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
  19 // std
  20 #include <algorithm>
  21
  22 // qt
  23 #include <QApplication>
  24
  25 // gdcm
  26 #include <gdcmFile.h>
  27 #if GDCM_MAJOR_VERSION >= 2
  28 #include <gdcmReader.h>
  29 #include <gdcmTag.h>
  30 #include <gdcmAttribute.h>
  31 #else
  32 #include <gdcm.h>
  33 #include <gdcmSQItem.h>
  34 #endif
  35
  36 // vtk
  37 #include <vtkVersion.h>
  38 #include <vtkSmartPointer.h>
  39 #include <vtkAppendPolyData.h>
  40 #include <vtkCellArray.h>
  41 #include <vtkMetaImageWriter.h>
  42 #include <vtkMetaImageReader.h>
  43 #include <vtkPolyDataWriter.h>
  44 #include <vtkImageData.h>
  45 #include <vtkImageCast.h>
  46 #include <vtkImageGaussianSmooth.h>
  47
  48 // clitk
  49 #include "clitkCommon.h"
  50 #include "clitkCommon.h"
  51 #include "clitkDicomRT_StructureSet.h"
  52 #include "vvMeshReader.h"
  53 #include "vvProgressDialog.h"
  54
  55 //------------------------------------------------------------------------------
  56 vvMeshReader::vvMeshReader() :
  57 vtk_mode(false)
  58 {}
  59 //------------------------------------------------------------------------------
  60
  61
  62 //------------------------------------------------------------------------------
  63 void vvMeshReader::Update()
  64 {
  65   //Show a progress bar only when opening a DC-struct (ie. multiple contours)
  66   vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
  67   this->start();
  68   while (this->isRunning()) {
  69     progress.SetProgress(result.size(),selected_contours.size());
  70     this->wait(50);
  71     qApp->processEvents();
  72   }
  73 }
  74 //------------------------------------------------------------------------------
  75
  76
  77 //------------------------------------------------------------------------------
  78 void vvMeshReader::run()
  79 {
  80   ///Verify the important stuff has been set
  81   assert(filename != "");
  82   if (vtk_mode) { //Read vtkPolyData
  83     vvMesh::Pointer m=vvMesh::New();
  84     m->ReadFromVTK(filename.c_str());
  85     if (vf) m->propagateContour(vf);
  86     m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
  87     result.push_back(m);
  88   } else { //Read a Dicom-struct file
  89     assert(selected_contours.size() > 0);
  90     assert(image);
  91     std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
  92     for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
  93          i!=contour_stacks.end(); i++) {
  94       (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
  95       (*i)->ComputeMeshes();
  96       if (vf) (*i)->propagateContour(vf);
  97       result.push_back(*i);
  98     }
  99   }
 100 }
 101 //------------------------------------------------------------------------------
 102
 103
 104 //------------------------------------------------------------------------------
 105 std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
 106 {
 107   assert(filename!="");
 108   std::vector<std::pair<int, std::string> > roi_names;
 109
 110 #if CLITK_USE_SYSTEM_GDCM == 1
 111
 112   // Read RT-struct data
 113   vtkSmartPointer<vtkGDCMPolyDataReader> areader = vtkGDCMPolyDataReader::New();
 114   areader->SetFileName(filename.c_str());
 115   areader->Update();
 116
 117   // get info on roi names
 118   vtkRTStructSetProperties * p = areader->GetRTStructSetProperties();
 119   int n = p->GetNumberOfStructureSetROIs();
 120
 121   for(unsigned int i=0; i<n; i++) {
 122     std::string name = p->GetStructureSetROIName(i);
 123     int nb = p->GetStructureSetROINumber(i);
 124     roi_names.push_back(make_pair(nb,name));
 125   }
 126
 127 #else
 128 #if GDCM_MAJOR_VERSION >= 2
 129
 130     // duplicate code from  clitk::DicomRT_StructureSet::Read
 131     gdcm::Reader * reader = new gdcm::Reader;
 132     reader->SetFileName( filename.c_str() );
 133     reader->Read();
 134
 135     const gdcm::DataSet &ds = reader->GetFile().GetDataSet();
 136
 137     // Check file type
 138     //Verify if the file is a RT-Structure-Set dicom file
 139     gdcm::File * mFile = &(reader->GetFile());
 140     gdcm::MediaStorage ms;
 141     ms.SetFromFile(*mFile);
 142     if( ms != gdcm::MediaStorage::RTStructureSetStorage )
 143       {
 144         std::cerr << "Error. the file " << filename
 145                   << " 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])"
 146                   << std::endl;
 147         exit(0);
 148       }
 149
 150     gdcm::Attribute<0x8,0x60> modality;
 151     modality.SetFromDataSet( ds );
 152     if( modality.GetValue() != "RTSTRUCT" )
 153       {
 154         std::cerr << "Error. the file " << filename
 155                   << " is not a Dicom Struct ? (must have 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])"
 156                   << std::endl;
 157         exit(0);
 158       }
 159
 160     gdcm::Attribute<0x20,0x10> studyid;
 161     studyid.SetFromDataSet( ds );
 162
 163     gdcm::Tag tssroisq(0x3006,0x0020);
 164     // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
 165     bool b = ds.FindDataElement(tssroisq);
 166     if (!b) { // FIXME
 167       clitkExceptionMacro("Error: tag 0x3006,0x0020 [ Structure Set ROI Sequence ] not found");
 168     }
 169
 170     const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
 171     gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
 172     assert(roi_seq); // FIXME error message
 173
 174     for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
 175       {
 176          gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
 177
 178         const gdcm::Item & sitem = roi_seq->GetItem(ridx+1); // Item start at #1
 179
 180         const gdcm::DataSet& snestedds = sitem.GetNestedDataSet();
 181         const gdcm::DataSet& nestedds = item.GetNestedDataSet();
 182
 183         if( snestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
 184           {
 185             // const gdcm::DataElement & a = nestedds.GetDataElement(gdcm::Tag(0x3006,0x26));
 186             // DD(a.GetValue());
 187
 188             gdcm::Attribute<0x3006,0x26> roiname;
 189             roiname.SetFromDataSet( snestedds );
 190             std::string name = roiname.GetValue();      // 0x3006,0x0026 = [ROI Name]
 191             gdcm::Attribute<0x3006,0x0022> roinumber;
 192             roinumber.SetFromDataSet( snestedds );
 193             int nb = roinumber.GetValue();  // 0x3006,0x0022 = [ROI Number]
 194
 195             roi_names.push_back(make_pair(nb,name));
 196           }
 197       }
 198
 199     delete reader;
 200
 201 #else
 202   gdcm::File reader;
 203   reader.SetFileName(filename.c_str());
 204   reader.SetMaxSizeLoadEntry(16384);
 205   reader.Load();
 206
 207   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 208   assert(roi_info);
 209   // DD("ici");
 210   //int n=0;
 211   for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
 212     if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
 213       roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
 214 #endif
 215 #endif
 216
 217   return roi_names;
 218 }
 219 //------------------------------------------------------------------------------
 220
 221
 222 //------------------------------------------------------------------------------
 223 std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
 224 {
 225   std::vector<vvMesh::Pointer> result;
 226 #if GDCM_MAJOR_VERSION >= 2
 227   gdcm::Reader reader;
 228   reader.SetFileName(filename.c_str());
 229   reader.Read();
 230
 231   const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
 232
 233   gdcm::SmartPointer<gdcm::SequenceOfItems> rois = ds.GetDataElement(gdcm::Tag(0x3006,0x39)).GetValueAsSQ();
 234   gdcm::SmartPointer<gdcm::SequenceOfItems> roi_info = ds.GetDataElement(gdcm::Tag(0x3006,0x20)).GetValueAsSQ();
 235   assert(rois); // TODO error message
 236   assert(roi_info); // TODO error message
 237   assert(rois->GetNumberOfItems() == roi_info->GetNumberOfItems());
 238
 239   for (unsigned ridx = 0; ridx < rois->GetNumberOfItems(); ++ridx)
 240     {
 241       vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
 242       const gdcm::DataSet& ds_rois = rois->GetItem( ridx + 1).GetNestedDataSet();
 243       const gdcm::DataSet& ds_roi_info = roi_info->GetItem( ridx + 1).GetNestedDataSet();
 244
 245       gdcm::Attribute<0x3006,0x84> roinumber;
 246       roinumber.SetFromDataSet(ds_rois);
 247       if (std::find(selected_contours.begin(), selected_contours.end(), roinumber.GetValue()) != selected_contours.end()) //Only read selected ROIs
 248         {
 249           gdcm::Attribute<0x3006,0x2a> trgb;
 250           trgb.SetFromDataSet(ds_rois);
 251           vvMesh::Pointer current_roi=vvMesh::New();
 252           current_roi->r = trgb[0] / 255.0;
 253           current_roi->g = trgb[1] / 255.0;
 254           current_roi->b = trgb[2] / 255.0;
 255
 256           gdcm::Attribute<0x3006,0x26> tstructure_name;
 257           tstructure_name.SetFromDataSet(ds_roi_info);
 258           current_roi->structure_name = tstructure_name.GetValue();
 259
 260           gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ds_rois.GetDataElement(gdcm::Tag(0x3006,0x40)).GetValueAsSQ();
 261           double z0=-1; //Used to determine spacing between slices, assumed to be constant
 262           for (unsigned j = 0; j < roi_seq->GetNumberOfItems(); ++j)
 263             {
 264               gdcm::Item & item_roi_seq = roi_seq->GetItem(j + 1); // Item starts at 1
 265               const gdcm::DataSet& ds_roi_seq = item_roi_seq.GetNestedDataSet();
 266               gdcm::Attribute<0x3006,0x42> tcontour_type;
 267               tcontour_type.SetFromDataSet(ds_roi_seq);
 268               std::string contour_type = tcontour_type.GetValue();
 269               if (contour_type=="CLOSED_PLANAR ")
 270                 {
 271                   gdcm::Attribute<0x3006,0x46> tpoint_number;
 272                   tpoint_number.SetFromDataSet(ds_roi_seq);
 273                   const gdcm::DataElement & points_data = ds_roi_seq.GetDataElement(gdcm::Tag(0x3006,0x50));
 274                   gdcm::Attribute<0x3006,0x50> tpoints;
 275                   tpoints.SetFromDataElement(points_data);
 276                   assert(tpoints.GetNumberOfValues() == static_cast<unsigned int>(tpoint_number.GetValue()) * 3);
 277                   const double* points = tpoints.GetValues();
 278                   if (z0 == -1) //First contour
 279                     z0=points[2];
 280                   else
 281                     if (current_roi->GetSpacing()==-1 && points[2] != z0 )
 282                       current_roi->SetSpacing(points[2]-z0);
 283                   vtkPolyData * contour=vtkPolyData::New();
 284                   contour->Allocate(); //for cell structures
 285                   contour->SetPoints(vtkPoints::New());
 286                   vtkIdType ids[2];
 287                   for (unsigned idx = 0; idx < tpoints.GetNumberOfValues(); idx += 3)
 288                     {
 289                       contour->GetPoints()->InsertNextPoint(points[idx], points[idx+1], points[idx+2]);
 290                       ids[0] = idx / 3;
 291                       ids[1] = (ids[0] + 1) % tpoint_number.GetValue(); //0-1,1-2,...,n-1-0
 292                       contour->GetLines()->InsertNextCell(2, ids);
 293                     }
 294 #if VTK_MAJOR_VERSION <= 5
 295                   append->AddInput(contour);
 296 #else
 297                   append->AddInputData(contour);
 298 #endif
 299                 }
 300               else
 301                 if (contour_type == "POINT ")
 302                   ; // silently ignore POINT type since we don't need them at the moment
 303                 else
 304                   std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
 305             }
 306           append->Update();
 307           current_roi->AddMesh(append->GetOutput());
 308           result.push_back(current_roi);
 309         }
 310       else
 311         {
 312           //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
 313         }
 314     }
 315 #else
 316   gdcm::File reader;
 317   reader.SetFileName(filename.c_str());
 318   reader.SetMaxSizeLoadEntry(16384);
 319   reader.Load();
 320
 321   gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
 322   ///We need to iterate both on the contours themselves, and on the contour info
 323   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 324   gdcm::SQItem* k=roi_info->GetFirstSQItem();
 325   for(gdcm::SQItem* i=rois->GetFirstSQItem(); i!=0; i=rois->GetNextSQItem()) { //loop over ROIS
 326     assert(k!=0);
 327     vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
 328     std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
 329     int roi_number;
 330     ss >> roi_number;
 331     if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
 332       vvMesh::Pointer current_roi=vvMesh::New();
 333       std::vector<double> rgb=clitk::parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
 334       assert(rgb.size()==3);
 335       current_roi->r=rgb[0]/255;
 336       current_roi->g=rgb[1]/255;
 337       current_roi->b=rgb[2]/255;
 338       current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
 339       gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
 340       double z0=-1; //Used to determine spacing between slices, assumed to be constant
 341       for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
 342         std::string contour_type=j->GetEntryValue(0x3006,0x0042);
 343         if (contour_type=="CLOSED_PLANAR ") {
 344           int point_number=clitk::parse_value<int>(j->GetEntryValue(0x3006,0x0046));
 345           std::vector<float> points=clitk::parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
 346           assert(points.size() == static_cast<unsigned int>(point_number)*3);
 347           if (z0 == -1) //First contour
 348             z0=points[2];
 349           //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
 350           //sometimes there is more than one closed contour per slice
 351           else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
 352             current_roi->SetSpacing(points[2]-z0);
 353           vtkPolyData * contour=vtkPolyData::New();
 354           contour->Allocate(); //for cell structures
 355           contour->SetPoints(vtkPoints::New());
 356           vtkIdType ids[2];
 357           for (unsigned int idx=0; idx<points.size(); idx+=3) {
 358             contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
 359             ids[0]=idx/3;
 360             ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
 361             contour->GetLines()->InsertNextCell(2,ids);
 362           }
 363           append->AddInput(contour);
 364         } else if (contour_type == "POINT ")
 365           ; // silently ignore POINT type since we don't need them at the moment
 366         else
 367           std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
 368       }
 369       append->Update();
 370       current_roi->AddMesh(append->GetOutput());
 371       result.push_back(current_roi);
 372     } else {
 373       //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
 374     }
 375     k=roi_info->GetNextSQItem(); //increment the second loop variable
 376   }
 377 #endif
 378   return result;
 379 }
 380