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
 *
 */

// $Id: dist2ascii.cc,v 1.1 2006-08-22 10:15:15 wollny Exp $

/*! \brief eva-downscale

\sa eva-downscale3d.cc

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


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

#include <string>
#include <stack>
#include <stdexcept>

#include <iostream>
#include <fstream>

#include <libmona/monaHistory.hh>
#include <libmona/monaException.hh>
#include <libmona/monaPopt.hh>
#include <libmona/3DVector.hh>
#include <libmona/filter.hh>
#include <libmona/fnameana.hh>
#include <libmona/2DImageWrap.hh>

#include <libmona/filter2dstack.hh>
#include <libmona/filetools.hh>


using namespace std; 
using namespace mona; 


void append_data(const C2DImageWrap& image, size_t z, float scale, ostream& outfile)
{
	const C2DUSImage *src = image.getC2DUSImage(); 
	if (!src) {
		stringstream msg; 
		msg << "input image " << z << "is not result of a distance transform"; 
		throw runtime_error(msg.str()); 
	}
	float iscale = 1.0 / scale; 
	
	C2DUSImage::const_iterator p = src->begin(); 
	
	for (size_t y = 0; y < src->get_size().y; ++y)
		for (size_t x = 0; x < src->get_size().x; ++x, ++p) 
			if (*p > 0)
				outfile << x << " " << y << " " << z << " " << *p * iscale << "\n";
}

int main(int argc, const char *args[])
{
	string in_filename; 
	string out_filename; 
	float scale; 
	
	C2DImageIOPluginHandler imageio; 
	
	// define options
	popt::COptions options;
	options.push_back(popt::option( in_filename, "in-file", 'i', "input file name", "")); 
	options.push_back(popt::option( out_filename, "out-file", 'o', "output file name", "output.txt")); 
	options.push_back(popt::option( scale, "scale", 's', "fixed point scale of distcance transform", "256.0"));
	
	
	vector<string> unknown_args; 
	popt::parse_options(argc, args, options, unknown_args);
	
	
	if (!unknown_args.empty()) {
		cverr() << "unknown arguments given\n"; 
		return -1; 
	}
	
	if (in_filename.empty()) {
		cverr() << "No input file given, run '" << args[0] << " --help' to get help\n"; 
		return -1; 
	}
	
	if (out_filename.empty()) {
		cverr() << "No output filename given, run '" << args[0] << " --help' to get help\n"; 
		return -1; 
	}
	
	
	try {
		
		ofstream os( out_filename.c_str(), ios::out ); 
				
		C2DImageList in_imagebuffer; 
		size_t start_filenum = 0; 
		size_t end_filenum  = 0; 
		size_t format_width = 0; 
 		
		std::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);
		

		// read all the files
		for (size_t i = start_filenum; i < end_filenum; ++i) {
			
			cvmsg() << "read " << i << " out of [" << start_filenum << ", " << end_filenum << "]\n"; 
			string src_name = create_filename(src_basename.c_str(), i);
			
			auto_ptr<C2DImageList> in_image_list(imageio.load(src_name));
			
			if (!in_image_list.get() || !in_image_list->size()) {
				cverr() << "expected " << end_filenum - start_filenum << " images, got only" << i - start_filenum <<"\n"; 
				break;
			}
			append_data(*in_image_list->begin(), i, scale, os ); 
		}
		
		
		cvmsg() << '\n'; 
		return EXIT_SUCCESS; 
	}
	catch (const mona_runtime_error& e){
		cerr << args[0] << " error: " << e.what() << endl;
	}
	catch (const mona_fatal_error& e){
		cerr << args[0] << " fatal: " << e.what() << endl;
	}
	catch (const mona_exception& e){
		cerr << args[0] << " error: " << e.what() << endl;
	}
	catch (const runtime_error &e){
		cerr << args[0] << " runtime: " << e.what() << endl;
	}
	catch (const invalid_argument &e){
		cerr << args[0] << " error: " << e.what() << endl;
	}
	catch (const exception& e){
		cerr << args[0] << " error: " << e.what() << endl;
	}
	catch (...){
		cerr << args[0] << " unknown exception" << endl;
	}

	return EXIT_FAILURE;
}