vv/vvMeshReader.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18 #include <algorithm>
  19
  20 #include <QApplication>
  21
  22 #include <gdcmFile.h>
  23 #if GDCM_MAJOR_VERSION == 2
  24   #include <gdcmReader.h>
  25   #include <gdcmTag.h>
  26   #include <gdcmAttribute.h>
  27 #else
  28   #include <gdcm.h>
  29   #include <gdcmSQItem.h>
  30 #endif
  31
  32 #include <vtkSmartPointer.h>
  33 #include <vtkAppendPolyData.h>
  34 #include <vtkCellArray.h>
  35 #include <vtkMetaImageWriter.h>
  36 #include <vtkMetaImageReader.h>
  37 #include <vtkPolyDataWriter.h>
  38 #include <vtkImageData.h>
  39 #include <vtkImageCast.h>
  40 #include <vtkImageGaussianSmooth.h>
  41
  42 #include "clitkCommon.h"
  43 #include "vvMeshReader.h"
  44 #include "vvProgressDialog.h"
  45 #include <clitkCommon.h>
  46
  47 vvMeshReader::vvMeshReader() :
  48   vtk_mode(false)
  49 {}
  50
  51 void vvMeshReader::Update()
  52 {
  53   //Show a progress bar only when opening a DC-struct (ie. multiple contours)
  54   vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
  55   this->start();
  56   while (this->isRunning()) {
  57     progress.SetProgress(result.size(),selected_contours.size());
  58     this->wait(50);
  59     qApp->processEvents();
  60   }
  61 }
  62
  63 void vvMeshReader::run()
  64 {
  65   ///Verify the important stuff has been set
  66   assert(filename != "");
  67   if (vtk_mode) { //Read vtkPolyData
  68     vvMesh::Pointer m=vvMesh::New();
  69     m->ReadFromVTK(filename.c_str());
  70     if (vf) m->propagateContour(vf);
  71     m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
  72     result.push_back(m);
  73   } else { //Read a Dicom-struct file
  74     assert(selected_contours.size() > 0);
  75     assert(image);
  76     std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
  77     for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
  78          i!=contour_stacks.end(); i++) {
  79       (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
  80       (*i)->ComputeMeshes();
  81       if (vf) (*i)->propagateContour(vf);
  82       result.push_back(*i);
  83     }
  84   }
  85 }
  86
  87 std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
  88 {
  89   assert(filename!="");
  90   std::vector<std::pair<int, std::string> > roi_names;
  91 #if GDCM_MAJOR_VERSION == 2
  92   // duplicate code from  clitk::DicomRT_StructureSet::Read
  93   gdcm::Reader reader;
  94   reader.SetFileName( filename.c_str() );
  95   reader.Read();
  96
  97   const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
  98
  99   gdcm::Tag tssroisq(0x3006,0x0020);
 100   const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
 101   gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
 102   assert(roi_seq); // TODO error message
 103   for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
 104     {
 105     gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
 106     const gdcm::DataSet& nestedds = item.GetNestedDataSet();
 107     if( nestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
 108       {
 109       gdcm::Attribute<0x3006,0x26> roiname;
 110       roiname.SetFromDataSet( nestedds );
 111       std::string name = roiname.GetValue();      // 0x3006,0x0026 = [ROI Name]
 112       gdcm::Attribute<0x3006,0x0022> roinumber;
 113       roinumber.SetFromDataSet( nestedds );
 114       int nb = roinumber.GetValue();  // 0x3006,0x0022 = [ROI Number]
 115
 116       roi_names.push_back(make_pair(nb,name));
 117       }
 118     }
 119 #else
 120   gdcm::File reader;
 121   reader.SetFileName(filename.c_str());
 122   reader.SetMaxSizeLoadEntry(16384);
 123   reader.Load();
 124
 125   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 126   assert(roi_info);
 127   // DD("ici");
 128   //int n=0;
 129   for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
 130     if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
 131       roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
 132 #endif
 133   return roi_names;
 134 }
 135
 136 std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
 137 {
 138   std::vector<vvMesh::Pointer> result;
 139 #if GDCM_MAJOR_VERSION == 2
 140   gdcm::Reader reader;
 141   reader.SetFileName(filename.c_str());
 142   reader.Read();
 143
 144   const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
 145
 146   gdcm::SmartPointer<gdcm::SequenceOfItems> rois = ds.GetDataElement(gdcm::Tag(0x3006,0x39)).GetValueAsSQ();
 147   gdcm::SmartPointer<gdcm::SequenceOfItems> roi_info = ds.GetDataElement(gdcm::Tag(0x3006,0x20)).GetValueAsSQ();
 148   assert(rois); // TODO error message
 149   assert(roi_info); // TODO error message
 150   assert(rois->GetNumberOfItems() == roi_info->GetNumberOfItems());
 151
 152   for (unsigned ridx = 0; ridx < rois->GetNumberOfItems(); ++ridx)
 153   {
 154     vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
 155     const gdcm::DataSet& ds_rois = rois->GetItem( ridx + 1).GetNestedDataSet();
 156     const gdcm::DataSet& ds_roi_info = roi_info->GetItem( ridx + 1).GetNestedDataSet();
 157
 158     gdcm::Attribute<0x3006,0x84> roinumber;
 159     roinumber.SetFromDataSet(ds_rois);
 160     if (std::find(selected_contours.begin(), selected_contours.end(), roinumber.GetValue()) != selected_contours.end()) //Only read selected ROIs
 161     {
 162       gdcm::Attribute<0x3006,0x2a> trgb;
 163       trgb.SetFromDataSet(ds_rois);
 164       vvMesh::Pointer current_roi=vvMesh::New();
 165       current_roi->r = trgb[0] / 255;
 166       current_roi->g = trgb[1] / 255;
 167       current_roi->b = trgb[2] / 255;
 168
 169       gdcm::Attribute<0x3006,0x26> tstructure_name;
 170       tstructure_name.SetFromDataSet(ds_roi_info);
 171       current_roi->structure_name = tstructure_name.GetValue();
 172
 173       gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ds_rois.GetDataElement(gdcm::Tag(0x3006,0x40)).GetValueAsSQ();
 174       double z0=-1; //Used to determine spacing between slices, assumed to be constant
 175       for (unsigned j = 0; j < roi_seq->GetNumberOfItems(); ++j)
 176       {
 177         gdcm::Item & item_roi_seq = roi_seq->GetItem(j + 1); // Item starts at 1
 178         const gdcm::DataSet& ds_roi_seq = item_roi_seq.GetNestedDataSet();
 179         gdcm::Attribute<0x3006,0x42> tcontour_type;
 180         tcontour_type.SetFromDataSet(ds_roi_seq);
 181         std::string contour_type = tcontour_type.GetValue();
 182         if (contour_type=="CLOSED_PLANAR ")
 183         {
 184           gdcm::Attribute<0x3006,0x46> tpoint_number;
 185           tpoint_number.SetFromDataSet(ds_roi_seq);
 186           const gdcm::DataElement & points_data = ds_roi_seq.GetDataElement(gdcm::Tag(0x3006,0x50));
 187           gdcm::Attribute<0x3006,0x50> tpoints;
 188           tpoints.SetFromDataElement(points_data);
 189           assert(tpoints.GetNumberOfValues() == static_cast<unsigned int>(tpoint_number.GetValue()) * 3);
 190           const double* points = tpoints.GetValues();
 191           if (z0 == -1) //First contour
 192             z0=points[2];
 193           else
 194             if (current_roi->GetSpacing()==-1 && points[2] != z0 )
 195               current_roi->SetSpacing(points[2]-z0);
 196           vtkPolyData * contour=vtkPolyData::New();
 197           contour->Allocate(); //for cell structures
 198           contour->SetPoints(vtkPoints::New());
 199           vtkIdType ids[2];
 200           for (unsigned idx = 0; idx < tpoints.GetNumberOfValues(); idx += 3)
 201           {
 202             contour->GetPoints()->InsertNextPoint(points[idx], points[idx+1], points[idx+2]);
 203             ids[0] = idx / 3;
 204             ids[1] = (ids[0] + 1) % tpoint_number.GetValue(); //0-1,1-2,...,n-1-0
 205             contour->GetLines()->InsertNextCell(2, ids);
 206           }
 207           append->AddInput(contour);
 208         }
 209         else
 210           if (contour_type == "POINT ")
 211           ; // silently ignore POINT type since we don't need them at the moment
 212           else
 213             std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
 214       }
 215       append->Update();
 216       current_roi->AddMesh(append->GetOutput());
 217       result.push_back(current_roi);
 218     }
 219     else
 220     {
 221     //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
 222     }
 223   }
 224 #else
 225   gdcm::File reader;
 226   reader.SetFileName(filename.c_str());
 227   reader.SetMaxSizeLoadEntry(16384);
 228   reader.Load();
 229
 230   gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
 231   ///We need to iterate both on the contours themselves, and on the contour info
 232   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 233   gdcm::SQItem* k=roi_info->GetFirstSQItem();
 234   for(gdcm::SQItem* i=rois->GetFirstSQItem(); i!=0; i=rois->GetNextSQItem()) { //loop over ROIS
 235     assert(k!=0);
 236     vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
 237     std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
 238     int roi_number;
 239     ss >> roi_number;
 240     if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
 241       vvMesh::Pointer current_roi=vvMesh::New();
 242       std::vector<double> rgb=clitk::parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
 243       assert(rgb.size()==3);
 244       current_roi->r=rgb[0]/255;
 245       current_roi->g=rgb[1]/255;
 246       current_roi->b=rgb[2]/255;
 247       current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
 248       gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
 249       double z0=-1; //Used to determine spacing between slices, assumed to be constant
 250       for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
 251         std::string contour_type=j->GetEntryValue(0x3006,0x0042);
 252         if (contour_type=="CLOSED_PLANAR ") {
 253           int point_number=clitk::parse_value<int>(j->GetEntryValue(0x3006,0x0046));
 254           std::vector<float> points=clitk::parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
 255           assert(points.size() == static_cast<unsigned int>(point_number)*3);
 256           if (z0 == -1) //First contour
 257             z0=points[2];
 258           //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
 259           //sometimes there is more than one closed contour per slice
 260           else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
 261             current_roi->SetSpacing(points[2]-z0);
 262           vtkPolyData * contour=vtkPolyData::New();
 263           contour->Allocate(); //for cell structures
 264           contour->SetPoints(vtkPoints::New());
 265           vtkIdType ids[2];
 266           for (unsigned int idx=0; idx<points.size(); idx+=3) {
 267             contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
 268             ids[0]=idx/3;
 269             ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
 270             contour->GetLines()->InsertNextCell(2,ids);
 271           }
 272           append->AddInput(contour);
 273         } else if (contour_type == "POINT ")
 274           ; // silently ignore POINT type since we don't need them at the moment
 275         else
 276           std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
 277       }
 278       append->Update();
 279       current_roi->AddMesh(append->GetOutput());
 280       result.push_back(current_roi);
 281     } else {
 282       //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
 283     }
 284     k=roi_info->GetNextSQItem(); //increment the second loop variable
 285   }
 286 #endif
 287   return result;
 288 }
 289