/*
 #
 #  File        : itkSTMS_TemporalSetToImageSequence_Spine.txx
 #                ( C++ header file - STMS )
 #
 #  Description : STMS lib that implements the STMS filter and clustering.
 #                This file is a part of the STMS Library project.
 #                ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
 #
 #  [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
 #       « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
 #       Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
 #
 #  Copyright   : Thomas GRENIER - Simon MURE
 #                ( https://www.creatis.insa-lyon.fr/~grenier/ )
 #
 #  License     : CeCILL C
 #                ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
 #
 #  This software is governed by the CeCILL  license under French law and
 #  abiding by the rules of distribution of free software.  You can  use,
 #  modify and/ or redistribute the software under the terms of the CeCILL
 #  license as circulated by CEA, CNRS and INRIA at the following URL
 #  "http://www.cecill.info".
 #
 #  As a counterpart to the access to the source code and  rights to copy,
 #  modify and redistribute granted by the license, users are provided only
 #  with a limited warranty  and the software's author,  the holder of the
 #  economic rights,  and the successive licensors  have only  limited
 #  liability.
 #
 #  In this respect, the user's attention is drawn to the risks associated
 #  with loading,  using,  modifying and/or developing or reproducing the
 #  software by the user in light of its specific status of free software,
 #  that may mean  that it is complicated to manipulate,  and  that  also
 #  therefore means  that it is reserved for developers  and  experienced
 #  professionals having in-depth computer knowledge. Users are therefore
 #  encouraged to load and test the software's suitability as regards their
 #  requirements in conditions enabling the security of their systems and/or
 #  data to be ensured and,  more generally, to use and operate it in the
 #  same conditions as regards security.
 #
 #  The fact that you are presently reading this means that you have had
 #  knowledge of the CeCILL license and that you accept its terms.
 #
*/
/* Please don't forget to cite our work :
  @article {MURE-15a,
    title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
    journal = {Pattern Recognition Letters},
    volume = {68, Part 1},
    year = {2015},
    pages = {48 - 55},
    issn = {0167-8655},
    doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
    url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
    author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
}
*/
#ifndef itkSTMS_TemporalSetToImageSequenceSpine_txx
#define itkSTMS_TemporalSetToImageSequenceSpine_txx

#include "itkSTMS_TemporalSetToImageSequence_Spine.h"
#include "itkSTMS_ArgumentsAnalysis_Spine.h"

namespace itkSTMS_Spine
{

template < class ImageType, class ClassImageType >
itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType >
::itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl, SpatialSampleSetType* sp, RangeSampleSetType* ra,
                                      itkSTMS_Spine::ParamsAnalysisOutputType* params)
{
    this->stmsParameters = params;
    this->classSet       = cl;
    this->spatialSet     = sp;
    this->rangeSet       = ra;
}


template < class ImageType, class ClassImageType >
void
itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
::GenerateImageSequence()
{
    bool first = true;

    // Output images allocation
    ImagePointer image
            = ImageType::New();
    ReaderPointer reader
            = ReaderType::New();

    reader->SetFileName( *stmsParameters->images.begin() );
    reader->Update();
    image = reader->GetOutput();

    SpatialIndexType start, outIndex, classIndex;
    start.Fill(0);

    RegionType region;
    region.SetSize( image->GetBufferedRegion().GetSize());
    region.SetIndex(start);

    ClassRegionType classRegion;
    classRegion.SetSize( image->GetBufferedRegion().GetSize());
    classRegion.SetIndex( start );


    std::string outputPath, classPath;

    ClassImagePointer classImage
            = ClassImageType::New();

    classImage->SetRegions( classRegion );
    classImage->Allocate();
    classImage->FillBuffer( 15.0 );


    // Filetered image sequence and class image saving
    //    for( unsigned int i=1 ; i<=stmsParameters->numTimePoints ; ++i )
    //    {
    unsigned int i=1;
    for (std::list<std::string>::iterator it_images = stmsParameters->images.begin(); it_images != stmsParameters->images.end(); ++it_images)
    {
        outputPath = stmsParameters->outFolder+ it_images->substr( it_images->find_last_of("/"), it_images->length()-stmsParameters->imageExtension.length()-it_images->find_last_of("/") ) +
                "_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
                "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
                "_Z-"+std::to_string(stmsParameters->spScales[2])+
                "_R-"+std::to_string(stmsParameters->rScale)+"_"+
                std::to_string(i)+stmsParameters->imageExtension;

        ImagePointer outImage
                = ImageType::New();

        outImage->SetRegions( region );
        outImage->Allocate();
        outImage->FillBuffer( 15.0 );

        WriterPointer writer
                = WriterType::New();
        writer->SetFileName( outputPath );

        //#pragma omp parrallel for ...
        for(unsigned int j=0 ; j<classSet->size() ; ++j)
        {
            for( unsigned int k=0 ; k<stmsParameters->dim ; ++k)
            {
                outIndex[k]   = (IndexType)( round(spatialSet->at(j)[k]*stmsParameters->spScales[k]) );

                if( first )
                    classIndex[k] = outIndex[k];
            }

            outImage->SetPixel( outIndex, rangeSet->at( classSet->at(j)-1 )[i-1]*stmsParameters->rScale );

            if( first )
                classImage->SetPixel(classIndex, classSet->at(j));
        }

        writer->SetInput( outImage );
        writer->Update();

        if( first )
        {
            classPath = stmsParameters->outFolder +
                    it_images->substr( it_images->find_last_of("/"), it_images->length()-stmsParameters->imageExtension.length()-it_images->find_last_of("/") ) +
                    "_Class_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
                    "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
                    "_Z-"+std::to_string(stmsParameters->spScales[2])+
                    "_R-"+std::to_string(stmsParameters->rScale)+"_"+
                    stmsParameters->imageExtension;

            ClassWriterPointer classWriter
                    = ClassWriterType::New();
            classWriter->SetFileName( classPath );

            classWriter->SetInput( classImage );
            classWriter->Update();
            first = false;
        }

        ++i;
    }
}

} // end of namespace itkSTMS

#endif