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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/dicom/quick_scan.h"
#include "file/dicom/definitions.h"
#include "file/dicom/element.h"
#include "file/dicom/csa_entry.h"
#include "debug.h"
namespace MR {
namespace File {
namespace Dicom {
bool QuickScan::read (const std::string& file_name, bool print_DICOM_fields, bool print_CSA_fields, bool print_Phoenix, bool force_read)
{
filename = file_name;
modality.clear();
patient.clear();
patient_ID.clear();
patient_DOB.clear();
study.clear();
study_date.clear();
study_ID.clear();
study_time.clear();
series.clear();
series_ref_UID.clear();
image_type.clear();
series_date.clear();
series_time.clear();
sequence.clear();
series_number = bits_alloc = dim[0] = dim[1] = data = 0;
transfer_syntax_supported = true;
{
Element item;
try {
item.set (filename, force_read);
std::string current_image_type;
bool in_frames = false;
while (item.read()) {
if (!item.ignore_when_parsing()) {
if (item.is (0x0008U, 0x0008U)) current_image_type = join (item.get_string(), " ");
else if (item.is (0x0008U, 0x0020U)) study_date = item.get_string (0);
else if (item.is (0x0008U, 0x0021U)) series_date = item.get_string (0);
else if (item.is (0x0008U, 0x0030U)) study_time = item.get_string (0);
else if (item.is (0x0008U, 0x0031U)) series_time = item.get_string (0);
else if (item.is (0x0008U, 0x0060U)) modality = item.get_string (0);
else if (item.is (0x0008U, 0x1030U)) study = item.get_string (0);
else if (item.is (0x0008U, 0x103EU)) series = item.get_string (0);
else if (item.is (0x0010U, 0x0010U)) patient = item.get_string (0);
else if (item.is (0x0010U, 0x0020U)) patient_ID = item.get_string (0);
else if (item.is (0x0010U, 0x0030U)) patient_DOB = item.get_string (0);
else if (item.is (0x0018U, 0x0024U)) sequence = item.get_string (0);
else if (item.is (0x0020U, 0x000DU)) study_UID = item.get_string (0);
else if (item.is (0x0020U, 0x000EU)) { if (item.is_in_series_ref_sequence()) series_ref_UID = item.get_string(0); }
else if (item.is (0x0020U, 0x0010U)) study_ID = item.get_string (0);
else if (item.is (0x0020U, 0x0011U)) series_number = item.get_uint (0);
else if (item.is (0x0028U, 0x0010U)) dim[1] = item.get_uint (0);
else if (item.is (0x0028U, 0x0011U)) dim[0] = item.get_uint (0);
else if (item.is (0x0028U, 0x0100U)) bits_alloc = item.get_uint (0);
else if (item.is (0x7FE0U, 0x0010U)) data = item.offset (item.data);
else if (item.is (0xFFFEU, 0xE000U)) {
if (item.parents.size() &&
item.parents.back().group == 0x5200U &&
item.parents.back().element == 0x9230U) { // multi-frame item
if (in_frames) ++image_type[current_image_type];
else in_frames = true;
}
}
}
if (print_DICOM_fields)
print (str(item));
if ((print_CSA_fields || print_Phoenix) && item.group == 0x0029U) {
if (item.element == 0x1010U ||
item.element == 0x1020U ||
item.element == 0x1110U ||
item.element == 0x1120U ||
item.element == 0x1210U ||
item.element == 0x1220U) {
CSAEntry entry (item.data, item.data + item.size);
while (entry.parse()) {
const bool is_phoenix = (strcmp ("MrPhoenixProtocol", entry.key()) == 0);
if ((print_Phoenix && is_phoenix) || (print_CSA_fields && !is_phoenix)) {
if (print_CSA_fields) {
print (str (entry));
} else {
const auto data = entry.get_string();
for (const auto& entry : data)
print (entry);
}
} else if (print_CSA_fields && is_phoenix) {
print (std::string("[CSA] ") + entry.key() + " (" + str(entry.num_items()) + " items): <");
const auto data = entry.get_string();
size_t line_count = 0;
for (const auto& entry : data) {
if (entry.size())
line_count += 1;
line_count += std::count (entry.begin(), entry.end(), '\n');
}
print (str(line_count) + " text lines>\n");
}
}
}
}
}
++image_type[current_image_type];
transfer_syntax_supported = item.transfer_syntax_supported;
}
catch (Exception& E) {
E.display (3);
return true;
}
}
check_app_exit_code();
return false;
}
std::ostream& operator<< (std::ostream& stream, const QuickScan& file)
{
stream << "file: \""
<< file.filename << "\" ["
<< file.modality << "]:\n patient: "
<< file.patient << " "
<< format_ID(file.patient_ID) << " - "
<< format_date (file.patient_DOB) << "\n study: "
<< ( file.study.size() ? file.study : "[unspecified]" ) << " "
<< format_ID(file.study_ID) << " - "
<< format_date (file.study_date) << " "
<< format_time (file.study_time) << "\n series: ["
<< file.series_number << "] "
<< ( file.series.size() ? file.series : "[unspecified]" ) << " - "
<< format_date (file.series_date) << " "
<< format_time (file.series_time) << "\n";
for (const auto& type : file.image_type)
stream << " image type: " << type.first << " [ " << type.second << " frames ]\n";
stream << " sequence: " << ( file.sequence.size() ? file.sequence : "[unspecified]" ) << "\n";
return stream;
}
}
}
}
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