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 #include <vtksys/SystemTools.hxx>
  49
  50 // itk
  51 #include <itkImage.h>
  52 #include <itkVTKImageToImageFilter.h>
  53
  54 // gdcm
  55 #include <vtkRTStructSetProperties.h>
  56 #include <vtkGDCMPolyDataReader.h>
  57 #include <vtkGDCMPolyDataWriter.h>
  58
  59 //--------------------------------------------------------------------
  60 template<class PixelType>
  61 clitk::Image2DicomRTStructFilter<PixelType>::Image2DicomRTStructFilter()
  62 {
  63   m_StructureSetFilename = "";
  64   m_DicomFolder = "";
  65   m_OutputFilename = "default-output.dcm";
  66   m_ThresholdValue = 0.5;
  67   m_SkipInitialStructuresFlag = false;
  68 }
  69 //--------------------------------------------------------------------
  70
  71
  72 //--------------------------------------------------------------------
  73 template<class PixelType>
  74 clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
  75 {
  76 }
  77 //--------------------------------------------------------------------
  78
  79
  80 //--------------------------------------------------------------------
  81 template<class PixelType>
  82 void
  83 clitk::Image2DicomRTStructFilter<PixelType>::SetROIType(std::string type)
  84 {
  85   m_ROIType = type;
  86 }
  87 //--------------------------------------------------------------------
  88
  89
  90 //--------------------------------------------------------------------
  91 template<class PixelType>
  92 void clitk::Image2DicomRTStructFilter<PixelType>::Update()
  93 {
  94   // Check this is a RT-Struct
  95   gdcm::Reader gdcm_reader;
  96   gdcm_reader.SetFileName(m_StructureSetFilename.c_str());
  97   if (!gdcm_reader.Read()) {
  98     clitkExceptionMacro("Error could not open the file '" << m_StructureSetFilename << std::endl);
  99   }
 100   gdcm::MediaStorage ms;
 101   ms.SetFromFile(gdcm_reader.GetFile());
 102   if (ms != gdcm::MediaStorage::RTStructureSetStorage) {
 103     clitkExceptionMacro("File '" << m_StructureSetFilename << "' is not a DICOM-RT-Struct file." << std::endl);
 104   }
 105
 106   // Read rt struct
 107   vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
 108   reader->SetFileName(m_StructureSetFilename.c_str());
 109   reader->Update();
 110
 111   // Get properties
 112   vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
 113   if (GetVerboseFlag()) {
 114     std::cout << "Number of structures in the dicom-rt-struct : "
 115               << p->GetNumberOfStructureSetROIs() << std::endl;
 116   }
 117
 118
 119   // number of additional contours
 120   int m = m_InputFilenames.size();
 121
 122   // Init writer
 123   vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
 124   int numMasks = reader->GetNumberOfOutputPorts() + m;
 125
 126   if (m_SkipInitialStructuresFlag) {
 127     numMasks = m;
 128   }
 129
 130   writer->SetNumberOfInputPorts(numMasks);
 131   writer->SetFileName(m_OutputFilename.c_str());
 132   writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
 133
 134   // List of already present rois
 135   vtkStringArray* roiNames = vtkStringArray::New();
 136   vtkStringArray* roiAlgorithms = vtkStringArray::New();
 137   vtkStringArray* roiTypes = vtkStringArray::New();
 138   roiNames->SetNumberOfValues(numMasks);
 139   roiAlgorithms->SetNumberOfValues(numMasks);
 140   roiTypes->SetNumberOfValues(numMasks);
 141
 142   // Convert the image into a mesh
 143   std::vector<vtkSmartPointer<vtkPolyData> > meshes;
 144   std::vector<std::string> m_ROINames;
 145   meshes.resize(m);
 146   m_ROINames.resize(m);
 147   for(unsigned int i=0; i<m; i++) {
 148
 149     // read image
 150     //    typedef float PixelType;
 151     //typedef itk::Image<PixelType, 3> ImageType;
 152     ImagePointer input = clitk::readImage<ImageType>(m_InputFilenames[i], false);
 153
 154     std::ostringstream oss;
 155     oss << vtksys::SystemTools::
 156       GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(m_InputFilenames[i]));
 157     std::string name = oss.str();
 158     m_ROINames[i] = name;
 159
 160     // convert to mesh
 161     typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
 162     typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
 163     convert->SetThresholdValue(m_ThresholdValue);
 164     convert->SetInput(input);
 165     convert->Update();
 166     meshes[i] = convert->GetOutputMesh();
 167     if (GetVerboseFlag()) {
 168       std::cout << "Mesh has " << meshes[i]->GetNumberOfLines() << " lines." << std::endl;
 169     }
 170
 171     /*
 172     // debug mesh write  FIXME
 173     vtkSmartPointer<vtkPolyDataWriter> wr = vtkSmartPointer<vtkPolyDataWriter>::New();
 174     wr->SetInputConnection(convert->GetOutputPort()); //psurface->GetOutputPort()
 175     wr->SetFileName("bidon.obj");
 176     wr->Update();
 177     wr->Write();
 178     */
 179   }
 180
 181   // Copy previous contours
 182   for (unsigned int i = 0; i < numMasks-m; ++i) {
 183 #if VTK_MAJOR_VERSION <= 5
 184     writer->SetInput(i, reader->GetOutput(i));
 185 #else
 186     writer->SetInputData(i, reader->GetOutput(i));
 187 #endif
 188     std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
 189     roiNames->InsertValue(i, theString);
 190     theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
 191     roiAlgorithms->InsertValue(i, theString);
 192     theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i);
 193     roiTypes->InsertValue(i, theString);
 194   }
 195
 196   // Add new ones
 197   for (unsigned int i = numMasks-m; i < numMasks; ++i) {
 198 #if VTK_MAJOR_VERSION <= 5
 199     writer->SetInput(i, meshes[i-numMasks+m]);
 200 #else
 201     writer->SetInputData(i, meshes[i-numMasks+m]);
 202 #endif
 203     roiNames->InsertValue(i, m_ROINames[i-numMasks+m]);
 204     roiAlgorithms->InsertValue(i, "CLITK_CREATED");
 205     roiTypes->InsertValue(i, m_ROIType);
 206   }
 207
 208   /*
 209   //  Visu DEBUG
 210   vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
 211   cubeMapper->SetInput( mesh );
 212   cubeMapper->SetScalarRange(0,7);
 213   vtkActor *cubeActor = vtkActor::New();
 214   cubeActor->SetMapper(cubeMapper);
 215   vtkProperty * property = cubeActor->GetProperty();
 216   property->SetRepresentationToWireframe();
 217
 218   vtkRenderer *renderer = vtkRenderer::New();
 219   vtkRenderWindow *renWin = vtkRenderWindow::New();
 220   renWin->AddRenderer(renderer);
 221
 222   vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
 223   iren->SetRenderWindow(renWin);
 224
 225   renderer->AddActor(cubeActor);
 226   renderer->ResetCamera();
 227   renderer->SetBackground(1,1,1);
 228
 229   renWin->SetSize(300,300);
 230
 231   renWin->Render();
 232   iren->Start();
 233   */
 234   // End visu
 235
 236   // Write (need to read dicom for slice id)
 237   vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
 238   writer->SetRTStructSetProperties(theProperties);
 239   if (GetVerboseFlag()) {
 240     std::cout << "Looking for dicom info, study instance "
 241               << p->GetStudyInstanceUID() << std::endl;
 242   }
 243   writer->InitializeRTStructSet(m_DicomFolder,
 244                                 reader->GetRTStructSetProperties()->GetStructureSetLabel(),
 245                                 reader->GetRTStructSetProperties()->GetStructureSetName(),
 246                                 roiNames, roiAlgorithms, roiTypes);
 247   writer->Write();
 248   reader->Delete();
 249   roiNames->Delete();
 250   roiTypes->Delete();
 251   roiAlgorithms->Delete();
 252   writer->Delete();
 253 }
 254 //--------------------------------------------------------------------
 255
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