Authors belong 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
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
#include <algorithm>
#include <QApplication>
-#include <gdcm.h>
-#include <gdcmSQItem.h>
+#include <gdcmFile.h>
+#if GDCM_MAJOR_VERSION == 2
+ #include <gdcmReader.h>
+ #include <gdcmTag.h>
+ #include <gdcmAttribute.h>
+#else
+ #include <gdcm.h>
+ #include <gdcmSQItem.h>
+#endif
#include <vtkSmartPointer.h>
#include <vtkAppendPolyData.h>
vvMesh::Pointer m=vvMesh::New();
m->ReadFromVTK(filename.c_str());
if (vf) m->propagateContour(vf);
- m->ComputeMasks(image->GetVTKImages()[0],true);
+ m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
result.push_back(m);
} else { //Read a Dicom-struct file
assert(selected_contours.size() > 0);
std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
{
assert(filename!="");
+ std::vector<std::pair<int, std::string> > roi_names;
+#if GDCM_MAJOR_VERSION == 2
+ // duplicate code from clitk::DicomRT_StructureSet::Read
+ gdcm::Reader reader;
+ reader.SetFileName( filename.c_str() );
+ reader.Read();
+
+ const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
+
+ 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();
+ if( nestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
+ {
+ 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]
+
+ roi_names.push_back(make_pair(nb,name));
+ }
+ }
+#else
gdcm::File reader;
reader.SetFileName(filename.c_str());
reader.SetMaxSizeLoadEntry(16384);
gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
assert(roi_info);
- std::vector<std::pair<int, std::string> > roi_names;
// DD("ici");
//int n=0;
for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
+#endif
return roi_names;
}
std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
{
+ std::vector<vvMesh::Pointer> result;
+#if GDCM_MAJOR_VERSION == 2
+ gdcm::Reader reader;
+ reader.SetFileName(filename.c_str());
+ reader.Read();
+
+ const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
+
+ gdcm::SmartPointer<gdcm::SequenceOfItems> rois = ds.GetDataElement(gdcm::Tag(0x3006,0x39)).GetValueAsSQ();
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_info = ds.GetDataElement(gdcm::Tag(0x3006,0x20)).GetValueAsSQ();
+ assert(rois); // TODO error message
+ assert(roi_info); // TODO error message
+ assert(rois->GetNumberOfItems() == roi_info->GetNumberOfItems());
+
+ for (unsigned ridx = 0; ridx < rois->GetNumberOfItems(); ++ridx)
+ {
+ vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
+ const gdcm::DataSet& ds_rois = rois->GetItem( ridx + 1).GetNestedDataSet();
+ const gdcm::DataSet& ds_roi_info = roi_info->GetItem( ridx + 1).GetNestedDataSet();
+
+ gdcm::Attribute<0x3006,0x84> roinumber;
+ roinumber.SetFromDataSet(ds_rois);
+ if (std::find(selected_contours.begin(), selected_contours.end(), roinumber.GetValue()) != selected_contours.end()) //Only read selected ROIs
+ {
+ gdcm::Attribute<0x3006,0x2a> trgb;
+ trgb.SetFromDataSet(ds_rois);
+ vvMesh::Pointer current_roi=vvMesh::New();
+ current_roi->r = trgb[0] / 255;
+ current_roi->g = trgb[1] / 255;
+ current_roi->b = trgb[2] / 255;
+
+ gdcm::Attribute<0x3006,0x26> tstructure_name;
+ tstructure_name.SetFromDataSet(ds_roi_info);
+ current_roi->structure_name = tstructure_name.GetValue();
+
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ds_rois.GetDataElement(gdcm::Tag(0x3006,0x40)).GetValueAsSQ();
+ double z0=-1; //Used to determine spacing between slices, assumed to be constant
+ for (unsigned j = 0; j < roi_seq->GetNumberOfItems(); ++j)
+ {
+ gdcm::Item & item_roi_seq = roi_seq->GetItem(j + 1); // Item starts at 1
+ const gdcm::DataSet& ds_roi_seq = item_roi_seq.GetNestedDataSet();
+ gdcm::Attribute<0x3006,0x42> tcontour_type;
+ tcontour_type.SetFromDataSet(ds_roi_seq);
+ std::string contour_type = tcontour_type.GetValue();
+ if (contour_type=="CLOSED_PLANAR ")
+ {
+ gdcm::Attribute<0x3006,0x46> tpoint_number;
+ tpoint_number.SetFromDataSet(ds_roi_seq);
+ const gdcm::DataElement & points_data = ds_roi_seq.GetDataElement(gdcm::Tag(0x3006,0x50));
+ gdcm::Attribute<0x3006,0x50> tpoints;
+ tpoints.SetFromDataElement(points_data);
+ assert(tpoints.GetNumberOfValues() == static_cast<unsigned int>(tpoint_number.GetValue()) * 3);
+ const double* points = tpoints.GetValues();
+ if (z0 == -1) //First contour
+ z0=points[2];
+ else
+ if (current_roi->GetSpacing()==-1 && points[2] != z0 )
+ current_roi->SetSpacing(points[2]-z0);
+ vtkPolyData * contour=vtkPolyData::New();
+ contour->Allocate(); //for cell structures
+ contour->SetPoints(vtkPoints::New());
+ vtkIdType ids[2];
+ for (unsigned idx = 0; idx < tpoints.GetNumberOfValues(); idx += 3)
+ {
+ contour->GetPoints()->InsertNextPoint(points[idx], points[idx+1], points[idx+2]);
+ ids[0] = idx / 3;
+ ids[1] = (ids[0] + 1) % tpoint_number.GetValue(); //0-1,1-2,...,n-1-0
+ contour->GetLines()->InsertNextCell(2, ids);
+ }
+ append->AddInput(contour);
+ }
+ else
+ if (contour_type == "POINT ")
+ ; // silently ignore POINT type since we don't need them at the moment
+ else
+ std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
+ }
+ append->Update();
+ current_roi->AddMesh(append->GetOutput());
+ result.push_back(current_roi);
+ }
+ else
+ {
+ //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
+ }
+ }
+#else
gdcm::File reader;
reader.SetFileName(filename.c_str());
reader.SetMaxSizeLoadEntry(16384);
reader.Load();
- std::vector<vvMesh::Pointer> result;
gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
///We need to iterate both on the contours themselves, and on the contour info
gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
}
k=roi_info->GetNextSQItem(); //increment the second loop variable
}
+#endif
return result;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff