common/clitkDicomRTStruct2ImageFilter.cxx

   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 #include <iterator>
  21 #include <algorithm>
  22
  23 // clitk
  24 #include "clitkDicomRTStruct2ImageFilter.h"
  25 #include "clitkImageCommon.h"
  26
  27 // vtk
  28 #include <vtkVersion.h>
  29 #include <vtkPolyDataToImageStencil.h>
  30 #include <vtkSmartPointer.h>
  31 #include <vtkImageStencil.h>
  32 #include <vtkLinearExtrusionFilter.h>
  33 #include <vtkMetaImageWriter.h>
  34
  35
  36 //--------------------------------------------------------------------
  37 clitk::DicomRTStruct2ImageFilter::DicomRTStruct2ImageFilter()
  38 {
  39   mROI = NULL;
  40   mWriteOutput = false;
  41   mCropMask = true;
  42 }
  43 //--------------------------------------------------------------------
  44
  45
  46 //--------------------------------------------------------------------
  47 clitk::DicomRTStruct2ImageFilter::~DicomRTStruct2ImageFilter()
  48 {
  49
  50 }
  51 //--------------------------------------------------------------------
  52
  53
  54 //--------------------------------------------------------------------
  55 bool clitk::DicomRTStruct2ImageFilter::ImageInfoIsSet() const
  56 {
  57   return mSize.size() && mSpacing.size() && mOrigin.size();
  58 }
  59 //--------------------------------------------------------------------
  60
  61
  62 //--------------------------------------------------------------------
  63 void clitk::DicomRTStruct2ImageFilter::SetWriteOutputFlag(bool b)
  64 {
  65   mWriteOutput = b;
  66 }
  67 //--------------------------------------------------------------------
  68
  69
  70 //--------------------------------------------------------------------
  71 void clitk::DicomRTStruct2ImageFilter::SetROI(clitk::DicomRT_ROI * roi)
  72 {
  73   mROI = roi;
  74 }
  75 //--------------------------------------------------------------------
  76
  77
  78 //--------------------------------------------------------------------
  79 void clitk::DicomRTStruct2ImageFilter::SetCropMaskEnabled(bool b)
  80 {
  81   mCropMask = b;
  82 }
  83 //--------------------------------------------------------------------
  84
  85
  86 //--------------------------------------------------------------------
  87 void clitk::DicomRTStruct2ImageFilter::SetOutputImageFilename(std::string s)
  88 {
  89   mOutputFilename = s;
  90   mWriteOutput = true;
  91 }
  92 //--------------------------------------------------------------------
  93
  94
  95 //--------------------------------------------------------------------
  96 void clitk::DicomRTStruct2ImageFilter::SetImage(vvImage::Pointer image)
  97 {
  98   if (image->GetNumberOfDimensions() != 3) {
  99     std::cerr << "Error. Please provide a 3D image." << std::endl;
 100     exit(0);
 101   }
 102   mSpacing.resize(3);
 103   mOrigin.resize(3);
 104   mSize.resize(3);
 105   for(unsigned int i=0; i<3; i++) {
 106     mSpacing[i] = image->GetSpacing()[i];
 107     mOrigin[i] = image->GetOrigin()[i];
 108     mSize[i] = image->GetSize()[i];
 109   }
 110 }
 111 //--------------------------------------------------------------------
 112
 113
 114 //--------------------------------------------------------------------
 115 void clitk::DicomRTStruct2ImageFilter::SetImageFilename(std::string f)
 116 {
 117   itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
 118   if (header->GetNumberOfDimensions() < 3) {
 119     std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
 120     exit(0);
 121   }
 122   if (header->GetNumberOfDimensions() > 3) {
 123     std::cerr << "Warning dimension > 3 are ignored" << std::endl;
 124   }
 125   mSpacing.resize(3);
 126   mOrigin.resize(3);
 127   mSize.resize(3);
 128   for(unsigned int i=0; i<3; i++) {
 129     mSpacing[i] = header->GetSpacing(i);
 130     mOrigin[i] = header->GetOrigin(i);
 131     mSize[i] = header->GetDimensions(i);
 132   }
 133 }
 134 //--------------------------------------------------------------------
 135
 136
 137 //--------------------------------------------------------------------
 138 void clitk::DicomRTStruct2ImageFilter::SetOutputOrigin(const double* origin)
 139 {
 140   std::copy(origin,origin+3,std::back_inserter(mOrigin));
 141 }
 142 //--------------------------------------------------------------------
 143
 144
 145 //--------------------------------------------------------------------
 146 void clitk::DicomRTStruct2ImageFilter::SetOutputSpacing(const double* spacing)
 147 {
 148   std::copy(spacing,spacing+3,std::back_inserter(mSpacing));
 149 }
 150 //--------------------------------------------------------------------
 151
 152
 153 //--------------------------------------------------------------------
 154 void clitk::DicomRTStruct2ImageFilter::SetOutputSize(const unsigned long* size)
 155 {
 156   std::copy(size,size+3,std::back_inserter(mSize));
 157 }
 158 //--------------------------------------------------------------------
 159
 160
 161 //--------------------------------------------------------------------
 162 void clitk::DicomRTStruct2ImageFilter::Update()
 163 {
 164   if (!mROI) {
 165     std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
 166     exit(0);
 167   }
 168   if (!ImageInfoIsSet()) {
 169     std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
 170     exit(0);
 171   }
 172
 173   // Get Mesh
 174   vtkPolyData * mesh = mROI->GetMesh();
 175
 176   // Get bounds
 177   double *bounds=mesh->GetBounds();
 178
 179   // Compute origin
 180   std::vector<double> origin;
 181   origin.resize(3);
 182   origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
 183   origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
 184   origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
 185
 186   // Compute extend
 187   std::vector<double> extend;
 188   extend.resize(3);
 189   extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
 190   extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
 191   extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
 192
 193   // If no crop, set initial image size/origin
 194   if (!mCropMask) {
 195     for(int i=0; i<3; i++) {
 196       origin[i] = mOrigin[i];
 197       extend[i] = mSize[i]-1;
 198     }
 199   }
 200
 201   // Create new output image
 202   mBinaryImage = vtkSmartPointer<vtkImageData>::New();
 203 #if VTK_MAJOR_VERSION <= 5
 204   mBinaryImage->SetScalarTypeToUnsignedChar();
 205 #endif
 206   mBinaryImage->SetOrigin(&origin[0]);
 207   mBinaryImage->SetSpacing(&mSpacing[0]);
 208   mBinaryImage->SetExtent(0, extend[0],
 209                           0, extend[1],
 210                           0, extend[2]);
 211 #if VTK_MAJOR_VERSION <= 5
 212   mBinaryImage->AllocateScalars();
 213 #else
 214   mBinaryImage->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
 215 #endif
 216
 217   memset(mBinaryImage->GetScalarPointer(), 0,
 218          mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
 219
 220   // Extrude
 221   vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
 222 #if VTK_MAJOR_VERSION <= 5
 223   extrude->SetInput(mesh);
 224 #else
 225   extrude->SetInputData(mesh);
 226 #endif
 227   ///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
 228   extrude->SetVector(0, 0, -mSpacing[2]);
 229
 230   // Binarization
 231   vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
 232   //The following line is extremely important
 233   //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
 234   sts->SetTolerance(0);
 235   sts->SetInformationInput(mBinaryImage);
 236 #if VTK_MAJOR_VERSION <= 5
 237   sts->SetInput(extrude->GetOutput());
 238 #else
 239   sts->SetInputConnection(extrude->GetOutputPort(0));
 240 #endif
 241   //sts->SetInput(mesh);
 242
 243   vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
 244 #if VTK_MAJOR_VERSION <= 5
 245   stencil->SetStencil(sts->GetOutput());
 246 #else
 247   stencil->SetStencilConnection(sts->GetOutputPort(0));
 248 #endif
 249 #if VTK_MAJOR_VERSION <= 5
 250   stencil->SetInput(mBinaryImage);
 251 #else
 252   stencil->SetInputData(mBinaryImage);
 253 #endif
 254   stencil->ReverseStencilOn();
 255   stencil->Update();
 256
 257   /*
 258   vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
 259   w->SetInput(stencil->GetOutput());
 260   w->SetFileName("binary2.mhd");
 261   w->Write();
 262   */
 263
 264   mBinaryImage->ShallowCopy(stencil->GetOutput());
 265
 266   if (mWriteOutput) {
 267     typedef itk::Image<unsigned char, 3> ImageType;
 268     typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
 269     ConnectorType::Pointer connector = ConnectorType::New();
 270     connector->SetInput(GetOutput());
 271     connector->Update();
 272     clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
 273   }
 274 }
 275 //--------------------------------------------------------------------
 276
 277
 278
 279 //--------------------------------------------------------------------
 280 vtkImageData * clitk::DicomRTStruct2ImageFilter::GetOutput()
 281 {
 282   assert(mBinaryImage);
 283   return mBinaryImage;
 284 }
 285 //--------------------------------------------------------------------
 286