/* -*- 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/>.
 *
 */

#include <libxml++/libxml++.h>
#include <mia/core/msgstream.hh>
#include <mia/core/cmdlineparser.hh>
#include <mia/internal/main.hh>
#include <mia/2d/segsetwithimages.hh>
#include <ostream>
#include <fstream>

using xmlpp::DomParser;

using namespace mia; 
using namespace std; 


const SProgramDescription g_description = {
        {pdi_group, "Tools for Myocardial Perfusion Analysis"}, 
	{pdi_short, "Evaluate the dice index between segmentations."}, 
	{pdi_description,	"This program is used to evaluate the per-frame dice index of "
	 "segmented regions of an image with respect to the segmentation of a reference frame "
	 "from the same series."}, 
	{pdi_example_descr,	"Evaluate the dice index of segmentation set segment.set with reference 30 and " 
	 "skipping the first two frames."}, 
	{pdi_example_code,	"-i segment.set -r 30 -k 2"}
}; 

float dice_value(const C2DUBImage& mask1, const C2DUBImage& mask2) 
{
	assert (mask1.get_size() == mask2.get_size()); 
	int schnitt = 0; 
	int sum = 0; 
	
	for (auto m1 = mask1.begin(), m2 = mask2.begin(); 
	     m1 != mask1.end(); ++m1, ++m2) {
	
		if (*m1) 
			++sum; 
		if (*m2) 
			++sum; 
		
		if (*m1 && *m2)
			++schnitt; 
	}
	
	return sum ? (2.0f * schnitt) / sum : 1.0f; 
}

int do_main( int argc, char *argv[] )
{
	string org_filename;
	int skip = 2; 
	size_t reference = 20; 

	CCmdOptionList options(g_description);
	options.add(make_opt( org_filename, "input", 'i', "original segmentation set", CCmdOptionFlags::required_input));
	options.add(make_opt( skip, "skip", 'k', "images to skip atthe bgin of the series")); 
	options.add(make_opt( reference, "reference", 'r', "reference image")); 
	options.set_stdout_is_result();
	if (options.parse(argc, argv) != CCmdOptionList::hr_no)
		return EXIT_SUCCESS; 


	CSegSetWithImages original(org_filename, true); 

	size_t real_skip = skip; 
	if (skip < 0) {
                // if RV peak is given in the segmentation file, use it, otherwiese use 
		// absolue value of skip 
		int sk = original.get_RV_peak(); 
		real_skip = (sk < 0 ) ? -skip : sk; 
	}
	
	auto original_frames = original.get_frames(); 
	
	if (reference < real_skip || reference >= original_frames.size())
		throw create_exception<invalid_argument>( "reference frame must be larger then skip=", 
						skip, " and smaller then the length of the series ", original_frames.size()); 
	

	C2DUBImage reference_mask = original_frames[reference].get_section_masks(1); 

	for (size_t i = real_skip; i < original_frames.size(); ++i)  {
		auto current = original_frames[i].get_section_masks(1);
		cout << dice_value(current, reference_mask) << '\n'; 
	}
	
	return EXIT_SUCCESS; 
}

MIA_MAIN(do_main); 
