Authors belongs to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
#include "clitkDicomRT_StructureSet.h"
#include <vtksys/SystemTools.hxx>
+#include "gdcmFile.h"
+#if GDCM_MAJOR_VERSION == 2
+#include "gdcmReader.h"
+#include "gdcmAttribute.h"
+#endif
//--------------------------------------------------------------------
clitk::DicomRT_StructureSet::DicomRT_StructureSet()
//--------------------------------------------------------------------
clitk::DicomRT_StructureSet::~DicomRT_StructureSet()
{
- for(uint i=0; i<mListOfROI.size(); i++) {
- delete mListOfROI[i];
- }
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::vector<clitk::DicomRT_ROI*> & clitk::DicomRT_StructureSet::GetListOfROI() const
+const std::vector<clitk::DicomRT_ROI::Pointer> & clitk::DicomRT_StructureSet::GetListOfROI() const
{
return mListOfROI;
}
void clitk::DicomRT_StructureSet::Read(const std::string & filename)
{
// Open DICOM
+#if GDCM_MAJOR_VERSION == 2
+ gdcm::Reader reader;
+ reader.SetFileName(filename.c_str());
+ reader.Read();
+
+ const gdcm::File & file = reader.GetFile();
+ const gdcm::DataSet & ds = file.GetDataSet();
+
+ // Check file type
+ //Verify if the file is a RT-Structure-Set dicom file
+ gdcm::MediaStorage ms;
+ ms.SetFromFile(file);
+ if( ms != gdcm::MediaStorage::RTStructureSetStorage )
+ {
+ std::cerr << "Error. the file " << filename
+ << " is not a Dicom Struct ? (must have a SOP Class UID [0008|0016] = 1.2.840.10008.5.1.4.1.1.481.3 ==> [RT Structure Set Storage])"
+ << std::endl;
+ exit(0);
+ }
+
+ gdcm::Attribute<0x8,0x60> modality;
+ modality.SetFromDataSet( ds );
+ if( modality.GetValue() != "RTSTRUCT" )
+ {
+ std::cerr << "Error. the file " << filename
+ << " is not a Dicom Struct ? (must have 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])"
+ << std::endl;
+ exit(0);
+ }
+
+ // Read global info
+ gdcm::Attribute<0x20,0x10> studyid;
+ studyid.SetFromDataSet( ds );
+ gdcm::Attribute<0x8,0x20> studytime;
+ studytime.SetFromDataSet( ds );
+ gdcm::Attribute<0x8,0x30> studydate;
+ studydate.SetFromDataSet( ds );
+ gdcm::Attribute<0x3006,0x02> label;
+ label.SetFromDataSet( ds );
+ gdcm::Attribute<0x3006,0x04> atname;
+ atname.SetFromDataSet( ds );
+ gdcm::Attribute<0x3006,0x09> time;
+ time.SetFromDataSet( ds );
+
+ mStudyID = studyid.GetValue();
+ mStudyTime = studytime.GetValue();
+ mStudyDate = studydate.GetValue();
+ mLabel = label.GetValue();
+ mName = atname.GetValue();
+ mTime = time.GetValue();
+
+ //----------------------------------
+ // Read all ROI Names and number
+ // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
+ gdcm::Tag tssroisq(0x3006,0x0020);
+ const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
+ assert(roi_seq); // TODO error message
+ for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
+ {
+ gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
+ const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+
+ gdcm::Attribute<0x3006,0x26> roiname;
+ roiname.SetFromDataSet( nestedds );
+ std::string name = roiname.GetValue(); // 0x3006,0x0026 = [ROI Name]
+ gdcm::Attribute<0x3006,0x0022> roinumber;
+ roinumber.SetFromDataSet( nestedds );
+ int nb = roinumber.GetValue(); // 0x3006,0x0022 = [ROI Number]
+ // Change number if needed
+
+ //TODO
+
+ // Check if such a number already exist
+ if (mMapOfROIName.find(nb) != mMapOfROIName.end()) {
+ std::cerr << "WARNING. A Roi already exist with the number "
+ << nb << ". I replace." << std::endl;
+ }
+ // Add in map
+ mMapOfROIName[nb] = name;
+ }
+ // DD(mMapOfROIName.size());
+
+ //----------------------------------
+ // Read all ROI
+ // 0x3006,0x0039 = [ ROI Contour Sequence ]
+ gdcm::Tag troicsq(0x3006,0x0039);
+ const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_contour_seq = roicsq.GetValueAsSQ();
+ assert(roi_contour_seq); // TODO error message
+ int n=0;
+ for(unsigned int ridx = 0; ridx < roi_contour_seq->GetNumberOfItems(); ++ridx)
+ {
+ gdcm::Item & item = roi_contour_seq->GetItem( ridx + 1); // Item starts at 1
+
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
+ roi->Read(mMapOfROIName, item);
+ mListOfROI.push_back(roi);
+ mMapOfROIIndex[roi->GetROINumber()] = n;
+ n++;
+ }
+
+#else
gdcm::File reader;
reader.SetFileName(filename.c_str());
reader.SetMaxSizeLoadEntry(16384); // Needed ...
mStudyTime = reader.GetValEntry(0x008,0x0020)->GetValue();
mStudyDate = reader.GetValEntry(0x008,0x0030)->GetValue();
mLabel = reader.GetValEntry(0x3006,0x002)->GetValue();
- mName = reader.GetValEntry(0x3006,0x004)->GetValue();
+ if (!reader.GetValEntry(0x3006,0x004)) {
+ mName = "Anonymous";
+ }
+ else {
+ mName = reader.GetValEntry(0x3006,0x004)->GetValue();
+ }
mTime = reader.GetValEntry(0x3006,0x009)->GetValue();
//----------------------------------
assert(roi_contour_seq); // TODO error message
int n=0;
for (gdcm::SQItem* r=roi_contour_seq->GetFirstSQItem(); r!=0; r=roi_contour_seq->GetNextSQItem()) {
- DicomRT_ROI * roi = new DicomRT_ROI;
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
roi->Read(mMapOfROIName, r);
mListOfROI.push_back(roi);
mMapOfROIIndex[roi->GetROINumber()] = n;
n++;
}
+#endif
}
//--------------------------------------------------------------------
color.push_back(0);
// Create ROI
- DicomRT_ROI * roi = new DicomRT_ROI;
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
roi->SetFromBinaryImage(im, max, oss.str(), color, n);
mListOfROI.push_back(roi);
mMapOfROIIndex[mListOfROI.size()-1] = max;
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff