/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2015 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 <iterator>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <ostream>
#include <cmath>
#include <list>
#include <cassert>
#include <boost/filesystem.hpp>
#include <libxml++/libxml++.h>

#include <mia/core.hh>
#include <mia/2d/segset.hh>
#include <mia/2d/imageio.hh>
#include <mia/2d/filter.hh>
#include <mia/internal/main.hh>

using namespace std;
using namespace mia;
using xmlpp::DomParser;
namespace bfs=boost::filesystem;


const SProgramDescription g_description = {
        {pdi_group, "Tools for Myocardial Perfusion Analysis"}, 
	{pdi_short, "Translate a segmentation by the given amount."}, 
	{pdi_description, "This program move the segmentation(s) of an image series by using a shift "
	"that is equal for all slices. The program also may remove images from the "
	"begin of the series. The program can be used to correct the segmentation "
	"of the images if the images where cropped."}, 
	{pdi_example_descr, "Shift the segmentations of a set segement.set by -20 pixels in "
	 "horizontal direction and -30 pixels in vertical direction (as if the images where "
	 "cropped starting at (20,30) and store it in translate.set. The shiftes files are "
	 "named translatedXXXX.png"},
	{pdi_example_code, "-i segment.set -o translate.set -g translated -S \"<20,30>\""}
}; 


CSegSet load_segmentation(const string& s)
{
	DomParser parser;
	parser.set_substitute_entities(); //We just want the text to be resolved/unescaped automatically.
	parser.parse_file(s);
	return CSegSet(*parser.get_document());
}

int do_main(int argc, char *argv[])
{
	string src_filename;
	string out_filename;
	string shift_filename("crop");
	size_t skip = 2;

	C2DFVector shift;
	const auto& imageio = C2DImageIOPluginHandler::instance();

	CCmdOptionList options(g_description);
	options.add(make_opt( src_filename, "in-file", 'i', "input segmentation set", 
			      CCmdOptionFlags::required_input, &imageio));
	options.add(make_opt( out_filename, "out-file", 'o', "input segmentation set", 
			      CCmdOptionFlags::required_output, &imageio));
	options.add(make_opt( shift_filename, "image-file", 'g', "output image filename base"));

	options.add(make_opt(shift, "shift", 'S', "shift of segmentation"));
	options.add(make_opt(skip, "skip", 'k', "skip frames at the beginning"));

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


	CSegSet src_segset = load_segmentation(src_filename);

	cvinfo() << "shift by " << shift << ", skip " << skip << " and rename to base " << shift_filename << "\n";
	CSegSet shifted = src_segset.shift_and_rename(skip, shift, shift_filename);

	unique_ptr<xmlpp::Document> outset(shifted.write());

	ofstream outfile(out_filename.c_str(), ios_base::out );
	if (outfile.good())
		outfile << outset->write_to_string_formatted();

	return outfile.good() ? EXIT_SUCCESS : EXIT_FAILURE;
}

MIA_MAIN(do_main); 
