);
> if( !ds.FindDataElement( tsqur ) )
> {
> return false;
> }
>
> const gdcm::DataElement &squr= ds.GetDataElement( tsqur );
> //std::cout << squr << std::endl;
> const gdcm::SequenceOfItems *sqi = squr.GetSequenceOfItems();
> if( !sqi || !sqi->GetNumberOfItems() )
> {
> return false;
> }
> //std::cout << sqi << std::endl;
>
> const gdcm::Item & item = sqi->GetItem(1);
> //std::cout << item << std::endl;
> const gdcm::DataSet& nestedds = item.GetNestedDataSet();
> //std::cout << nestedds << std::endl;
>
> gdcm::Tag tX0(0x0018,0x6018);
> gdcm::Tag tY0(0x0018,0x601a);
> gdcm::Tag tX1(0x0018,0x601c);
> gdcm::Tag tY1(0x0018,0x601e);
>
> if( (!nestedds.FindDataElement( tX0 ))||(!nestedds.FindDataElement( tY0
> ))||(!nestedds.FindDataElement( tX1 ))||(!nestedds.FindDataElement( tY1 )) )
> {
> return false;
> }
>
> const gdcm::DataElement& deX0 = nestedds.GetDataElement( tX0 );
> const gdcm::DataElement& deY0 = nestedds.GetDataElement( tY0 );
> const gdcm::DataElement& deX1 = nestedds.GetDataElement( tX1 );
> const gdcm::DataElement& deY1 = nestedds.GetDataElement( tY1 );
> //std::cout << deX0 << std::endl << deY0 << std::endl << << deX1 <<
> std::endl << deY1 << std::endl;
>
> //const gdcm::ByteValue *bvX0 = deX0.GetByteValue();
> //const gdcm::ByteValue *bvY0 = deY0.GetByteValue();
> //const gdcm::ByteValue *bvX1 = deX1.GetByteValue();
> //const gdcm::ByteValue *bvY1 = deY1.GetByteValue();
> //std::cout << bvX0 << std::endl << bvY0 << std::endl << bvX1 <<
> std::endl << bvY1 << std::endl;
>
> gdcm::Attribute<0x0018,0x6018> atX0;
> gdcm::Attribute<0x0018,0x601a> atY0;
> gdcm::Attribute<0x0018,0x601c> atX1;
> gdcm::Attribute<0x0018,0x601e> atY1;
> atX0.SetFromDataElement( deX0 );
> atY0.SetFromDataElement( deY0 );
> atX1.SetFromDataElement( deX1 );
> atY1.SetFromDataElement( deY1 );
> const uint32_t* X0 = atX0.GetValues();
> const uint32_t* Y0 = atY0.GetValues();
> const uint32_t* X1 = atX1.GetValues();
> const uint32_t* Y1 = atY1.GetValues();
> //std::cout << X0 << std::endl << Y0 << std::endl << X1 << std::endl <<
> Y1 << std::endl;
>
> X_min = static_cast<unsigned int>(X0[0]);
> Y_min = static_cast<unsigned int>(Y0[0]);
> X_max = static_cast<unsigned int>(X1[0]);
> Y_max = static_cast<unsigned int>(Y1[0]);
>
> std::cout << "X_min = " << X_min << std::endl;
> std::cout << "Y_min = " << Y_min << std::endl;
> std::cout << "X_max = " << X_max << std::endl;
> std::cout << "Y_max = " << Y_max << std::endl;
>
> return true;
> }
>
>
>
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