medical image analysis SVN (old)

/*
 * Copyright (c) 2007 Gert Wollny <gert.wollny at web.de>
 *
 * 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
 *
 */

// $Id: 3dimagefilter.cc,v 1.12 2006-07-12 13:44:23 wollny Exp $

/*! \brief mia-3dimagefilter

\sa mia-3dimagefilter.cc

\file mask.cc
\author G. Wollny, wollny eva.mpg.de, 2005
*/

#include <miaconfig.h>
#include <iostream>
#include <string>
#include <stdexcept>
#include <sstream>

#include <mia/3d/3dfilter.hh>
#include <mia/3d/3dimageio.hh>
#include <mia/core.hh>

using namespace std;
NS_MIA_USE; 

int main( int argc, const char *argv[] )
{

	string in_filename;
	string out_filename;
	string out_type; 

	bool help_plugins = false; 

	try {	
	        const C3DFilterPluginHandler::Instance& filter_plugins = C3DFilterPluginHandler::instance();
		const C3DImageIOPluginHandler::Instance& imageio = C3DImageIOPluginHandler::instance();
	
		stringstream filter_names; 
		
		filter_names << "filters in the order to be applied (out of: " << filter_plugins.get_plugin_names() << ")"; 
		
		CCmdOptionList options;
		options.push_back(make_opt( in_filename, "in-file", 'i', "input image(s) to be filtered", "input", true)); 
		options.push_back(make_opt( out_filename, "out-file", 'o', "output image(s) that have been filtered", "output", true)); 
		options.push_back(make_opt( out_type, imageio.get_set(), "type", 't',"output file type" , "type", false)); 	
		options.push_back(make_opt( help_plugins, "help-plugins", 0, "give some help about the filter plugins", NULL)); 
	

		options.parse(argc, argv);

		vector<const char *> filter_chain = options.get_remaining();

		cvdebug() << "IO supported types: " << imageio.get_plugin_names() << "\n"; 
		cvdebug() << "supported filters: " << filter_plugins.get_plugin_names() << "\n"; 

		if (help_plugins) {
			filter_plugins.print_help(cout);
			return EXIT_SUCCESS; 
		}

		if ( filter_chain.empty() ) 
			cvwarn() << "no filters given, just copy\n";

		if ( in_filename.empty() ) 
			throw runtime_error("'--in-image' ('i') option required");

		if ( out_filename.empty() ) 
			throw runtime_error("'--out-image' ('o') option required");
		
		//CHistory::instance().append(argv[0], "unknown", options);
		

		std::list<C3DFilterPlugin::ProductPtr> filters;

		for (vector<const char *>::const_iterator i = filter_chain.begin(); 
		     i != filter_chain.end(); ++i) {
			cvdebug() << "Prepare filter " << *i << std::endl; 
			C3DFilterPlugin::ProductPtr filter = filter_plugins.produce(*i); 
			if (!filter){
				std::stringstream error; 
				error << "Filter " << *i << " not found"; 
				throw invalid_argument(error.str());
			}
			filters.push_back(filter);
		}

		// read image
		C3DImageIOPluginHandler::Instance::PData  in_image_list = imageio.load(in_filename);

		
                if (in_image_list.get() && in_image_list->size()) {
			vector<const char *>::const_iterator filter_name = filter_chain.begin();
			for (std::list<C3DFilterPlugin::ProductPtr>::const_iterator f = filters.begin(); 
			     f != filters.end(); ++f, ++filter_name) {
				cvmsg() << "Run filter: " << *filter_name << "\n";
				for (C3DImageIOPluginHandler::Instance::Data::iterator i = in_image_list->begin(); 
				     i != in_image_list->end(); ++i)
					*i = (*f)->filter(**i);
			}
			
			if ( !imageio.save(out_type, out_filename, *in_image_list) ){
				string not_save = ("unable to save result to ") + out_filename;
				throw runtime_error(not_save);
			};
			
		}


		return EXIT_SUCCESS; 

	}
	catch (const runtime_error &e){
		cerr << argv[0] << " runtime: " << e.what() << endl;
	}
	catch (const invalid_argument &e){
		if (help_plugins) {
			C3DFilterPluginHandler::instance().print_help(cout);
			return EXIT_SUCCESS; 
		}
		cerr << argv[0] << " error: " << e.what() << endl;
	}
	catch (const exception& e){
		cerr << argv[0] << " error: " << e.what() << endl;
	}
	catch (...){
		cerr << argv[0] << " unknown exception" << endl;
	}

	return EXIT_FAILURE;
}