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   // number of additional contours
 119   int m = m_InputFilenames.size();
 120
 121   // Init writer
 122   vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
 123   int numMasks = reader->GetNumberOfOutputPorts() + m;
 124
 125   if (m_SkipInitialStructuresFlag) {
 126     numMasks = m;
 127   }
 128
 129   writer->SetNumberOfInputPorts(numMasks);
 130   writer->SetFileName(m_OutputFilename.c_str());
 131   writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
 132
 133   // List of already present rois
 134   vtkStringArray* roiNames = vtkStringArray::New();
 135   vtkStringArray* roiAlgorithms = vtkStringArray::New();
 136   vtkStringArray* roiTypes = vtkStringArray::New();
 137   roiNames->SetNumberOfValues(numMasks);
 138   roiAlgorithms->SetNumberOfValues(numMasks);
 139   roiTypes->SetNumberOfValues(numMasks);
 140
 141   // Convert the image into a mesh
 142   std::vector<vtkSmartPointer<vtkPolyData> > meshes;
 143   std::vector<std::string> m_ROINames;
 144   meshes.resize(m);
 145   m_ROINames.resize(m);
 146   for(unsigned int i=0; i<m; i++) {
 147
 148     // read image
 149     //    typedef float PixelType;
 150     //typedef itk::Image<PixelType, 3> ImageType;
 151     ImagePointer input = clitk::readImage<ImageType>(m_InputFilenames[i], false);
 152
 153     std::ostringstream oss;
 154     oss << vtksys::SystemTools::
 155       GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(m_InputFilenames[i]));
 156     std::string name = oss.str();
 157     m_ROINames[i] = name;
 158
 159     // convert to mesh
 160     typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
 161     typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
 162     convert->SetThresholdValue(m_ThresholdValue);
 163     convert->SetInput(input);
 164     convert->Update();
 165     meshes[i] = convert->GetOutputMesh();
 166     if (GetVerboseFlag()) {
 167       std::cout << "Mesh has " << meshes[i]->GetNumberOfLines() << " lines." << std::endl;
 168     }
 169
 170     /*
 171     // debug mesh write  FIXME
 172     vtkSmartPointer<vtkPolyDataWriter> wr = vtkSmartPointer<vtkPolyDataWriter>::New();
 173     wr->SetInputConnection(convert->GetOutputPort()); //psurface->GetOutputPort()
 174     wr->SetFileName("bidon.obj");
 175     wr->Update();
 176     wr->Write();
 177     */
 178   }
 179
 180   // Copy previous contours
 181   for (unsigned int i = 0; i < numMasks-m; ++i) {
 182 #if VTK_MAJOR_VERSION <= 5
 183     writer->SetInput(i, reader->GetOutput(i));
 184 #else
 185     writer->SetInputData(i, reader->GetOutput(i));
 186 #endif
 187     std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
 188     roiNames->InsertValue(i, theString);
 189     theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
 190     roiAlgorithms->InsertValue(i, theString);
 191     theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i);
 192     roiTypes->InsertValue(i, theString);
 193   }
 194
 195   // Add new ones
 196   for (unsigned int i = numMasks-m; i < numMasks; ++i) {
 197 #if VTK_MAJOR_VERSION <= 5
 198     writer->SetInput(i, meshes[i-numMasks+m]);
 199 #else
 200     writer->SetInputData(i, meshes[i-numMasks+m]);
 201 #endif
 202     roiNames->InsertValue(i, m_ROINames[i-numMasks+m]);
 203     roiAlgorithms->InsertValue(i, "CLITK_CREATED");
 204     roiTypes->InsertValue(i, m_ROIType);
 205   }
 206
 207   /*
 208   //  Visu DEBUG
 209   vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
 210   cubeMapper->SetInput( mesh );
 211   cubeMapper->SetScalarRange(0,7);
 212   vtkActor *cubeActor = vtkActor::New();
 213   cubeActor->SetMapper(cubeMapper);
 214   vtkProperty * property = cubeActor->GetProperty();
 215   property->SetRepresentationToWireframe();
 216
 217   vtkRenderer *renderer = vtkRenderer::New();
 218   vtkRenderWindow *renWin = vtkRenderWindow::New();
 219   renWin->AddRenderer(renderer);
 220
 221   vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
 222   iren->SetRenderWindow(renWin);
 223
 224   renderer->AddActor(cubeActor);
 225   renderer->ResetCamera();
 226   renderer->SetBackground(1,1,1);
 227
 228   renWin->SetSize(300,300);
 229
 230   renWin->Render();
 231   iren->Start();
 232   */
 233   // End visu
 234
 235   // Write (need to read dicom for slice id)
 236   vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
 237   writer->SetRTStructSetProperties(theProperties);
 238   if (GetVerboseFlag()) {
 239     std::cout << "Looking for dicom info, study instance "
 240               << p->GetStudyInstanceUID() << std::endl;
 241   }
 242   writer->InitializeRTStructSet(m_DicomFolder,
 243                                 reader->GetRTStructSetProperties()->GetStructureSetLabel(),
 244                                 reader->GetRTStructSetProperties()->GetStructureSetName(),
 245                                 roiNames, roiAlgorithms, roiTypes);
 246   writer->Write();
 247   reader->Delete();
 248   roiNames->Delete();
 249   roiTypes->Delete();
 250   roiAlgorithms->Delete();
 251   writer->Delete();
 252 }
 253 //--------------------------------------------------------------------
 254
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