Src/STMS_GrayLevelFiltering_Spine.cxx

   1 #include <iomanip>
   2 #include <ctime>
   3 #include "itkImage.h"
   4 #include "itkSTMS_ArgumentsAnalysis_Spine.h"
   5 #include "itkSTMS_ImageSequenceToTemporalSet_Spine.h"
   6 #include "itkSTMS_TemporalSetToImageSequence_Spine.h"
   7 #include "itkSTMS_BlurringSTMS_Spine.h"
   8
   9
  10 typedef float PixelType;
  11
  12 double gettime_hp()
  13 {
  14     struct timespec timestamp;
  15
  16     clock_gettime(CLOCK_REALTIME, &timestamp);
  17     return timestamp.tv_sec * 1000.0 + timestamp.tv_nsec * 1.0e-6;
  18 }
  19
  20 // Only --expDescription and --outFolder parameters are compulsory.
  21 /* --image ../../itkSTMS/Data/Images/Simu/Simu1.nii --image ../../itkSTMS/Data/Images/Simu/Simu2.nii --image ../../itkSTMS/Data/Images/Simu/Simu3.nii
  22 --image ../../itkSTMS/Data/Images/Simu/Simu4.nii --image ../../itkSTMS/Data/Images/Simu/Simu5.nii --image ../../itkSTMS/Data/Images/Simu/Simu6.nii
  23 --image ../../itkSTMS/Data/Images/Simu/Simu7.nii --image ../../itkSTMS/Data/Images/Simu/Simu8.nii --outFolder ../../itkSTMS/Data/Images/Simu_Outputs-Spine/
  24 --imageDimension 2 --xScale 1000 --yScale 1000 --rScale 0.5 --mask ../../itkSTMS/Data/Images/Simu/Mask.nii --imageExtension .nii
  25
  26 --image ../../itkSTMS/Data/Images/Simu/Simu1.nii --image ../../itkSTMS/Data/Images/Simu/Simu2.nii --image ../../itkSTMS/Data/Images/Simu/Simu3.nii
  27 --image ../../itkSTMS/Data/Images/Simu/Simu4.nii --image ../../itkSTMS/Data/Images/Simu/Simu5.nii --image ../../itkSTMS/Data/Images/Simu/Simu6.nii
  28 --image ../../itkSTMS/Data/Images/Simu/Simu7.nii --image ../../itkSTMS/Data/Images/Simu/Simu8.nii --outFolder ../../itkSTMS/Data/Images/Simu_Outputs-Spine/
  29 --imageDimension 2 --xScale 1000 --yScale 1000 --rScale 0.5 --imageExtension .nii
  30 */
  31 int main(int argc, char **argv){
  32     double dtime;
  33
  34     itkSTMS_Spine::itkSTMS_ArgumentsAnalysis* argsAnalysis
  35             = new itkSTMS_Spine::itkSTMS_ArgumentsAnalysis(argc, argv);
  36     argsAnalysis->Update();
  37
  38     itkSTMS_Spine::ParamsAnalysisOutputType* params
  39             = argsAnalysis->GetSTMSParams();
  40
  41
  42     switch(params->dim){
  43         case 2:
  44         {
  45             typedef itk::Image< PixelType, 2 >     ImageType2D;
  46             typedef itk::Image< unsigned int, 2 > MaskImageType2D;
  47
  48
  49             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexType            IndexType;
  50             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialType          SpatialType;
  51             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexSampleSetType   IndexSampleSetType;
  52             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialSampleSetType SpatialSampleSetType;
  53             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::RangeSampleSetType   RangeSampleSetType;
  54
  55             typedef itk::Image< IndexType, 2 >  ClassImageType2D;
  56
  57
  58             dtime=gettime_hp();
  59
  60             itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >* preProcess
  61                     = new itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D > ( params );
  62             preProcess->GenerateDataSets();
  63
  64             dtime = gettime_hp()-dtime;
  65             std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
  66
  67             IndexSampleSetType*   indexSet   = preProcess->GetIndexSet();
  68             IndexSampleSetType*   classSet   = preProcess->GetClassSet();
  69             IndexSampleSetType*   weightsSet = preProcess->GetWeightsSet();
  70             SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
  71             RangeSampleSetType*   rangeSet   = preProcess->GetRangeSet();
  72
  73
  74             dtime=gettime_hp();
  75
  76             itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >* stmsFilter
  77                     = new itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >
  78                     (indexSet, classSet, weightsSet, spatialSet, rangeSet,  params );
  79
  80             stmsFilter->GenerateData();
  81
  82             dtime = gettime_hp()-dtime;
  83             std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
  84
  85
  86
  87             dtime=gettime_hp();
  88
  89             itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >* postProcess
  90                     = new itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >(stmsFilter->GetClassMemory(),
  91                                                                                                        stmsFilter->GetSpatialMemory(),
  92                                                                                                        stmsFilter->GetRangeSet(),
  93                                                                                                        params );
  94
  95             postProcess->GenerateImageSequence();
  96
  97             dtime = gettime_hp()-dtime;
  98             std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
  99
 100             delete argsAnalysis;
 101             delete preProcess;
 102             delete stmsFilter;
 103             delete postProcess;
 104             break;
 105         }
 106
 107         case 3:
 108         {
 109             typedef itk::Image< PixelType, 3 >     ImageType3D;
 110             typedef itk::Image< unsigned int, 3 > MaskImageType3D;
 111
 112             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexType            IndexType;
 113             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialType          SpatialType;
 114             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexSampleSetType   IndexSampleSetType;
 115             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialSampleSetType SpatialSampleSetType;
 116             typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::RangeSampleSetType   RangeSampleSetType;
 117
 118
 119             dtime=gettime_hp();
 120
 121             itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >* preProcess
 122                     = new itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D > ( params );
 123             preProcess->GenerateDataSets();
 124
 125             dtime = gettime_hp()-dtime;
 126             std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
 127
 128             IndexSampleSetType*   indexSet   = preProcess->GetIndexSet();
 129             IndexSampleSetType*   classSet   = preProcess->GetClassSet();
 130             IndexSampleSetType*   weightsSet = preProcess->GetWeightsSet();
 131             SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
 132             RangeSampleSetType*   rangeSet   = preProcess->GetRangeSet();
 133
 134
 135
 136
 137             dtime=gettime_hp();
 138
 139             itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >* stmsFilter
 140                     = new itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >
 141                     (indexSet, classSet, weightsSet, spatialSet, rangeSet,  params );
 142
 143             stmsFilter->GenerateData();
 144
 145             dtime = gettime_hp()-dtime;
 146             std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
 147
 148
 149             dtime=gettime_hp();
 150
 151             itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >* postProcess
 152                     = new itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >(stmsFilter->GetClassMemory(),
 153                                                                                                       stmsFilter->GetSpatialMemory(),
 154                                                                                                       stmsFilter->GetRangeSet(),
 155                                                                                                       params );
 156
 157             postProcess->GenerateImageSequence();
 158
 159             dtime = gettime_hp()-dtime;
 160             std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
 161
 162
 163             delete argsAnalysis;
 164             delete preProcess;
 165             delete stmsFilter;
 166             delete postProcess;
 167             break;
 168         }
 169
 170         default:
 171         {
 172             delete argsAnalysis;
 173
 174             std::cout << std::endl << "Image dimensionality should be equal to 2 or 3.";
 175             std::exit( EXIT_FAILURE );
 176             break;
 177         }
 178     }
 179
 180     return EXIT_SUCCESS;
 181 }