def header_getter(field, header):
data_element = header.get_data_element(field)
dtype = data_element.VALUE_REPRESENTATION.value
data = data_element.value
if ("String" in dtype and "Decimal" not in dtype and "Code" not in dtype
or dtype == "Unknown"):
dtype = "STRING"
elif "Code String" in dtype:
dtype = "LIST"
else:
dtype = "NORMAL"
if isinstance(data, (tuple, list)):
data = ([ScanningSequence(elem).name for elem in data]
if field == "ScanningSequence" or field == (0x0018, 0x0020)
else [SequenceVariant(elem).name
for elem in data] if field == "SequenceVariant"
or field == (0x0018, 0x0021) else data)
else:
data = (ScanningSequence(data).name
if field == "ScanningSequence" or field == (0x0018, 0x0020)
else SequenceVariant(data).name if field == "SequenceVariant"
or field == (0x0018, 0x0021) else data)
return data or None, dtype
def test_sequence_variant_base_choices(self):
"""
`Sequence Variant`_ is a `Code String (CS)`_ data element and therfores
has a limited number of possible values.
.. _Sequence Variant: https://dicom.innolitics.com/ciods/mr-image/mr-image/00180021
.. _Code String (CS): http://northstar-www.dartmouth.edu/doc/idl/html_6.2/Value_Representations.html
"""
field = self.series._meta.get_field("sequence_variant")
self.assertEqual(field.base_field.choices, SequenceVariant.choices())
class Series(DicomEntity):
"""
A model to represent a single instance of the Series_ entity.
.. _Series: http://dicom.nema.org/dicom/2013/output/chtml/part03/chapter_A.html
"""
#: `Series Instance UID
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/0020000e>`_
#: value.
uid = models.CharField(
max_length=64,
unique=True,
validators=[digits_and_dots_only],
verbose_name="Series Instance UID",
help_text=help_text.SERIES_UID,
)
#: `Series Number
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00200011>`_
#: value.
number = models.PositiveIntegerField(
blank=True,
null=True,
verbose_name="Series Number",
help_text=help_text.SERIES_NUMBER,
)
#: `Series Description
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/0008103e>`_
#: value.
description = models.CharField(
max_length=64,
blank=True,
null=True,
verbose_name="Series Description",
help_text=help_text.SERIES_DESCRIPTION,
)
#: `Series Date
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00080021>`_
#: value.
date = models.DateField(
blank=True, null=True, help_text=help_text.SERIES_DATE
)
#: `Series Time
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00080021>`_
#: value.
time = models.TimeField(
blank=True, null=True, help_text=help_text.SERIES_TIME
)
#: `Echo Time
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180081>`_
#: value.
echo_time = models.FloatField(
blank=True,
null=True,
validators=[MinValueValidator(0)],
help_text=help_text.ECHO_TIME,
)
#: `Echo Train Length
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180091>`_
#: value.
echo_train_length = models.PositiveIntegerField(
blank=True, null=True, help_text=help_text.ECHO_TRAIN_LENGTH
)
#: `Inversion Time
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180082>`_
#: value.
inversion_time = models.FloatField(
blank=True,
null=True,
validators=[MinValueValidator(0)],
help_text=help_text.INVERSION_TIME,
)
#: `Repetition Time
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180080>`_
#: value.
repetition_time = models.FloatField(
blank=True,
null=True,
validators=[MinValueValidator(0)],
help_text=help_text.REPETITION_TIME,
)
#: `Scanning Sequence
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180020>`_
#: value.
scanning_sequence = ChoiceArrayField(
models.CharField(max_length=2, choices=ScanningSequence.choices()),
size=5,
help_text=help_text.SCANNING_SEQUENCE,
blank=True,
null=True,
)
#: `Sequence Variant
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180021>`_
#: value.
sequence_variant = ChoiceArrayField(
models.CharField(max_length=4, choices=SequenceVariant.choices()),
size=6,
help_text=help_text.SEQUENCE_VARIANT,
blank=True,
null=True,
)
#: `Pixel Spacing
#: <https://dicom.innolitics.com/ciods/mr-image/image-plane/00280030>`_
#: value.
pixel_spacing = ArrayField(
models.FloatField(validators=[MinValueValidator(0)]),
size=2,
help_text=help_text.PIXEL_SPACING,
blank=True,
null=True,
)
#: `Slice Thickness
#: <https://dicom.innolitics.com/ciods/mr-image/image-plane/00180050>`_
#: value.
slice_thickness = models.FloatField(
validators=[MinValueValidator(0)],
help_text=help_text.SLICE_THICKNESS,
blank=True,
null=True,
)
#: `Manufacturer
#: <https://dicom.innolitics.com/ciods/mr-image/device/00500010/00080070>`_
#: value.
manufacturer = models.CharField(
max_length=64, blank=True, null=True, help_text=help_text.MANUFACTURER
)
#: `Manufacturer's Model Name
#: <https://dicom.innolitics.com/ciods/mr-image/device/00500010/00081090>`_
#: value.
manufacturer_model_name = models.CharField(
max_length=64,
blank=True,
null=True,
help_text=help_text.MANUFACTURER_MODEL_NAME,
)
#: `Magnetic Field Strength
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180087>`_
#: value.
magnetic_field_strength = models.FloatField(
null=True,
blank=True,
validators=[MinValueValidator(0)],
help_text=help_text.MAGNETIC_FIELD_STRENGTH,
)
#: `Device Serial Number
#: <https://dicom.innolitics.com/ciods/mr-image/device/00500010/00181000>`_
#: value.
device_serial_number = models.CharField(
max_length=64,
blank=True,
null=True,
help_text=help_text.DEVICE_SERIAL_NUMBER,
)
#: `Body Part Examined
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00180015>`_
#: value.
body_part_examined = models.CharField(
max_length=16,
blank=True,
null=True,
help_text=help_text.BODY_PART_EXAMINED,
)
#: `Patient Position
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00185100>`_
#: value.
patient_position = models.CharField(
max_length=4,
choices=PatientPosition.choices(),
blank=True,
null=True,
help_text=help_text.PATIENT_POSITION,
)
#: `Modality
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00080060>`_
#: value.
modality = models.CharField(
max_length=10, choices=Modality.choices(), help_text=help_text.MODALITY
)
#: `Institution Name
#: <https://dicom.innolitics.com/ciods/mr-image/general-equipment/00080080>`_
#: value.
institution_name = models.CharField(
max_length=64,
blank=True,
null=True,
help_text=help_text.INSTITUTE_NAME,
)
#: `Operator's Name
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00081070>`_
#: value.
operators_name = models.JSONField(
blank=True, null=True, help_text=help_text.OPERATORS_NAME
)
#: `Protocol Name
#: <https://dicom.innolitics.com/ciods/mr-image/general-series/00181030>`_
#: value.
protocol_name = models.CharField(
max_length=64, blank=True, null=True, help_text=help_text.PROTOCOL_NAME
)
#: `Flip Angle
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00181314>`_
#: value.
flip_angle = models.FloatField(
null=True, blank=True, help_text=help_text.FLIP_ANGLE
)
#: `Pulse Sequence Name
#: <https://dicom.innolitics.com/ciods/enhanced-mr-color-image/mr-pulse-sequence/00189005>`_
#: value.
pulse_sequence_name = models.CharField(
max_length=64,
blank=True,
null=True,
help_text=help_text.PULSE_SEQUENCE_NAME,
)
#: `Sequence Name
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180024>`_
#: value.
sequence_name = models.CharField(
max_length=64, blank=True, null=True, help_text=help_text.SEQUENCE_NAME
)
#: `MR Acquisition Type
#: <https://dicom.innolitics.com/ciods/mr-image/mr-image/00180023>`_
#: value.
MR_ACQUISITION_2D = "2D"
MR_ACQUISITION_3D = "3D"
MR_ACQUISITION_TYPE_CHOICES = (
(MR_ACQUISITION_2D, "2D"),
(MR_ACQUISITION_3D, "3D"),
)
mr_acquisition_type = models.CharField(
max_length=2,
choices=MR_ACQUISITION_TYPE_CHOICES,
blank=True,
null=True,
help_text=help_text.MR_ACQUISITION_TYPE,
verbose_name="MR Acquisition Type",
)
#: The :class:`~django_dicom.models.study.Study` instance to which this
#: series belongs.
study = models.ForeignKey(
"django_dicom.Study", on_delete=models.PROTECT, blank=True, null=True
)
#: The :class:`~django_dicom.models.patient.Patient` instance to which this
#: series belongs.
patient = models.ForeignKey(
"django_dicom.Patient", on_delete=models.PROTECT, blank=True, null=True
)
#: A dictionary of DICOM data element keywords to be used to populate
#: a created instance's fields.
FIELD_TO_HEADER = {
"uid": "SeriesInstanceUID",
"date": "SeriesDate",
"time": "SeriesTime",
"description": "SeriesDescription",
"number": "SeriesNumber",
"mr_acquisition_type": "MRAcquisitionType",
"pulse_sequence_name": (0x0019, 0x109C),
}
# Cached :class:`~dicom_parser.series.Series` instance.
_instance = None
logger = logging.getLogger("data.dicom.series")
class Meta:
ordering = (
"-date",
"time",
"number",
)
verbose_name_plural = "Series"
indexes = [
models.Index(fields=["uid"]),
models.Index(fields=["date", "time"]),
]
def __str__(self) -> str:
"""
Returns the str representation of this instance.
Returns
-------
str
This instance's string representation
"""
return self.uid
def get_absolute_url(self) -> str:
"""
Returns the absolute URL for this instance.
For more information see the `Django documentation`_.
.. _Django documentation:
https://docs.djangoproject.com/en/3.0/ref/models/instances/#get-absolute-url
Returns
-------
str
This instance's absolute URL path
"""
return reverse("dicom:series-detail", args=[str(self.id)])
def save(self, *args, **kwargs) -> None:
"""
Overrides :meth:`~django_dicom.models.dicom_entity.DicomEntity.save` to
create any missing related DICOM entities if required.
"""
header = kwargs.get("header")
if header and self.missing_relation:
if not self.patient:
self.patient, _ = header.get_or_create_patient()
if not self.study:
self.study, _ = header.get_or_create_study()
super().save(*args, **kwargs)
def get_path(self) -> Path:
"""
Returns the base directory containing the images composing this series.
Returns
-------
str
This series's base directory path
"""
sample_image = self.image_set.first()
dcm_path = (
sample_image.dcm.name
if os.getenv("USE_S3")
else sample_image.dcm.path
)
return Path(dcm_path).parent
def get_scanning_sequence_display(self) -> list:
"""
Returns the display valuse of this instance's
:attr:`~django_dicom.models.series.Series.scanning_sequence` attribute.
Returns
-------
list
Verbose scanning sequence values
"""
if self.scanning_sequence:
return [
ScanningSequence[sequence].value
if getattr(ScanningSequence, sequence, False)
else sequence
for sequence in self.scanning_sequence
]
def get_sequence_variant_display(self) -> list:
"""
Returns the display valuse of this instance's
:attr:`~django_dicom.models.series.Series.sequence_variant` attribute.
Returns
-------
list
Verbose sequence variant values
"""
if self.sequence_variant:
return [
SequenceVariant[variant].value
if getattr(SequenceVariant, variant, False)
else variant
for variant in self.sequence_variant
]
@property
def path(self) -> Path:
"""
Returns the base path of this series' images.
Returns
-------
:class:`pathlib.Path`
Series directory path
"""
return self.get_path()
@property
def instance(self) -> DicomSeries:
"""
Caches the created :class:`dicom_parser.series.Series`
instance to prevent multiple reades.
Returns
-------
:class:`dicom_parser.series.Series`
Series information
"""
if not isinstance(self._instance, DicomSeries):
self._instance = DicomSeries(self.path)
return self._instance
@property
def data(self) -> np.ndarray:
"""
Returns the :attr:`dicom_parser.series.Series.data` property's value.
Returns
-------
:class:`np.ndarray`
Series data
"""
return self.instance.data
@property
def datetime(self) -> datetime:
"""
Returns a :class:`datetime.datetime` object by combining the values of
the :attr:`~django_dicom.models.series.Series.date` and
:attr:`~django_dicom.models.series.Series.time` fields.
Returns
-------
:class:`datetime.datetime`
Series datetime
"""
time = self.time or datetime.min.time()
if self.date:
return datetime.combine(self.date, time, tzinfo=pytz.UTC)
@property
def missing_relation(self) -> bool:
"""
Returns whether this instance misses an associated
:class:`~django_dicom.models.patient.Patient` or
:class:`~django_dicom.models.study.Study`.
Returns
-------
bool
Whether this instance has missing relationships
"""
return not (self.patient and self.study)
@property
def spatial_resolution(self) -> tuple:
"""
Returns the 3D spatial resolution of the instance by combining the
values of the :attr:`~django_dicom.models.series.Series.pixel_spacing`
and :attr:`~django_dicom.models.series.Series.slice_thickness` fields.
Returns
-------
tuple
(x, y, z) resolution in millimeters
"""
if self.pixel_spacing and self.slice_thickness:
return tuple(self.pixel_spacing + [self.slice_thickness])
elif self.pixel_spacing:
return tuple(self.pixel_spacing)
class SeriesFilter(filters.FilterSet):
"""
Provides filtering functionality for the
:class:`~django_dicom.views.series.SeriesViewSet`.
Available filters are:
* *id*: Primary key
* *uid*: Series Instance UID
* *patient_id*: Related :class:`~django_dicom.models.patient.Patient`
instance's primary key
* *study_uid*: Related :class:`~django_dicom.models.study.Study`
instance's :attr:`~django_dicom.models.study.Study.uid` value
* *study_description*: Related
:class:`~django_dicom.models.study.Study` instance's
:attr:`~django_dicom.models.study.Study.description` value
(in-icontains)
* *modality*: Any of the values defined in
:class:`~dicom_parser.utils.code_strings.modality.Modality`
* *description*: Series description value (contains, icontains, or
exact)
* *number*: Series number value
* *protocol_name*: Protocol name value (contains)
* *scanning_sequence*: Any combination of the values defined in
:class:`~dicom_parser.utils.code_strings.scanning_sequence.ScanningSequence`
* *sequence_variant*: Any combination of the values defined in
:class:`~dicom_parser.utils.code_strings.sequence_variant.SequenceVariant`
* *echo_time*: :attr:`~django_dicom.models.series.Series.echo_time`
value
* *inversion_time*:
:attr:`~django_dicom.models.series.Series.inversion_time` value
* *repetition_time*:
:attr:`~django_dicom.models.series.Series.repetition_time` value
* *flip_angle*: Any of the existing
:attr:`~django_dicom.models.series.Series.flip_angle` in the database
* *created_after_date*: Create after date
* *date*: Exact :attr:`~django_dicom.models.series.Series.date` value
* *created_before_date*: Create before date
* *created_after_time*: Create after time
* *created_before_time*: Create before time
* *manufacturer*: Any of the existing
:attr:`~django_dicom.models.series.Series.manufacturer` in the
database
* *manufacturer_model_name*: Any of the existing
:attr:`~django_dicom.models.series.Series.manufacturer_model_name` in
the database
* *device_serial_number*: Any of the existing
:attr:`~django_dicom.models.series.Series.device_serial_number` in
the database
* *institution_name*: Any of the existing
:attr:`~django_dicom.models.series.Series.institution_name` in the
database
* *pulse_sequence_name*:
:attr:`~django_dicom.models.series.Series.pulse_sequence_name` value
(in-icontains)
* *sequence_name*:
:attr:`~django_dicom.models.series.Series.sequence_name` value
(in-icontains)
"""
study_uid = filters.CharFilter("study__uid",
lookup_expr="exact",
label="Study UID")
study_description = CharInFilter(
field_name="study__description",
lookup_expr="in",
label="Study description icontains",
method=filter_in_string,
)
modality = filters.ChoiceFilter("modality", choices=Modality.choices())
description = filters.LookupChoiceFilter(lookup_choices=[
("contains", "Contains (case-sensitive)"),
("icontains", "Contains (case-insensitive)"),
("exact", "Exact"),
])
protocol_name = filters.CharFilter("protocol_name", lookup_expr="contains")
scanning_sequence = filters.MultipleChoiceFilter(
"scanning_sequence",
choices=ScanningSequence.choices(),
conjoined=True,
method=filter_array,
)
sequence_variant = filters.MultipleChoiceFilter(
"sequence_variant",
choices=SequenceVariant.choices(),
conjoined=True,
method=filter_array,
)
flip_angle = filters.AllValuesFilter("flip_angle")
created_after_date = filters.DateFilter("date", lookup_expr="gte")
date = filters.DateFilter("date")
created_before_date = filters.DateFilter("date", lookup_expr="lte")
created_after_time = filters.TimeFilter("time", lookup_expr="gte")
created_before_time = filters.TimeFilter("time", lookup_expr="lte")
manufacturer = filters.AllValuesFilter("manufacturer")
manufacturer_model_name = filters.AllValuesFilter(
"manufacturer_model_name")
magnetic_field_strength = filters.AllValuesFilter(
"magnetic_field_strength")
device_serial_number = filters.AllValuesFilter("device_serial_number")
institution_name = filters.AllValuesFilter("institution_name")
pulse_sequence_name = CharInFilter(
field_name="pulse_sequence_name",
lookup_expr="icontains",
method=filter_in_string,
)
sequence_name = CharInFilter(
field_name="sequence_name",
lookup_expr="icontains",
method=filter_in_string,
)
pixel_spacing = filters.RangeFilter("pixel_spacing__0")
slice_thickness = filters.RangeFilter("slice_thickness")
repetition_time = filters.RangeFilter("repetition_time")
inversion_time = filters.RangeFilter("inversion_time")
echo_time = filters.RangeFilter("echo_time")
header_fields = filters.CharFilter("image", method=filter_header)
class Meta:
model = Series
fields = (
"id",
"uid",
"patient_id",
"study_uid",
"study_description",
"modality",
"description",
"protocol_name",
"number",
"created_after_date",
"created_before_date",
"created_after_time",
"created_before_time",
"echo_time",
"inversion_time",
"repetition_time",
"slice_thickness",
"pixel_spacing",
"scanning_sequence",
"sequence_variant",
"flip_angle",
"manufacturer",
"manufacturer_model_name",
"magnetic_field_strength",
"device_serial_number",
"institution_name",
"patient__id",
"pulse_sequence_name",
"sequence_name",
)