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   mDirection.resize(3);
 106   for(unsigned int i=0; i<3; i++) {
 107     mSpacing[i] = image->GetSpacing()[i];
 108     mOrigin[i] = image->GetOrigin()[i];
 109     mSize[i] = image->GetSize()[i];
 110     mDirection[i].resize(3);
 111     for(unsigned int j=0; j<3; j++)
 112       mDirection[i][j] = image->GetDirection()[i][j];
 113   }
 114 }
 115 //--------------------------------------------------------------------
 116
 117
 118 //--------------------------------------------------------------------
 119 void clitk::DicomRTStruct2ImageFilter::SetImageFilename(std::string f)
 120 {
 121   itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
 122   if (header->GetNumberOfDimensions() < 3) {
 123     std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
 124     exit(0);
 125   }
 126   if (header->GetNumberOfDimensions() > 3) {
 127     std::cerr << "Warning dimension > 3 are ignored" << std::endl;
 128   }
 129   mSpacing.resize(3);
 130   mOrigin.resize(3);
 131   mSize.resize(3);
 132   mDirection.resize(3);
 133   for(unsigned int i=0; i<3; i++) {
 134     mSpacing[i] = header->GetSpacing(i);
 135     mOrigin[i] = header->GetOrigin(i);
 136     mSize[i] = header->GetDimensions(i);
 137     mDirection[i].resize(3);
 138     for(unsigned int j=0; j<3; j++)
 139       mDirection[i][j] = header->GetDirection(i)[j];
 140   }
 141 }
 142 //--------------------------------------------------------------------
 143
 144
 145 //--------------------------------------------------------------------
 146 void clitk::DicomRTStruct2ImageFilter::SetOutputOrigin(const double* origin)
 147 {
 148   std::copy(origin,origin+3,std::back_inserter(mOrigin));
 149 }
 150 //--------------------------------------------------------------------
 151
 152
 153 //--------------------------------------------------------------------
 154 void clitk::DicomRTStruct2ImageFilter::SetOutputSpacing(const double* spacing)
 155 {
 156   std::copy(spacing,spacing+3,std::back_inserter(mSpacing));
 157 }
 158 //--------------------------------------------------------------------
 159
 160
 161 //--------------------------------------------------------------------
 162 void clitk::DicomRTStruct2ImageFilter::SetOutputSize(const unsigned long* size)
 163 {
 164   std::copy(size,size+3,std::back_inserter(mSize));
 165 }
 166 //--------------------------------------------------------------------
 167
 168
 169 //--------------------------------------------------------------------
 170 void clitk::DicomRTStruct2ImageFilter::Update()
 171 {
 172   if (!mROI) {
 173     std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
 174     exit(0);
 175   }
 176   if (!ImageInfoIsSet()) {
 177     std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
 178     exit(0);
 179   }
 180
 181   // Get Mesh
 182   vtkPolyData * mesh = mROI->GetMesh();
 183
 184   // Get bounds
 185   double *bounds=mesh->GetBounds();
 186
 187   //Change mOrigin, mSize and mSpacing with respect to the directions
 188   // Spacing is influenced by input direction
 189   std::vector<double> tempSpacing;
 190   tempSpacing.resize(3);
 191   for(int i=0; i<3; i++) {
 192     tempSpacing[i] = 0.0;
 193     for(int j=0; j<3; j++) {
 194       tempSpacing[i] += mDirection[i][j] * mSpacing[j];
 195     }
 196   }
 197   for(int i=0; i<3; i++)
 198     mSpacing[i] = tempSpacing[i];
 199
 200   // Size is influenced by affine transform matrix and input direction
 201   // Size is converted to double, transformed and converted back to size type.
 202   std::vector<double> tempSize;
 203   tempSize.resize(3);
 204   for(int i=0; i<3; i++) {
 205     tempSize[i] = 0.0;
 206     for(int j=0; j<3; j++) {
 207       tempSize[i] += mDirection[i][j] * mSize[j];
 208     }
 209   }
 210   for(int i=0; i<3; i++) {
 211     if (tempSize[i] < 0.0) {
 212       tempSize[i] *= -1;
 213       mOrigin[i] += mSpacing[i]*(tempSize[i] -1);
 214       mSpacing[i] *= -1;
 215     }
 216     mSize[i] = lrint(tempSize[i]);
 217   }
 218
 219   // Compute origin
 220   std::vector<double> origin;
 221   origin.resize(3);
 222   origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
 223   origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
 224   origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
 225
 226   // Compute extend
 227   std::vector<double> extend;
 228   extend.resize(3);
 229   extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
 230   extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
 231   extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
 232
 233   // If no crop, set initial image size/origin
 234   if (!mCropMask) {
 235     for(int i=0; i<3; i++) {
 236       origin[i] = mOrigin[i];
 237       extend[i] = mSize[i]-1;
 238     }
 239   }
 240
 241   // Create new output image
 242   mBinaryImage = vtkSmartPointer<vtkImageData>::New();
 243 #if VTK_MAJOR_VERSION <= 5
 244   mBinaryImage->SetScalarTypeToUnsignedChar();
 245 #endif
 246   mBinaryImage->SetOrigin(&origin[0]);
 247   mBinaryImage->SetSpacing(&mSpacing[0]);
 248   mBinaryImage->SetExtent(0, extend[0],
 249                           0, extend[1],
 250                           0, extend[2]);
 251 #if VTK_MAJOR_VERSION <= 5
 252   mBinaryImage->AllocateScalars();
 253 #else
 254   mBinaryImage->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
 255 #endif
 256
 257   memset(mBinaryImage->GetScalarPointer(), 0,
 258          mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
 259
 260   // Extrude
 261   vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
 262 #if VTK_MAJOR_VERSION <= 5
 263   extrude->SetInput(mesh);
 264 #else
 265   extrude->SetInputData(mesh);
 266 #endif
 267   ///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
 268   extrude->SetVector(0, 0, -mSpacing[2]);
 269
 270   // Binarization
 271   vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
 272   //The following line is extremely important
 273   //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
 274   sts->SetTolerance(0);
 275   sts->SetInformationInput(mBinaryImage);
 276 #if VTK_MAJOR_VERSION <= 5
 277   sts->SetInput(extrude->GetOutput());
 278 #else
 279   sts->SetInputConnection(extrude->GetOutputPort(0));
 280 #endif
 281   //sts->SetInput(mesh);
 282
 283   vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
 284 #if VTK_MAJOR_VERSION <= 5
 285   stencil->SetStencil(sts->GetOutput());
 286 #else
 287   stencil->SetStencilConnection(sts->GetOutputPort(0));
 288 #endif
 289 #if VTK_MAJOR_VERSION <= 5
 290   stencil->SetInput(mBinaryImage);
 291 #else
 292   stencil->SetInputData(mBinaryImage);
 293 #endif
 294   stencil->ReverseStencilOn();
 295   stencil->Update();
 296
 297   /*
 298   vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
 299   w->SetInput(stencil->GetOutput());
 300   w->SetFileName("binary2.mhd");
 301   w->Write();
 302   */
 303
 304   mBinaryImage->ShallowCopy(stencil->GetOutput());
 305
 306   if (mWriteOutput) {
 307     typedef itk::Image<unsigned char, 3> ImageType;
 308     typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
 309     ConnectorType::Pointer connector = ConnectorType::New();
 310     connector->SetInput(GetOutput());
 311     connector->Update();
 312     clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
 313   }
 314 }
 315 //--------------------------------------------------------------------
 316
 317
 318
 319 //--------------------------------------------------------------------
 320 vtkImageData * clitk::DicomRTStruct2ImageFilter::GetOutput()
 321 {
 322   assert(mBinaryImage);
 323   return mBinaryImage;
 324 }
 325 //--------------------------------------------------------------------
 326