From 3d1a811fcee80cb36cb8938a529d69c482f4fea2 Mon Sep 17 00:00:00 2001 From: David Sarrut Date: Fri, 3 Feb 2012 07:57:12 +0100 Subject: [PATCH] Replace old gdcm code with vtkGDCMPolyData --- vv/vvMeshReader.cxx | 300 ++++++++++++++++++++++++++++++-------------- 1 file changed, 205 insertions(+), 95 deletions(-) diff --git a/vv/vvMeshReader.cxx b/vv/vvMeshReader.cxx index 040ba50..736dbcf 100644 --- a/vv/vvMeshReader.cxx +++ b/vv/vvMeshReader.cxx @@ -14,21 +14,26 @@ - 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 +#include +#include +#include #else - #include - #include +#include +#include #endif +// vtk #include #include #include @@ -39,17 +44,25 @@ #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() { + DD("vvMeshReader::Update"); + //Show a progress bar only when opening a DC-struct (ie. multiple contours) vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1)); this->start(); @@ -59,7 +72,10 @@ void vvMeshReader::Update() qApp->processEvents(); } } +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ void vvMeshReader::run() { ///Verify the important stuff has been set @@ -83,39 +99,130 @@ void vvMeshReader::run() } } } +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ std::vector > vvMeshReader::GetROINames() { assert(filename!=""); std::vector > roi_names; + DD(GDCM_MAJOR_VERSION); + DD(CLITK_USE_SYSTEM_GDCM); + #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(); + // Read RT-struct data + DD("before read"); + vtkSmartPointer reader = vtkGDCMPolyDataReader::New(); + reader->SetFileName(filename.c_str()); + reader->Update(); + DD("after read"); - gdcm::Tag tssroisq(0x3006,0x0020); - const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq ); - gdcm::SmartPointer 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) ) ) + // get info on roi names + vtkRTStructSetProperties * p = reader->GetRTStructSetProperties(); + DD(p->GetNumberOfStructureSetROIs()); + DD(p->GetStructureSetROIName(0)); + DD(p->GetStructureSetROINumber(0)); + int n = p->GetNumberOfStructureSetROIs(); + DD(n); + + for(unsigned int i=0; iGetStructureSetROIName(i); + int nb = p->GetStructureSetROINumber(i); + roi_names.push_back(make_pair(nb,name)); + } + + // ==================== + + if (false) { + // duplicate code from clitk::DicomRT_StructureSet::Read + gdcm::Reader * reader = new gdcm::Reader; + reader->SetFileName( filename.c_str() ); + reader->Read(); + DD("after gdcm read"); + + const gdcm::DataSet &ds = reader->GetFile().GetDataSet(); + + DD("after ds"); + DD(ds.IsEmpty()); + + // 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" ) { - 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 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])" + << std::endl; + exit(0); } + + gdcm::Attribute<0x20,0x10> studyid; + studyid.SetFromDataSet( ds ); + DD(studyid.GetValue()); + + 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 ); + DD("after ssroisq"); + gdcm::SmartPointer roi_seq = ssroisq.GetValueAsSQ(); + assert(roi_seq); // FIXME error message + + DD(roi_seq->GetNumberOfItems()); + + for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx) + { + DD(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(); + + DD(nestedds.IsEmpty()); + + if( snestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) ) + { + DD("tag found"); + // 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] + DD(name); + gdcm::Attribute<0x3006,0x0022> roinumber; + roinumber.SetFromDataSet( snestedds ); + int nb = roinumber.GetValue(); // 0x3006,0x0022 = [ROI Number] + DD(nb); + + roi_names.push_back(make_pair(nb,name)); + } + } + + delete reader; + + } + #else gdcm::File reader; reader.SetFileName(filename.c_str()); @@ -132,7 +239,10 @@ std::vector > vvMeshReader::GetROINames() #endif return roi_names; } +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ std::vector vvMeshReader::readSelectedContours() { std::vector result; @@ -150,77 +260,77 @@ std::vector vvMeshReader::readSelectedContours() 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; + 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<0x3006,0x26> tstructure_name; - tstructure_name.SetFromDataSet(ds_roi_info); - current_roi->structure_name = tstructure_name.GetValue(); + 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::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<0x3006,0x26> 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); + } + 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 { - 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); - } - append->AddInput(contour); + //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl; } - 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()); -- 2.45.1