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