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 <vtkSmartPointer.h>
  38 #include <vtkAppendPolyData.h>
  39 #include <vtkCellArray.h>
  40 #include <vtkMetaImageWriter.h>
  41 #include <vtkMetaImageReader.h>
  42 #include <vtkPolyDataWriter.h>
  43 #include <vtkImageData.h>
  44 #include <vtkImageCast.h>
  45 #include <vtkImageGaussianSmooth.h>
  46
  47 // clitk
  48 #include "clitkCommon.h"
  49 #include "clitkCommon.h"
  50 #include "clitkDicomRT_StructureSet.h"
  51 #include "vvMeshReader.h"
  52 #include "vvProgressDialog.h"
  53
  54 //------------------------------------------------------------------------------
  55 vvMeshReader::vvMeshReader() :
  56 vtk_mode(false)
  57 {}
  58 //------------------------------------------------------------------------------
  59
  60
  61 //------------------------------------------------------------------------------
  62 void vvMeshReader::Update()
  63 {
  64   DD("vvMeshReader::Update");
  65
  66   //Show a progress bar only when opening a DC-struct (ie. multiple contours)
  67   vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
  68   this->start();
  69   while (this->isRunning()) {
  70     progress.SetProgress(result.size(),selected_contours.size());
  71     this->wait(50);
  72     qApp->processEvents();
  73   }
  74 }
  75 //------------------------------------------------------------------------------
  76
  77
  78 //------------------------------------------------------------------------------
  79 void vvMeshReader::run()
  80 {
  81   ///Verify the important stuff has been set
  82   assert(filename != "");
  83   if (vtk_mode) { //Read vtkPolyData
  84     vvMesh::Pointer m=vvMesh::New();
  85     m->ReadFromVTK(filename.c_str());
  86     if (vf) m->propagateContour(vf);
  87     m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
  88     result.push_back(m);
  89   } else { //Read a Dicom-struct file
  90     assert(selected_contours.size() > 0);
  91     assert(image);
  92     std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
  93     for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
  94          i!=contour_stacks.end(); i++) {
  95       (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
  96       (*i)->ComputeMeshes();
  97       if (vf) (*i)->propagateContour(vf);
  98       result.push_back(*i);
  99     }
 100   }
 101 }
 102 //------------------------------------------------------------------------------
 103
 104
 105 //------------------------------------------------------------------------------
 106 std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
 107 {
 108   assert(filename!="");
 109   std::vector<std::pair<int, std::string> > roi_names;
 110   DD(GDCM_MAJOR_VERSION);
 111   DD(CLITK_USE_SYSTEM_GDCM);
 112
 113 #if CLITK_USE_SYSTEM_GDCM == 1
 114   // Read RT-struct data
 115   DD("before read");
 116   vtkSmartPointer<vtkGDCMPolyDataReader> areader = vtkGDCMPolyDataReader::New();
 117   areader->SetFileName(filename.c_str());
 118   areader->Update();
 119   DD("after read");
 120
 121   // get info on roi names
 122   vtkRTStructSetProperties * p = areader->GetRTStructSetProperties();
 123   DD(p->GetNumberOfStructureSetROIs());
 124   DD(p->GetStructureSetROIName(0));
 125   DD(p->GetStructureSetROINumber(0));
 126   int n = p->GetNumberOfStructureSetROIs();
 127   DD(n);
 128
 129   for(unsigned int i=0; i<n; i++) {
 130     std::string name = p->GetStructureSetROIName(i);
 131     int nb = p->GetStructureSetROINumber(i);
 132     roi_names.push_back(make_pair(nb,name));
 133   }
 134
 135 #else
 136 #if GDCM_MAJOR_VERSION == 2
 137
 138     // duplicate code from  clitk::DicomRT_StructureSet::Read
 139     gdcm::Reader * reader = new gdcm::Reader;
 140     reader->SetFileName( filename.c_str() );
 141     reader->Read();
 142
 143     const gdcm::DataSet &ds = reader->GetFile().GetDataSet();
 144
 145     // Check file type
 146     //Verify if the file is a RT-Structure-Set dicom file
 147     gdcm::File * mFile = &(reader->GetFile());
 148     gdcm::MediaStorage ms;
 149     ms.SetFromFile(*mFile);
 150     if( ms != gdcm::MediaStorage::RTStructureSetStorage )
 151       {
 152         std::cerr << "Error. the file " << filename
 153                   << " 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])"
 154                   << std::endl;
 155         exit(0);
 156       }
 157
 158     gdcm::Attribute<0x8,0x60> modality;
 159     modality.SetFromDataSet( ds );
 160     if( modality.GetValue() != "RTSTRUCT" )
 161       {
 162         std::cerr << "Error. the file " << filename
 163                   << " is not a Dicom Struct ? (must have 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])"
 164                   << std::endl;
 165         exit(0);
 166       }
 167
 168     gdcm::Attribute<0x20,0x10> studyid;
 169     studyid.SetFromDataSet( ds );
 170
 171     gdcm::Tag tssroisq(0x3006,0x0020);
 172     // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
 173     bool b = ds.FindDataElement(tssroisq);
 174     if (!b) { // FIXME
 175       clitkExceptionMacro("Error: tag 0x3006,0x0020 [ Structure Set ROI Sequence ] not found");
 176     }
 177
 178     const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
 179     gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
 180     assert(roi_seq); // FIXME error message
 181
 182     for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
 183       {
 184          gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
 185
 186         const gdcm::Item & sitem = roi_seq->GetItem(ridx+1); // Item start at #1
 187
 188         const gdcm::DataSet& snestedds = sitem.GetNestedDataSet();
 189         const gdcm::DataSet& nestedds = item.GetNestedDataSet();
 190
 191         if( snestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
 192           {
 193             // const gdcm::DataElement & a = nestedds.GetDataElement(gdcm::Tag(0x3006,0x26));
 194             // DD(a.GetValue());
 195
 196             gdcm::Attribute<0x3006,0x26> roiname;
 197             roiname.SetFromDataSet( snestedds );
 198             std::string name = roiname.GetValue();      // 0x3006,0x0026 = [ROI Name]
 199             gdcm::Attribute<0x3006,0x0022> roinumber;
 200             roinumber.SetFromDataSet( snestedds );
 201             int nb = roinumber.GetValue();  // 0x3006,0x0022 = [ROI Number]
 202
 203             roi_names.push_back(make_pair(nb,name));
 204           }
 205       }
 206
 207     delete reader;
 208
 209 #else
 210   gdcm::File reader;
 211   reader.SetFileName(filename.c_str());
 212   reader.SetMaxSizeLoadEntry(16384);
 213   reader.Load();
 214
 215   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 216   assert(roi_info);
 217   // DD("ici");
 218   //int n=0;
 219   for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
 220     if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
 221       roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
 222 #endif
 223 #endif
 224
 225   return roi_names;
 226
 227 }
 228 //------------------------------------------------------------------------------
 229
 230
 231 //------------------------------------------------------------------------------
 232 std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
 233 {
 234   std::vector<vvMesh::Pointer> result;
 235 #if GDCM_MAJOR_VERSION == 2
 236
 237 #if CLITK_USE_SYSTEM_GDCM == 0
 238
 239   clitkExceptionMacro("ERROR ! You need to compile vv with itk4 + system_gdcm to use this function");
 240
 241 #endif
 242
 243   gdcm::Reader reader;
 244   reader.SetFileName(filename.c_str());
 245   reader.Read();
 246
 247   const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
 248
 249   gdcm::SmartPointer<gdcm::SequenceOfItems> rois = ds.GetDataElement(gdcm::Tag(0x3006,0x39)).GetValueAsSQ();
 250   gdcm::SmartPointer<gdcm::SequenceOfItems> roi_info = ds.GetDataElement(gdcm::Tag(0x3006,0x20)).GetValueAsSQ();
 251   assert(rois); // TODO error message
 252   assert(roi_info); // TODO error message
 253   assert(rois->GetNumberOfItems() == roi_info->GetNumberOfItems());
 254
 255   for (unsigned ridx = 0; ridx < rois->GetNumberOfItems(); ++ridx)
 256     {
 257       vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
 258       const gdcm::DataSet& ds_rois = rois->GetItem( ridx + 1).GetNestedDataSet();
 259       const gdcm::DataSet& ds_roi_info = roi_info->GetItem( ridx + 1).GetNestedDataSet();
 260
 261       gdcm::Attribute<0x3006,0x84> roinumber;
 262       roinumber.SetFromDataSet(ds_rois);
 263       if (std::find(selected_contours.begin(), selected_contours.end(), roinumber.GetValue()) != selected_contours.end()) //Only read selected ROIs
 264         {
 265           gdcm::Attribute<0x3006,0x2a> trgb;
 266           trgb.SetFromDataSet(ds_rois);
 267           vvMesh::Pointer current_roi=vvMesh::New();
 268           current_roi->r = trgb[0] / 255.0;
 269           current_roi->g = trgb[1] / 255.0;
 270           current_roi->b = trgb[2] / 255.0;
 271
 272           gdcm::Attribute<0x3006,0x26> tstructure_name;
 273           tstructure_name.SetFromDataSet(ds_roi_info);
 274           current_roi->structure_name = tstructure_name.GetValue();
 275
 276           gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ds_rois.GetDataElement(gdcm::Tag(0x3006,0x40)).GetValueAsSQ();
 277           double z0=-1; //Used to determine spacing between slices, assumed to be constant
 278           for (unsigned j = 0; j < roi_seq->GetNumberOfItems(); ++j)
 279             {
 280               gdcm::Item & item_roi_seq = roi_seq->GetItem(j + 1); // Item starts at 1
 281               const gdcm::DataSet& ds_roi_seq = item_roi_seq.GetNestedDataSet();
 282               gdcm::Attribute<0x3006,0x42> tcontour_type;
 283               tcontour_type.SetFromDataSet(ds_roi_seq);
 284               std::string contour_type = tcontour_type.GetValue();
 285               if (contour_type=="CLOSED_PLANAR ")
 286                 {
 287                   gdcm::Attribute<0x3006,0x46> tpoint_number;
 288                   tpoint_number.SetFromDataSet(ds_roi_seq);
 289                   const gdcm::DataElement & points_data = ds_roi_seq.GetDataElement(gdcm::Tag(0x3006,0x50));
 290                   gdcm::Attribute<0x3006,0x50> tpoints;
 291                   tpoints.SetFromDataElement(points_data);
 292                   assert(tpoints.GetNumberOfValues() == static_cast<unsigned int>(tpoint_number.GetValue()) * 3);
 293                   const double* points = tpoints.GetValues();
 294                   if (z0 == -1) //First contour
 295                     z0=points[2];
 296                   else
 297                     if (current_roi->GetSpacing()==-1 && points[2] != z0 )
 298                       current_roi->SetSpacing(points[2]-z0);
 299                   vtkPolyData * contour=vtkPolyData::New();
 300                   contour->Allocate(); //for cell structures
 301                   contour->SetPoints(vtkPoints::New());
 302                   vtkIdType ids[2];
 303                   for (unsigned idx = 0; idx < tpoints.GetNumberOfValues(); idx += 3)
 304                     {
 305                       contour->GetPoints()->InsertNextPoint(points[idx], points[idx+1], points[idx+2]);
 306                       ids[0] = idx / 3;
 307                       ids[1] = (ids[0] + 1) % tpoint_number.GetValue(); //0-1,1-2,...,n-1-0
 308                       contour->GetLines()->InsertNextCell(2, ids);
 309                     }
 310                   append->AddInput(contour);
 311                 }
 312               else
 313                 if (contour_type == "POINT ")
 314                   ; // silently ignore POINT type since we don't need them at the moment
 315                 else
 316                   std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
 317             }
 318           append->Update();
 319           current_roi->AddMesh(append->GetOutput());
 320           result.push_back(current_roi);
 321         }
 322       else
 323         {
 324           //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
 325         }
 326     }
 327 #else
 328   gdcm::File reader;
 329   reader.SetFileName(filename.c_str());
 330   reader.SetMaxSizeLoadEntry(16384);
 331   reader.Load();
 332
 333   gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
 334   ///We need to iterate both on the contours themselves, and on the contour info
 335   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 336   gdcm::SQItem* k=roi_info->GetFirstSQItem();
 337   for(gdcm::SQItem* i=rois->GetFirstSQItem(); i!=0; i=rois->GetNextSQItem()) { //loop over ROIS
 338     assert(k!=0);
 339     vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
 340     std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
 341     int roi_number;
 342     ss >> roi_number;
 343     if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
 344       vvMesh::Pointer current_roi=vvMesh::New();
 345       std::vector<double> rgb=clitk::parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
 346       assert(rgb.size()==3);
 347       current_roi->r=rgb[0]/255;
 348       current_roi->g=rgb[1]/255;
 349       current_roi->b=rgb[2]/255;
 350       current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
 351       gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
 352       double z0=-1; //Used to determine spacing between slices, assumed to be constant
 353       for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
 354         std::string contour_type=j->GetEntryValue(0x3006,0x0042);
 355         if (contour_type=="CLOSED_PLANAR ") {
 356           int point_number=clitk::parse_value<int>(j->GetEntryValue(0x3006,0x0046));
 357           std::vector<float> points=clitk::parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
 358           assert(points.size() == static_cast<unsigned int>(point_number)*3);
 359           if (z0 == -1) //First contour
 360             z0=points[2];
 361           //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
 362           //sometimes there is more than one closed contour per slice
 363           else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
 364             current_roi->SetSpacing(points[2]-z0);
 365           vtkPolyData * contour=vtkPolyData::New();
 366           contour->Allocate(); //for cell structures
 367           contour->SetPoints(vtkPoints::New());
 368           vtkIdType ids[2];
 369           for (unsigned int idx=0; idx<points.size(); idx+=3) {
 370             contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
 371             ids[0]=idx/3;
 372             ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
 373             contour->GetLines()->InsertNextCell(2,ids);
 374           }
 375           append->AddInput(contour);
 376         } else if (contour_type == "POINT ")
 377           ; // silently ignore POINT type since we don't need them at the moment
 378         else
 379           std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
 380       }
 381       append->Update();
 382       current_roi->AddMesh(append->GetOutput());
 383       result.push_back(current_roi);
 384     } else {
 385       //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
 386     }
 387     k=roi_info->GetNextSQItem(); //increment the second loop variable
 388   }
 389 #endif
 390   return result;
 391 }
 392