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