/*
 #
 #  File        : itkSTMS_TemporalSetToImageSequence.h
 #                ( 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_TemporalSetToImageSequence_h
#define itkSTMS_TemporalSetToImageSequence_h

#include <string>
#include <vector>
#include <algorithm>
#include <math.h>

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIteratorWithIndex.h"


#ifndef STMS_NUMBERING_FORM_ONE
#define STMS_NUMBERING_FORM_ONE "1"
#endif

namespace itkSTMS
{
    template < class ImageType, class ClassImageType, class OutputImageType=ImageType>
    class itkSTMS_TemporalSetToImageSequence
    {
    public:
        // Reader and writer typedefs
        typedef itk::ImageFileReader< ImageType >       ReaderType;
        typedef typename ReaderType::Pointer            ReaderPointer;
        typedef itk::ImageFileWriter< OutputImageType > WriterType;
        typedef typename WriterType::Pointer            WriterPointer;
        typedef itk::ImageFileWriter< ClassImageType >  ClassWriterType;
        typedef typename ClassWriterType::Pointer       ClassWriterPointer;

        // Sample set typedefs
        typedef unsigned int                        IndexType;
        typedef float                               SpatialType;
        typedef typename ImageType::PixelType       PixelType;

        typedef std::vector< SpatialType >          SpatialVectorType;
        typedef std::vector< PixelType >            RangeVectorType;

        typedef std::vector< IndexType >            IndexSampleSetType;
        typedef std::vector< SpatialVectorType >    SpatialSampleSetType;
        typedef std::vector< RangeVectorType >      RangeSampleSetType;

        // Image typedefs
        typedef typename ImageType::IndexType       SpatialIndexType;
        typedef typename ImageType::RegionType      RegionType;

        typedef typename ImageType::Pointer         ImagePointer;
        typedef typename ImageType::ConstPointer    ImageConstPointer;
        typedef typename ImageType::SizeType        SizeType;

        typedef typename ClassImageType::Pointer    ClassImagePointer;
        typedef typename ClassImageType::RegionType ClassRegionType;


        // Methods
        itkSTMS_TemporalSetToImageSequence( IndexSampleSetType*   cl,
                                            SpatialSampleSetType* sp,
                                            RangeSampleSetType*   ra,
                                            itkSTMS::ParamsAnalysisOutputType* params,
                                            itkSTMS::ParserOutputType*         desc   );

        void GenerateImageSequence();

        //! To generate CSV File from all classes. The file contains the class ID, the number of pixels of this class and then all filtered values along time.
        //! You can pass a delimiter (ie a record separator) to this function.
        void GenerateCSVFile(const std::string &delimiter = std::string(", "));

    private:
        // Attributes
        itkSTMS::ParserOutputType*         expDescription;
        itkSTMS::ParamsAnalysisOutputType* stmsParameters;

        IndexSampleSetType*      classSet;
        SpatialSampleSetType*    spatialSet;
        RangeSampleSetType*      rangeSet;

    };  // end of class itkSTMS_TemporalSetToImageSequence
} // end of namespace itkstms

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkSTMS_TemporalSetToImageSequence.txx"
#endif

#endif