common/clitkImage2DicomRTStructFilter.txx

   1 /*=========================================================================
   2   Program:         vv http://www.creatis.insa-lyon.fr/rio/vv
   3   Main authors :   XX XX XX
   4
   5   Authors belongs to:
   6   - University of LYON           http://www.universite-lyon.fr/
   7   - Léon Bérard cancer center    http://www.centreleonberard.fr
   8   - CREATIS CNRS laboratory      http://www.creatis.insa-lyon.fr
   9
  10   This software is distributed WITHOUT ANY WARRANTY; without even
  11   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  12   PURPOSE.  See the copyright notices for more information.
  13
  14   It is distributed under dual licence
  15   - BSD       http://www.opensource.org/licenses/bsd-license.php
  16   - CeCILL-B  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17
  18   =========================================================================*/
  19
  20 // std
  21 #include <iterator>
  22 #include <algorithm>
  23
  24 // clitk
  25 #include "clitkImage2DicomRTStructFilter.h"
  26 #include "clitkBinaryImageToMeshFilter.h"
  27 #include "clitkImageCommon.h"
  28 #include "vvFromITK.h"
  29
  30 // vtk
  31 #include <vtkPolyDataToImageStencil.h>
  32 #include <vtkSmartPointer.h>
  33 #include <vtkImageStencil.h>
  34 #include <vtkLinearExtrusionFilter.h>
  35 #include <vtkMetaImageWriter.h>
  36 #include <vtkImageData.h>
  37
  38 // FIXME to remove
  39 #include "vtkPolyDataMapper.h"
  40 #include "vtkPolyDataMapper2D.h"
  41 #include "vtkRenderWindowInteractor.h"
  42 #include "vtkPolyDataReader.h"
  43 #include "vtkRenderWindow.h"
  44 #include "vtkRenderer.h"
  45 #include "vtkCamera.h"
  46 #include "vtkProperty.h"
  47 #include "vtkProperty2D.h"
  48
  49 // itk
  50 #include <itkImage.h>
  51 #include <itkVTKImageToImageFilter.h>
  52
  53 // gdcm
  54 #include <vtkGDCMPolyDataWriter.h>
  55
  56 //--------------------------------------------------------------------
  57 template<class PixelType>
  58 clitk::Image2DicomRTStructFilter<PixelType>::Image2DicomRTStructFilter()
  59 {
  60   DD("Image2DicomRTStructFilter Const");
  61 }
  62 //--------------------------------------------------------------------
  63
  64
  65 //--------------------------------------------------------------------
  66 template<class PixelType>
  67 clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
  68 {
  69   DD("Image2DicomRTStructFilter Destructor");
  70 }
  71 //--------------------------------------------------------------------
  72
  73
  74 //--------------------------------------------------------------------
  75 template<class PixelType>
  76 void clitk::Image2DicomRTStructFilter<PixelType>::Update()
  77 {
  78   DD("Image2DicomRTStructFilter::GenerateData");
  79
  80   // Read rt struct
  81   vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
  82   reader->SetFileName(m_StructureSetFilename.c_str());
  83   reader->Update();
  84   DD("reader done");
  85
  86   // Get properties
  87   vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
  88   DD(p->GetNumberOfStructureSetROIs());
  89   DD(p->GetStructureSetROIName(0));
  90   DD(p->GetStructureSetROINumber(0));
  91
  92   // Init writer
  93   vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
  94   int numMasks = reader->GetNumberOfOutputPorts() + 1;//add one more
  95   DD(numMasks);
  96
  97   // numMasks = 3; //FIXME temporary
  98
  99   writer->SetNumberOfInputPorts(numMasks);
 100   writer->SetFileName(m_OutputFilename.c_str());
 101   writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
 102
 103   // List of already present rois
 104   vtkStringArray* roiNames = vtkStringArray::New();
 105   vtkStringArray* roiAlgorithms = vtkStringArray::New();
 106   vtkStringArray* roiTypes = vtkStringArray::New();
 107   roiNames->SetNumberOfValues(numMasks);
 108   roiAlgorithms->SetNumberOfValues(numMasks);
 109   roiTypes->SetNumberOfValues(numMasks);
 110
 111   typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
 112   typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
 113   convert->SetInput(m_Input);
 114   DD("Update");
 115   convert->Update();
 116   DD("here");
 117   DD("end update");
 118   vtkPolyData* mesh = convert->GetOutputMesh();
 119   DD(mesh->GetNumberOfVerts());
 120   DD(mesh->GetNumberOfLines());
 121   DD(mesh->GetNumberOfPolys());
 122   DD(mesh->GetNumberOfStrips());
 123
 124   // Add on (FIXME) to replace with binary image
 125   // vtkPolyData* blank = vtkPolyData::New();
 126   // writer->SetInput(0, blank);
 127   writer->SetInput(0, mesh);
 128   roiNames->InsertValue(0, "blank");
 129   roiAlgorithms->InsertValue(0, "blank");
 130   roiTypes->InsertValue(0, "ORGAN");
 131
 132   for (unsigned int i = 1; i < numMasks; ++i) {
 133     // DD(i);
 134     writer->SetInput(i, reader->GetOutput(i-1));
 135     std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i-1);
 136     roiNames->InsertValue(i, theString);
 137     theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i-1);
 138     roiAlgorithms->InsertValue(i, theString);
 139     theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i-1);
 140     roiTypes->InsertValue(i, theString);
 141   }
 142
 143
 144   /*
 145   //  Visu
 146   vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
 147   cubeMapper->SetInput( mesh );
 148   cubeMapper->SetScalarRange(0,7);
 149   vtkActor *cubeActor = vtkActor::New();
 150   cubeActor->SetMapper(cubeMapper);
 151   vtkProperty * property = cubeActor->GetProperty();
 152   property->SetRepresentationToWireframe();
 153
 154   vtkRenderer *renderer = vtkRenderer::New();
 155   vtkRenderWindow *renWin = vtkRenderWindow::New();
 156   renWin->AddRenderer(renderer);
 157
 158   vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
 159   iren->SetRenderWindow(renWin);
 160
 161   renderer->AddActor(cubeActor);
 162   renderer->ResetCamera();
 163   renderer->SetBackground(1,1,1);
 164
 165   renWin->SetSize(300,300);
 166
 167   renWin->Render();
 168   iren->Start();
 169   */
 170
 171
 172   // End visu
 173
 174
 175   vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
 176   DD(p->GetStudyInstanceUID());
 177   writer->SetRTStructSetProperties(theProperties);
 178   /*writer->InitializeRTStructSet2(p,"./",
 179                                  reader->GetRTStructSetProperties()->GetStructureSetLabel(),
 180                                  reader->GetRTStructSetProperties()->GetStructureSetName(),
 181                                  roiNames, roiAlgorithms, roiTypes);*/
 182   writer->InitializeRTStructSet(m_DicomFolder,
 183                                 reader->GetRTStructSetProperties()->GetStructureSetLabel(),
 184                                 reader->GetRTStructSetProperties()->GetStructureSetName(),
 185                                 roiNames, roiAlgorithms, roiTypes);
 186
 187   DD("after init");
 188   writer->Write();
 189   DD("write done");
 190
 191   reader->Delete();
 192   roiNames->Delete();
 193   roiTypes->Delete();
 194   //theProperties->Delete();
 195   roiAlgorithms->Delete();
 196   //blank->Delete();
 197   writer->Delete();
 198
 199   ////////////////////
 200
 201
 202   /*
 203
 204   // DicomRTStruct
 205   DD(m_StructureSet->GetName());
 206   clitk::DicomRT_ROI * roi = m_StructureSet->GetROIFromROINumber(1); // Aorta
 207   DD(roi->GetName());
 208   DD(roi->GetROINumber());
 209
 210
 211   // Get
 212
 213
 214
 215
 216   // Add an image to the roi
 217   vvImage::Pointer im = vvImageFromITK<3, PixelType>(m_Input);
 218   roi->SetImage(im);
 219
 220   // Get one contour
 221   DD("Compute Mesh");
 222   roi->ComputeContoursFromImage(); // FIXME do the set mesh for the moment (to change)
 223   // roi->ComputeMeshFromContour();
 224   vtkSmartPointer<vtkPolyData> mesh = roi->GetMesh();
 225   DD("done");
 226
 227   // Change the mesh (shift by 10);
 228   // const vtkSmartPointer<vtkPoints> & points = mesh->GetPoints();
 229   // for(uint i=0; i<mesh->GetNumberOfVerts (); i++) {
 230   //   DD(i);
 231   //   double * p = points->GetPoint(i);
 232   //   p[0] += 30;
 233   //   points->SetPoint(i, p);
 234   // }
 235   roi->SetName("TOTO");
 236   roi->SetDicomUptodateFlag(true); // indicate that dicom info must be updated from the mesh.
 237
 238   // Convert to dicom ?
 239   DD("TODO");
 240
 241   // Write
 242   structset->Write("toto.dcm");
 243   */
 244 }
 245 //--------------------------------------------------------------------
 246
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