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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 <iomanip>
#include "command.h"
#include "datatype.h"
#include "image.h"
#include "image_helpers.h"
#include "memory.h"
#include "stats.h"
#include "types.h"
#include "algo/histogram.h"
#include "algo/loop.h"
#include "file/ofstream.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Compute images statistics";
ARGUMENTS
+ Argument ("image",
"the input image from which statistics will be computed.")
.type_image_in ();
OPTIONS
+ Stats::Options
+ OptionGroup ("Additional options for mrstats")
+ Option ("allvolumes", "generate statistics across all image volumes, rather than one set of statistics per image volume");
}
using value_type = Stats::value_type;
using complex_type = Stats::complex_type;
class Volume_loop
{ NOMEMALIGN
public:
Volume_loop (Image<complex_type>& 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<complex_type>& image;
const bool is_4D;
bool status;
};
void run_volume (Stats::Stats& stats, Image<complex_type>& data, Image<bool>& mask)
{
if (mask.valid()) {
for (auto l = Loop(0,3) (data, mask); l; ++l) {
if (mask.value())
stats (data.value());
}
} else {
for (auto l = Loop(0,3) (data); l; ++l)
stats (data.value());
}
}
void run ()
{
auto header = Header::open (argument[0]);
if (header.ndim() > 4)
throw Exception ("mrstats is not designed to handle images greater than 4D");
const bool is_complex = header.datatype().is_complex();
auto data = header.get_image<complex_type>();
const bool ignorezero = get_options("ignorezero").size();
auto opt = get_options ("mask");
Image<bool> mask;
if (opt.size()) {
mask = Image<bool>::open (opt[0][0]);
check_dimensions (mask, header, 0, 3);
}
vector<std::string> fields;
opt = get_options ("output");
for (size_t n = 0; n < opt.size(); ++n)
fields.push_back (opt[n][0]);
if (App::log_level && fields.empty())
Stats::print_header (is_complex);
if (get_options ("allvolumes").size()) {
Stats::Stats stats (is_complex, ignorezero);
for (auto i = Volume_loop (data); i; ++i)
run_volume (stats, data, mask);
stats.print (data, fields);
} else {
for (auto i = Volume_loop (data); i; ++i) {
Stats::Stats stats (is_complex, ignorezero);
run_volume (stats, data, mask);
stats.print (data, fields);
}
}
}
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