Merge branch 'master' of ssh://git.creatis.insa-lyon.fr/STMS

[STMS.git] / Lib / PrePostProcessing / itkSTMS_TemporalSetToImageSequence.txx

diff --git a/Lib/PrePostProcessing/itkSTMS_TemporalSetToImageSequence.txx b/Lib/PrePostProcessing/itkSTMS_TemporalSetToImageSequence.txx
index 2d5131821dafa43f4ff2b394f9b137b0ed8f0e49..115918763c8368d28107ba013fb5d0bac3d73e15 100755 (executable)
--- a/Lib/PrePostProcessing/itkSTMS_TemporalSetToImageSequence.txx
+++ b/Lib/PrePostProcessing/itkSTMS_TemporalSetToImageSequence.txx
@@ -67,8 +67,8 @@
 namespace itkSTMS
 {
 
-template < class ImageType, class ClassImageType >
-itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType >
+template < class ImageType, class ClassImageType, class OutputImageType>
+itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType, OutputImageType >
 ::itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl, SpatialSampleSetType* sp, RangeSampleSetType* ra,
                                       itkSTMS::ParamsAnalysisOutputType* params, itkSTMS::ParserOutputType* desc )
 {
@@ -81,9 +81,9 @@ itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType >
 }
 
 
-template < class ImageType, class ClassImageType >
+template < class ImageType, class ClassImageType, class OutputImageType >
 void
-itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
+itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType, OutputImageType >
 ::GenerateImageSequence()
 {
     bool first = true;
@@ -114,9 +114,7 @@ itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
 
     std::string outputPath, classPath;
 
-    ClassImagePointer classImage
-            = ClassImageType::New();
-
+    ClassImagePointer classImage          = ClassImageType::New();
     classImage->SetRegions( classRegion );
     classImage->Allocate();
     classImage->FillBuffer( 15.0 );
@@ -128,23 +126,22 @@ itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
             "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
             "_Z-"+std::to_string((unsigned int)stmsParameters->spScales[2])+
             "_R-"+std::to_string(stmsParameters->rScale)+
-            expDescription->outputImageExtension;
+            expDescription->outputClassExtension;
 
-    ClassWriterPointer classWriter
-            = ClassWriterType::New();
+    ClassWriterPointer classWriter         = ClassWriterType::New();
     classWriter->SetFileName( classPath );
 
     // Filetered image sequence and class image saving
     for( unsigned int i=1 ; i<=stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1; ++i )
     {
         char buffer[6];
-        int n;
+         // int n;
 
-        if( sizeof(STMS_NUMBERING_FORM_ONE) == 6 ) n=sprintf (buffer, "%05d", i + stmsParameters->startTimePoint - 1);
-        if( sizeof(STMS_NUMBERING_FORM_ONE) == 5 ) n=sprintf (buffer, "%04d", i + stmsParameters->startTimePoint - 1);
-        if( sizeof(STMS_NUMBERING_FORM_ONE) == 4 ) n=sprintf (buffer, "%03d", i + stmsParameters->startTimePoint - 1);
-        if( sizeof(STMS_NUMBERING_FORM_ONE) == 3 ) n=sprintf (buffer, "%02d", i + stmsParameters->startTimePoint - 1);
-        if( sizeof(STMS_NUMBERING_FORM_ONE) == 2 ) n=sprintf (buffer, "%01d", i + stmsParameters->startTimePoint - 1);
+        if( sizeof(STMS_NUMBERING_FORM_ONE) == 6 ) sprintf( buffer, "%05d", i + stmsParameters->startTimePoint - 1);
+        if( sizeof(STMS_NUMBERING_FORM_ONE) == 5 ) sprintf( buffer, "%04d", i + stmsParameters->startTimePoint - 1);
+        if( sizeof(STMS_NUMBERING_FORM_ONE) == 4 ) sprintf( buffer, "%03d", i + stmsParameters->startTimePoint - 1);
+        if( sizeof(STMS_NUMBERING_FORM_ONE) == 3 ) sprintf( buffer, "%02d", i + stmsParameters->startTimePoint - 1);
+        if( sizeof(STMS_NUMBERING_FORM_ONE) == 2 ) sprintf( buffer, "%01d", i + stmsParameters->startTimePoint - 1);
 
         outputPath = expDescription->experimentPath+expDescription->outputFolder+
                 expDescription->outputCommonRoot+
@@ -154,15 +151,14 @@ itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
                 "_R-"+std::to_string(stmsParameters->rScale)+"_"+
                 buffer+expDescription->outputImageExtension;
 
-        ImagePointer outImage
-                = ImageType::New();
 
+
+        typename OutputImageType::Pointer outImage           = OutputImageType::New();
         outImage->SetRegions( region );
         outImage->Allocate();
-        outImage->FillBuffer( 15.0 );
+        outImage->FillBuffer( 0 );
 
-        WriterPointer writer
-                = WriterType::New();
+        WriterPointer writer            = WriterType::New();
         writer->SetFileName( outputPath );
 
         //#pragma omp parrallel for ...
@@ -176,7 +172,7 @@ itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
                     classIndex[k] = outIndex[k];
             }
 
-            outImage->SetPixel( outIndex, rangeSet->at( classSet->at(j)-1 )[i-1]*stmsParameters->rScale );
+            outImage->SetPixel( outIndex, static_cast<typename OutputImageType::PixelType>(rangeSet->at( classSet->at(j)-1 )[i-1]*stmsParameters->rScale) );
 
             if( first )
                 classImage->SetPixel(classIndex, classSet->at(j));
@@ -195,9 +191,9 @@ itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
 }
 
 
-template < class ImageType, class ClassImageType>
+template < class ImageType, class ClassImageType, class OutputImageType>
 void
-itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
+itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType, OutputImageType>
 ::GenerateCSVFile(const std::string &delimiter)
 {
     std::string CSVFilename = expDescription->experimentPath+expDescription->outputFolder+
@@ -207,13 +203,14 @@ itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
             "_Z-"+std::to_string((unsigned int)stmsParameters->spScales[2])+
             "_R-"+std::to_string(stmsParameters->rScale)+".csv";
 
-    std::cout << "Writing CSV File (classID, nb of pixels, values of time serie), : " << CSVFilename << std::endl;
+    std::cout << "Writing CSV File (classID, nb of pixels, values of time serie) : " << CSVFilename << std::endl;
     std::ofstream ofs;
     ofs.open (CSVFilename.c_str(), std::ofstream::out | std::ofstream::trunc);
 
     for(unsigned int j=0 ; j<rangeSet->size() ; ++j)
     {
         ofs << j+1 << delimiter << std::count (classSet->begin(), classSet->end(), j+1);
+        ofs << delimiter << stmsParameters->startTimePoint << delimiter << stmsParameters->numTimePoints;
         for( unsigned int i=1 ; i<=stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1; ++i )
            ofs << delimiter << rangeSet->at(j)[i-1]*stmsParameters->rScale ;
         ofs << std::endl;