#ifndef __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__
#define __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__

#include "bbSlicer_EXPORT.h"
#include "bbtkAtomicBlackBox.h"

#include <vector>
#include <cstdlib>
#include <dlfcn.h>
#include <sstream>
#include <fstream>
#include <iostream>

#include <ModuleDescriptionUtilities.h>
#include <ModuleDescriptionParser.h>
#include <ModuleParameterGroup.h>
#include <ModuleDescription.h>
#include <ModuleParameter.h>

#include "CreationTool.h"

namespace bbSlicer {

    class bbSlicer_EXPORT MRIBiasFieldCorrection
    :
    public bbtk::AtomicBlackBox {
        BBTK_BLACK_BOX_INTERFACE ( MRIBiasFieldCorrection , bbtk::AtomicBlackBox ) ;

        // GENERATED ARGS        
        
BBTK_DECLARE_INPUT ( InputImage , std::string );
BBTK_DECLARE_INPUT ( InputMask , std::string );
BBTK_DECLARE_INPUT ( OutputImage , std::string );
BBTK_DECLARE_INPUT ( AlgorithmType , std::string );
BBTK_DECLARE_INPUT ( ShrinkFactor , int );
BBTK_DECLARE_INPUT ( MaximumNumberOfIterations , int );
BBTK_DECLARE_INPUT ( NumberOfFittingLevels , int );
BBTK_DECLARE_INPUT ( WienerFilterNoise , double );
BBTK_DECLARE_INPUT ( FullWidthAtHalfMaximum , double );
BBTK_DECLARE_INPUT ( ConvergenceThreshold , double );

        // EO GENERATED ARGS

        BBTK_PROCESS ( Process ) ;
        void Process ( ) ;
    private:
        void execute ( std::string lib , int _argc , char * _argv[] ) ;
    } ;

    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MRIBiasFieldCorrection , bbtk::AtomicBlackBox ) ;
    BBTK_NAME ( "MRIBiasFieldCorrection" ) ;
    BBTK_AUTHOR ( "Sylvain Jaume (MIT)" ) ;
    BBTK_DESCRIPTION ( "Corrects 3D MRI images corrupted by MRI gain field effect.  This module removes the slow-varying intensity variation from a 3D image.  The output image has a higher contrast locally and the visualization and reading of the image are improved.  This is an important pre-processinbg step for image operations requiring intensity perfect images, such as the Expectation Maximization segmentation (see EMSegment module). The N3 and N4 methods are described in N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction, Tustison N., Gee J., Insight Journal, 2009. http://hdl.handle.net/10380/3053 The Slicer code was contributed by Sylvain Jaume (MIT) for NA-MIC (http://na-mic.org)." ) ;
    BBTK_CATEGORY ( "Legacy.Filtering" ) ;

    // GENERATED DESCRPTION
    
BBTK_INPUT(MRIBiasFieldCorrection , InputImage , "InputImage" , std::string, "");
BBTK_INPUT(MRIBiasFieldCorrection , InputMask , "InputMask" , std::string, "");
BBTK_INPUT(MRIBiasFieldCorrection , OutputImage , "OutputImage" , std::string, "");
BBTK_INPUT(MRIBiasFieldCorrection , AlgorithmType , "AlgorithmType" , std::string, "");
BBTK_INPUT(MRIBiasFieldCorrection , ShrinkFactor , "ShrinkFactor" , int, "");
BBTK_INPUT(MRIBiasFieldCorrection , MaximumNumberOfIterations , "MaximumNumberOfIterations" , int, "");
BBTK_INPUT(MRIBiasFieldCorrection , NumberOfFittingLevels , "NumberOfFittingLevels" , int, "");
BBTK_INPUT(MRIBiasFieldCorrection , WienerFilterNoise , "WienerFilterNoise" , double, "");
BBTK_INPUT(MRIBiasFieldCorrection , FullWidthAtHalfMaximum , "FullWidthAtHalfMaximum" , double, "");
BBTK_INPUT(MRIBiasFieldCorrection , ConvergenceThreshold , "ConvergenceThreshold" , double, "");

    // EO GENERATED DESCRIPTION

    BBTK_END_DESCRIBE_BLACK_BOX ( MRIBiasFieldCorrection ) ;
}

#endif // __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__