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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 "file/path.h"
#include "file/dicom/element.h"
#include "file/dicom/quick_scan.h"
#include "file/dicom/image.h"
#include "file/dicom/series.h"
#include "file/dicom/study.h"
#include "file/dicom/patient.h"
#include "file/dicom/tree.h"
namespace MR {
namespace File {
namespace Dicom {
std::shared_ptr<Patient> Tree::find (const std::string& patient_name, const std::string& patient_ID, const std::string& patient_DOB)
{
for (size_t n = 0; n < size(); n++) {
bool match = true;
if (patient_name == (*this)[n]->name) {
if (patient_ID.size() && (*this)[n]->ID.size())
if (patient_ID != (*this)[n]->ID)
match = false;
if (match) {
if (patient_DOB.size() && (*this)[n]->DOB.size())
if (patient_DOB != (*this)[n]->DOB)
match = false;
}
if (match)
return (*this)[n];
}
}
push_back (std::shared_ptr<Patient> (new Patient (patient_name, patient_ID, patient_DOB)));
return back();
}
void Tree::read_dir (const std::string& filename, ProgressBar& progress)
{
try {
Path::Dir folder (filename);
std::string entry;
while ((entry = folder.read_name()).size()) {
std::string name (Path::join (filename, entry));
if (Path::is_dir (name))
read_dir (name, progress);
else {
try {
read_file (name);
}
catch (Exception& E) {
E.display (3);
}
}
++progress;
}
}
catch (Exception& E) {
throw Exception (E, "error opening DICOM folder \"" + filename + "\": " + strerror (errno));
}
}
void Tree::read_file (const std::string& filename)
{
QuickScan reader;
if (reader.read (filename)) {
INFO ("error reading file \"" + filename + "\" - ignored");
return;
}
if (! (reader.dim[0] && reader.dim[1] && reader.bits_alloc && reader.data)) {
INFO ("DICOM file \"" + filename + "\" does not seem to contain image data - ignored");
return;
}
std::shared_ptr<Patient> patient = find (reader.patient, reader.patient_ID, reader.patient_DOB);
std::shared_ptr<Study> study = patient->find (reader.study, reader.study_ID, reader.study_UID, reader.study_date, reader.study_time);
for (const auto& image_type : reader.image_type) {
std::shared_ptr<Series> series = study->find (reader.series, reader.series_number, image_type.first,
reader.series_ref_UID, reader.modality, reader.series_date, reader.series_time);
std::shared_ptr<Image> image (new Image);
image->filename = filename;
image->series = series.get();
image->sequence_name = reader.sequence;
image->image_type = image_type.first;
image->transfer_syntax_supported = reader.transfer_syntax_supported;
series->push_back (image);
}
}
void Tree::read (const std::string& filename)
{
description = filename;
ProgressBar progress ("scanning DICOM folder \"" + shorten (filename) + "\"", 0);
if (Path::is_dir (filename))
read_dir (filename, progress);
else {
try {
read_file (filename);
}
catch (Exception) {
}
}
if (size() > 0)
return;
throw Exception ("no DICOM images found in \"" + filename + "\"");
}
std::ostream& operator<< (std::ostream& stream, const Tree& item)
{
stream << "FileSet " << item.description << ":\n";
for (size_t n = 0; n < item.size(); n++)
stream << *item[n];
return stream;
}
}
}
}
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