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 test_detect_sequence_with_unknown_modality_returns_none(self):
header = Header(TEST_IMAGE_PATH)
header.raw.Modality = "UNKNOWN"
with warnings.catch_warnings():
warnings.simplefilter("ignore")
result = header.detect_sequence()
self.assertIsNone(result)
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 setUpClass(cls):
cls.csa_parser = CsaParser()
# Read a sample header
cls.header = Header(TEST_EP2D_IMAGE_PATH)
csa_series_info_tag = SIEMENS_PRIVATE_TAGS["CSASeriesHeaderInfo"]
raw_csa_header = cls.header.get(csa_series_info_tag, parsed=False)
csa_header = CsaHeader(raw_csa_header)
cls.parsed = csa_header.parse()
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 __init__(self, raw):
"""
The Image class should be initialized with either a string or a
:class:`~pathlib.Path` instance representing the path of a .dcm file.
Another option is to initialize it with a :class:`~pydicom.FileDataset`
instance, however, in that case make sure that the `stop_before_pixels`
parameter is set to False, otherwise reading pydicom's `pixel_array`
will fail.
Parameters
----------
raw : str, pathlib.Path, or pydicom.FileDataset
A single DICOM image.
parser : type, optional
An object with a public `parse()` method that may be used to parse
data elements, by default Parser.
"""
self.raw = read_file(raw, read_data=True)
self.header = Header(self.raw)
self.warnings = []
self._data = self.read_raw_data()
class Image:
"""
This class represents a single DICOM image (i.e. `.dcm` file) and provides
unified access to it's header information and data.
"""
def __init__(self, raw):
"""
The Image class should be initialized with either a string or a
:class:`~pathlib.Path` instance representing the path of a .dcm file.
Another option is to initialize it with a :class:`~pydicom.FileDataset`
instance, however, in that case make sure that the `stop_before_pixels`
parameter is set to False, otherwise reading pydicom's `pixel_array`
will fail.
Parameters
----------
raw : str, pathlib.Path, or pydicom.FileDataset
A single DICOM image.
parser : type, optional
An object with a public `parse()` method that may be used to parse
data elements, by default Parser.
"""
self.raw = read_file(raw, read_data=True)
self.header = Header(self.raw)
self.warnings = []
self._data = self.read_raw_data()
def read_raw_data(self) -> np.ndarray:
"""
Reads the pixel array data as returned by pydicom.
Returns
-------
np.ndarray
Pixel array data
"""
try:
return self.raw.pixel_array
except (AttributeError, ValueError) as exception:
warning = messages.DATA_READ_FAILURE.format(exception=exception)
warnings.warn(warning)
if warning not in self.warnings:
self.warnings.append(warning)
def fix_data(self) -> np.ndarray:
"""
Applies any required transformation to the data.
Returns
-------
np.ndarray
Pixel array data
"""
if self.is_mosaic:
mosaic = Mosaic(self._data, self.header)
return mosaic.fold()
return self._data
def get_default_relative_path(self) -> Path:
patient_uid = self.header.get("PatientID")
series_uid = self.header.get("SeriesInstanceUID")
name = str(self.header.get("InstanceNumber", 0)) + ".dcm"
return Path(patient_uid, series_uid, name)
@property
def is_mosaic(self) -> bool:
"""
Checks whether a 3D volume is encoded as a 2D Mosaic.
For more information, see the
:class:`~dicom_parser.utils.siemens.mosaic.Mosaic`
class.
Returns
-------
bool
Whether the image is a mosaic encoded volume
"""
return "MOSAIC" in self.header.get("ImageType")
@property
def is_fmri(self) -> bool:
"""
Returns True for fMRI images according to their header information.
Returns
-------
bool
Whether this image represents fMRI data.
"""
return self.header.detected_sequence == "fMRI"
@property
def data(self) -> np.ndarray:
"""
Returns the pixel data array after having applied any required
transformations.
Returns
-------
np.ndarray
Pixel data array.
"""
return self.fix_data()
@property
def default_relative_path(self) -> Path:
return self.get_default_relative_path()
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)
def test_incorrect_raw_input_raises_type_error(self):
bad_inputs = 6, 4.2, ("/some/path", ), ["/another/path"], None
for bad_input in bad_inputs:
with self.assertRaises(TypeError):
Header(bad_input)
def test_instantiation_with_path_instance(self):
path = Path(TEST_IMAGE_PATH)
header = Header(path)
self.assertIsInstance(header.raw, pydicom.FileDataset)
def test_instantiation_with_string_path(self):
header = Header(TEST_IMAGE_PATH)
self.assertIsInstance(header.raw, pydicom.FileDataset)
def setUpClass(cls):
cls.raw = pydicom.dcmread(TEST_IMAGE_PATH, stop_before_pixels=True)
cls.header = Header(cls.raw)
def test_get_with_a_missing_csa_header_returns_none(self):
header = Header(TEST_GE_LOCALIZER_PATH)
result = header.get("CSASeriesHeaderInfo")
self.assertIsNone(result)
def test_get_with_a_csa_header_returns_dict(self):
header = Header(TEST_IMAGE_PATH)
result = header.get("CSASeriesHeaderInfo")
self.assertIsInstance(result, dict)