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