def populate_new_fields(apps, schema_editor):
Series = apps.get_model("django_dicom", "Series")
for series in Series.objects.all():
header = DicomHeader(str(series.image_set.first().dcm))
series.pulse_sequence_name = header.get((0x0019, 0x109C))
series.sequence_name = header.get((0x0018, 0x0024))
series.save()
def get_or_create_from_dcm(self,
path: Path,
autoremove: bool = True) -> Tuple:
"""
Gets or creates an :class:`~django_dicom.models.image.Image` instance
based on the contents of the provided *.dcm* path.
Parameters
----------
path : :class:`pathlib.Path`
Local *.dcm* file path
autoremove : bool, optional
Whether to remove the local copy of the *.dcm* file under
MEDIA_ROOT if creation fails, by default True
Returns
-------
Tuple[Image, bool]
image, created
"""
header = DicomHeader(path)
uid = header.get("SOPInstanceUID")
try:
existing = self.get(uid=uid)
except ObjectDoesNotExist:
new_instance = self.create_from_dcm(path, autoremove=autoremove)
return new_instance, True
else:
return existing, False
def instance(self) -> DicomHeader:
"""
Caches the created :class:`dicom_parser.header.Header` instance to
prevent multiple reades.
Returns
-------
:class:`dicom_parser.header.Header`
Header information
"""
if not isinstance(self._instance, DicomHeader):
dcm_path = (self.image.dcm.name
if os.getenv("USE_S3") else self.image.dcm.path)
self._instance = DicomHeader(dcm_path)
return self._instance
def scan_subject_to_session(apps, schema_editor):
Subject = get_subject_model()
Scan = apps.get_model("django_mri", "Scan")
Session = apps.get_model("django_mri", "Session")
for scan in Scan.objects.all():
subject = Subject.objects.filter(
id_number=scan.dicom.patient.uid
).first()
first_image = scan.dicom.image_set.first().dcm.path
header = DicomHeader(first_image)
date = header.get("StudyDate") or header.get("SeriesDate")
try:
time = header.get("StudyTime")
except ValueError:
time = datetime.time()
else:
if not time:
time = datetime.time()
session_time = datetime.datetime.combine(date, time)
if not subject:
session = Session.objects.create(time=session_time)
scan.session_id = session.id
else:
session = subject.mri_session_set.filter(
time=session_time
).first()
if not session:
session = Session.objects.create(
subject_id=subject.id, time=session_time
)
else:
existing_scan_number = Scan.objects.filter(
session_id=session.id, number=scan.number
)
if existing_scan_number:
session = Session.objects.create(
subject_id=subject.id, time=session_time
)
scan.session_id = session.id
scan.save()
def import_path(
self,
path: Path,
progressbar: bool = True,
report: bool = True,
persistent: bool = True,
force_patient_uid: bool = False,
) -> QuerySet:
"""
Iterates the given directory tree and imports any *.dcm* files found
within it.
Parameters
----------
path : :class:`pathlib.Path`
Base path for recursive *.dcm* import
progressbar : bool, optional
Whether to display a progressbar or not, by default True
report : bool, optional
Whether to print out a summary report when finished or not, by
default True
persistent : bool, optional
Whether to continue and raise a warning or to raise an exception
when failing to read a DICOM file's header
force_patient_uid : bool, optional
If patient UID for an existing image doesn't match the DB value,
change the DB value to match that of the imported image
Returns
-------
:class:`~django.db.models.query.QuerySet`
The created :class:`~django_dicom.models.image.Image` instances
"""
# Create an iterator
iterator = Path(path).rglob("*.dcm")
if progressbar:
# Create a progressbar wrapped iterator using tqdm
iterator = create_progressbar(iterator, unit="image")
if report:
counter = {"created": 0, "existing": 0}
# Keep a list of all the created images' primary keys
created_ids = []
# Keep a list of patient UID mismatches to log
patient_uid_mismatch = []
for dcm_path in iterator:
# Atomic image import
# For more information see:
# https://docs.djangoproject.com/en/3.0/topics/db/transactions/#controlling-transactions-explicitly
with transaction.atomic():
try:
image, created = self.get_or_create_from_dcm(
dcm_path, autoremove=True)
except InvalidDicomError as e:
if persistent:
IMPORT_LOGGER.warning(e)
continue
else:
raise
if report:
counter_key = "created" if created else "existing"
counter[counter_key] += 1
if created:
created_ids.append(image.id)
else:
if image.patient.uid not in patient_uid_mismatch:
# Validate patient UID for existing images
header = DicomHeader(dcm_path)
patient_uid = header.get("PatientID")
if patient_uid != image.patient.uid:
# Log patient UID mismatch
image_uid = header.get("SOPInstanceUID")
message = PATIENT_UID_MISMATCH.format(
image_uid=image_uid,
db_value=image.patient.uid,
patient_uid=patient_uid,
)
IMPORT_LOGGER.warning(message)
patient_uid_mismatch.append(image.patient.uid)
if report:
self.report_import_path_results(path, counter)
return self.filter(id__in=created_ids)