File: 2dmultiimagevar.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 <cmath>
#include <mia/core.hh>
#include <mia/2d.hh>
#include <mia/internal/main.hh>

NS_MIA_USE;
using namespace std;


const SProgramDescription g_description = {
        {pdi_group, "Analysis, filtering, combining, and segmentation of 2D images"}, 
	{pdi_short, "Evaluate the intensity variation of pixels in a series of images."}, 
	{pdi_description, "This program evaluates the pixel-wise accumulated intensity "
	 "variation of a set of image given on the command line. "
	 "If the input image files contain more then one image all images are used. "
	 "All images must be of the same size."}, 
	{pdi_example_descr, "Evaluate the pixel-vise intensity variation of images i1.png, i2.png, "
	 "i3.png, and i4.png and store the result to var.v."}, 
	{pdi_example_code, "-o var.v i1.png i2.png i3.png i4.png"}
}; 


class CVarAccumulator : public TFilter<bool> {
public:
	CVarAccumulator():
		m_n(0)
	{
	}

	template <typename T>
	bool operator () (const T2DImage<T>& image) {
		if (!m_n) {
			m_sum = C2DDImage(image.get_size(), image);
			m_sum2 = C2DDImage(image.get_size());
		}else if (image.get_size() != m_sum.get_size()) {
			throw create_exception<invalid_argument>( "input images differ in size");
		}

		transform(image.begin(), image.end(), m_sum.begin(), m_sum.begin(), 
			  [](double x, double y){return x + y;});
		
		transform(image.begin(), image.end(), m_sum2.begin(), m_sum2.begin(), 
			  [](double x, double y){return x * x + y;});
		++m_n;
		return true;
	}

	P2DImage result()const
	{
		C2DFImage *image = new C2DFImage( m_sum.get_size());
		P2DImage result(image);
		transform(m_sum.begin(), m_sum.end(), m_sum2.begin(), image->begin(), 
			  [this](double sum, double sum2){return (sum2 - sum * sum/m_n)/(m_n - 1);}); 
		transform(image->begin(), image->end(), image->begin(),  
			  [](double x) {return sqrt(x);}); 
		return result;

	}
private:
	C2DDImage m_sum;
	C2DDImage m_sum2;
	size_t m_n;
};

int do_main( int argc, char *argv[] )
{
	
	string out_filename;
	string out_type("vista");

	const auto& imageio = C2DImageIOPluginHandler::instance();


	CCmdOptionList options(g_description);
	options.add(make_opt( out_filename, "out-file", 'o', "output image ", 
			      CCmdOptionFlags::required_output, &imageio));

	if (options.parse(argc, argv, "image", &imageio) != CCmdOptionList::hr_no)
		return EXIT_SUCCESS; 


	if (options.get_remaining().empty())
		throw runtime_error("no input images given ...");

	auto input_images = options.get_remaining();

	CVarAccumulator ic;

	for (auto  i = input_images.begin(); i != input_images.end(); ++i) {
		cvmsg() << "Load " << *i << "\r";
		auto in_image_list = imageio.load(*i);
		if (in_image_list.get() && in_image_list->size()) {
			accumulate(ic, **in_image_list->begin());
		}
	}
	cvmsg() << "\n";

	if (save_image(out_filename, ic.result()))
		return EXIT_SUCCESS;
	else
		cerr << argv[0] << " fatal: unable to output image to " <<  out_filename << endl;

	return EXIT_SUCCESS;
}

MIA_MAIN(do_main);