File: 2dnrreg.cc

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/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2014 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 <mia/core.hh>
#include <mia/2d.hh>
#include <mia/internal/main.hh>
#include <sstream>
#include <iomanip>
#include <boost/algorithm/minmax_element.hpp>

NS_MIA_USE
using namespace boost; 
using namespace std; 

const SProgramDescription g_description = {
        {pdi_group, "2D Image Registration"}, 
	{pdi_short, "Non-linear registration of two 2D images."}, 
	{pdi_description, "This program is used to run a model based non-rigid registration of two 2D images. "
	"Optimization is done using a time marching algorithm. "
	 "Remark: The implementation currently only supports a per pixel transformation and "
	 "it is not well tested."}, 
	{pdi_example_descr, "Register image test.v to image ref.v and write the registered image to reg.v. "
	 "Start registration at the smallest size above 16 pixel and ssd as cost function."}, 
	{pdi_example_code, "-i test.v -r ref.v -o reg.v -s 16 -c ssd"}
	
}; 

// set op the command line parameters and run the registration 
int do_main(int argc, char **argv)
{

	CCmdOptionList options(g_description);
	string src_filename; 
	string out_filename; 
	string def_filename; 
	string ref_filename; 
	string mov_filename; 
	string cost_function("ssd"); 
	string regmodel("navier"); 
	string timestep("fluid"); 
	int start_size = 16; 
	EInterpolation interpolator = ip_bspline3; 
	int max_iter = 200; 
	float epsilon = 0.01; 
	bool save_steps = false; 

	const C2DImageCostPluginHandler::Instance& icph = C2DImageCostPluginHandler::instance(); 

	options.add(make_opt( src_filename, "in-file", 'i', "input image (floating image)", "template", true));
	options.add(make_opt( ref_filename, "ref-file", 'r', "reference image", "reference", true));
	options.add(make_opt( def_filename, "def-file", 'd', "deformed inpout image", NULL, false));
	options.add(make_opt( out_filename, "out-file", 'o', "output vector field", "output", true));
	options.add(make_opt( mov_filename, "mov-file", 0, "movie generator image", NULL, false));
	options.add(make_opt( regmodel, "regmodel", 'm', "registration model", "model", false));
	options.add(make_opt( timestep, "timestep", 't', "time setp", "timestep", false));
	options.add(make_opt( start_size, "mgsize", 's', "multigrid start size", "start", false));
	options.add(make_opt( max_iter, "max-iter", 'n', ",maximum number of iterations", "iter", false));
	options.add(make_opt( cost_function, "cost", 'c', "cost function", "cost", false)); 
	options.add(make_opt( interpolator, GInterpolatorTable ,"interpolator", 'p', 
					"image interpolator", "interpolator", false)); 
	options.add(make_opt( epsilon, "epsilon", 'e', "relative accuracy to stop registration at a multi-grid level", NULL, false)); 
	options.add(make_opt( save_steps, "save-steps", 0, "save the steps of the registration in images", NULL, false));

	options.parse(argc, argv);

	P2DImageCost cost = icph.produce(cost_function.c_str());
	P2DRegModel model = C2DRegModelPluginHandler::instance().produce(regmodel.c_str()); 
	P2DRegTimeStep time_step = C2DRegTimeStepPluginHandler::instance().produce(timestep.c_str()); 
	
	if (!cost || !model || !time_step)
		return EXIT_FAILURE;

	
	const C2DImageIOPluginHandler::Instance& imageio = C2DImageIOPluginHandler::instance(); 
	typedef C2DImageIOPluginHandler::Instance::PData PImageVector; 


	PImageVector reference = imageio.load(ref_filename); 
	PImageVector source    = imageio.load(src_filename); 
	PImageVector movie; 

	if (!mov_filename.empty() ) {
		movie = imageio.load(mov_filename); 
	}

	if (!movie && save_steps)
		movie = source; 
	
	if (!reference || reference->size() < 1) {
		cerr << "no image found in " << ref_filename << "\n"; 
		return EXIT_FAILURE;
	}

	if (!source || source->size() < 1) {
		cerr << "no image found in " << src_filename << "\n"; 
		return EXIT_FAILURE;
	}
	
	std::shared_ptr<C2DInterpolatorFactory > ipf(create_2dinterpolation_factory(interpolator)); 
	if (!ipf)
		throw invalid_argument("unknown interpolator requested"); 

	C2DImageRegister reg(start_size, *cost, max_iter, *model, *time_step, *ipf, epsilon, save_steps, 
			     (!movie || movie->empty()) ?  P2DImage() : *movie->begin());

	P2DFVectorfield regfield = reg(**source->begin(), **reference->begin()); 
	C2DIOVectorfield outfield(*regfield);
	
	 if (!C2DVFIOPluginHandler::instance().save("", out_filename, outfield)){
		cerr << "Unable to save result vector field to " << out_filename << "\n"; 
		return EXIT_FAILURE; 
	}
	
	if (!def_filename.empty()) {
		C2DImageVector vimg;
		vimg.push_back(filter(FDeformer2D(*regfield, *ipf), **source->begin())); 
		if (!imageio.save("", def_filename, vimg)) {
			cerr << "Unable to save result image to " << def_filename << "\n"; 
			return EXIT_FAILURE; 
		}
			
	}
	return EXIT_SUCCESS; 
}

MIA_MAIN(do_main);