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/* Copyright (c) 2008-2022 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 "phase_encoding.h"
#include "math/math.h"
namespace MR
{
namespace PhaseEncoding
{
using namespace App;
const OptionGroup ImportOptions = OptionGroup ("Options for importing phase-encode tables")
+ Option ("import_pe_table", "import a phase-encoding table from file")
+ Argument ("file").type_file_in()
+ Option ("import_pe_eddy", "import phase-encoding information from an EDDY-style config / index file pair")
+ Argument ("config").type_file_in()
+ Argument ("indices").type_file_in();
const OptionGroup SelectOptions = OptionGroup ("Options for selecting volumes based on phase-encoding")
+ Option ("pe", "select volumes with a particular phase encoding; "
"this can be three comma-separated values (for i,j,k components of vector direction) or four (direction & total readout time)")
+ Argument ("desc").type_sequence_float();
const OptionGroup ExportOptions = OptionGroup ("Options for exporting phase-encode tables")
+ Option ("export_pe_table", "export phase-encoding table to file")
+ Argument ("file").type_file_out()
+ Option ("export_pe_eddy", "export phase-encoding information to an EDDY-style config / index file pair")
+ Argument ("config").type_file_out()
+ Argument ("indices").type_file_out();
void clear_scheme (Header& header)
{
auto erase = [&] (const std::string& s) { auto it = header.keyval().find (s); if (it != header.keyval().end()) header.keyval().erase (it); };
erase ("pe_scheme");
erase ("PhaseEncodingDirection");
erase ("TotalReadoutTime");
}
Eigen::MatrixXd parse_scheme (const Header& header)
{
Eigen::MatrixXd PE;
const auto it = header.keyval().find ("pe_scheme");
if (it != header.keyval().end()) {
try {
PE = parse_matrix (it->second);
} catch (Exception& e) {
throw Exception (e, "malformed PE scheme in image \"" + header.name() + "\"");
}
if (ssize_t(PE.rows()) != ((header.ndim() > 3) ? header.size(3) : 1))
throw Exception ("malformed PE scheme in image \"" + header.name() + "\" - number of rows does not equal number of volumes");
} else {
const auto it_dir = header.keyval().find ("PhaseEncodingDirection");
if (it_dir != header.keyval().end()) {
const auto it_time = header.keyval().find ("TotalReadoutTime");
const size_t cols = it_time == header.keyval().end() ? 3 : 4;
Eigen::Matrix<default_type, Eigen::Dynamic, 1> row (cols);
row.head(3) = Axes::id2dir (it_dir->second);
if (it_time != header.keyval().end())
row[3] = to<default_type>(it_time->second);
PE.resize ((header.ndim() > 3) ? header.size(3) : 1, cols);
PE.rowwise() = row.transpose();
}
}
return PE;
}
Eigen::MatrixXd get_scheme (const Header& header)
{
DEBUG ("searching for suitable phase encoding data...");
using namespace App;
Eigen::MatrixXd result;
try {
const auto opt_table = get_options ("import_pe_table");
if (opt_table.size())
result = load (opt_table[0][0], header);
const auto opt_eddy = get_options ("import_pe_eddy");
if (opt_eddy.size()) {
if (opt_table.size())
throw Exception ("Phase encoding table can be provided using either -import_pe_table or -import_pe_eddy option, but NOT both");
result = load_eddy (opt_eddy[0][0], opt_eddy[0][1], header);
}
if (!opt_table.size() && !opt_eddy.size())
result = parse_scheme (header);
}
catch (Exception& e) {
throw Exception (e, "error importing phase encoding table for image \"" + header.name() + "\"");
}
if (!result.rows())
return result;
if (result.cols() < 3)
throw Exception ("unexpected phase encoding table matrix dimensions");
INFO ("found " + str (result.rows()) + "x" + str (result.cols()) + " phase encoding table");
return result;
}
Eigen::MatrixXd eddy2scheme (const Eigen::MatrixXd& config, const Eigen::Array<int, Eigen::Dynamic, 1>& indices)
{
if (config.cols() != 4)
throw Exception ("Expected 4 columns in EDDY-format phase-encoding config file");
Eigen::MatrixXd result (indices.size(), 4);
for (ssize_t row = 0; row != indices.size(); ++row) {
if (indices[row] > config.rows())
throw Exception ("Malformed EDDY-style phase-encoding information: Index exceeds number of config entries");
result.row(row) = config.row(indices[row]-1);
}
return result;
}
void export_commandline (const Header& header)
{
auto check = [&](const Eigen::MatrixXd& m) -> const Eigen::MatrixXd& {
if (!m.rows())
throw Exception ("no phase-encoding information found within image \"" + header.name() + "\"");
return m;
};
auto scheme = parse_scheme (header);
auto opt = get_options ("export_pe_table");
if (opt.size())
save (check (scheme), header, opt[0][0]);
opt = get_options ("export_pe_eddy");
if (opt.size())
save_eddy (check (scheme), header, opt[0][0], opt[0][1]);
}
}
}
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