Lib/PrePostProcessing/itkSTMS_TemporalSetToImageSequence.txx

   1 /*
   2  #
   3  #  File        : itkSTMS_TemporalSetToImageSequence.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_TemporalSetToImageSequence_txx
  61 #define itkSTMS_TemporalSetToImageSequence_txx
  62
  63 #include "itkSTMS_TemporalSetToImageSequence.h"
  64 #include "itkSTMS_XMLFileParser.h"
  65 #include "itkSTMS_ArgumentsAnalysis.h"
  66
  67 namespace itkSTMS
  68 {
  69
  70 template < class ImageType, class ClassImageType >
  71 itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType >
  72 ::itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl, SpatialSampleSetType* sp, RangeSampleSetType* ra,
  73                                       itkSTMS::ParamsAnalysisOutputType* params, itkSTMS::ParserOutputType* desc )
  74 {
  75     this->stmsParameters = params;
  76     this->expDescription = desc;
  77
  78     this->classSet   = cl;
  79     this->spatialSet = sp;
  80     this->rangeSet   = ra;
  81 }
  82
  83
  84 template < class ImageType, class ClassImageType >
  85 void
  86 itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
  87 ::GenerateImageSequence()
  88 {
  89     bool first = true;
  90
  91     // Output images allocation
  92     ImagePointer image
  93             = ImageType::New();
  94     ReaderPointer reader
  95             = ReaderType::New();
  96
  97     std::string imagePath = expDescription->experimentPath+expDescription->inputFolder+expDescription->inputCommonRoot+STMS_NUMBERING_FORM_ONE+expDescription->imageExtension;
  98
  99     reader->SetFileName( imagePath );
 100     reader->Update();
 101     image = reader->GetOutput();
 102
 103     SpatialIndexType start, outIndex, classIndex;
 104     start.Fill(0);
 105
 106     RegionType region;
 107     region.SetSize( image->GetBufferedRegion().GetSize());
 108     region.SetIndex(start);
 109
 110     ClassRegionType classRegion;
 111     classRegion.SetSize( image->GetBufferedRegion().GetSize());
 112     classRegion.SetIndex( start );
 113
 114
 115     std::string outputPath, classPath;
 116
 117     ClassImagePointer classImage
 118             = ClassImageType::New();
 119
 120     classImage->SetRegions( classRegion );
 121     classImage->Allocate();
 122     classImage->FillBuffer( 15.0 );
 123
 124
 125     classPath = expDescription->experimentPath+expDescription->outputFolder+
 126             expDescription->outputCommonRoot+
 127             "_Class_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
 128             "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
 129             "_Z-"+std::to_string((unsigned int)stmsParameters->spScales[2])+
 130             "_R-"+std::to_string(stmsParameters->rScale)+
 131             expDescription->outputImageExtension;
 132
 133     ClassWriterPointer classWriter
 134             = ClassWriterType::New();
 135     classWriter->SetFileName( classPath );
 136
 137     // Filetered image sequence and class image saving
 138     for( unsigned int i=1 ; i<=stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1; ++i )
 139     {
 140         char buffer[6];
 141         int n;
 142
 143         if( sizeof(STMS_NUMBERING_FORM_ONE) == 6 ) n=sprintf (buffer, "%05d", i + stmsParameters->startTimePoint - 1);
 144         if( sizeof(STMS_NUMBERING_FORM_ONE) == 5 ) n=sprintf (buffer, "%04d", i + stmsParameters->startTimePoint - 1);
 145         if( sizeof(STMS_NUMBERING_FORM_ONE) == 4 ) n=sprintf (buffer, "%03d", i + stmsParameters->startTimePoint - 1);
 146         if( sizeof(STMS_NUMBERING_FORM_ONE) == 3 ) n=sprintf (buffer, "%02d", i + stmsParameters->startTimePoint - 1);
 147         if( sizeof(STMS_NUMBERING_FORM_ONE) == 2 ) n=sprintf (buffer, "%01d", i + stmsParameters->startTimePoint - 1);
 148
 149         outputPath = expDescription->experimentPath+expDescription->outputFolder+
 150                 expDescription->outputCommonRoot+
 151                 "_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
 152                 "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
 153                 "_Z-"+std::to_string((unsigned int)stmsParameters->spScales[2])+
 154                 "_R-"+std::to_string(stmsParameters->rScale)+"_"+
 155                 buffer+expDescription->outputImageExtension;
 156
 157         ImagePointer outImage
 158                 = ImageType::New();
 159
 160         outImage->SetRegions( region );
 161         outImage->Allocate();
 162         outImage->FillBuffer( 15.0 );
 163
 164         WriterPointer writer
 165                 = WriterType::New();
 166         writer->SetFileName( outputPath );
 167
 168         //#pragma omp parrallel for ...
 169         for(unsigned int j=0 ; j<classSet->size() ; ++j)
 170         {
 171             for( unsigned int k=0 ; k<stmsParameters->dim ; ++k)
 172             {
 173                 outIndex[k]   = (IndexType)( round(spatialSet->at(j)[k]*stmsParameters->spScales[k]) );
 174
 175                 if( first )
 176                     classIndex[k] = outIndex[k];
 177             }
 178
 179             outImage->SetPixel( outIndex, rangeSet->at( classSet->at(j)-1 )[i-1]*stmsParameters->rScale );
 180
 181             if( first )
 182                 classImage->SetPixel(classIndex, classSet->at(j));
 183         }
 184
 185         writer->SetInput( outImage );
 186         writer->Update();
 187
 188         if( first )
 189         {
 190             classWriter->SetInput( classImage );
 191             classWriter->Update();
 192             first = false;
 193         }
 194     }
 195 }
 196
 197
 198 template < class ImageType, class ClassImageType>
 199 void
 200 itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
 201 ::GenerateCSVFile(const std::string &delimiter)
 202 {
 203     std::string CSVFilename = expDescription->experimentPath+expDescription->outputFolder+
 204             expDescription->outputCommonRoot+
 205             "_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
 206             "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
 207             "_Z-"+std::to_string((unsigned int)stmsParameters->spScales[2])+
 208             "_R-"+std::to_string(stmsParameters->rScale)+".csv";
 209
 210     std::cout << "Writing CSV File (classID, nb of pixels, values of time serie), : " << CSVFilename << std::endl;
 211     std::ofstream ofs;
 212     ofs.open (CSVFilename.c_str(), std::ofstream::out | std::ofstream::trunc);
 213
 214     for(unsigned int j=0 ; j<rangeSet->size() ; ++j)
 215     {
 216         ofs << j+1 << delimiter << std::count (classSet->begin(), classSet->end(), j+1);
 217         for( unsigned int i=1 ; i<=stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1; ++i )
 218            ofs << delimiter << rangeSet->at(j)[i-1]*stmsParameters->rScale ;
 219         ofs << std::endl;
 220     }
 221
 222     ofs.close();
 223
 224 }
 225
 226
 227 } // end of namespace itkSTMS
 228
 229 #endif