- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
+ ===========================================================================**/
+
+// std
#include <algorithm>
+// qt
#include <QApplication>
+// gdcm
#include <gdcmFile.h>
-#if GDCM_MAJOR_VERSION == 2
- #include <gdcmReader.h>
- #include <gdcmTag.h>
- #include <gdcmAttribute.h>
+#if GDCM_MAJOR_VERSION >= 2
+#include <gdcmReader.h>
+#include <gdcmTag.h>
+#include <gdcmAttribute.h>
#else
- #include <gdcm.h>
- #include <gdcmSQItem.h>
+#include <gdcm.h>
+#include <gdcmSQItem.h>
#endif
+// vtk
+#include <vtkVersion.h>
#include <vtkSmartPointer.h>
#include <vtkAppendPolyData.h>
#include <vtkCellArray.h>
#include <vtkImageCast.h>
#include <vtkImageGaussianSmooth.h>
+// clitk
+#include "clitkCommon.h"
#include "clitkCommon.h"
+#include "clitkDicomRT_StructureSet.h"
#include "vvMeshReader.h"
#include "vvProgressDialog.h"
-#include <clitkCommon.h>
+//------------------------------------------------------------------------------
vvMeshReader::vvMeshReader() :
- vtk_mode(false)
+vtk_mode(false)
{}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvMeshReader::Update()
{
//Show a progress bar only when opening a DC-struct (ie. multiple contours)
qApp->processEvents();
}
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvMeshReader::run()
{
///Verify the important stuff has been set
}
}
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
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();
+#if CLITK_USE_SYSTEM_GDCM == 1
- 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) ) )
+ // Read RT-struct data
+ vtkSmartPointer<vtkGDCMPolyDataReader> areader = vtkGDCMPolyDataReader::New();
+ areader->SetFileName(filename.c_str());
+ areader->Update();
+
+ // get info on roi names
+ vtkRTStructSetProperties * p = areader->GetRTStructSetProperties();
+ int n = p->GetNumberOfStructureSetROIs();
+
+ for(unsigned int i=0; i<n; i++) {
+ std::string name = p->GetStructureSetROIName(i);
+ int nb = p->GetStructureSetROINumber(i);
+ roi_names.push_back(make_pair(nb,name));
+ }
+
+#else
+#if GDCM_MAJOR_VERSION >= 2
+
+ // duplicate code from clitk::DicomRT_StructureSet::Read
+ gdcm::Reader * reader = new gdcm::Reader;
+ reader->SetFileName( filename.c_str() );
+ reader->Read();
+
+ const gdcm::DataSet &ds = reader->GetFile().GetDataSet();
+
+ // Check file type
+ //Verify if the file is a RT-Structure-Set dicom file
+ gdcm::File * mFile = &(reader->GetFile());
+ gdcm::MediaStorage ms;
+ ms.SetFromFile(*mFile);
+ if( ms != gdcm::MediaStorage::RTStructureSetStorage )
{
- 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));
+ 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);
+ }
+
+ gdcm::Attribute<0x20,0x10> studyid;
+ studyid.SetFromDataSet( ds );
+
+ gdcm::Tag tssroisq(0x3006,0x0020);
+ // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
+ bool b = ds.FindDataElement(tssroisq);
+ if (!b) { // FIXME
+ clitkExceptionMacro("Error: tag 0x3006,0x0020 [ Structure Set ROI Sequence ] not found");
}
+
+ const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
+ assert(roi_seq); // FIXME 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::Item & sitem = roi_seq->GetItem(ridx+1); // Item start at #1
+
+ const gdcm::DataSet& snestedds = sitem.GetNestedDataSet();
+ const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+
+ if( snestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
+ {
+ // const gdcm::DataElement & a = nestedds.GetDataElement(gdcm::Tag(0x3006,0x26));
+ // DD(a.GetValue());
+
+ gdcm::Attribute<0x3006,0x26> roiname;
+ roiname.SetFromDataSet( snestedds );
+ std::string name = roiname.GetValue(); // 0x3006,0x0026 = [ROI Name]
+ gdcm::Attribute<0x3006,0x0022> roinumber;
+ roinumber.SetFromDataSet( snestedds );
+ int nb = roinumber.GetValue(); // 0x3006,0x0022 = [ROI Number]
+
+ roi_names.push_back(make_pair(nb,name));
+ }
+ }
+
+ delete reader;
+
#else
gdcm::File reader;
reader.SetFileName(filename.c_str());
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
+#endif
+
return roi_names;
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
{
std::vector<vvMesh::Pointer> result;
-#if GDCM_MAJOR_VERSION == 2
+#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] / 255.0;
+ current_roi->g = trgb[1] / 255.0;
+ current_roi->b = trgb[2] / 255.0;
+
+ 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);
+ }
+#if VTK_MAJOR_VERSION <= 5
+ append->AddInput(contour);
+#else
+ append->AddInputData(contour);
+#endif
+ }
+ 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());
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff