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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/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 {
vector<std::shared_ptr<Series>> select_cmdline (const Tree& tree)
{
vector<std::shared_ptr<Series>> series;
if (tree.size() == 0)
throw Exception ("DICOM tree its empty");
//ENVVAR name: DICOM_PATIENT
//ENVVAR when reading DICOM data, match the PatientName entry against
//ENVVAR the string provided
const char* patient_from_env = getenv ("DICOM_PATIENT");
//ENVVAR name: DICOM_ID
//ENVVAR when reading DICOM data, match the PatientID entry against
//ENVVAR the string provided
const char* patid_from_env = getenv ("DICOM_ID");
//ENVVAR name: DICOM_STUDY
//ENVVAR when reading DICOM data, match the StudyName entry against
//ENVVAR the string provided
const char* study_from_env = getenv ("DICOM_STUDY");
//ENVVAR name: DICOM_SERIES
//ENVVAR when reading DICOM data, match the SeriesName entry against
//ENVVAR the string provided
const char* series_from_env = getenv ("DICOM_SERIES");
if (patient_from_env || patid_from_env || study_from_env || series_from_env) {
// select using environment variables:
vector<std::shared_ptr<Patient>> patient;
for (size_t i = 0; i < tree.size(); i++) {
if ( (!patient_from_env || match (patient_from_env, tree[i]->name, true)) &&
(!patid_from_env || match (patid_from_env, tree[i]->ID, true)) )
patient.push_back (tree[i]);
}
if (patient.empty())
throw Exception ("no matching patients in DICOM dataset \"" + tree.description + "\"");
if (patient.size() > 1)
throw Exception ("too many matching patients in DICOM dataset \"" + tree.description + "\"");
vector<std::shared_ptr<Study>> study;
for (size_t i = 0; i < patient[0]->size(); i++) {
if (!study_from_env || match (study_from_env, (*patient[0])[i]->name, true))
study.push_back ((*patient[0])[i]);
}
if (study.empty())
throw Exception ("no matching studies in DICOM dataset \"" + tree.description + "\"");
if (study.size() > 1)
throw Exception ("too many matching studies in DICOM dataset \"" + tree.description + "\"");
for (size_t i = 0; i < study[0]->size(); i++) {
if (!series_from_env || match (series_from_env, (*study[0])[i]->name, true))
series.push_back ((*study[0])[i]);
}
if (series.empty())
throw Exception ("no matching studies in DICOM dataset \"" + tree.description + "\"");
return series;
}
// select interactively:
std::string buf;
const Patient* patient_p = nullptr;
if (tree.size() > 1) {
while (patient_p == nullptr) {
fprintf(stderr, "Select patient (q to abort):\n");
for (size_t i = 0; i < tree.size(); i++) {
fprintf (stderr, " %2" PRI_SIZET " - %s %s %s\n",
i+1,
tree[i]->name.c_str(),
format_ID(tree[i]->ID).c_str(),
format_date (tree[i]->DOB).c_str() );
}
std::cerr << "? ";
std::cin >> buf;
if (buf[0] == 'q' || buf[0] == 'Q')
throw CancelException();
if (isdigit (buf[0])) {
int n = to<int>(buf) - 1;
if (n <= (int) tree.size())
patient_p = tree[n].get();
}
if (!patient_p)
fprintf (stderr, "invalid selection - try again\n");
}
}
else
patient_p = tree[0].get();
const Patient& patient (*patient_p);
if (tree.size() > 1) {
fprintf (stderr, "patient: %s %s %s\n",
patient.name.c_str(),
format_ID (patient.ID).c_str(),
format_date (patient.DOB).c_str() );
}
const Study* study_p = nullptr;
if (patient.size() > 1) {
while (study_p == nullptr) {
fprintf (stderr, "Select study (q to abort):\n");
for (size_t i = 0; i < patient.size(); i++) {
fprintf (stderr, " %4" PRI_SIZET " - %s %s %s %s\n",
i+1,
( patient[i]->name.size() ? patient[i]->name.c_str() : "unnamed" ),
format_ID (patient[i]->ID).c_str(),
format_date (patient[i]->date).c_str(),
format_time (patient[i]->time).c_str() );
}
std::cerr << "? ";
std::cin >> buf;
if (buf[0] == 'q' || buf[0] == 'Q')
throw CancelException();
if (isdigit (buf[0])) {
int n = to<int>(buf) - 1;
if (n <= (int) patient.size())
study_p = patient[n].get();
}
if (!study_p)
fprintf (stderr, "invalid selection - try again\n");
}
}
else
study_p = patient[0].get();
const Study& study(*study_p);
if (patient.size() > 1) {
fprintf (stderr, "study: %s %s %s %s\n",
( study.name.size() ? study.name.c_str() : "unnamed" ),
format_ID (study.ID).c_str(),
format_date (study.date).c_str(),
format_time (study.time).c_str() );
}
if (study.size() > 1) {
while (series.size() == 0) {
fprintf (stderr, "Select series ('q' to abort):\n");
for (size_t i = 0; i < study.size(); i++) {
fprintf (stderr, " %2" PRI_SIZET " - %4" PRI_SIZET " %s images %8s %s (%s) [%" PRI_SIZET "] %s\n",
i,
study[i]->size(),
( study[i]->modality.size() ? study[i]->modality.c_str() : "" ),
format_time (study[i]->time).c_str(),
( study[i]->name.size() ? study[i]->name.c_str() : "unnamed" ),
( (*study[i])[0]->sequence_name.size() ? (*study[i])[0]->sequence_name.c_str() : "?" ),
study[i]->number, study[i]->image_type.c_str());
}
std::cerr << "? ";
std::cin >> buf;
if (buf[0] == 'q' || buf[0] == 'Q')
throw CancelException();
if (isdigit (buf[0])) {
vector<uint32_t> seq;
try {
seq = parse_ints<uint32_t> (buf);
for (size_t i = 0; i < seq.size(); i++) {
if (seq[i] < 0 || seq[i] >= (uint32_t) study.size()) {
series.clear();
break;
}
series.push_back (study[seq[i]]);
}
}
catch (Exception) {
seq.clear();
}
}
if (series.size() == 0)
fprintf (stderr, "Invalid selection - please try again\n");
}
}
else series.push_back (study[0]);
return series;
}
vector<std::shared_ptr<Series>> (*select_func) (const Tree& tree) = select_cmdline;
}
}
}
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