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/* Copyright (c) 2008-2025 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#include "command.h"
#include "header.h"
#include "image.h"
#include "algo/histogram.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Generate a histogram of image intensities";
ARGUMENTS
+ Argument ("image", "the input image from which the histogram will be computed").type_image_in()
+ Argument ("hist", "the output histogram file").type_file_out();
OPTIONS
+ Algo::Histogram::Options
+ OptionGroup ("Additional options for mrhistogram")
+ Option ("allvolumes", "generate one histogram across all image volumes, rather than one per image volume");
}
class Volume_loop { MEMALIGN(Volume_loop)
public:
Volume_loop (Image<float>& in) :
image (in),
is_4D (in.ndim() == 4),
status (true)
{
if (is_4D)
image.index(3) = 0;
}
void operator++ ()
{
if (is_4D) {
image.index(3)++;
} else {
assert (status);
status = false;
}
}
operator bool() const
{
if (is_4D)
return (image.index(3) >= 0 && image.index(3) < image.size(3));
else
return status;
}
private:
Image<float>& image;
const bool is_4D;
bool status;
};
template <class Functor>
void run_volume (Functor& functor, Image<float>& data, Image<bool>& mask)
{
if (mask.valid()) {
for (auto l = Loop(0,3) (data, mask); l; ++l) {
if (mask.value())
functor (float(data.value()));
}
} else {
for (auto l = Loop(0,3) (data); l; ++l)
functor (float(data.value()));
}
}
void run ()
{
auto header = Header::open (argument[0]);
if (header.ndim() > 4)
throw Exception ("mrhistogram is not designed to handle images greater than 4D");
if (header.datatype().is_complex())
throw Exception ("histogram generation not supported for complex data types");
auto data = header.get_image<float>();
const bool allvolumes = get_options ("allvolumes").size();
size_t nbins = get_option_value ("bins", 0);
auto opt = get_options ("mask");
Image<bool> mask;
if (opt.size()) {
mask = Image<bool>::open (opt[0][0]);
check_dimensions (mask, header, 0, 3);
}
File::OFStream output (argument[1]);
output << "# " << App::command_history_string << "\n";
Algo::Histogram::Calibrator calibrator (nbins, get_options ("ignorezero").size());
opt = get_options ("template");
if (opt.size()) {
calibrator.from_file (opt[0][0]);
} else {
for (auto v = Volume_loop(data); v; ++v)
run_volume (calibrator, data, mask);
// If getting min/max using all volumes, but generating a single histogram per volume,
// then want the automatic calculation of bin width to be based on the number of
// voxels per volume, rather than the total number of values sent to the calibrator
calibrator.finalize (header.ndim() > 3 && !allvolumes ? header.size(3) : 1,
header.datatype().is_integer() && header.intensity_offset() == 0.0 && header.intensity_scale() == 1.0);
}
nbins = calibrator.get_num_bins();
if (!nbins)
throw Exception (std::string("No histogram bins constructed") +
((get_options ("ignorezero").size() || get_options ("bins").size()) ?
"." :
"; you might want to use the -ignorezero or -bins option."));
for (size_t i = 0; i != nbins; ++i)
output << (calibrator.get_min() + ((i+0.5) * calibrator.get_bin_width())) << ",";
output << "\n";
if (allvolumes) {
Algo::Histogram::Data histogram (calibrator);
for (auto v = Volume_loop(data); v; ++v)
run_volume (histogram, data, mask);
for (size_t i = 0; i != nbins; ++i)
output << histogram[i] << ",";
output << "\n";
} else {
for (auto v = Volume_loop(data); v; ++v) {
Algo::Histogram::Data histogram (calibrator);
run_volume (histogram, data, mask);
for (size_t i = 0; i != nbins; ++i)
output << histogram[i] << ",";
output << "\n";
}
}
}
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