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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 "image.h"
#include "ordered_thread_queue.h"
#include "progressbar.h"
#include "interp/linear.h"
#include "dwi/tractography/file.h"
#include "dwi/tractography/properties.h"
using namespace MR;
using namespace MR::DWI;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";
SYNOPSIS = "Apply a spatial transformation to a tracks file";
ARGUMENTS
+ Argument ("tracks", "the input track file.").type_tracks_in()
+ Argument ("transform", "the image containing the transform.").type_image_in()
+ Argument ("output", "the output track file").type_tracks_out();
}
using value_type = float;
using TrackType = Tractography::Streamline<value_type>;
class Loader { MEMALIGN(Loader)
public:
Loader (const std::string& file) : reader (file, properties) {}
bool operator() (TrackType& item) {
return reader (item);
}
Tractography::Properties properties;
protected:
Tractography::Reader<value_type> reader;
};
class Warper { MEMALIGN(Warper)
public:
Warper (const Image<value_type>& warp) :
interp (warp) { }
bool operator () (const TrackType& in, TrackType& out) {
out.clear();
out.set_index (in.get_index());
out.weight = in.weight;
for (size_t n = 0; n < in.size(); ++n) {
auto vertex = pos(in[n]);
if (vertex.allFinite())
out.push_back (vertex);
}
return true;
}
Eigen::Matrix<value_type,3,1> pos (const Eigen::Matrix<value_type,3,1>& x) {
Eigen::Matrix<value_type,3,1> p;
if (interp.scanner (x)) {
interp.index(3) = 0; p[0] = interp.value();
interp.index(3) = 1; p[1] = interp.value();
interp.index(3) = 2; p[2] = interp.value();
}
return p;
}
protected:
Interp::Linear< Image<value_type> > interp;
};
class Writer { MEMALIGN(Writer)
public:
Writer (const std::string& file, const Tractography::Properties& properties) :
progress ("applying spatial transformation to tracks",
properties.find("count") == properties.end() ? 0 : to<size_t>(properties.find ("count")->second)),
writer (file, properties) { }
bool operator() (const TrackType& item) {
writer (item);
++progress;
return true;
}
protected:
ProgressBar progress;
Tractography::Properties properties;
Tractography::Writer<value_type> writer;
};
void run ()
{
Loader loader (argument[0]);
auto data = Image<value_type>::open (argument[1]).with_direct_io (3);
Warper warper (data);
Writer writer (argument[2], loader.properties);
Thread::run_ordered_queue (
loader,
Thread::batch (TrackType(), 1024),
Thread::multi (warper),
Thread::batch (TrackType(), 1024),
writer);
}
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