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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 "algo/threaded_loop.h"
#include "interp/linear.h"
using namespace MR;
using namespace App;
class TransformBase { MEMALIGN(TransformBase)
public:
virtual ~TransformBase(){}
virtual Eigen::Vector3d transform_point (const Eigen::Vector3d& input) = 0;
};
class Warp : public TransformBase { MEMALIGN(Warp)
public:
Warp (Image<default_type>& in) : interp (in) {}
Eigen::Vector3d transform_point (const Eigen::Vector3d &input) {
Eigen::Vector3d output;
if (interp.scanner (input))
output = interp.row(3);
else
output.fill (NaN);
return output;
}
protected:
Interp::Linear<Image<default_type> > interp;
};
class Linear : public TransformBase { MEMALIGN(Linear)
public:
Linear (const transform_type& transform) : transform (transform) {}
Eigen::Vector3d transform_point (const Eigen::Vector3d &input) {
Eigen::Vector3d output = transform * input;
return output;
}
const transform_type transform;
};
void usage ()
{
AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";
SYNOPSIS = "Compose any number of linear transformations and/or warps into a single transformation";
DESCRIPTION
+ "Any linear transforms must be supplied as a 4x4 matrix in a text file (e.g. as per the output of mrregister). "
"Any warp fields must be supplied as a 4D image representing a deformation field (e.g. as output from mrrregister -nl_warp)."
+ "Input transformations should be provided to the command in the order in which they would be applied "
"to an image if they were to be applied individually."
+ "If all input transformations are linear, and the -template option is not provided, then the file output by "
"the command will also be a linear transformation saved as a 4x4 matrix in a text file. If a template image is "
"supplied, then the output will always be a deformation field. If at least one of the inputs is a warp field, "
"then the output will be a deformation field, which will be defined on the grid of the last input warp image "
"supplied if the -template option is not used.";
ARGUMENTS
+ Argument ("input", "the input transforms (either linear or non-linear warps).").type_file_in().allow_multiple()
+ Argument ("output", "the output file (may be a linear transformation text file, or a deformation warp field image, depending on usage)").type_various();
OPTIONS
+ Option ("template", "define the output grid defined by a template image")
+ Argument ("image").type_image_in();
}
using value_type = float;
void run ()
{
vector<std::unique_ptr<TransformBase>> transform_list;
std::unique_ptr<Header> template_header;
for (size_t i = 0; i < argument.size() - 1; ++i) {
try {
template_header.reset (new Header (Header::open (argument[i])));
auto image = Image<default_type>::open (argument[i]);
if (image.ndim() != 4)
throw Exception ("input warp is not a 4D image");
if (image.size(3) != 3)
throw Exception ("input warp should have 3 volumes in the 4th dimension");
std::unique_ptr<TransformBase> transform (new Warp (image));
transform_list.push_back (std::move (transform));
} catch (Exception& E) {
try {
std::unique_ptr<TransformBase> transform (new Linear (load_transform (argument[i])));
transform_list.push_back (std::move (transform));
} catch (Exception& E) {
throw Exception ("error reading input file: " + str(argument[i]) + ". Does not appear to be a 4D warp image or 4x4 linear transform.");
}
}
}
auto opt = get_options("template");
if (opt.size()) {
template_header.reset (new Header (Header::open (opt[0][0])));
// no template is supplied and there are input warps, then make sure the last transform in the list is a warp
} else if (template_header) {
if (!dynamic_cast<Warp*> (transform_list[transform_list.size() - 1].get()))
throw Exception ("Output deformation field grid not defined. When composing warps either use the -template "
"option to define the output deformation field grid, or ensure the last input transformation is a warp.");
}
// all inputs are linear so compose and output as text file
if (!template_header) {
transform_type composed = dynamic_cast<Linear*>(transform_list[transform_list.size() - 1].get())->transform;
ssize_t index = transform_list.size() - 2;
ProgressBar progress ("composing linear transformations", transform_list.size());
progress++;
while (index >= 0) {
composed = dynamic_cast<Linear*>(transform_list[index].get())->transform * composed;
index--;
progress++;
}
save_transform (composed, argument[argument.size() - 1]);
} else {
Header output_header (*template_header);
output_header.ndim() = 4;
output_header.size(3) = 3;
output_header.datatype() = DataType::Float32;
Image<float> output = Image<value_type>::create (argument [argument.size() - 1], output_header);
Transform template_transform (output);
for (auto i = Loop ("composing transformations", output, 0, 3) (output); i ; ++i) {
Eigen::Vector3d voxel ((default_type) output.index(0),
(default_type) output.index(1),
(default_type) output.index(2));
Eigen::Vector3d position = template_transform.voxel2scanner * voxel;
ssize_t index = transform_list.size() - 1;
while (index >= 0) {
position = transform_list[index]->transform_point (position);
index--;
}
output.row(3) = position;
}
}
}
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