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   m_StructureSetFilename = "";
  61   m_DicomFolder = "";
  62   m_OutputFilename = "default-output.dcm";
  63   m_ThresholdValue = 0.5;
  64 }
  65 //--------------------------------------------------------------------
  66
  67
  68 //--------------------------------------------------------------------
  69 template<class PixelType>
  70 clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
  71 {
  72 }
  73 //--------------------------------------------------------------------
  74
  75
  76 //--------------------------------------------------------------------
  77 template<class PixelType>
  78 void
  79 clitk::Image2DicomRTStructFilter<PixelType>::SetROIName(std::string name, std::string type)
  80 {
  81   m_ROIName = name;
  82   m_ROIType = type;
  83 }
  84 //--------------------------------------------------------------------
  85
  86
  87 //--------------------------------------------------------------------
  88 template<class PixelType>
  89 void clitk::Image2DicomRTStructFilter<PixelType>::Update()
  90 {
  91   // Check this is a RT-Struct
  92   gdcm::Reader gdcm_reader;
  93   gdcm_reader.SetFileName(m_StructureSetFilename.c_str());
  94   if (!gdcm_reader.Read()) {
  95     clitkExceptionMacro("Error could not open the file '" << m_StructureSetFilename << std::endl);
  96   }
  97   gdcm::MediaStorage ms;
  98   ms.SetFromFile(gdcm_reader.GetFile());
  99   if (ms != gdcm::MediaStorage::RTStructureSetStorage) {
 100     clitkExceptionMacro("File '" << m_StructureSetFilename << "' is not a DICOM-RT-Struct file." << std::endl);
 101   }
 102
 103   // Read rt struct
 104   vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
 105   reader->SetFileName(m_StructureSetFilename.c_str());
 106   reader->Update();
 107
 108   // Get properties
 109   vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
 110   if (GetVerboseFlag()) {
 111     std::cout << "Number of structures in the dicom-rt-struct : "
 112               << p->GetNumberOfStructureSetROIs() << std::endl;
 113   }
 114
 115   // Init writer
 116   vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
 117   int numMasks = reader->GetNumberOfOutputPorts() + 1;//add one more
 118   writer->SetNumberOfInputPorts(numMasks);
 119   writer->SetFileName(m_OutputFilename.c_str());
 120   writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
 121
 122   // List of already present rois
 123   vtkStringArray* roiNames = vtkStringArray::New();
 124   vtkStringArray* roiAlgorithms = vtkStringArray::New();
 125   vtkStringArray* roiTypes = vtkStringArray::New();
 126   roiNames->SetNumberOfValues(numMasks);
 127   roiAlgorithms->SetNumberOfValues(numMasks);
 128   roiTypes->SetNumberOfValues(numMasks);
 129
 130   // Convert the image into a mesh
 131   typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
 132   typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
 133   convert->SetThresholdValue(m_ThresholdValue);
 134   convert->SetInput(m_Input);
 135   convert->Update();
 136   vtkPolyData* mesh = convert->GetOutputMesh();
 137   if (GetVerboseFlag()) {
 138     std::cout << "Mesh has " << mesh->GetNumberOfLines() << " lines." << std::endl;
 139   }
 140
 141   // Copy previous contours
 142   for (unsigned int i = 0; i < numMasks-1; ++i) {
 143     writer->SetInput(i, reader->GetOutput(i));
 144     std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
 145     roiNames->InsertValue(i, theString);
 146     theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
 147     roiAlgorithms->InsertValue(i, theString);
 148     theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i);
 149     roiTypes->InsertValue(i, theString);
 150   }
 151
 152   // Add new one
 153   int last = numMasks-1;
 154   writer->SetInput(last, mesh);
 155   roiNames->InsertValue(last, m_ROIName);
 156   roiAlgorithms->InsertValue(last, "CLITK_CREATED");
 157   roiTypes->InsertValue(last, m_ROIType);
 158
 159   /*
 160   //  Visu DEBUG
 161   vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
 162   cubeMapper->SetInput( mesh );
 163   cubeMapper->SetScalarRange(0,7);
 164   vtkActor *cubeActor = vtkActor::New();
 165   cubeActor->SetMapper(cubeMapper);
 166   vtkProperty * property = cubeActor->GetProperty();
 167   property->SetRepresentationToWireframe();
 168
 169   vtkRenderer *renderer = vtkRenderer::New();
 170   vtkRenderWindow *renWin = vtkRenderWindow::New();
 171   renWin->AddRenderer(renderer);
 172
 173   vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
 174   iren->SetRenderWindow(renWin);
 175
 176   renderer->AddActor(cubeActor);
 177   renderer->ResetCamera();
 178   renderer->SetBackground(1,1,1);
 179
 180   renWin->SetSize(300,300);
 181
 182   renWin->Render();
 183   iren->Start();
 184   */
 185   // End visu
 186
 187   // Write (need to read dicom for slice id)
 188   vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
 189   writer->SetRTStructSetProperties(theProperties);
 190   if (GetVerboseFlag()) {
 191     std::cout << "Looking for dicom info, study instance "
 192               << p->GetStudyInstanceUID() << std::endl;
 193   }
 194   writer->InitializeRTStructSet(m_DicomFolder,
 195                                 reader->GetRTStructSetProperties()->GetStructureSetLabel(),
 196                                 reader->GetRTStructSetProperties()->GetStructureSetName(),
 197                                 roiNames, roiAlgorithms, roiTypes);
 198   writer->Write();
 199   reader->Delete();
 200   roiNames->Delete();
 201   roiTypes->Delete();
 202   roiAlgorithms->Delete();
 203   writer->Delete();
 204 }
 205 //--------------------------------------------------------------------
 206
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