Src/STMS_GrayLevelFiltering.cxx

   1 /*
   2  #
   3  #  File        : STMS_GrayLevelFiltering.cxx
   4  #                ( C++ example 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 V2.1
  18  #                ( http://www.cecill.info/licences/Licence_CeCILL_V2.1-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 #include <iomanip>
  61 #include <ctime>
  62
  63 #define STMS_NUMBERING_FORM_ONE "0001"
  64
  65 #include "itkImage.h"
  66 #include "itkSTMS_ArgumentsAnalysis.h"
  67 #include "itkSTMS_ImageSequenceToTemporalSet.h"
  68 #include "itkSTMS_TemporalSetToImageSequence.h"
  69 #include "itkSTMS_BlurringSTMS.h"
  70
  71 #include <array>
  72
  73
  74
  75 typedef float PixelType;
  76 typedef unsigned char OutputPixelType2D;
  77 typedef float OutputPixelType3D;
  78
  79
  80 double gettime_hp()
  81 {
  82     struct timespec timestamp;
  83
  84     clock_gettime(CLOCK_REALTIME, &timestamp);
  85     return timestamp.tv_sec * 1000.0 + timestamp.tv_nsec * 1.0e-6;
  86 }
  87
  88 // Only --expDescription and numTimePoints parameter are compulsory.
  89
  90 //--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/P43_Parser.xml --imageDimension 2 --xScale 20 --yScale 20 --rScale 1 --epsilon 0.1 --maxIt 20 --numTimePoints 25 --merge
  91
  92 //--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/L43_3_Parser.xml --imageDimension 3 --xScale 1000 --yScale 1000 --zScale 1000 --rScale 0.75 --epsilon 0.1 --maxIt 50 --numTimePoints 25 --merge
  93 //--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/Simu_Parser.xml --imageDimension 2 --xScale 255 --yScale 255 --rScale 0.4 --epsilon 0.01 --maxIt 50 --numTimePoints 8
  94 //--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/G1_Parser.xml --imageDimension 3 --xScale 1000 --yScale 1000 --zScale 1000 --rScale 0.15 --epsilon 0.01 --maxIt 50 --numTimePoints 8
  95
  96 // --expDescription E:/Documents/Creatis/Projets/15_MUST/Data_Cardiac/Parser_AIF_Cardiac.xml --imageDimension 2 --xScale 10 --yScale 10 --rScale 10 --numTimePoints 80
  97
  98 int main(int argc, char **argv){
  99     double dtime;
 100
 101     std::cout << "The Numbering form is set to numbers like = " << STMS_NUMBERING_FORM_ONE << std::endl;
 102     std::cout << "size : " << sizeof(STMS_NUMBERING_FORM_ONE) << std::endl;
 103
 104
 105     itkSTMS::itkSTMS_ArgumentsAnalysis* argsAnalysis
 106             = new itkSTMS::itkSTMS_ArgumentsAnalysis(argc, argv);
 107     argsAnalysis->Update();
 108
 109     itkSTMS::ParamsAnalysisOutputType* params
 110             = argsAnalysis->GetSTMSParams();
 111
 112
 113     switch(params->dim){
 114         case 2:
 115         {
 116             typedef itk::Image< PixelType, 2 >          ImageType2D;
 117             typedef itk::Image< OutputPixelType2D, 2 >  OutputImageType2D;
 118             typedef itk::Image< unsigned char, 2 >      MaskImageType2D;
 119
 120
 121             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexType            IndexType;
 122             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialType          SpatialType;
 123             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexSampleSetType   IndexSampleSetType;
 124             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialSampleSetType SpatialSampleSetType;
 125             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::RangeSampleSetType   RangeSampleSetType;
 126
 127             typedef itk::Image< IndexType, 2 >  ClassImageType2D;
 128
 129
 130             dtime=gettime_hp();
 131
 132             itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >* preProcess
 133                     = new itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D > ( params );
 134             preProcess->GenerateDataSets();
 135
 136             dtime = gettime_hp()-dtime;
 137             std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
 138
 139             IndexSampleSetType*   indexSet   = preProcess->GetIndexSet();
 140             IndexSampleSetType*   classSet   = preProcess->GetClassSet();
 141             IndexSampleSetType*   weightsSet = preProcess->GetWeightsSet();
 142             SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
 143             RangeSampleSetType*   rangeSet   = preProcess->GetRangeSet();
 144
 145
 146             dtime=gettime_hp();
 147
 148             itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >* stmsFilter
 149                     = new itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >
 150                     (indexSet, classSet, weightsSet, spatialSet, rangeSet,  params, preProcess->GetExperimentDescription());
 151
 152             stmsFilter->GenerateData();
 153
 154             dtime = gettime_hp()-dtime;
 155             std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
 156
 157
 158             dtime=gettime_hp();
 159
 160             itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D, OutputImageType2D >* postProcess
 161                     = new itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D, OutputImageType2D>(stmsFilter->GetClassMemory(),
 162                                                                                                        stmsFilter->GetSpatialMemory(),
 163                                                                                                        stmsFilter->GetRangeSet(),
 164                                                                                                        params,
 165                                                                                                        preProcess->GetExperimentDescription());
 166
 167             postProcess->GenerateImageSequence();
 168             if(preProcess->GetExperimentDescription()->outputCSV == "true"  )
 169                 postProcess->GenerateCSVFile();
 170
 171             dtime = gettime_hp()-dtime;
 172             std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
 173
 174             delete argsAnalysis;
 175             delete preProcess;
 176             delete stmsFilter;
 177             delete postProcess;
 178             break;
 179         }
 180
 181         case 3:
 182         {
 183             typedef itk::Image< PixelType, 3 >     ImageType3D;
 184             typedef itk::Image< OutputPixelType3D, 3 >     OutputImageType3D;
 185             typedef itk::Image< unsigned char, 3 > MaskImageType3D;
 186
 187             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexType            IndexType;
 188             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialType          SpatialType;
 189             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexSampleSetType   IndexSampleSetType;
 190             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialSampleSetType SpatialSampleSetType;
 191             typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::RangeSampleSetType   RangeSampleSetType;
 192
 193
 194             dtime=gettime_hp();
 195
 196             itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >* preProcess
 197                     = new itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D > ( params );
 198             preProcess->GenerateDataSets();
 199
 200             dtime = gettime_hp()-dtime;
 201             std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
 202
 203             IndexSampleSetType*   indexSet   = preProcess->GetIndexSet();
 204             IndexSampleSetType*   classSet   = preProcess->GetClassSet();
 205             IndexSampleSetType*   weightsSet = preProcess->GetWeightsSet();
 206             SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
 207             RangeSampleSetType*   rangeSet   = preProcess->GetRangeSet();
 208
 209
 210
 211
 212             dtime=gettime_hp();
 213
 214             itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >* stmsFilter
 215                     = new itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >
 216                     (indexSet, classSet, weightsSet, spatialSet, rangeSet,  params, preProcess->GetExperimentDescription());
 217
 218             stmsFilter->GenerateData();
 219
 220             dtime = gettime_hp()-dtime;
 221             std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
 222
 223
 224             dtime=gettime_hp();
 225
 226             itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D, OutputImageType3D>* postProcess
 227                     = new itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D, OutputImageType3D >(stmsFilter->GetClassMemory(),
 228                                                                                                       stmsFilter->GetSpatialMemory(),
 229                                                                                                       stmsFilter->GetRangeSet(),
 230                                                                                                       params,
 231                                                                                                       preProcess->GetExperimentDescription());
 232
 233             postProcess->GenerateImageSequence();
 234             if(preProcess->GetExperimentDescription()->outputCSV == "true"  )
 235                 postProcess->GenerateCSVFile();
 236
 237             dtime = gettime_hp()-dtime;
 238             std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
 239
 240
 241             delete argsAnalysis;
 242             delete preProcess;
 243             delete stmsFilter;
 244             delete postProcess;
 245             break;
 246         }
 247
 248         default:
 249         {
 250             delete argsAnalysis;
 251
 252             std::cout << std::endl << "Image dimensionality should be equal to 2 or 3.";
 253             std::exit( EXIT_FAILURE );
 254             break;
 255         }
 256     }
 257
 258     return EXIT_SUCCESS;
 259 }