/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2015 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/>.
 *
 */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <mia/core/type_traits.hh>
#include <mia/3d/fifof/regiongrow.hh>

NS_BEGIN(regiongrow_fifof)

NS_MIA_USE;
using namespace std;
using namespace boost;
namespace bfs=boost::filesystem;

static char const * plugin_name = "regiongrow";


C2DRegiongrowFifoFilter::C2DRegiongrowFifoFilter(const CProbabilityVector probmap,
			float low, float seed, int cls, int depth):
	C2DImageFifoFilter(1, 1, depth),
	m_probmap(probmap),
	m_low(low),
	m_seed(seed),
	m_class(cls),
	m_depth(depth), 
	m_slice_emls(0)
{
	m_shape = C3DShapePluginHandler::instance().produce("6n");
}

template <typename T, bool is_float>
struct FTransform {
	FTransform(CProbabilityVector::value_type map):
		m_map(map),
		m_maxidx(map.size()-1)
	{
		assert((size_t)m_maxidx < map.size());
	}

	double operator () (T x) const {
		if (x <= 0)
			return m_map[0];
		if (x <= m_maxidx)
			return m_map[x];
		return m_map[m_maxidx];
	}
	CProbabilityVector::value_type m_map;
	T m_maxidx;
};

template <typename T>
struct FTransform<T, true> {
	FTransform(CProbabilityVector::value_type /*map*/)
	{
		throw invalid_argument("C2DRegiongrowFifoFilter doesn't support float input images");
	}

	double operator () (T /*x*/) const {
		throw invalid_argument("C2DRegiongrowFifoFilter doesn't support float input images");
	}
};


template <typename T>
int C2DRegiongrowFifoFilter::operator ()( const T2DImage<T>& image)
{
	const bool is_float = std::is_floating_point<T>::value;
	transform(image.begin(), image.end(), m_in_buffer.begin(),
		  FTransform<T, is_float>(m_probmap[m_class]));

	transform(m_in_buffer.begin(), m_in_buffer.begin() + image.size(),
		  m_out_buffer.begin(),
		  m_seed);
	return 0;
}

void C2DRegiongrowFifoFilter::do_push(::boost::call_traits<P2DImage>::param_type x)
{
	TRACE("C2DRegiongrowFifoFilter::do_push");
	mia::accumulate(*this, *x);
}

void C2DRegiongrowFifoFilter::do_initialize(::boost::call_traits<P2DImage>::param_type x)
{
	TRACE("C2DRegiongrowFifoFilter::do_initialize");
	m_slice_size = x->get_size();
	m_slice_emls = m_slice_size.x * m_slice_size.y;
	C3DBounds buf_size(m_slice_size.x, m_slice_size.y, m_depth + 1);
	m_in_buffer = C3DDImage(buf_size);
	m_out_buffer = C3DBitImage(buf_size);
}

void C2DRegiongrowFifoFilter::seed_env(const C3DBounds& center, queue<C3DBounds>& seeds) const
{
	C3DShape::const_iterator sb = m_shape->begin();
	C3DShape::const_iterator se = m_shape->end();

	while (sb != se) {
		C3DBounds x(center.x + sb->x, center.y + sb->y, center.z + sb->z);
		++sb;
		if (x.z >= get_end())
			continue;
		if ( m_slice_size.y <= x.y || m_slice_size.x <= x.x)
			continue;
		if (!m_out_buffer(x) && m_in_buffer(x) >= m_low)
			seeds.push(x);
	}
}

void  C2DRegiongrowFifoFilter::grow()
{
	queue<C3DBounds> seeds;
	C3DBitImage::const_iterator i = m_out_buffer.begin();
	
	for (size_t z = 0; z < get_end(); ++z)
		for (size_t y = 0; y < m_slice_size.y; ++y)
			for (size_t x = 0; x < m_slice_size.x; ++x, ++i) {
				if (*i)
					seed_env(C3DBounds(x,y,z), seeds);
			}

	while (!seeds.empty()) {
		C3DBounds x = seeds.front();
		cvdebug() << "add " << x << "\n";
		seeds.pop();
		if (!m_out_buffer(x)) {
			m_out_buffer(x) = true;
			seed_env(x, seeds);
		}
	}
}

P2DImage C2DRegiongrowFifoFilter::do_filter()
{
	TRACE("C2DRegiongrowFifoFilter::do_filter");
	cvdebug() << "Range: [" << get_start() << ", " << get_end() << "]\n";
	grow();
	C2DBitImage *result = new C2DBitImage(m_slice_size);
	copy(m_out_buffer.begin_at(0,0,get_start()),  m_out_buffer.begin_at(0,0, get_start() + 1), result->begin());
	return P2DImage(result);
}

void C2DRegiongrowFifoFilter::shift_buffer()
{
	TRACE("C2DRegiongrowFifoFilter::shift_buffer");
	copy_backward(m_in_buffer.begin(), m_in_buffer.end() - m_slice_emls, m_in_buffer.end());
	copy_backward(m_out_buffer.begin(), m_out_buffer.end() - m_slice_emls, m_out_buffer.end());
}

class C2DRegiongrowFifoFilterPlugin : public C2DFifoFilterPlugin {
public:
	C2DRegiongrowFifoFilterPlugin();
private:
	virtual const string do_get_descr() const;
	virtual C2DImageFifoFilter *do_create()const;

	string m_map;
	float m_low;
	float m_seed;
	int m_class;
	int m_depth;
};


C2DRegiongrowFifoFilterPlugin::C2DRegiongrowFifoFilterPlugin():
	C2DFifoFilterPlugin(plugin_name),
	m_low(0.5f),
	m_seed(0.98),
	m_class(2),
	m_depth(10)
{
	add_parameter("map", new CStringParameter(m_map, CCmdOptionFlags::required_input, "seed class map"));
	add_parameter("low", make_oci_param(m_low, .0f, 1.0f, false,
						 "low threshold for acceptance probability"));
	add_parameter("seed", make_oci_param(m_seed, .0f, 1.0f, false,
						 "threshold for seed probability"));

	add_parameter("class", make_lc_param(m_class, 0, false, "class to be segmented"));
	add_parameter("depth", make_lc_param(m_depth, 1, false, "number of slices to keep during processing"));
}


const string C2DRegiongrowFifoFilterPlugin::do_get_descr() const
{
	return "Run a region-growing filter on a stack of images that comprise "
		"a 3D image.  The region growing is based on class probabilities obtained from "
		"a c-means classification of the pixel intensities. One seed thresh is use to initiate "
		"a region, and another (lower) threshold is used to stop the region growing. "
		"By holding a number of 3D slices in the working memory to allow the region to grow \""
		"backwards \" in the stack a Quasi-3D processing is achieved. However, with complex "
		"structures the region growing may not properly be segmented.";
}

C2DImageFifoFilter *C2DRegiongrowFifoFilterPlugin::do_create()const
{
	return  new C2DRegiongrowFifoFilter(CProbabilityVector(m_map),
					    m_low, m_seed, m_class, m_depth);
}


extern "C" EXPORT CPluginBase *get_plugin_interface()
{
	return new C2DRegiongrowFifoFilterPlugin();
}
NS_END
