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header.cpp
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header.cpp
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/* Copyright (c) 2008-2021 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 "header.h"
#include <cctype>
#include <set>
#include "app.h"
#include "axes.h"
#include "mrtrix.h"
#include "phase_encoding.h"
#include "stride.h"
#include "transform.h"
#include "image_io/default.h"
#include "image_io/scratch.h"
#include "file/name_parser.h"
#include "file/path.h"
#include "formats/list.h"
#include "dwi/gradient.h"
namespace MR
{
bool Header::do_realign_transform = true;
void Header::check (const Header& H) const
{
if (ndim() != H.ndim())
throw Exception ("dimension mismatch between image files for \"" + name() + "\"");
for (size_t n = 0; n < ndim(); ++n) {
if (size(n) != H.size(n))
throw Exception ("dimension mismatch between image files for \"" + name() + "\"");
if (stride(n) != H.stride(n))
throw Exception ("data strides differs image files for \"" + name() + "\"");
if (std::isfinite(spacing(n)) && std::isfinite(H.spacing(n)) && spacing(n) != H.spacing(n))
WARN ("voxel dimensions differ between image files for \"" + name() + "\"");
}
if ((transform().matrix() - H.transform().matrix()).cwiseAbs().maxCoeff() > 1.0e-6)
WARN ("transform matrices differ between image files for \"" + name() + "\"");;
if (datatype() != H.datatype())
throw Exception ("data types differ between image files for \"" + name() + "\"");
if (intensity_offset() != H.intensity_offset() || intensity_scale() != H.intensity_scale())
throw Exception ("scaling coefficients differ between image files for \"" + name() + "\"");
}
namespace {
std::string resolve_slice_timing (const std::string& one, const std::string& two)
{
if (one == "variable" || two == "variable")
return "variable";
vector<std::string> one_split = split (one, ",");
vector<std::string> two_split = split (two, ",");
if (one_split.size() != two_split.size()) {
DEBUG ("Slice timing vectors of inequal length");
return "invalid";
}
// Siemens CSA reports with 2.5ms precision = 0.0025s
// Allow slice times to vary by 1.5x this amount, but no more
for (size_t i = 0; i != one_split.size(); ++i) {
default_type f_one, f_two;
try {
f_one = to<default_type> (one_split[i]);
f_two = to<default_type> (two_split[i]);
} catch (Exception& e) {
DEBUG ("Error converting slice timing vector to floating-point");
return "invalid";
}
const default_type diff = abs (f_two - f_one);
if (diff > 0.00375) {
DEBUG ("Supra-threshold difference of " + str(diff) + "s in slice times");
return "variable";
}
}
return one;
}
}
void Header::merge_keyval (const Header& H)
{
std::map<std::string, std::string> new_keyval;
std::set<std::string> unique_comments;
for (const auto& item : keyval()) {
if (item.first == "comments") {
new_keyval.insert (item);
const auto comments = split_lines (item.second);
for (const auto& c : comments)
unique_comments.insert (c);
} else if (item.first != "command_history") {
new_keyval.insert (item);
}
}
for (const auto& item : H.keyval()) {
if (item.first == "comments") {
const auto comments = split_lines (item.second);
for (const auto& c : comments) {
if (unique_comments.find (c) == unique_comments.end()) {
add_line (new_keyval["comments"], c);
unique_comments.insert (c);
}
}
} else {
auto it = keyval().find (item.first);
if (it == keyval().end() || it->second == item.second)
new_keyval.insert (item);
else if (item.first == "SliceTiming")
new_keyval["SliceTiming"] = resolve_slice_timing (item.second, it->second);
else
new_keyval[item.first] = "variable";
}
}
std::swap (keyval_, new_keyval);
}
namespace {
std::string short_description (const Header& H)
{
vector<std::string> dims;
for (size_t n = 0; n < H.ndim(); ++n)
dims.push_back (str(H.size(n)));
vector<std::string> vox;
for (size_t n = 0; n < H.ndim(); ++n)
vox.push_back (str(H.spacing(n)));
return " with dimensions " + join (dims, "x") + ", voxel spacing " + join (vox, "x") + ", datatype " + H.datatype().specifier();
}
}
Header Header::open (const std::string& image_name)
{
if (image_name.empty())
throw Exception ("no name supplied to open image!");
Header H;
try {
INFO ("opening image \"" + image_name + "\"...");
File::ParsedName::List list;
const auto num = list.parse_scan_check (image_name);
const Formats::Base** format_handler = Formats::handlers;
size_t item_index = 0;
H.name() = list[item_index].name();
for (; *format_handler; format_handler++) {
if ( (H.io = (*format_handler)->read (H)) )
break;
}
if (!*format_handler)
throw Exception ("unknown format for image \"" + H.name() + "\"");
assert (H.io);
H.format_ = (*format_handler)->description;
if (num.size()) {
const Header template_header (H);
// Convenient to know a priori which loop index corresponds to which image axis
// This needs to detect unity-sized axes and flag the loop to concatenate data along that axis
vector<size_t> loopindex2axis;
size_t axis;
for (axis = 0; axis != H.ndim(); ++axis) {
if (H.size (axis) == 1) {
loopindex2axis.push_back (axis);
if (loopindex2axis.size() == num.size())
break;
}
}
for (; loopindex2axis.size() < num.size(); ++axis)
loopindex2axis.push_back (axis);
std::reverse (loopindex2axis.begin(), loopindex2axis.end());
// Reimplemented support for [] notation using recursive function calls
// Note that the very first image header has already been opened before this function is
// invoked for the first time; "vector<Header>& this_data" is used to propagate this
// data to deeper layers when necessary
std::function<void(Header&, vector<Header>&, const size_t)>
import = [&] (Header& result, vector<Header>& this_data, const size_t loop_index) -> void
{
if (loop_index == num.size()-1) {
vector<std::unique_ptr<ImageIO::Base>> ios;
if (this_data.size())
ios.push_back (std::move (this_data[0].io));
for (size_t i = this_data.size(); i != size_t(num[loop_index]); ++i) {
Header header (template_header);
std::unique_ptr<ImageIO::Base> io_handler;
header.name() = list[++item_index].name();
header.keyval().clear();
if (!(io_handler = (*format_handler)->read (header)))
throw Exception ("image specifier contains mixed format files");
assert (io_handler);
template_header.check (header);
this_data.push_back (std::move (header));
ios.push_back (std::move (io_handler));
}
result = concatenate (this_data, loopindex2axis[loop_index], false);
result.io = std::move (ios[0]);
for (size_t i = 1; i != ios.size(); ++i)
result.io->merge (*ios[i]);
return;
} // End branch for when loop_index is the maximum, ie. innermost loop
// For each coordinate along this axis, need to concatenate headers from the
// next lower axis
vector<Header> nested_data;
// The nested concatenation may still include the very first header that has already been read;
// this needs to be propagated through to the nested call
if (this_data.size()) {
assert (this_data.size() == 1);
nested_data.push_back (std::move (this_data[0]));
this_data.clear();
}
for (size_t i = 0; i != size_t(num[loop_index]); ++i) {
Header temp;
import (temp, nested_data, loop_index+1);
this_data.push_back (std::move (temp));
nested_data.clear();
}
result = concatenate (this_data, loopindex2axis[loop_index], false);
result.io = std::move (this_data[0].io);
for (size_t i = 1; i != size_t(num[loop_index]); ++i)
result.io->merge (*this_data[i].io);
};
vector<Header> headers;
headers.push_back (std::move (H));
import (H, headers, 0);
H.name() = image_name;
} // End branching for [] notation
H.sanitise();
if (do_realign_transform)
H.realign_transform();
}
catch (CancelException& e) { throw; }
catch (Exception& E) {
throw Exception (E, "error opening image \"" + image_name + "\"");
}
INFO ("image \"" + H.name() + "\" opened" + short_description (H));
return H;
}
namespace {
inline bool check_strides_match (const vector<ssize_t>& a, const vector<ssize_t>& b)
{
size_t n = 0;
for (; n < std::min (a.size(), b.size()); ++n)
if (a[n] != b[n]) return false;
for (size_t i = n; i < a.size(); ++i)
if (a[i] > 1) return false;
for (size_t i = n; i < b.size(); ++i)
if (b[i] > 1) return false;
return true;
}
}
Header Header::create (const std::string& image_name, const Header& template_header, bool add_to_command_history)
{
if (image_name.empty())
throw Exception ("no name supplied to open image!");
Header H (template_header);
const auto previous_datatype = H.datatype();
try {
INFO ("creating image \"" + image_name + "\"...");
if (add_to_command_history) {
// Make sure the current command is not concatenated more than once
const auto command_history = split_lines (H.keyval()["command_history"]);
if (!(command_history.size() && command_history.back() == App::command_history_string))
add_line (H.keyval()["command_history"], App::command_history_string);
}
H.keyval()["mrtrix_version"] = App::mrtrix_version;
if (App::project_version)
H.keyval()["project_version"] = App::project_version;
H.sanitise();
File::NameParser parser;
parser.parse (image_name);
vector<uint32_t> Pdim (parser.ndim());
vector<int> Hdim (H.ndim());
for (size_t i = 0; i < H.ndim(); ++i)
Hdim[i] = H.size(i);
H.name() = image_name;
const vector<ssize_t> strides (Stride::get_symbolic (H));
const Formats::Base** format_handler = Formats::handlers;
for (; *format_handler; format_handler++)
if ((*format_handler)->check (H, H.ndim() - Pdim.size()))
break;
if (!*format_handler) {
const std::string basename = Path::basename (image_name);
const size_t extension_index = basename.find_last_of (".");
if (extension_index == std::string::npos)
throw Exception ("unknown format for image \"" + image_name + "\" (no file extension specified)");
else
throw Exception ("unknown format for image \"" + image_name + "\" (unsupported file extension: " + basename.substr (extension_index) + ")");
}
const vector<ssize_t> strides_aftercheck (Stride::get_symbolic (H));
if (!check_strides_match (strides, strides_aftercheck)) {
INFO("output strides for image " + image_name + " modified to " + str(strides_aftercheck) +
" - requested strides " + str(strides) + " are not supported in " + (*format_handler)->description + " format");
}
H.datatype().set_byte_order_native();
int a = 0;
for (size_t n = 0; n < Pdim.size(); ++n) {
while (a < int(H.ndim()) && H.stride(a))
a++;
Pdim[n] = Hdim[a++];
}
parser.calculate_padding (Pdim);
const bool split_4d_schemes = (parser.ndim() == 1 && template_header.ndim() == 4);
Eigen::MatrixXd dw_scheme, pe_scheme;
try {
dw_scheme = DWI::parse_DW_scheme (template_header);
} catch (Exception&) {
DWI::clear_DW_scheme (H);
}
try {
pe_scheme = PhaseEncoding::parse_scheme (template_header);
} catch (Exception&) {
PhaseEncoding::clear_scheme (H);
}
if (split_4d_schemes) {
try {
DWI::check_DW_scheme (template_header, dw_scheme);
DWI::set_DW_scheme (H, dw_scheme.row (0));
} catch (Exception&) {
dw_scheme.resize (0, 0);
DWI::clear_DW_scheme (H);
}
try {
PhaseEncoding::check (template_header, pe_scheme);
PhaseEncoding::set_scheme (H, pe_scheme.row (0));
} catch (Exception&) {
pe_scheme.resize (0, 0);
PhaseEncoding::clear_scheme (H);
}
}
Header header (H);
vector<uint32_t> num (Pdim.size());
if (image_name != "-")
H.name() = parser.name (num);
H.io = (*format_handler)->create (H);
assert (H.io);
H.format_ = (*format_handler)->description;
auto get_next = [](decltype(num)& pos, const decltype(Pdim)& limits) {
size_t axis = 0;
while (axis < limits.size()) {
pos[axis]++;
if (pos[axis] < limits[axis])
return true;
pos[axis] = 0;
axis++;
}
return false;
};
size_t counter = 0;
while (get_next (num, Pdim)) {
header.name() = parser.name (num);
++counter;
if (split_4d_schemes) {
if (dw_scheme.rows())
DWI::set_DW_scheme (header, dw_scheme.row (counter));
if (pe_scheme.rows())
PhaseEncoding::set_scheme (header, pe_scheme.row (counter));
}
std::shared_ptr<ImageIO::Base> io_handler ((*format_handler)->create (header));
assert (io_handler);
H.io->merge (*io_handler);
}
if (Pdim.size()) {
int a = 0, n = 0;
ssize_t next_stride = 0;
for (size_t i = 0; i < H.ndim(); ++i) {
if (H.stride(i)) {
++n;
next_stride = std::max (next_stride, abs (H.stride(i)));
}
}
H.axes_.resize (n + Pdim.size());
for (size_t i = 0; i < Pdim.size(); ++i) {
while (H.stride(a))
++a;
H.size(a) = Pdim[i];
H.stride(a) = ++next_stride;
}
H.name() = image_name;
}
if (split_4d_schemes) {
DWI::set_DW_scheme (H, dw_scheme);
PhaseEncoding::set_scheme (H, pe_scheme);
}
H.io->set_image_is_new (true);
H.io->set_readwrite (true);
H.sanitise();
}
catch (Exception& E) {
throw Exception (E, "error creating image \"" + image_name + "\"");
}
DataType new_datatype = H.datatype();
if (new_datatype != previous_datatype) {
new_datatype.unset_flag (DataType::BigEndian);
new_datatype.unset_flag (DataType::LittleEndian);
if (new_datatype != previous_datatype)
WARN (std::string ("requested datatype (") + previous_datatype.specifier() + ") not supported - substituting with " + H.datatype().specifier());
}
INFO ("image \"" + H.name() + "\" created" + short_description (H));
return H;
}
Header Header::scratch (const Header& template_header, const std::string& label)
{
Header H (template_header);
H.name() = label;
H.reset_intensity_scaling();
H.sanitise();
H.format_ = "scratch image";
H.io = make_unique<ImageIO::Scratch> (H);
return H;
}
std::ostream& operator<< (std::ostream& stream, const Header& H)
{
stream << "\"" << H.name() << "\", " << H.datatype().specifier() << ", size [ ";
for (size_t n = 0; n < H.ndim(); ++n) stream << H.size(n) << " ";
stream << "], voxel size [ ";
for (size_t n = 0; n < H.ndim(); ++n) stream << H.spacing(n) << " ";
stream << "], strides [ ";
for (size_t n = 0; n < H.ndim(); ++n) stream << H.stride(n) << " ";
stream << "]";
return stream;
}
std::string Header::description (bool print_all) const
{
std::string desc (
"************************************************\n"
"Image name: \"" + name() + "\"\n"
"************************************************\n");
desc += " Dimensions: ";
size_t i;
for (i = 0; i < ndim(); i++) {
if (i) desc += " x ";
desc += str (size(i));
}
desc += "\n Voxel size: ";
for (i = 0; i < ndim(); i++) {
if (i) desc += " x ";
desc += std::isnan (spacing(i)) ? "?" : str (spacing(i), 6);
}
desc += "\n";
desc += " Data strides: [ ";
auto strides (Stride::get (*this));
Stride::symbolise (strides);
for (i = 0; i < ndim(); i++)
desc += stride(i) ? str (strides[i]) + " " : "? ";
desc += "]\n";
if (io) {
desc += std::string(" Format: ") + (format() ? format() : "undefined") + "\n";
desc += std::string (" Data type: ") + ( datatype().description() ? datatype().description() : "invalid" ) + "\n";
desc += " Intensity scaling: offset = " + str (intensity_offset()) + ", multiplier = " + str (intensity_scale()) + "\n";
}
desc += " Transform: ";
for (size_t i = 0; i < 3; i++) {
if (i) desc += " ";
for (size_t j = 0; j < 4; j++) {
char buf[14], buf2[14];
snprintf (buf, 14, "%.4g", transform() (i,j));
snprintf (buf2, 14, "%12.10s", buf);
desc += buf2;
}
desc += "\n";
}
for (const auto& p : keyval()) {
std::string key = " " + p.first + ": ";
if (key.size() < 21)
key.resize (21, ' ');
const auto entries = split_lines (p.second);
if (entries.size()) {
bool shorten = (!print_all && entries.size() > 5);
desc += key + entries[0] + "\n";
if (entries.size() > 5) {
key = " [" + str(entries.size()) + " entries] ";
if (key.size() < 21)
key.resize (21, ' ');
}
else key = " ";
for (size_t n = 1; n < (shorten ? size_t(2) : entries.size()); ++n) {
desc += key + entries[n] + "\n";
key = " ";
}
if (!print_all && entries.size() > 5) {
desc += key + "...\n";
for (size_t n = entries.size()-2; n < entries.size(); ++n )
desc += key + entries[n] + "\n";
}
} else {
desc += key + "(empty)\n";
}
}
return desc;
}
void Header::sanitise_voxel_sizes ()
{
if (ndim() < 3) {
INFO ("image contains fewer than 3 dimensions - adding extra dimensions");
axes_.resize (3);
}
if (!std::isfinite (spacing(0)) || !std::isfinite (spacing(1)) || !std::isfinite (spacing(2))) {
WARN ("invalid voxel sizes - resetting to sane defaults");
default_type mean_vox_size = 0.0;
size_t num_valid_vox = 0;
for (size_t i = 0; i < 3; ++i) {
if (std::isfinite(spacing(i))) {
++num_valid_vox;
mean_vox_size += spacing(i);
}
}
mean_vox_size = num_valid_vox ? mean_vox_size / num_valid_vox : 1.0;
for (size_t i = 0; i < 3; ++i)
if (!std::isfinite(spacing(i)))
spacing(i) = mean_vox_size;
}
}
void Header::sanitise_transform ()
{
if (!transform().matrix().allFinite()) {
WARN ("transform matrix contains invalid entries - resetting to sane defaults");
transform() = Transform::get_default (*this);
}
// check that cosine vectors are unit length (to some precision):
bool rescale_cosine_vectors = false;
for (size_t i = 0; i < 3; ++i) {
auto length = transform().matrix().col(i).head<3>().norm();
if (abs (length-1.0) > 1.0e-6)
rescale_cosine_vectors = true;
}
// if unit length, rescale and modify voxel sizes accordingly:
if (rescale_cosine_vectors) {
INFO ("non unit cosine vectors detected - normalising and rescaling voxel sizes to match");
for (size_t i = 0; i < 3; ++i) {
auto length = transform().matrix().col(i).head(3).norm();
transform().matrix().col(i).head(3) /= length;
spacing(i) *= length;
}
}
}
void Header::realign_transform ()
{
// find which row of the transform is closest to each scanner axis:
Axes::get_permutation_to_make_axial (transform(), realign_perm_, realign_flip_);
// check if image is already near-axial, return if true:
if (realign_perm_[0] == 0 && realign_perm_[1] == 1 && realign_perm_[2] == 2 &&
!realign_flip_[0] && !realign_flip_[1] && !realign_flip_[2])
return;
auto M (transform());
auto translation = M.translation();
// modify translation vector:
for (size_t i = 0; i < 3; ++i) {
if (realign_flip_[i]) {
const default_type length = (size(i)-1) * spacing(i);
auto axis = M.matrix().col (i);
for (size_t n = 0; n < 3; ++n) {
axis[n] = -axis[n];
translation[n] -= length*axis[n];
}
}
}
// switch and/or invert rows if needed:
for (size_t i = 0; i < 3; ++i) {
auto row = M.matrix().row(i).head<3>();
row = Eigen::RowVector3d (row[realign_perm_[0]], row[realign_perm_[1]], row[realign_perm_[2]]);
if (realign_flip_[i])
stride(i) = -stride(i);
}
// copy back transform:
transform() = std::move (M);
// switch axes to match:
Axis a[] = {
axes_[realign_perm_[0]],
axes_[realign_perm_[1]],
axes_[realign_perm_[2]]
};
axes_[0] = a[0];
axes_[1] = a[1];
axes_[2] = a[2];
INFO ("Axes and transform of image \"" + name() + "\" altered to approximate RAS coordinate system");
// If there's any phase encoding direction information present in the
// header, it's necessary here to update it according to the
// flips / permutations that have taken place
auto pe_scheme = PhaseEncoding::get_scheme (*this);
if (pe_scheme.rows()) {
for (ssize_t row = 0; row != pe_scheme.rows(); ++row) {
Eigen::VectorXd new_line (pe_scheme.row (row));
for (ssize_t axis = 0; axis != 3; ++axis) {
new_line[axis] = pe_scheme(row, realign_perm_[axis]);
if (new_line[axis] && realign_flip_[realign_perm_[axis]])
new_line[axis] = -new_line[axis];
}
pe_scheme.row (row) = new_line;
}
PhaseEncoding::set_scheme (*this, pe_scheme);
INFO ("Phase encoding scheme modified to conform to MRtrix3 internal header transform realignment");
}
// If there's any slice encoding direction information present in the
// header, that's also necessary to update here
auto slice_encoding_it = keyval().find ("SliceEncodingDirection");
if (slice_encoding_it != keyval().end()) {
const Eigen::Vector3 orig_dir (Axes::id2dir (slice_encoding_it->second));
Eigen::Vector3 new_dir;
for (size_t axis = 0; axis != 3; ++axis)
new_dir[axis] = orig_dir[realign_perm_[axis]] * (realign_flip_[realign_perm_[axis]] ? -1.0 : 1.0);
slice_encoding_it->second = Axes::dir2id (new_dir);
INFO ("Slice encoding direction has been modified to conform to MRtrix3 internal header transform realignment");
}
}
Header concatenate (const vector<Header>& headers, const size_t axis_to_concat, const bool permit_datatype_mismatch)
{
Exception e ("Unable to concatenate " + str(headers.size()) + " images along axis " + str(axis_to_concat) + ": ");
auto datatype_test = [&] (const bool condition)
{
if (condition && !permit_datatype_mismatch) {
e.push_back ("Mismatched data types");
throw e;
}
return condition;
};
auto concat_scheme = [] (Eigen::MatrixXd& existing, const Eigen::MatrixXd& extra)
{
if (!existing.rows())
return;
if (!extra.rows() || (extra.cols() != existing.cols())) {
existing.resize (0, 0);
return;
}
existing.conservativeResize (existing.rows() + extra.rows(), existing.cols());
existing.bottomRows (extra.rows()) = extra;
};
if (headers.empty())
return Header();
size_t global_max_nonunity_dim = 0;
for (const auto& H : headers) {
if (axis_to_concat > H.ndim() + 1) {
e.push_back ("Image \"" + H.name() + "\" is only " + str(H.ndim()) + "D");
throw e;
}
ssize_t this_max_nonunity_dim;
for (this_max_nonunity_dim = H.ndim()-1; this_max_nonunity_dim >= 0 && H.size (this_max_nonunity_dim) <= 1; --this_max_nonunity_dim);
global_max_nonunity_dim = std::max (global_max_nonunity_dim, size_t(std::max (ssize_t(0), this_max_nonunity_dim)));
}
Header result (headers[0]);
if (axis_to_concat >= result.ndim()) {
result.ndim() = axis_to_concat + 1;
result.size(axis_to_concat) = 1;
}
result.stride (axis_to_concat) = result.ndim()+1;
for (size_t axis = 0; axis != result.ndim(); ++axis) {
if (axis != axis_to_concat && result.size (axis) <= 1) {
for (const auto& H : headers) {
if (H.ndim() > axis) {
result.size(axis) = H.size (axis);
result.spacing(axis) = H.spacing (axis);
break;
}
}
}
}
Eigen::MatrixXd dw_scheme, pe_scheme;
if (axis_to_concat == 3) {
try {
dw_scheme = DWI::get_DW_scheme (result);
} catch (Exception&) { }
try {
pe_scheme = PhaseEncoding::get_scheme (result);
} catch (Exception&) { }
}
for (size_t i = 1; i != headers.size(); ++i) {
const Header& H (headers[i]);
// Check that dimensions of image are compatible with concatenation
for (size_t axis = 0; axis <= global_max_nonunity_dim; ++axis) {
if (axis != axis_to_concat && axis < H.ndim() && H.size (axis) != result.size (axis)) {
e.push_back ("Images \"" + result.name() + "\" and \"" + H.name() + "\" have inequal sizes along axis " + str(axis_to_concat) + " (" + str(result.size (axis)) + " vs " + str(H.size (axis)) + ")");
throw e;
}
}
// Expand the image along the axis of concatenation
result.size (axis_to_concat) += H.ndim() <= axis_to_concat ? 1 : H.size (axis_to_concat);
// Concatenate 4D schemes if necessary
if (axis_to_concat == 3) {
try {
const auto extra_dw = DWI::parse_DW_scheme (H);
concat_scheme (dw_scheme, extra_dw);
} catch (Exception&) {
dw_scheme.resize (0, 0);
}
try {
const auto extra_pe = PhaseEncoding::get_scheme (H);
concat_scheme (pe_scheme, extra_pe);
} catch (Exception&) {
pe_scheme.resize (0, 0);
}
}
// Resolve key-value pairs
result.merge_keyval (H);
// Resolve discrepancies in datatype;
// also throw an exception if such mismatch is not permitted
if (datatype_test (!result.datatype().is_complex() && H.datatype().is_complex()))
result.datatype().set_flag (DataType::Complex);
if (datatype_test (result.datatype().is_integer() && !result.datatype().is_signed() && H.datatype().is_signed()))
result.datatype().set_flag (DataType::Signed);
if (datatype_test (result.datatype().is_integer() && H.datatype().is_floating_point()))
result.datatype() = H.datatype();
if (datatype_test (result.datatype().bytes() < H.datatype().bytes()))
result.datatype() = (result.datatype()() & DataType::Attributes) + (H.datatype()() & DataType::Type);
}
if (axis_to_concat == 3) {
DWI::set_DW_scheme (result, dw_scheme);
PhaseEncoding::set_scheme (result, pe_scheme);
}
return result;
}
}