/* -*- 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 <sstream>
#include <ostream>
#include <fstream>
#include <mia/core.hh>
#include <mia/core/cmeans.hh>
#include <mia/core/cmdlineparser.hh>
#include <mia/internal/main.hh>
#include <mia/2d.hh>

NS_MIA_USE;
using namespace std;

const SProgramDescription g_description = {
	
	{pdi_group, "Processing of series of 2D images in a 3D fashion (out-of-core)"}, 
	{pdi_short, "Calculate the c-means classification for a series of images."}, 
	
	
	{pdi_description, "This program first evaluates a sparse histogram of an input image "
         "series, then runs a c-means classification over the histogram and then writes the "
	 "probability mapping for thr original intensity values"
        }, 
	
	{pdi_example_descr,"Run the program over images imageXXXX.png with the sparse histogram, "
         "threshold the lower 5% bins (if available), run cmeans with three classes on the non-zero "
         "pixels."}, 
	
	{pdi_example_code, "-i image0000.png -o cmeans,txt --histogram-tresh=5 --classes 3"}
}; 



int do_main( int argc, char *argv[] )
{
	string out_probmap;
	string in_filename;

        float histogram_thresh = 5;
	
	CMeans::PInitializer class_center_initializer;

	
	const C2DImageIOPluginHandler::Instance& 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 filtered", 
			      CCmdOptionFlags::required_input, &imageio));
	options.add(make_opt( out_probmap, "out-probmap", 'o', "Save probability map to this file", 
			      CCmdOptionFlags::required_output));

	
        options.set_group("Parameters");
        options.add(make_opt( histogram_thresh, EParameterBounds::bf_closed_interval, {0,50},
			      "histogram-thresh", 'T',
                              "Percent of the extrem parts of the histogram to be collapsed "
			      "into the respective last histogram bin."));
        
        options.add(make_opt( class_center_initializer, "kmeans:nc=3", "classes", 'C',
			      "C-means class initializer"));
       
	 
	if (options.parse(argc, argv) != CCmdOptionList::hr_no)
		return EXIT_SUCCESS; 
	
	size_t start_filenum = 0;
	size_t end_filenum  = 0;
	size_t format_width = 0;

	string src_basename = get_filename_pattern_and_range(in_filename, start_filenum, end_filenum, format_width);
		
	if (start_filenum >= end_filenum)
		throw invalid_argument(string("no files match pattern ") + src_basename);


        CSparseHistogram histo;
        size_t n_pixels = 0; 
        for (size_t i = start_filenum; i < end_filenum; ++i) {
                string src_name = create_filename(src_basename.c_str(), i);
                C2DImageIOPluginHandler::Instance::PData  in_image_list = imageio.load(src_name);
                cvmsg() << "Read:" << src_name << "\r";
                if (in_image_list.get() && in_image_list->size()) {
                        for (auto k = in_image_list->begin(); k != in_image_list->end(); ++k)
                                n_pixels += accumulate(histo, **k);
                }
        }
	
        auto chistogram = histo.get_compressed_histogram();
	
        size_t n_cut_off = static_cast<size_t>(floor(n_pixels / 100.0 * histogram_thresh));
	
	
	size_t ni = 0; 
	auto ii = chistogram.begin(); 
        while ( ni < n_cut_off && ii != chistogram.end()) {
		ni += ii->second;
                ++ii; 
        }
	
	size_t ne = 0; 
	auto ie = chistogram.end() - 1;
        while ( ne < n_cut_off && ie !=  ii) {
		ne += ie->second;
                --ie;
        }

	CSparseHistogram::Compressed threshed_histo(ii, ie);

	CMeans::DVector class_centers; 
	
	CMeans cmeans(0.00001, class_center_initializer);
	CMeans::SparseProbmap pv = cmeans.run(threshed_histo,  class_centers);

	pv.save(out_probmap); 
	
	return EXIT_SUCCESS;
}

MIA_MAIN(do_main); 

        
