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/* -*- mia-c++ -*-
*
* This file is part of MIA - a toolbox for medical image analysis
* Copyright (c) Leipzig, Madrid 1999-2016 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 <iostream>
#include <iomanip>
#include <string>
#include <sstream>
#include <stdexcept>
#include <mia/core.hh>
#include <mia/2d/imageio.hh>
NS_MIA_USE
using namespace std;
using namespace boost;
const SProgramDescription g_description = {
{pdi_group, "Analysis, filtering, combining, and segmentation of 2D images"},
{pdi_short, "Evaluate average intensities of an image series."},
{pdi_description, "Evaluate average intensities of an image series"
"This program is used to evaluate the average intensity and its variation of a series "
"of images in a given masked region."},
};
struct C2DStat : public TFilter<bool> {
typedef pair<size_t, double> TCollector;
typedef map<size_t, TCollector> TSliceStat;
C2DStat(const C2DUBImage& mask):
m_mask(mask)
{
}
template <typename T>
bool operator ()(const T2DImage<T>& image)
{
if (image.get_size() != m_mask.get_size())
throw invalid_argument("Input image and mask differ in size");
typename T2DImage<T>::const_iterator i = image.begin();
typename T2DImage<T>::const_iterator e = image.end();
C2DUBImage::const_iterator m = m_mask.begin();
TSliceStat slice;
while (i != e) {
if (*m) {
size_t idx = *m - 1;
++slice[idx].first;
slice[idx].second += *i;
}
++i;
++m;
}
m_counter.push_back(slice);
cvmsg() << "Got " << m_counter.size() << "slices\n";
return true;
}
const vector<TSliceStat>& result() const {
return m_counter;
}
private:
C2DUBImage m_mask;
vector<TSliceStat> m_counter;
};
/* Revision string */
const char revision[] = "not specified";
int do_main( int argc, char *argv[] )
{
string in_filename;
string mask_filename;
const auto& image2dio = C2DImageIOPluginHandler::instance();
CCmdOptionList options(g_description);
options.add(make_opt( in_filename, "in-files", 'i', "input image(s)",
CCmdOptionFlags::required_input, &image2dio));
options.add(make_opt( mask_filename, "mask-file", 'm', "mask image, must be of type byte",
CCmdOptionFlags::required_input, &image2dio));
options.set_stdout_is_result();
if (options.parse(argc, argv, "image") != CCmdOptionList::hr_no)
return EXIT_SUCCESS;
if (!options.get_remaining().empty())
throw runtime_error("unknown option given ...");
CHistory::instance().append(argv[0], revision, options);
size_t start_filenum = 0;
size_t end_filenum = 0;
size_t format_width = 0;
std::string src_basename = get_filename_pattern_and_range(in_filename, start_filenum, end_filenum, format_width);
if (start_filenum >= end_filenum)
throw invalid_argument(string("no files match pattern ") + src_basename);
char new_line = cverb.show_debug() ? '\n' : '\r';
C2DImageIOPluginHandler::Instance::PData mask_image_list = image2dio.load(mask_filename);
if (!mask_image_list.get() || mask_image_list->empty())
throw invalid_argument("no mask found");
const C2DImage *mask_image = mask_image_list->begin()->get();
const C2DUBImage *mask = dynamic_cast<const C2DUBImage *>( mask_image );
if (!mask)
throw create_exception<invalid_argument>("Mask image must be an image with pixel type byte, but pixel type '",
CPixelTypeDict.get_name(mask_image->get_pixel_type()),
"' was provided.");
C2DStat stat(*mask);
for (size_t i = start_filenum; i < end_filenum; ++i) {
string src_name = create_filename(src_basename.c_str(), i);
cvmsg() << new_line << "Read: " << i <<" out of "<< "["
<< start_filenum<< "," << end_filenum << "] = " << src_name ;
C2DImageIOPluginHandler::Instance::PData in_image_list = image2dio.load(src_name);
if (in_image_list.get() && in_image_list->size()) {
accumulate(stat, **in_image_list->begin());
}
}
cvmsg() << "\n";
const vector<C2DStat::TSliceStat>& ss = stat.result();
for (vector<C2DStat::TSliceStat>::const_iterator i = ss.begin(); i != ss.end(); ++i) {
for (C2DStat::TSliceStat::const_iterator k = i->begin(); k != i->end(); ++k) {
cout << k->second.second / k->second.first << " ";
}
cout << "\n";
}
return EXIT_SUCCESS;
}
#include <mia/internal/main.hh>
MIA_MAIN(do_main);
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