[ITK-users] [Insight-users] GDCM custom tag dictionary

[Harnish, Roy]

Hi,

I'm revisiting the thread below since I'm having trouble getting the DicomImageReadPrintTags.cxx example to use the .dic file I provide. I am trying to correctly interpret the (0119,1030) tag from a dicom file.  The element is very similar to an ImageOrientationPatient, but defines direction cosines for slices in addition to rows and columns. I'm wondering if I should continue trying to specify my own .dic (or is it XML?), of if there is an alternative. Perhaps I could try to parse the output ((0119|1030)  is: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==) as a 9 element DS. Syntax suggestions for that would be much appreciated.

Yours,

Roy


This is a comparison of dcmdumps:

cbl-mbp-3369:data rharnish$ dcmdump dce.dcm | grep 0119,1030
(0119,1030) DS [-1\-0\0\-0\-1\0\0\0\1]                  #  22, 9 Unknown Tag & Data
cbl-mbp-3369:data rharnish$ dcmdump dce.dcm | grep ImageOri
(0020,0037) DS [-1\-0\0\-0\-1\0]                        #  16, 6 ImageOrientationPatient
cbl-mbp-3369:data rharnish$ 


This is the modified version of DicomImageReadPrintTags.cxx I'm using:

#include "itkImageFileReader.h"
#include "itkGDCMImageIO.h"
#include "itkMetaDataObject.h"

#include "gdcmGlobal.h"

int
main (int argc, char* argv[])
{
  if (argc < 2)
    {
      std::cerr << "Usage: " << argv[0] << " DicomFile [user defined dict]" << std::endl;
      return EXIT_FAILURE;
    }

  typedef unsigned short PixelType;
  const unsigned int Dimension = 3;

  typedef itk::Image<PixelType, Dimension> ImageType;

  if (argc == 3)
    {
      // Specify a path where XML dicts can be found (Part 3/4 & 6)
      gdcm::Global::GetInstance ().Prepend (itksys::SystemTools::GetFilenamePath (argv[2]).c_str ());
      // Load them !
      gdcm::Global::GetInstance ().LoadResourcesFiles ();

      std::cout << argv[2] << std::endl;
      std::cout << itksys::SystemTools::GetFilenamePath (argv[2]).c_str () << std::endl;
    }

  typedef itk::ImageFileReader<ImageType> ReaderType;
  ReaderType::Pointer reader = ReaderType::New ();
  typedef itk::GDCMImageIO ImageIOType;
  ImageIOType::Pointer dicomIO = ImageIOType::New ();
  dicomIO->LoadSequencesOn ();
  dicomIO->LoadPrivateTagsOn ();

  reader->SetFileName (argv[1]);
  reader->SetImageIO (dicomIO);

  try
    {
      reader->Update ();
    }
  catch (itk::ExceptionObject &ex)
    {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
    }

  std::cout << "has key: " << dicomIO->GetMetaDataDictionary ().HasKey ("0119|1030") << std::endl;

  typedef itk::MetaDataDictionary DictionaryType;
  const DictionaryType & dictionary = dicomIO->GetMetaDataDictionary ();
  typedef itk::MetaDataObject<std::string> MetaDataStringType;

  DictionaryType::ConstIterator itr = dictionary.Begin ();
  DictionaryType::ConstIterator end = dictionary.End ();

  // try to print value of 0119|1030
  std::string entryId = "0119|1030";
  DictionaryType::ConstIterator tagItr = dictionary.Find (entryId);
  if (tagItr != end)
    {
      MetaDataStringType::ConstPointer entryvalue = dynamic_cast<const MetaDataStringType *> (tagItr->second.GetPointer ());

      if (entryvalue)
	{
	  std::string tagvalue = entryvalue->GetMetaDataObjectValue ();
	  std::cout << "(" << entryId << ") ";
	  std::cout << " is: " << tagvalue.c_str () << std::endl;
	}

    }

  // try to print value of ImageOrientationPatient
  entryId = "0020|0037";
  tagItr = dictionary.Find (entryId);
  if (tagItr != end)
    {
      MetaDataStringType::ConstPointer entryvalue = dynamic_cast<const MetaDataStringType *> (tagItr->second.GetPointer ());

      if (entryvalue)
	{
	  std::string tagvalue = entryvalue->GetMetaDataObjectValue ();
	  std::cout << "(" << entryId << ") ";
	  std::cout << " is: " << tagvalue.c_str () << std::endl;
	}

    }

  return EXIT_SUCCESS;
}


This is the program output:

/Users/rharnish/Projects/itkImageProcessing/io/DicomTags/data/test.dic
/Users/rharnish/Projects/itkImageProcessing/io/DicomTags/data
has key: 1
(0119|1030)  is: LTFcLTBcMFwtMFwtMVwwXDBcMFwxIA==
(0020|0037)  is: -1\-0\0\-0\-1\0


This is the contents of test.dic:

0119 1030 DS 9 3DDirectionCosines






Angela.Y Wang wrote:
> I am trying to read processed data in dicom file format and would like
> to create a GDCM dictionary for the private tags.  In a previous
> message, it was suggested to create a custom tag dictionary and put it
> in the GDCM search path.  Could somebody please tell me how to go about
> doing this?


Hi Angela,

	I have added an example on how to user dynamically loaded user defined 
DICOM dictionary:

$ cvs ci -m"ENH: Add example on how to use a user defined dict" 

/cvsroot/Insight/Insight/Examples/IO/DicomImageReadPrintTags.cxx,v  <-- 
  DicomImageReadPrintTags.cxx
new revision: 1.16; previous revision: 1.15
/cvsroot/Insight/Insight/Examples/IO/itk.dic,v  <--  itk.dic
initial revision: 1.1


	You should be able to now type in:

$ ./bin/DicomImageReadPrintTags /path/to/012345.002.050 
/path/to/Insight/Examples/IO/itk.dic

First argument is the DICOM file, second (optional) argument is a user 
defined dictionary which should look like:

http://public.kitware.com/cgi-bin/viewcvs.cgi/*checkout*/Examples/IO/itk.dic?rev=1.1&root=Insight

HTH
Mathieu