X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvMeshReader.cxx;h=0feabf3fac5dc8123b5c12b4f468ebf2c97432bd;hb=93f793e07c285d87a02d72864cf11c13adf4a304;hp=152a9a3860e1758ebf74abb64ee22b0b6f7e0a93;hpb=7fb3f08a03ea03edb40f5e73d59381c5a92935fb;p=clitk.git diff --git a/vv/vvMeshReader.cxx b/vv/vvMeshReader.cxx index 152a9a3..0feabf3 100644 --- a/vv/vvMeshReader.cxx +++ b/vv/vvMeshReader.cxx @@ -3,7 +3,7 @@ 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 @@ -14,14 +14,27 @@ - BSD See included LICENSE.txt file - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html -======================================================================-====*/ + ===========================================================================**/ + +// std #include +// qt #include +// gdcm +#include +#if GDCM_MAJOR_VERSION == 2 +#include +#include +#include +#else #include #include +#endif +// vtk +#include #include #include #include @@ -32,15 +45,21 @@ #include #include +// clitk +#include "clitkCommon.h" #include "clitkCommon.h" +#include "clitkDicomRT_StructureSet.h" #include "vvMeshReader.h" #include "vvProgressDialog.h" -#include +//------------------------------------------------------------------------------ vvMeshReader::vvMeshReader() : - vtk_mode(false) +vtk_mode(false) {} +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ void vvMeshReader::Update() { //Show a progress bar only when opening a DC-struct (ie. multiple contours) @@ -52,7 +71,10 @@ void vvMeshReader::Update() qApp->processEvents(); } } +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ void vvMeshReader::run() { ///Verify the important stuff has been set @@ -61,7 +83,7 @@ void vvMeshReader::run() 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); @@ -76,10 +98,107 @@ void vvMeshReader::run() } } } +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ std::vector > vvMeshReader::GetROINames() { assert(filename!=""); + std::vector > roi_names; + +#if CLITK_USE_SYSTEM_GDCM == 1 + + // Read RT-struct data + vtkSmartPointer 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; iGetStructureSetROIName(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 ) + { + 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 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()); reader.SetMaxSizeLoadEntry(16384); @@ -87,23 +206,118 @@ std::vector > vvMeshReader::GetROINames() gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020); assert(roi_info); - std::vector > 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 +#endif + return roi_names; } +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ std::vector vvMeshReader::readSelectedContours() { + std::vector 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 rois = ds.GetDataElement(gdcm::Tag(0x3006,0x39)).GetValueAsSQ(); + gdcm::SmartPointer 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 append=vtkSmartPointer::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 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(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()); reader.SetMaxSizeLoadEntry(16384); reader.Load(); - std::vector 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); @@ -160,6 +374,7 @@ std::vector vvMeshReader::readSelectedContours() } k=roi_info->GetNextSQItem(); //increment the second loop variable } +#endif return result; }