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 }
  66 //--------------------------------------------------------------------
  67
  68
  69 //--------------------------------------------------------------------
  70 template<class PixelType>
  71 clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
  72 {
  73 }
  74 //--------------------------------------------------------------------
  75
  76
  77 //--------------------------------------------------------------------
  78 template<class PixelType>
  79 void
  80 clitk::Image2DicomRTStructFilter<PixelType>::SetROIType(std::string type)
  81 {
  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
 116   // number of additional contours
 117   int m = m_InputFilenames.size();
 118
 119   // Init writer
 120   vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
 121   int numMasks = reader->GetNumberOfOutputPorts() + m;
 122   writer->SetNumberOfInputPorts(numMasks);
 123   writer->SetFileName(m_OutputFilename.c_str());
 124   writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
 125
 126   // List of already present rois
 127   vtkStringArray* roiNames = vtkStringArray::New();
 128   vtkStringArray* roiAlgorithms = vtkStringArray::New();
 129   vtkStringArray* roiTypes = vtkStringArray::New();
 130   roiNames->SetNumberOfValues(numMasks);
 131   roiAlgorithms->SetNumberOfValues(numMasks);
 132   roiTypes->SetNumberOfValues(numMasks);
 133
 134   // Convert the image into a mesh
 135   std::vector<vtkSmartPointer<vtkPolyData> > meshes;
 136   std::vector<std::string> m_ROINames;
 137   meshes.resize(m);
 138   m_ROINames.resize(m);
 139   for(unsigned int i=0; i<m; i++) {
 140
 141     // read image
 142     //    typedef float PixelType;
 143     //typedef itk::Image<PixelType, 3> ImageType;
 144     ImagePointer input = clitk::readImage<ImageType>(m_InputFilenames[i], false);
 145
 146     std::ostringstream oss;
 147     oss << vtksys::SystemTools::
 148       GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(m_InputFilenames[i]));
 149     std::string name = oss.str();
 150     m_ROINames[i] = name;
 151
 152     // convert to mesh
 153     typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
 154     typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
 155     convert->SetThresholdValue(m_ThresholdValue);
 156     convert->SetInput(input);
 157     convert->Update();
 158     meshes[i] = convert->GetOutputMesh();
 159     if (GetVerboseFlag()) {
 160       std::cout << "Mesh has " << meshes[i]->GetNumberOfLines() << " lines." << std::endl;
 161     }
 162
 163     /*
 164     // debug mesh write  FIXME
 165     vtkSmartPointer<vtkPolyDataWriter> wr = vtkSmartPointer<vtkPolyDataWriter>::New();
 166     wr->SetInputConnection(convert->GetOutputPort()); //psurface->GetOutputPort()
 167     wr->SetFileName("bidon.obj");
 168     wr->Update();
 169     wr->Write();
 170     */
 171   }
 172
 173   // Copy previous contours
 174   for (unsigned int i = 0; i < numMasks-m; ++i) {
 175     writer->SetInput(i, reader->GetOutput(i));
 176     std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
 177     roiNames->InsertValue(i, theString);
 178     theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
 179     roiAlgorithms->InsertValue(i, theString);
 180     theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i);
 181     roiTypes->InsertValue(i, theString);
 182   }
 183
 184   // Add new ones
 185   for (unsigned int i = numMasks-m; i < numMasks; ++i) {
 186     writer->SetInput(i, meshes[i-numMasks+m]);
 187     roiNames->InsertValue(i, m_ROINames[i-numMasks+m]);
 188     roiAlgorithms->InsertValue(i, "CLITK_CREATED");
 189     roiTypes->InsertValue(i, m_ROIType);
 190   }
 191
 192   /*
 193   //  Visu DEBUG
 194   vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
 195   cubeMapper->SetInput( mesh );
 196   cubeMapper->SetScalarRange(0,7);
 197   vtkActor *cubeActor = vtkActor::New();
 198   cubeActor->SetMapper(cubeMapper);
 199   vtkProperty * property = cubeActor->GetProperty();
 200   property->SetRepresentationToWireframe();
 201
 202   vtkRenderer *renderer = vtkRenderer::New();
 203   vtkRenderWindow *renWin = vtkRenderWindow::New();
 204   renWin->AddRenderer(renderer);
 205
 206   vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
 207   iren->SetRenderWindow(renWin);
 208
 209   renderer->AddActor(cubeActor);
 210   renderer->ResetCamera();
 211   renderer->SetBackground(1,1,1);
 212
 213   renWin->SetSize(300,300);
 214
 215   renWin->Render();
 216   iren->Start();
 217   */
 218   // End visu
 219
 220   // Write (need to read dicom for slice id)
 221   vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
 222   writer->SetRTStructSetProperties(theProperties);
 223   if (GetVerboseFlag()) {
 224     std::cout << "Looking for dicom info, study instance "
 225               << p->GetStudyInstanceUID() << std::endl;
 226   }
 227   writer->InitializeRTStructSet(m_DicomFolder,
 228                                 reader->GetRTStructSetProperties()->GetStructureSetLabel(),
 229                                 reader->GetRTStructSetProperties()->GetStructureSetName(),
 230                                 roiNames, roiAlgorithms, roiTypes);
 231   writer->Write();
 232   reader->Delete();
 233   roiNames->Delete();
 234   roiTypes->Delete();
 235   roiAlgorithms->Delete();
 236   writer->Delete();
 237 }
 238 //--------------------------------------------------------------------
 239
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 242