medical image analysis SVN (old)

/* -*- mona-c++  -*-
 * Copyright (c) Leipzig, Madrid 2004 - 2008 
 * Max-Planck-Institute for Human Cognitive and Brain Science	
 * Max-Planck-Institute for Evolutionary Anthropology 
 * BIT, ETSI Telecomunicacion, UPM
 *
 * This program 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 2 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *
 */

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

#include <memory>
#include <vector>
#include <numeric>

#include <libmona/filter_plugin2d.hh>
#include <libmona/2DImageWrap.hh>

#include <libmona/monaException.hh>
#include <libmona/monaHistory.hh>

using namespace mona; 
using namespace std; 

C2DImageWrap and_image(const C2DBitImage& image_1, const C2DBitImage& image_2, bool & nempty)
{
	if (image_1.get_size() != image_2.get_size()) 
		throw invalid_argument("input images need to be of the same size"); 
	
	C2DBitImage *result = new C2DBitImage(image_1.get_size()); 
	
	transform(image_1.begin(), image_1.end(), image_2.begin(), result->begin(), logical_and<bool>()); 
	nempty = accumulate(result->begin(), result->end(), false, logical_or<bool>());

	return C2DImageWrap(result); 
}

int main(int argc, const char *argv[])
{
	string a_filename; 
	string b_filename; 
	string out_filename; 
	string dilate_shape; 
	string out_type; 
	
	try {
		C2DImageIOPluginHandler imageio;
		
		popt::COptions options;
		options.push_back(popt::option( a_filename, "file1", '1', "input image 1", NULL )); 
		options.push_back(popt::option( b_filename, "file2", '2', "input image 2", NULL )); 
		options.push_back(popt::option( out_filename, "out-file", 'o', "border image", NULL )); 
		options.push_back(popt::option( dilate_shape, "dilate", 'd', "dilate shape", "4n")); 
		options.push_back(popt::option( out_type, imageio.get_set(), "type", 't',"output file type" , NULL)); 	
		

		vector<string> unknown_opts; 
			
		popt::parse_options(argc, argv, options, unknown_opts);

		if (!unknown_opts.empty())
			throw mona_fatal_error("Unknown options given"); 
		
		if (a_filename.empty() || b_filename.empty() ||out_filename.empty())
			throw mona_fatal_error("2 input files and an output file required"); 
		
	
		C2DImageFilterHandler filter_plugins;
		
		auto_ptr<C2DImageList> image_list_1(imageio.load(a_filename));
		if (!image_list_1.get() || image_list_1->empty()) 
			throw mona_fatal_error(string("No images found in ") + a_filename); 
		
		auto_ptr<C2DImageList> image_list_2(imageio.load(b_filename));
		if (!image_list_2.get() || image_list_2->empty()) 
			throw mona_fatal_error(string("No images found in ") + b_filename); 

		if (out_type.empty())
			out_type = image_list_1->get_sourceformat(); 

		
		stringstream filter_descr; 
		filter_descr << "dilate:shape=" << dilate_shape; 
		
		C2DImageFilterFactory::ProductPtr filter = C2DImageFilterFactory::produce(filter_descr.str().c_str(), filter_plugins); 
		if (!filter)
			throw invalid_argument(string("Unable to create dilate filter from:") +filter_descr.str()); 
		
		C2DImageWrap image_wrap_1 = filter->filter(*image_list_1->begin()); 
		C2DImageWrap image_wrap_2 = filter->filter(*image_list_2->begin()); 
		
		C2DBitImage *image_1 = image_wrap_1.getC2DBitImage(); 
		if (!image_1)
			throw invalid_argument("Input image 1 needs to be in bit representation"); 
		
		C2DBitImage *image_2 = image_wrap_2.getC2DBitImage(); 
		if (!image_2)
			throw invalid_argument("Input image 2 needs to be in bit representation"); 
		
		
		C2DImageList out_list; 
		bool nempty = false; 
		out_list.push_back(and_image(*image_1, *image_2, nempty)); 
		
		if ( !imageio.save(out_type, out_list, out_filename) ){
			string not_save = ("unable to save result to ") + out_filename;
			throw mona_runtime_error(not_save);
		};
		
		return EXIT_SUCCESS; 
	}


	catch (const mona_runtime_error& e){
		 cverr() << argv[0] << " error: " << e.what() << endl;
	} 
	 catch (const mona_fatal_error& e){
		cverr() << argv[0] << " fatal: " << e.what() << endl;
	}
	catch (const mona_exception& e){
		cverr() << argv[0] << " error: " << e.what() << endl;
	}
	catch (const invalid_argument &e){
		cverr() << argv[0] << " error: " << e.what() << endl;
	}
	catch (const exception& e){
		cverr() << argv[0] << " error: " << e.what() << endl;
	}
 	catch (...){
 		cverr() << argv[0] << " unknown exception" << endl;
 	}

	return EXIT_FAILURE;


}