File: 2dseries2dordermedian.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/>.
 *
 */

#define VSTREAM_DOMAIN "SER2DGRADMedian"

#include <iostream>
#include <fstream>
#include <iomanip>
#include <string>
#include <limits>
#include <sstream>
#include <stdexcept>
#include <boost/algorithm/minmax_element.hpp>

#include <mia/internal/main.hh>
#include <mia/2d/filterchain.hh>
#include <mia/2d/imageio.hh>
#include <mia/2d/segsetwithimages.hh>
#include <mia/core.hh>

using namespace std;
using namespace mia;

const SProgramDescription g_description = {
	{pdi_group, "Tools for Myocardial Perfusion Analysis"}, 
	
	{pdi_short, "Evaluate time-intensity median 2nd order derivative of a series."}, 

	{pdi_description,"This program evaluates the pixel-wise median of the absolute values of the gauss filtered "
	 "2nd order temporal derivative of a series of images. In addition, it can be used to "
	 "output the time-intensity curve of a given pixel."
	 "The program supports slice-wise spacial pre-filtering by giving additional filters as free "
	 "parameters (filter/2dimage)."}, 

	{pdi_example_descr,"Evaluate the median of the 2nd order derivative of the series given in segmentation set "
	 "segment.set after filtering with a Gaussian of width 3. In addition write "
	 "the time intensity curve of pixel <128,64> to curve.txt."}, 
	

	 {pdi_example_code, "-i segment.set -o gradmedian.exr -g 1 --itc-file curve.txt --itc-loc \"<128,64>\""}
}; 

template <typename T>
struct fabsdelta {
	T operator () (T x, T y) const {
		return fabs(x - y);
	}
};
struct C2DAccumulator : public TFilter<bool> {
	typedef vector<double> CBuffer;

	C2DAccumulator(size_t n, size_t gauss_width):
		m_min(numeric_limits<float>::max()),
		m_max(-numeric_limits<float>::max()),
		m_n(n - 1),
		m_initialized(false)
	{
		if (gauss_width > 0) {
			stringstream gauss_descr;
			gauss_descr << "gauss:w=" << gauss_width;
			gauss = C1DSpacialKernelPluginHandler::instance().produce(gauss_descr.str().c_str());
		}

	}

	template <typename T>
	bool operator ()(const T2DImage<T>& image)
	{
		if (!m_initialized) {
			m_field.resize(image.size());
			m_size = image.get_size();
			m_initialized = true;
		}

		if (image.get_size() != m_size)
			throw invalid_argument("Input images are not all of same size");

		typename T2DImage<T>::const_iterator i = image.begin();
		typename T2DImage<T>::const_iterator e = image.end();
		vector<CBuffer>::iterator v = m_field.begin();

		for(; i != e; ++i, ++v)
			v->push_back(*i);

		pair<typename T2DImage<T>::const_iterator, typename T2DImage<T>::const_iterator>
			src_minmax = ::boost::minmax_element(image.begin(), image.end());
		if (m_min > *src_minmax.first)
			m_min = *src_minmax.first;
		if (m_max < *src_minmax.second)
			m_max = *src_minmax.second;

		return true;
	}

	CBuffer get_curve_at(const C2DBounds& loc) const {
		if (loc.x < m_size.x && loc.y < m_size.y) {
			return m_field[loc.y * m_size.x + loc.x];
		}
		throw invalid_argument("get_curve_at: requested point outside image area\n");
	}

	CBuffer absgradient_2(const CBuffer& x) {
		CBuffer result;
		for (size_t i = 1; i < x.size() - 1; ++i) {
			result.push_back(abs(x[i+1] + x[i-1] - 2 * x[i]));
		}
		return result;
	}

	void evaluate_gradients()
	{
		vector<CBuffer>::iterator v = m_field.begin();
		vector<CBuffer>::iterator e = m_field.end();

		while ( v != e ) {
			if (gauss) {
				gauss->apply_inplace(*v);
			}
			*v = absgradient_2(*v);
			++v;
		}
	}

	static float median( CBuffer::iterator begin,
			     CBuffer::iterator end, size_t len)
	{
		if (len & 1) {
			CBuffer::iterator i = begin + (len - 1) / 2;
			std::nth_element(begin, i, end);
			return *i;
		}else {
			CBuffer::iterator i1 = begin + len / 2 - 1;
			CBuffer::iterator i2 = begin + len / 2;
			std::nth_element(begin, i1, end);
			std::nth_element(begin, i2, end);
			return (*i1 + *i2) / 2.0;
		}
	}

	P2DImage  result() {
		float range = 255.0 / (m_max - m_min);

		C2DFImage *median2order = new C2DFImage(m_size);

		C2DFImage::iterator ii = median2order->begin();
		vector<CBuffer>::iterator iv = m_field.begin();
		vector<CBuffer>::iterator ev = m_field.end();
		while (iv != ev) {
			*ii++ = range * median(iv->begin(), iv->end(), m_n);
			++iv;
		}
		return P2DImage(median2order);
	}

private:
	C2DBounds m_size;
	float m_min;
	float m_max;
	vector<CBuffer> m_field;
	size_t m_n;
	bool m_initialized;
	std::shared_ptr<C1DFilterKernel > gauss;
};

int do_main( int argc, char *argv[] )
{

	string in_filename;
	string out_filename;
	string out_type;
	bool crop;
	size_t skip = 0;
	size_t enlarge_boundary = 5;
	size_t gauss_width = 1;
	C2DBounds itc_location;
	string itc_file;


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

	CCmdOptionList options(g_description);
	options.add(make_opt( in_filename, "in-file", 'i', "input segmentation set", CCmdOptionFlags::required_input));
	options.add(make_opt( out_filename, "out-file", 'o', "output image name", CCmdOptionFlags::required_output, &imageio));
	options.add(make_opt( skip, "skip", 'k', "Skip files at the beginning"));
	options.add(make_opt( enlarge_boundary,  "enlarge-boundary", 'e', "Enlarge cropbox by number of pixels"));
	options.add(make_opt( crop, "crop", 'c', "crop image before running statistics"));
	options.add(make_opt( gauss_width, "gauss", 'g', "gauss filter width for moothing the gradient"));
	options.add(make_opt( itc_file, "itc-file", 0, "intensity time curve output file"));
	options.add(make_opt( itc_location, "itc-loc", 0, "intensity time curve output pixel coordinates"));


	if (options.parse(argc, argv, "filter", &C2DFilterPluginHandler::instance()) != CCmdOptionList::hr_no)
		return EXIT_SUCCESS; 

	C2DImageFilterChain filter_chain(options.get_remaining());

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

	CSegSetWithImages  segset(in_filename, true);

	if (crop) {
		C2DBoundingBox box = segset.get_boundingbox();
		box.enlarge(enlarge_boundary);
		stringstream crop_descr;
		crop_descr << "crop:"
			   << "start=[" << box.get_grid_begin()
			   << "],end=[" << box.get_grid_end() << "]";
		cvdebug() << "Crop with " << crop_descr.str() << "\r";

		filter_chain.push_front(crop_descr.str().c_str());
	}

	if (skip >= segset.get_images().size())
		throw invalid_argument("Skip is equal or larger then image series");

	auto iimages = segset.get_images().begin();
	auto eimages = segset.get_images().end();
	advance(iimages, skip);

	C2DAccumulator acc(distance(iimages, eimages), gauss_width);
	for (; iimages != eimages; ++iimages) {

		P2DImage in_image = *iimages;
		if (!filter_chain.empty() )
			in_image = filter_chain.run(in_image);
		mia::accumulate(acc, *in_image);
	}

	C2DAccumulator::CBuffer itc_absolute;
	if (!itc_file.empty())
		itc_absolute = acc.get_curve_at(itc_location);

	acc.evaluate_gradients();
	auto itc_d2 = acc.get_curve_at(itc_location);

	P2DImage  result = acc.result();

	if (!itc_file.empty()) {
		auto itc_d2help = acc.absgradient_2(itc_absolute);
		ofstream itc(itc_file.c_str(), ios_base::out);

		auto ia = itc_absolute.begin() + 1;
		auto id2 = itc_d2.begin();
		auto ihelp = itc_d2help.begin();
		while (id2 != itc_d2.end()) {
			itc << *ia++ << " " << *id2++ << " " << *ihelp++ << "\n";
		}
	}

	if (save_image(out_filename, result))
		return  EXIT_SUCCESS;
	return  EXIT_FAILURE;

}

MIA_MAIN(do_main);