/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2016 Gert Wollny
 *
 * MIA is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with MIA; if not, see <http://www.gnu.org/licenses/>.
 *
 */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <fstream>
#include <cstdlib>
#include <string>
//#include <dlfcn.h>
#include <algorithm>

#include <mia/2d/fuzzyseg.hh>
#include <mia/core/cmdlineparser.hh>

NS_MIA_USE
using namespace std;

const SProgramDescription g_description = {
	{pdi_group, "Analysis, filtering, combining, and segmentation of 2D images"}, 
	{pdi_short, "A fuzzy c-means segmentation of a 2D image"}, 
	{pdi_description, "This program runs a combined fuzzy c-means clustering and "
	 "B-field correction to facilitate a fuzzy segmentation of 2D image. cf D.L. "
	 "Pham and J.L.Prince, \"An adaptive fuzzy C-means algorithm for image "
	 "segmentation in the presence of intensity inhomogeneities\", Pat. Rec. "
	 "Let., 20:57-68,1999"}, 
	{pdi_example_descr, "Run a 5-class segmentation over input image input.v "
	 "and store the class probability images in cls.v and the B0-field corrected "
	 "image in b0.v."}, 
	{pdi_example_code, "-i input.v -c 5 -o b0.v -c cls.v"}
}; 

int do_main( int argc, char *argv[] )
{


	string in_filename;
	string out_filename;
	string gain_filename;
	string cls_filename;
	int    noOfClasses = 3;
	SFuzzySegParams params; 

	const auto& imageio = C2DImageIOPluginHandler::instance();



	CCmdOptionList options(g_description);
	options.set_group("File-IO"); 
	options.add(make_opt( in_filename, "in-file", 'i',
			      "input image(s) to be segmenetd", CCmdOptionFlags::required_input, &imageio));
	options.add(make_opt( cls_filename, "cls-file", 'c',
			      "output class probability images (floating point values and multi-image)", 
			      CCmdOptionFlags::output, &imageio));
	options.add(make_opt( out_filename, "b0-file", 'o', "image corrected for intensity non-uniformity", 
			      CCmdOptionFlags::output, &imageio ));
	options.add(make_opt( gain_filename, "gain-file", 'g', "gain field (floating point valued)", 
			      CCmdOptionFlags::output, &imageio ));

	options.set_group("Parameters"); 
	options.add(make_opt( noOfClasses, "no-of-classes", 'n',
			      "number of classes"));
	options.add(make_opt( params.residuum, "residuum", 'r', "relative residuum"));
	options.add(make_opt( params.lambda1, "l1", 0, "Penalize magnitude of intensity inhomogeinity correction"));
	options.add(make_opt( params.lambda2, "l2", 0, "Smoothness of intensity inhomogeinity correction"));

	if (options.parse(argc, argv) != CCmdOptionList::hr_no)
		return EXIT_SUCCESS; 

	// required options (anything that has no default value)
	if ( in_filename.empty() )
		throw runtime_error("'--in-file'  ('i') option required\n");
	if ( in_filename.empty() )
		throw runtime_error("'--cls-file' ('c') option required\n");


	C2DImageIOPluginHandler::Instance::PData inImage_list = imageio.load(in_filename);

	if (!inImage_list.get() || !inImage_list->size() ) {
		string not_found = ("No supported data found in ") + in_filename;
		throw runtime_error(not_found);
	}

	// segment image
	if (inImage_list->size() > 1)
		cvwarn() << "Only segmenting first input image\n";

	C2DImageVector classes;
	P2DImage gain; 
	P2DImage b0_corrected = fuzzy_segment_2d(**inImage_list->begin(), noOfClasses, params, classes, gain);

	if (!out_filename.empty()) {

		// save corrected image to out-file
		C2DImageIOPluginHandler::Instance::Data out_list;

		out_list.push_back(b0_corrected);
		if ( !imageio.save(out_filename, out_list) ){

			string not_save = ("unable to save result to ") + out_filename;
			throw runtime_error(not_save);

		};

	};

	//CHistory::instance().append(argv[0], revision, opts);

	if ( !imageio.save(cls_filename, classes) ){
		string not_save = ("unable to save result to ") + cls_filename;
		throw runtime_error(not_save);

	}

	if (!gain_filename.empty()) {
		if (!save_image(gain_filename, gain)) 
			throw create_exception<runtime_error>( "unable to save gain field to '", gain_filename, "'"); 
	}
	
	return EXIT_SUCCESS;

}

#include <mia/internal/main.hh>
MIA_MAIN(do_main); 
