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: 3d22dimage.cc,v 1.7 2006-07-12 13:44:25 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 <stdexcept>
#include <iomanip>

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

#include <libmona/filter_plugin2d.hh>
#include <libmona/2DImageWrap.hh>
#include <libmona/3DImagePtr.hh>
#include <libmona/fnameana.hh>

#include <libmona/filetools.hh>

using namespace std; 
using namespace mona; 

class C2DImageSaver: public TUnaryImageFilter<bool> {
public: 
	C2DImageSaver(const string& basename, const string& type, const C2DImageIOPluginHandler& imageio2d); 
	
	template <class Image3D>
	bool operator () (const Image3D& image)const; 
private: 
	string _M_basename; 
	string _M_type; 
	const C2DImageIOPluginHandler& _M_imageio2d; 
};

C2DImageSaver::C2DImageSaver(const string& basename, const string& type, const C2DImageIOPluginHandler& imageio2d):
	_M_basename(basename), 
	_M_type(type), 
	_M_imageio2d(imageio2d)
{
}

template <class Image3D>
bool C2DImageSaver::operator () (const Image3D& image)const 
{
	typedef T2DImage<typename Image3D::value_type> OutImage; 
	
	
	for (size_t z = 0; z < image.get_size().z; ++z) {
		OutImage *r = new OutImage(C2DBounds( image.get_size().x, image.get_size().y)); 
		C2DImageList out_images; 
		out_images.push_back(C2DImageWrap(r));

		image.get_data_plane_xy(z, &(*r)(0,0), r->size());
		for (typename OutImage::iterator i= r->begin(); 
		     i != r->end(); ++i)
			if (*i < 0)
				*i = 0; 
		
		stringstream fname; 
		fname << _M_basename << setfill ('0') << setw (4) << z << "." <<_M_type; 
		cvmsg() << "save " << fname.str() << '\n'; 
		if (!_M_imageio2d.save(_M_type, out_images, fname.str(), NULL))
			return false; 
	}
	return true; 
}

int main(int argc, const char *args[])
{
	string in_filename; 
	string out_filename; 
	string type; 
	vector<int> new_size; 

	try {
		C2DImageIOPluginHandler imageio2d;
		string types = string("data type to convert to ( ") + imageio2d.supported_formats() + ")";
		
		
		// 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-basename", 'o', "output base name", "basename")); 
		options.push_back(popt::option( type, imageio2d.get_set(), "type", 't',"output file type" , "png")); 	
		
		
		vector<string> unknows_args; 
		popt::parse_options(argc, args, options, unknows_args);
		
		if (!unknows_args.empty()) {
			cverr() << "Unknown arguments: "; 
			for (vector<string>::const_iterator i = unknows_args.begin(); i !=  unknows_args.end(); 
			     ++i)
				cverb << *i << " "; 
			cverb << "\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; 
		}
		
		// now start the fun part 
		//first count the number of slices
		C3DImageIOPluginHandler imageio3d; 
		
		auto_ptr<C3DImageList> in_image(imageio3d.load(in_filename)); 
		if (in_image.get() && !in_image->empty()) {
			C2DImageSaver saver(out_filename, type, imageio2d); 
			
			return !wrap_filter(saver, *in_image->begin()); 
		}
		
	}
	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;
}