Lib/PrePostProcessing/itkSTMS_TemporalSetToImageSequence_Spine.txx

   1 /*
   2  #
   3  #  File        : itkSTMS_TemporalSetToImageSequence_Spine.txx
   4  #                ( C++ header file - STMS )
   5  #
   6  #  Description : STMS lib that implements the STMS filter and clustering.
   7  #                This file is a part of the STMS Library project.
   8  #                ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
   9  #
  10  #  [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
  11  #       « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
  12  #       Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
  13  #
  14  #  Copyright   : Thomas GRENIER - Simon MURE
  15  #                ( https://www.creatis.insa-lyon.fr/~grenier/ )
  16  #
  17  #  License     : CeCILL C
  18  #                ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
  19  #
  20  #  This software is governed by the CeCILL  license under French law and
  21  #  abiding by the rules of distribution of free software.  You can  use,
  22  #  modify and/ or redistribute the software under the terms of the CeCILL
  23  #  license as circulated by CEA, CNRS and INRIA at the following URL
  24  #  "http://www.cecill.info".
  25  #
  26  #  As a counterpart to the access to the source code and  rights to copy,
  27  #  modify and redistribute granted by the license, users are provided only
  28  #  with a limited warranty  and the software's author,  the holder of the
  29  #  economic rights,  and the successive licensors  have only  limited
  30  #  liability.
  31  #
  32  #  In this respect, the user's attention is drawn to the risks associated
  33  #  with loading,  using,  modifying and/or developing or reproducing the
  34  #  software by the user in light of its specific status of free software,
  35  #  that may mean  that it is complicated to manipulate,  and  that  also
  36  #  therefore means  that it is reserved for developers  and  experienced
  37  #  professionals having in-depth computer knowledge. Users are therefore
  38  #  encouraged to load and test the software's suitability as regards their
  39  #  requirements in conditions enabling the security of their systems and/or
  40  #  data to be ensured and,  more generally, to use and operate it in the
  41  #  same conditions as regards security.
  42  #
  43  #  The fact that you are presently reading this means that you have had
  44  #  knowledge of the CeCILL license and that you accept its terms.
  45  #
  46 */
  47 /* Please don't forget to cite our work :
  48   @article {MURE-15a,
  49     title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
  50     journal = {Pattern Recognition Letters},
  51     volume = {68, Part 1},
  52     year = {2015},
  53     pages = {48 - 55},
  54     issn = {0167-8655},
  55     doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
  56     url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
  57     author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
  58 }
  59 */
  60 #ifndef itkSTMS_TemporalSetToImageSequenceSpine_txx
  61 #define itkSTMS_TemporalSetToImageSequenceSpine_txx
  62
  63 #include "itkSTMS_TemporalSetToImageSequence_Spine.h"
  64 #include "itkSTMS_ArgumentsAnalysis_Spine.h"
  65
  66 namespace itkSTMS_Spine
  67 {
  68
  69 template < class ImageType, class ClassImageType >
  70 itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType >
  71 ::itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl, SpatialSampleSetType* sp, RangeSampleSetType* ra,
  72                                       itkSTMS_Spine::ParamsAnalysisOutputType* params)
  73 {
  74     this->stmsParameters = params;
  75     this->classSet       = cl;
  76     this->spatialSet     = sp;
  77     this->rangeSet       = ra;
  78 }
  79
  80
  81 template < class ImageType, class ClassImageType >
  82 void
  83 itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
  84 ::GenerateImageSequence()
  85 {
  86     bool first = true;
  87
  88     // Output images allocation
  89     ImagePointer image
  90             = ImageType::New();
  91     ReaderPointer reader
  92             = ReaderType::New();
  93
  94     reader->SetFileName( *stmsParameters->images.begin() );
  95     reader->Update();
  96     image = reader->GetOutput();
  97
  98     SpatialIndexType start, outIndex, classIndex;
  99     start.Fill(0);
 100
 101     RegionType region;
 102     region.SetSize( image->GetBufferedRegion().GetSize());
 103     region.SetIndex(start);
 104
 105     ClassRegionType classRegion;
 106     classRegion.SetSize( image->GetBufferedRegion().GetSize());
 107     classRegion.SetIndex( start );
 108
 109
 110     std::string outputPath, classPath;
 111
 112     ClassImagePointer classImage
 113             = ClassImageType::New();
 114
 115     classImage->SetRegions( classRegion );
 116     classImage->Allocate();
 117     classImage->FillBuffer( 15.0 );
 118
 119
 120     // Filetered image sequence and class image saving
 121     //    for( unsigned int i=1 ; i<=stmsParameters->numTimePoints ; ++i )
 122     //    {
 123     unsigned int i=1;
 124     for (std::list<std::string>::iterator it_images = stmsParameters->images.begin(); it_images != stmsParameters->images.end(); ++it_images)
 125     {
 126         outputPath = stmsParameters->outFolder+ it_images->substr( it_images->find_last_of("/"), it_images->length()-stmsParameters->imageExtension.length()-it_images->find_last_of("/") ) +
 127                 "_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
 128                 "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
 129                 "_Z-"+std::to_string(stmsParameters->spScales[2])+
 130                 "_R-"+std::to_string(stmsParameters->rScale)+"_"+
 131                 std::to_string(i)+stmsParameters->imageExtension;
 132
 133         ImagePointer outImage
 134                 = ImageType::New();
 135
 136         outImage->SetRegions( region );
 137         outImage->Allocate();
 138         outImage->FillBuffer( 15.0 );
 139
 140         WriterPointer writer
 141                 = WriterType::New();
 142         writer->SetFileName( outputPath );
 143
 144         //#pragma omp parrallel for ...
 145         for(unsigned int j=0 ; j<classSet->size() ; ++j)
 146         {
 147             for( unsigned int k=0 ; k<stmsParameters->dim ; ++k)
 148             {
 149                 outIndex[k]   = (IndexType)( round(spatialSet->at(j)[k]*stmsParameters->spScales[k]) );
 150
 151                 if( first )
 152                     classIndex[k] = outIndex[k];
 153             }
 154
 155             outImage->SetPixel( outIndex, rangeSet->at( classSet->at(j)-1 )[i-1]*stmsParameters->rScale );
 156
 157             if( first )
 158                 classImage->SetPixel(classIndex, classSet->at(j));
 159         }
 160
 161         writer->SetInput( outImage );
 162         writer->Update();
 163
 164         if( first )
 165         {
 166             classPath = stmsParameters->outFolder +
 167                     it_images->substr( it_images->find_last_of("/"), it_images->length()-stmsParameters->imageExtension.length()-it_images->find_last_of("/") ) +
 168                     "_Class_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
 169                     "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
 170                     "_Z-"+std::to_string(stmsParameters->spScales[2])+
 171                     "_R-"+std::to_string(stmsParameters->rScale)+"_"+
 172                     stmsParameters->imageExtension;
 173
 174             ClassWriterPointer classWriter
 175                     = ClassWriterType::New();
 176             classWriter->SetFileName( classPath );
 177
 178             classWriter->SetInput( classImage );
 179             classWriter->Update();
 180             first = false;
 181         }
 182
 183         ++i;
 184     }
 185 }
 186
 187 } // end of namespace itkSTMS
 188
 189 #endif