#include <iomanip>
#include <ctime>
#include "itkImage.h"
#include "itkSTMS_ArgumentsAnalysis_Spine.h"
#include "itkSTMS_ImageSequenceToTemporalSet_Spine.h"
#include "itkSTMS_TemporalSetToImageSequence_Spine.h"
#include "itkSTMS_BlurringSTMS_Spine.h"


typedef float PixelType;

double gettime_hp()
{
    struct timespec timestamp;

    clock_gettime(CLOCK_REALTIME, &timestamp);
    return timestamp.tv_sec * 1000.0 + timestamp.tv_nsec * 1.0e-6;
}

// Only --expDescription and --outFolder parameters are compulsory.
/* --image ../../itkSTMS/Data/Images/Simu/Simu1.nii --image ../../itkSTMS/Data/Images/Simu/Simu2.nii --image ../../itkSTMS/Data/Images/Simu/Simu3.nii
--image ../../itkSTMS/Data/Images/Simu/Simu4.nii --image ../../itkSTMS/Data/Images/Simu/Simu5.nii --image ../../itkSTMS/Data/Images/Simu/Simu6.nii
--image ../../itkSTMS/Data/Images/Simu/Simu7.nii --image ../../itkSTMS/Data/Images/Simu/Simu8.nii --outFolder ../../itkSTMS/Data/Images/Simu_Outputs-Spine/
--imageDimension 2 --xScale 1000 --yScale 1000 --rScale 0.5 --mask ../../itkSTMS/Data/Images/Simu/Mask.nii --imageExtension .nii

--image ../../itkSTMS/Data/Images/Simu/Simu1.nii --image ../../itkSTMS/Data/Images/Simu/Simu2.nii --image ../../itkSTMS/Data/Images/Simu/Simu3.nii
--image ../../itkSTMS/Data/Images/Simu/Simu4.nii --image ../../itkSTMS/Data/Images/Simu/Simu5.nii --image ../../itkSTMS/Data/Images/Simu/Simu6.nii
--image ../../itkSTMS/Data/Images/Simu/Simu7.nii --image ../../itkSTMS/Data/Images/Simu/Simu8.nii --outFolder ../../itkSTMS/Data/Images/Simu_Outputs-Spine/
--imageDimension 2 --xScale 1000 --yScale 1000 --rScale 0.5 --imageExtension .nii
*/
int main(int argc, char **argv){
    double dtime;

    itkSTMS_Spine::itkSTMS_ArgumentsAnalysis* argsAnalysis
            = new itkSTMS_Spine::itkSTMS_ArgumentsAnalysis(argc, argv);
    argsAnalysis->Update();

    itkSTMS_Spine::ParamsAnalysisOutputType* params
            = argsAnalysis->GetSTMSParams();


    switch(params->dim){
        case 2:
        {
            typedef itk::Image< PixelType, 2 >     ImageType2D;
            typedef itk::Image< unsigned int, 2 > MaskImageType2D;


            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexType            IndexType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialType          SpatialType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexSampleSetType   IndexSampleSetType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialSampleSetType SpatialSampleSetType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::RangeSampleSetType   RangeSampleSetType;

            typedef itk::Image< IndexType, 2 >  ClassImageType2D;


            dtime=gettime_hp();

            itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >* preProcess
                    = new itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D > ( params );
            preProcess->GenerateDataSets();

            dtime = gettime_hp()-dtime;
            std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;

            IndexSampleSetType*   indexSet   = preProcess->GetIndexSet();
            IndexSampleSetType*   classSet   = preProcess->GetClassSet();
            IndexSampleSetType*   weightsSet = preProcess->GetWeightsSet();
            SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
            RangeSampleSetType*   rangeSet   = preProcess->GetRangeSet();


            dtime=gettime_hp();

            itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >* stmsFilter
                    = new itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >
                    (indexSet, classSet, weightsSet, spatialSet, rangeSet,  params );

            stmsFilter->GenerateData();

            dtime = gettime_hp()-dtime;
            std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;



            dtime=gettime_hp();

            itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >* postProcess
                    = new itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >(stmsFilter->GetClassMemory(),
                                                                                                       stmsFilter->GetSpatialMemory(),
                                                                                                       stmsFilter->GetRangeSet(),
                                                                                                       params );

            postProcess->GenerateImageSequence();

            dtime = gettime_hp()-dtime;
            std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;

            delete argsAnalysis;
            delete preProcess;
            delete stmsFilter;
            delete postProcess;
            break;
        }

        case 3:
        {
            typedef itk::Image< PixelType, 3 >     ImageType3D;
            typedef itk::Image< unsigned int, 3 > MaskImageType3D;

            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexType            IndexType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialType          SpatialType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexSampleSetType   IndexSampleSetType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialSampleSetType SpatialSampleSetType;
            typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::RangeSampleSetType   RangeSampleSetType;


            dtime=gettime_hp();

            itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >* preProcess
                    = new itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D > ( params );
            preProcess->GenerateDataSets();

            dtime = gettime_hp()-dtime;
            std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;

            IndexSampleSetType*   indexSet   = preProcess->GetIndexSet();
            IndexSampleSetType*   classSet   = preProcess->GetClassSet();
            IndexSampleSetType*   weightsSet = preProcess->GetWeightsSet();
            SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
            RangeSampleSetType*   rangeSet   = preProcess->GetRangeSet();




            dtime=gettime_hp();

            itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >* stmsFilter
                    = new itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >
                    (indexSet, classSet, weightsSet, spatialSet, rangeSet,  params );

            stmsFilter->GenerateData();

            dtime = gettime_hp()-dtime;
            std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;


            dtime=gettime_hp();

            itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >* postProcess
                    = new itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >(stmsFilter->GetClassMemory(),
                                                                                                      stmsFilter->GetSpatialMemory(),
                                                                                                      stmsFilter->GetRangeSet(),
                                                                                                      params );

            postProcess->GenerateImageSequence();

            dtime = gettime_hp()-dtime;
            std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;


            delete argsAnalysis;
            delete preProcess;
            delete stmsFilter;
            delete postProcess;
            break;
        }

        default:
        {
            delete argsAnalysis;

            std::cout << std::endl << "Image dimensionality should be equal to 2 or 3.";
            std::exit( EXIT_FAILURE );
            break;
        }
    }

    return EXIT_SUCCESS;
}