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/*
Copyright 2008 Brain Research Institute, Melbourne, Australia
Written by J-Donald Tournier, 27/06/08.
This file is part of MRtrix.
MRtrix is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
MRtrix is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with MRtrix. If not, see <http://www.gnu.org/licenses/>.
15-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* handle files even when any of the study, series or patient description fields are blank
19-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* various sanity checks to ignore non-image DICOM files
15-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* add shorten() function to reduce long filenames
*/
#include <glibmm/fileutils.h>
#include <glibmm/stringutils.h>
#include <glibmm/miscutils.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 {
RefPtr<Patient> Tree::find (const String& patient_name, const String& patient_ID, const String& patient_DOB)
{
bool match;
for (guint n = 0; n < size(); n++) {
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 (RefPtr<Patient> (new Patient (patient_name, patient_ID, patient_DOB)));
return (back());
}
void Tree::read_dir (const String& filename)
{
try {
Glib::Dir folder (filename);
String entry;
while ((entry = folder.read_name()).size()) {
String name (Glib::build_filename (filename, entry));
if (Glib::file_test (name, Glib::FILE_TEST_IS_DIR)) read_dir (name);
else {
try { read_file (name); }
catch (Exception) { }
}
ProgressBar::inc();
}
}
catch (...) { throw Exception ("error opening DICOM folder \"" + filename + "\": " + Glib::strerror (errno)); }
}
void Tree::read_file (const String& filename)
{
QuickScan reader;
if (reader.read (filename)) {
info ("error reading file \"" + filename + "\" - assuming not DICOM");
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;
}
RefPtr<Patient> patient = find (reader.patient, reader.patient_ID, reader.patient_DOB);
RefPtr<Study> study = patient->find (reader.study, reader.study_ID, reader.study_date, reader.study_time);
RefPtr<Series> series = study->find (reader.series, reader.series_number, reader.modality, reader.series_date, reader.series_time);
RefPtr<Image> image (new Image);
image->filename = filename;
image->series = series.get();
image->sequence_name = reader.sequence;
series->push_back (image);
}
void Tree::read (const String& filename)
{
ProgressBar::init (0, "scanning DICOM set \"" + shorten (filename) + "\"");
if (Glib::file_test (filename, Glib::FILE_TEST_IS_DIR)) read_dir (filename);
else {
try { read_file (filename); }
catch (Exception) { }
}
ProgressBar::done();
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 (guint n = 0; n < item.size(); n++) stream << (*item[n]);
return (stream);
}
}
}
}
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