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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/loop.h"
#include "progressbar.h"
#include "dwi/gradient.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "J-Donald Tournier (jdtournier@gmail.com) and Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Concatenate several images into one";
ARGUMENTS
+ Argument ("image1", "the first input image.")
.type_image_in()
+ Argument ("image2", "additional input image(s).")
.type_image_in()
.allow_multiple()
+ Argument ("output", "the output image.")
.type_image_out ();
EXAMPLES
+ Example ("Concatenate individual 3D volumes into a single 4D image series",
"mrcat volume*.mif series.mif",
"The wildcard characters will find all images in the current working directory with names that "
"begin with \"volume\" and end with \".mif\"; the mrcat command will receive these as a list of "
"input file names, from which it will produce a 4D image where the input volumes have been "
"concatenated along axis 3 (the fourth axis; the spatial axes are 0, 1 & 2).");
OPTIONS
+ Option ("axis",
"specify axis along which concatenation should be performed. By default, "
"the program will use the last non-singleton, non-spatial axis of any of "
"the input images - in other words axis 3 or whichever axis (greater than 3) "
"of the input images has size greater than one.")
+ Argument ("axis").type_integer (0)
+ DataType::options();
}
template <typename value_type>
void write (vector<Header>& in,
const size_t axis,
Header& header_out)
{
auto image_out = Image<value_type>::create (header_out.name(), header_out);
size_t axis_offset = 0;
for (size_t i = 0; i != in.size(); i++) {
auto image_in = in[i].get_image<value_type>();
auto copy_func = [&axis, &axis_offset](decltype(image_in)& in, decltype(image_out)& out)
{
out.index (axis) = axis < in.ndim() ? in.index (axis) + axis_offset : axis_offset;
out.value() = in.value();
};
ThreadedLoop ("concatenating \"" + image_in.name() + "\"", image_in, 0, std::min<size_t> (image_in.ndim(), image_out.ndim()))
.run (copy_func, image_in, image_out);
if (axis < image_in.ndim())
axis_offset += image_in.size (axis);
else {
++axis_offset;
image_out.index (axis) = axis_offset;
}
}
}
void run ()
{
size_t num_images = argument.size()-1;
vector<Header> headers;
ssize_t max_axis_nonunity = 0;
for (size_t i = 0; i != num_images; ++i) {
Header H = Header::open (argument[i]);
ssize_t a;
for (a = ssize_t(H.ndim())-1; a >= 0 && H.size (a) <= 1; a--);
max_axis_nonunity = std::max (max_axis_nonunity, a);
headers.push_back (std::move (H));
}
const size_t axis = get_option_value ("axis", std::max (size_t(3), size_t(std::max (ssize_t(0), max_axis_nonunity))));
Header header_out = concatenate (headers, axis, true);
header_out.name() = std::string (argument[num_images]);
header_out.datatype() = DataType::from_command_line (header_out.datatype());
if (header_out.intensity_offset() == 0.0 && header_out.intensity_scale() == 1.0 && !header_out.datatype().is_floating_point()) {
switch (header_out.datatype()() & DataType::Type) {
case DataType::Bit:
case DataType::UInt8:
case DataType::UInt16:
case DataType::UInt32:
if (header_out.datatype().is_signed())
write<int32_t> (headers, axis, header_out);
else
write<uint32_t> (headers, axis, header_out);
break;
case DataType::UInt64:
if (header_out.datatype().is_signed())
write<int64_t> (headers, axis, header_out);
else
write<uint64_t> (headers, axis, header_out);
break;
}
} else {
if (header_out.datatype().is_complex())
write<cdouble> (headers, axis, header_out);
else
write<double> (headers, axis, header_out);
}
}
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