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mitkDicomSeriesReader.patch
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• santos
Jul 1 2010, 1:27 PM
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4 KB
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mitkDicomSeriesReader.patch
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Index: mitk/Core/Code/IO/mitkDicomSeriesReader.txx
===================================================================
--- mitk/Core/Code/IO/mitkDicomSeriesReader.txx (revision 24101)
+++ mitk/Core/Code/IO/mitkDicomSeriesReader.txx (working copy)
@@ -22,27 +22,77 @@
#include <itkImageSeriesReader.h>
+#include <gdcmSorter.h>
+#include <gdcmScanner.h>
+
namespace mitk
{
template <typename PixelType>
void DicomSeriesReader::LoadDicom(const StringContainer &filenames, DataNode &node)
{
- typedef itk::Image<PixelType, 3> ImageType;
+ typedef itk::Image<PixelType, 4> ImageType;
typedef itk::ImageSeriesReader<ImageType> ReaderType;
+ /******** Workaround for 4D data ***************/
+ gdcm::Sorter sorter;
+
+ sorter.SetSortFunction(DicomSeriesReader::GdcmSortFunction);
+ sorter.Sort(filenames);
+
+ gdcm::Tag acq_time(0x0008,0x0032);
+ gdcm::Scanner scanner;
+
+ scanner.AddTag(acq_time);
+ scanner.Scan(sorter.GetFilenames());
+
+ std::list<StringContainer> decomposed_filenames;
+ const StringContainer::const_iterator f_end = sorter.GetFilenames().end();
+ const char *act_value = scanner.GetValue(sorter.GetFilenames().front().c_str(), acq_time);
+ unsigned int volume_count = 1u;
+
+ decomposed_filenames.push_back(StringContainer());
+ decomposed_filenames.back().push_back(sorter.GetFilenames().front());
+
+ for (StringContainer::const_iterator f_it = ++sorter.GetFilenames().begin(); f_it != f_end; ++f_it)
+ {
+ const char *value = scanner.GetValue(f_it->c_str(), acq_time);
+
+ if (strcmp(act_value, value))
+ {
+ act_value = value;
+ decomposed_filenames.push_back(StringContainer());
+ ++volume_count;
+ }
+
+ decomposed_filenames.back().push_back(*f_it);
+ }
+ /******** End: Workaround for 4D data **********/
+
DcmIoType::Pointer io = DcmIoType::New();
typename ReaderType::Pointer reader = ReaderType::New();
- reader->SetFileNames(filenames);
reader->SetImageIO(io);
reader->ReverseOrderOff();
- reader->Update();
+ const std::list<StringContainer>::const_iterator df_end = decomposed_filenames.end();
mitk::Image::Pointer image = mitk::Image::New();
+ unsigned int act_volume = 1u;
- image->InitializeByItk(reader->GetOutput());
- image->SetImportVolume(reader->GetOutput()->GetBufferPointer());
+ reader->SetFileNames(decomposed_filenames.front());
+ reader->Update();
+ image->InitializeByItk(reader->GetOutput(), 1, volume_count);
+ image->SetImportVolume(reader->GetOutput()->GetBufferPointer(), 0u);
+
+ MITK_INFO << "Volume dimension: [" << image->GetDimension(0) << ", " << image->GetDimension(1) << ", " << image->GetDimension(2) << ", " << image->GetDimension(3) << "]";
+
+ for (std::list<StringContainer>::iterator df_it = ++decomposed_filenames.begin(); df_it != df_end; ++df_it)
+ {
+ reader->SetFileNames(*df_it);
+ reader->Update();
+ image->SetImportVolume(reader->GetOutput()->GetBufferPointer(), act_volume++);
+ }
+
node.SetData(image);
}
Index: mitk/Core/Code/IO/mitkDicomSeriesReader.h
===================================================================
--- mitk/Core/Code/IO/mitkDicomSeriesReader.h (revision 24111)
+++ mitk/Core/Code/IO/mitkDicomSeriesReader.h (working copy)
@@ -27,6 +27,8 @@
#include <itkDICOMImageIO2.h>
#endif
+#include <gdcmDataSet.h>
+
namespace mitk
{
@@ -94,6 +96,12 @@
*/
template <typename PixelType>
static void LoadDicom(const StringContainer &filenames, DataNode &node);
+
+ /*
+ * Auxiliary sort function for Gdcm Dicom sorting. It is used for sorting
+ * 4D Dicom data.
+ */
+ static bool GdcmSortFunction(const gdcm::DataSet &ds1, const gdcm::DataSet &ds2);
};
}
Index: mitk/Core/Code/IO/mitkDicomSeriesReader.cpp
===================================================================
--- mitk/Core/Code/IO/mitkDicomSeriesReader.cpp (revision 24101)
+++ mitk/Core/Code/IO/mitkDicomSeriesReader.cpp (working copy)
@@ -19,6 +19,8 @@
#include <itkGDCMSeriesFileNames.h>
+#include <gdcmAttribute.h>
+
namespace mitk
{
@@ -151,5 +153,27 @@
return name_generator->GetFileNames(series_uid);
}
+bool DicomSeriesReader::GdcmSortFunction(const gdcm::DataSet &ds1, const gdcm::DataSet &ds2)
+{
+ gdcm::Attribute<0x0008,0x0032> acq_time1; // Acquisition time
+ gdcm::Attribute<0x0020,0x0032> image_pos1; // Image Position (Patient)
+
+ acq_time1.Set(ds1);
+ image_pos1.Set(ds1);
+
+ gdcm::Attribute<0x0008,0x0032> acq_time2;
+ gdcm::Attribute<0x0020,0x0032> image_pos2;
+
+ acq_time2.Set(ds2);
+ image_pos2.Set(ds2);
+
+ if (acq_time1 == acq_time2)
+ {
+ return image_pos1 < image_pos2;
+ }
+
+ return acq_time1 < acq_time2;
+}
+
}

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mitkDicomSeriesReader.patch (4 KB)

Event Timeline

• santos added a comment.Jul 1 2010, 1:27 PM

Modifications to DicomSeriesReader in order to make it 4D compatible.

MITK · MIC · IMSY · DKFZ