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://oncora1.lyon.fnclcc.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 <gdcm.h>
  23 #include <gdcmSQItem.h>
  24
  25 #include <vtkSmartPointer.h>
  26 #include <vtkAppendPolyData.h>
  27 #include <vtkCellArray.h>
  28 #include <vtkMetaImageWriter.h>
  29 #include <vtkMetaImageReader.h>
  30 #include <vtkPolyDataWriter.h>
  31 #include <vtkImageData.h>
  32 #include <vtkImageCast.h>
  33 #include <vtkImageGaussianSmooth.h>
  34
  35 #include "clitkCommon.h"
  36 #include "vvMeshReader.h"
  37 #include "vvProgressDialog.h"
  38
  39 vvMeshReader::vvMeshReader() :
  40   vtk_mode(false)
  41 {}
  42
  43 void vvMeshReader::Update()
  44 {
  45   //Show a progress bar only when opening a DC-struct (ie. multiple contours)
  46   vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
  47   this->start();
  48   while (this->isRunning()) {
  49     progress.SetProgress(result.size(),selected_contours.size());
  50     this->wait(50);
  51     qApp->processEvents();
  52   }
  53 }
  54
  55 void vvMeshReader::run()
  56 {
  57   ///Verify the important stuff has been set
  58   assert(filename != "");
  59   if (vtk_mode) { //Read vtkPolyData
  60     vvMesh::Pointer m=vvMesh::New();
  61     m->ReadFromVTK(filename.c_str());
  62     if (vf) m->propagateContour(vf);
  63     m->ComputeMasks(image->GetVTKImages()[0],true);
  64     result.push_back(m);
  65   } else { //Read a Dicom-struct file
  66     assert(selected_contours.size() > 0);
  67     assert(image);
  68     std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
  69     for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
  70          i!=contour_stacks.end(); i++) {
  71       (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
  72       (*i)->ComputeMeshes();
  73       if (vf) (*i)->propagateContour(vf);
  74       result.push_back(*i);
  75     }
  76   }
  77 }
  78
  79 template<class ElementType>
  80 ElementType parse_value(std::string str)
  81 {
  82   std::istringstream parser(str);
  83   ElementType value;
  84   parser >> value;
  85   assert(!parser.fail());
  86   return value;
  87 }
  88
  89 template<class ElementType>
  90 std::vector<ElementType> parse_string(std::string str,char delim)
  91 {
  92   std::istringstream ss(str);
  93   std::string token;
  94   std::vector<ElementType> result;
  95   while (getline(ss,token,delim)) {
  96     result.push_back(parse_value<ElementType>(token));
  97   }
  98   return result;
  99 }
 100
 101 std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
 102 {
 103   assert(filename!="");
 104   gdcm::File reader;
 105   reader.SetFileName(filename.c_str());
 106   reader.SetMaxSizeLoadEntry(16384);
 107   reader.Load();
 108
 109   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 110   assert(roi_info);
 111   std::vector<std::pair<int, std::string> > roi_names;
 112   // DD("ici");
 113   //int n=0;
 114   for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
 115     if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
 116       roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
 117   return roi_names;
 118 }
 119
 120 std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
 121 {
 122   gdcm::File reader;
 123   reader.SetFileName(filename.c_str());
 124   reader.SetMaxSizeLoadEntry(16384);
 125   reader.Load();
 126
 127   std::vector<vvMesh::Pointer> result;
 128   gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
 129   ///We need to iterate both on the contours themselves, and on the contour info
 130   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
 131   gdcm::SQItem* k=roi_info->GetFirstSQItem();
 132   for(gdcm::SQItem* i=rois->GetFirstSQItem(); i!=0; i=rois->GetNextSQItem()) { //loop over ROIS
 133     assert(k!=0);
 134     vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
 135     std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
 136     int roi_number;
 137     ss >> roi_number;
 138     if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
 139       vvMesh::Pointer current_roi=vvMesh::New();
 140       std::vector<double> rgb=parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
 141       assert(rgb.size()==3);
 142       current_roi->r=rgb[0]/255;
 143       current_roi->g=rgb[1]/255;
 144       current_roi->b=rgb[2]/255;
 145       current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
 146       gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
 147       double z0=-1; //Used to determine spacing between slices, assumed to be constant
 148       for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
 149         std::string contour_type=j->GetEntryValue(0x3006,0x0042);
 150         if (contour_type=="CLOSED_PLANAR ") {
 151           int point_number=parse_value<int>(j->GetEntryValue(0x3006,0x0046));
 152           std::vector<float> points=parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
 153           assert(points.size() == static_cast<unsigned int>(point_number)*3);
 154           if (z0 == -1) //First contour
 155             z0=points[2];
 156           //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
 157           //sometimes there is more than one closed contour per slice
 158           else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
 159             current_roi->SetSpacing(points[2]-z0);
 160           vtkPolyData * contour=vtkPolyData::New();
 161           contour->Allocate(); //for cell structures
 162           contour->SetPoints(vtkPoints::New());
 163           vtkIdType ids[2];
 164           for (unsigned int idx=0; idx<points.size(); idx+=3) {
 165             contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
 166             ids[0]=idx/3;
 167             ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
 168             contour->GetLines()->InsertNextCell(2,ids);
 169           }
 170           append->AddInput(contour);
 171         } else if (contour_type == "POINT ")
 172           ; // silently ignore POINT type since we don't need them at the moment
 173         else
 174           std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
 175       }
 176       append->Update();
 177       current_roi->AddMesh(append->GetOutput());
 178       result.push_back(current_roi);
 179     } else {
 180       //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
 181     }
 182     k=roi_info->GetNextSQItem(); //increment the second loop variable
 183   }
 184   return result;
 185 }
 186