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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 "math/math.h"
#include "image.h"
#include "ordered_thread_queue.h"
#include "thread.h"
#include "dwi/tractography/file.h"
#include "dwi/tractography/properties.h"
#include "dwi/tractography/resampling/arc.h"
#include "dwi/tractography/resampling/downsampler.h"
#include "dwi/tractography/resampling/endpoints.h"
#include "dwi/tractography/resampling/fixed_num_points.h"
#include "dwi/tractography/resampling/fixed_step_size.h"
#include "dwi/tractography/resampling/resampling.h"
#include "dwi/tractography/resampling/upsampler.h"
using namespace MR;
using namespace App;
using namespace DWI::Tractography;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au) and J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Resample each streamline in a track file to a new set of vertices";
DESCRIPTION
+ "It is necessary to specify precisely ONE of the command-line options for "
"controlling how this resampling takes place; this may be either increasing "
"or decreasing the number of samples along each streamline, or may involve "
"changing the positions of the samples according to some specified trajectory."
+ "Note that because the length of a streamline is calculated based on the sums of "
"distances between adjacent vertices, resampling a streamline to a new set of "
"vertices will typically change the quantified length of that streamline; the "
"magnitude of the difference will typically depend on the discrepancy in the "
"number of vertices, with less vertices leading to a shorter length (due to "
"taking chordal lengths of curved trajectories).";
ARGUMENTS
+ Argument ("in_tracks", "the input track file").type_tracks_in()
+ Argument ("out_tracks", "the output resampled tracks").type_tracks_out();
OPTIONS
+ Resampling::ResampleOption;
// TODO Resample according to an exemplar streamline
}
using value_type = float;
class Worker
{ NOMEMALIGN
public:
Worker (const std::unique_ptr<Resampling::Base>& in) :
resampler (in->clone()) { }
Worker (const Worker& that) :
resampler (that.resampler->clone()) { }
bool operator() (const Streamline<value_type>& in, Streamline<value_type>& out) const {
(*resampler) (in, out);
return true;
}
private:
std::unique_ptr<Resampling::Base> resampler;
};
class Receiver
{ NOMEMALIGN
public:
Receiver (const std::string& path, const Properties& properties) :
writer (path, properties),
progress ("resampling streamlines") { }
bool operator() (const Streamline<value_type>& tck) {
auto progress_message = [&](){ return "resampling streamlines (count: " + str(writer.count) + ", skipped: " + str(writer.total_count - writer.count) + ")"; };
writer (tck);
progress.set_text (progress_message());
return true;
}
private:
Writer<value_type> writer;
ProgressBar progress;
};
void run ()
{
Properties properties;
Reader<value_type> read (argument[0], properties);
const std::unique_ptr<Resampling::Base> resampler (Resampling::get_resampler());
Worker worker (resampler);
Receiver receiver (argument[1], properties);
Thread::run_ordered_queue (read,
Thread::batch (Streamline<value_type>()),
Thread::multi (worker),
Thread::batch (Streamline<value_type>()),
receiver);
}
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