itk/clitkCropLikeImageFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ===========================================================================**/
  18
  19 #ifndef CLITKCROPLIKEIMAGEFILTER_TXX
  20 #define CLITKCROPLIKEIMAGEFILTER_TXX
  21
  22 // clitk
  23 #include "clitkCommon.h"
  24 #include "clitkPasteImageFilter.h"
  25
  26 //--------------------------------------------------------------------
  27 template <class ImageType>
  28 clitk::CropLikeImageFilter<ImageType>::
  29 CropLikeImageFilter():itk::ImageToImageFilter<ImageType, ImageType>() {
  30   this->SetNumberOfRequiredInputs(1);
  31   m_LikeImage = NULL;
  32   m_LikeFilenameIsGiven = false;
  33   this->SetBackgroundValue(typename PixelTraits<typename ImageType::PixelType>::ValueType(0));
  34   m_CropAlongThisDimension.resize(ImageType::ImageDimension);
  35   for(uint i=0; i<ImageType::ImageDimension; i++)
  36     m_CropAlongThisDimension[i] = true;
  37 }
  38 //--------------------------------------------------------------------
  39
  40
  41 //--------------------------------------------------------------------
  42 template <class ImageType>
  43 void
  44 clitk::CropLikeImageFilter<ImageType>::
  45 SetCropLikeFilename(std::string f)
  46 {
  47   m_LikeFilename = f;
  48   m_LikeFilenameIsGiven = true;
  49 }
  50 //--------------------------------------------------------------------
  51
  52
  53 //--------------------------------------------------------------------
  54 template <class ImageType>
  55 void
  56 clitk::CropLikeImageFilter<ImageType>::
  57 SetCropLikeImage(const itk::ImageBase<ImageType::ImageDimension> * like)
  58 {
  59   m_LikeImage = like;
  60 }
  61 //--------------------------------------------------------------------
  62
  63
  64 //--------------------------------------------------------------------
  65 template <class ImageType>
  66 void
  67 clitk::CropLikeImageFilter<ImageType>::
  68 SetCropLikeImage(const itk::ImageBase<ImageType::ImageDimension> * like, int axe)
  69 {
  70   m_LikeImage = like;
  71   for(uint i=0; i<ImageType::ImageDimension; i++)
  72     m_CropAlongThisDimension[i] = false;
  73   m_CropAlongThisDimension[axe] = true;
  74 }
  75 //--------------------------------------------------------------------
  76
  77
  78 //--------------------------------------------------------------------
  79 template <class ImageType>
  80 void
  81 clitk::CropLikeImageFilter<ImageType>::
  82 GenerateInputRequestedRegion() {
  83   // Needed because output region can be larger than input
  84   ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
  85   input->SetRequestedRegion(input->GetLargestPossibleRegion());
  86 }
  87 //--------------------------------------------------------------------
  88
  89
  90 //--------------------------------------------------------------------
  91 template <class ImageType>
  92 void
  93 clitk::CropLikeImageFilter<ImageType>::
  94 GenerateOutputInformation() {
  95   // Get input pointers
  96   ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
  97
  98   // Get output pointer
  99   ImagePointer output = this->GetOutput(0);
 100
 101   // Get input info
 102   typename ImageType::SizeType likeSize;
 103   typename ImageType::IndexType likeStart;
 104   typename ImageType::PointType likeOrigin;
 105   typename ImageType::SpacingType likeSpacing;
 106   if (m_LikeImage) {
 107     likeSize = m_LikeImage->GetLargestPossibleRegion().GetSize();
 108     likeStart = m_LikeImage->GetLargestPossibleRegion().GetIndex();
 109     likeOrigin = m_LikeImage->GetOrigin();
 110     likeSpacing = m_LikeImage->GetSpacing();
 111     output->CopyInformation(m_LikeImage);
 112   }
 113   else {
 114     // Only load the header (allows to use 'like' with any image type)
 115     if (m_LikeFilenameIsGiven) {
 116       itk::ImageIOBase::Pointer header = readImageHeader(m_LikeFilename);
 117       for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 118         likeSize[i] = header->GetDimensions(i);
 119         likeStart[i] = 0;//header->GetIORegion().GetIndex()[i];
 120         likeOrigin[i] = header->GetOrigin(i);
 121         likeSpacing[i] = header->GetSpacing(i);
 122       }
 123     }
 124     else {
 125       clitkExceptionMacro("You should provide SetCropLikeFilename or SetCropLike to CropLikeImageFilter");
 126     }
 127   }
 128
 129   // Check spacing
 130   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 131     if (likeSpacing[i] != input->GetSpacing()[i]) {
 132       clitkExceptionMacro("Images must have the same spacing, but input's spacing(" << i
 133                           <<") is " << input->GetSpacing()[i] << " while the spacing(" << i
 134                           << ") of 'like' is " << likeSpacing[i] << ".");
 135     }
 136   }
 137
 138   // Check that we must crop along each dimension. If not, we use the
 139   // size of the input image
 140   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 141     if (m_CropAlongThisDimension[i] == false) {
 142       likeStart[i] = input->GetLargestPossibleRegion().GetIndex()[i];
 143       likeSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
 144     }
 145   }
 146
 147   // Define output region
 148   m_OutputRegion.SetIndex(likeStart);
 149   m_OutputRegion.SetSize(likeSize);
 150   output->SetRegions(m_OutputRegion);
 151   output->SetRequestedRegion(m_OutputRegion);
 152   output->SetBufferedRegion(m_OutputRegion);
 153   output->SetSpacing(likeSpacing);
 154   output->SetOrigin(likeOrigin);
 155   output->Allocate(); // Needed ?
 156
 157   // get startpoint source/dest
 158   // for each dim
 159   // if source < dest -> start from dest, compute in source
 160   // if source > dest -> start from source, compute in dest
 161   m_StartDestIndex = output->GetLargestPossibleRegion().GetIndex();
 162   m_StartSourceIndex = input->GetLargestPossibleRegion().GetIndex();
 163   PointType m_StartPointInSource;
 164   PointType m_StartPointInDest;
 165   m_StartSourceIndex = input->GetLargestPossibleRegion().GetIndex();
 166   input->TransformIndexToPhysicalPoint(m_StartSourceIndex, m_StartPointInSource);
 167   m_StartDestIndex = output->GetLargestPossibleRegion().GetIndex();
 168   output->TransformIndexToPhysicalPoint(m_StartDestIndex, m_StartPointInDest);
 169   IndexType startDestInSource;
 170   IndexType startSourceInDest;
 171   input->TransformPhysicalPointToIndex(m_StartPointInDest, startDestInSource);
 172   output->TransformPhysicalPointToIndex(m_StartPointInSource, startSourceInDest);
 173   for(int i=0; i<ImageType::ImageDimension; i++) {
 174     if (m_StartPointInSource[i] < m_StartPointInDest[i]) {
 175       m_StartSourceIndex[i] = startDestInSource[i];
 176     }
 177     else {
 178       m_StartDestIndex[i] = startSourceInDest[i];
 179     }
 180   }
 181   m_Region.SetIndex(m_StartSourceIndex);
 182
 183   // Stop index
 184   m_StopSourceIndex = input->GetLargestPossibleRegion().GetIndex()+
 185     input->GetLargestPossibleRegion().GetSize();
 186   m_StopDestIndex = output->GetLargestPossibleRegion().GetIndex()+
 187     output->GetLargestPossibleRegion().GetSize();
 188   PointType m_StopPointInSource;
 189   PointType m_StopPointInDest;
 190   input->TransformIndexToPhysicalPoint(m_StopSourceIndex, m_StopPointInSource);
 191   output->TransformIndexToPhysicalPoint(m_StopDestIndex, m_StopPointInDest);
 192   IndexType stopDestInSource;
 193   IndexType stopSourceInDest;
 194   input->TransformPhysicalPointToIndex(m_StopPointInDest, stopDestInSource);
 195   output->TransformPhysicalPointToIndex(m_StopPointInSource, stopSourceInDest);
 196
 197   for(int i=0; i<ImageType::ImageDimension; i++) {
 198     if (m_StopPointInSource[i] > m_StopPointInDest[i]) {
 199       m_StopSourceIndex[i] = stopDestInSource[i];
 200     }
 201     else {
 202       m_StopDestIndex[i] = stopSourceInDest[i];
 203     }
 204   }
 205
 206   // Set size to the region we want to paste
 207   SizeType s;
 208   for(int i=0; i<ImageType::ImageDimension; i++)
 209     s[i] = m_StopSourceIndex[i]-m_StartSourceIndex[i];
 210   m_Region.SetSize(s);
 211
 212 }
 213 //--------------------------------------------------------------------
 214
 215 //--------------------------------------------------------------------
 216 template <class ImageType>
 217 void
 218 clitk::CropLikeImageFilter<ImageType>::
 219 GenerateData() {
 220   // Get input pointers
 221   ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
 222
 223   // Get output pointer, fill with Background
 224   ImagePointer output = this->GetOutput(0);
 225
 226   output->FillBuffer(GetBackgroundValue());
 227
 228   // Paste image inside
 229   typedef clitk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
 230   typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
 231   //pasteFilter->ReleaseDataFlagOn(); // change nothing ?
 232   //  pasteFilter->InPlaceOn(); // makt it seg fault
 233   pasteFilter->SetSourceImage(input);
 234   pasteFilter->SetDestinationImage(output);
 235   pasteFilter->SetDestinationIndex(m_StartDestIndex);
 236   pasteFilter->SetSourceRegion(m_Region);
 237   pasteFilter->Update();
 238
 239   // Get (graft) output (SetNthOutput does not fit here because of Origin).
 240   this->GraftOutput(pasteFilter->GetOutput());
 241 }
 242 //--------------------------------------------------------------------
 243
 244
 245 //--------------------------------------------------------------------
 246 template<class ImageType>
 247 typename ImageType::Pointer
 248 clitk::ResizeImageLike(const ImageType * input,
 249                        const itk::ImageBase<ImageType::ImageDimension> * like,
 250                        typename ImageType::PixelType backgroundValue)
 251 {
 252   typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
 253   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 254   cropFilter->SetInput(input);
 255   cropFilter->SetCropLikeImage(like);
 256   cropFilter->SetBackgroundValue(backgroundValue);
 257   cropFilter->Update();
 258   return cropFilter->GetOutput();
 259 }
 260 //--------------------------------------------------------------------
 261
 262
 263 //--------------------------------------------------------------------
 264 template<class ImageType>
 265 typename ImageType::Pointer
 266 clitk::ResizeImageLike(const ImageType * input,
 267                        typename itk::ImageBase<ImageType::ImageDimension>::RegionType * region,
 268                        typename ImageType::PixelType backgroundValue)
 269 {
 270   typename ImageType::Pointer output = ImageType::New();
 271   output->CopyInformation(input);
 272   typename ImageType::RegionType reg;
 273   reg.SetIndex(region->GetIndex());
 274   reg.SetSize(region->GetSize());
 275   output->SetRegions(reg);
 276   output->Allocate();
 277   return clitk::ResizeImageLike<ImageType>(input, output, backgroundValue);
 278 }
 279 //--------------------------------------------------------------------
 280
 281
 282 //--------------------------------------------------------------------
 283 template<class ImageType>
 284 typename ImageType::Pointer
 285 clitk::ResizeImageLike(const ImageType * input,
 286                        typename itk::BoundingBox<unsigned long, ImageType::ImageDimension>::Pointer bb,
 287                        typename ImageType::PixelType BG)
 288 {
 289   typename ImageType::RegionType region;
 290   clitk::ComputeRegionFromBB<ImageType>(input, bb, region);
 291   typename ImageType::Pointer output = ImageType::New();
 292   output->CopyInformation(input);
 293   output->SetRegions(region);
 294   output->Allocate();
 295   return clitk::ResizeImageLike<ImageType>(input, output, BG);
 296 }
 297 //--------------------------------------------------------------------
 298
 299 #endif //#define CLITKCROPLIKEIMAGEFILTER_TXX