def __init__(
self,
method: Union[Code, CodedConcept],
parent_specimen_id: str,
parent_specimen_type: Union[Code, CodedConcept],
issuer_of_parent_specimen_id: Optional[IssuerOfIdentifier] = None
):
"""
Parameters
----------
method: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
Method used to sample the examined specimen from a parent specimen
parent_specimen_id: str
Identifier of the parent specimen
parent_specimen_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
Type of the parent specimen
issuer_of_parent_specimen_id: highdicom.content.IssuerOfIdentifier, optional
Issuer who created the parent specimen
""" # noqa
super().__init__()
# CID 8110
method_item = CodeContentItem(
name=codes.DCM.SamplingMethod,
value=method
)
self.append(method_item)
parent_specimen_identitier_item = TextContentItem(
name=codes.DCM.ParentSpecimenIdentifier,
value=parent_specimen_id
)
self.append(parent_specimen_identitier_item)
if issuer_of_parent_specimen_id is not None:
try:
entity_id = issuer_of_parent_specimen_id.UniversalEntityID
except AttributeError:
entity_id = issuer_of_parent_specimen_id.LocalNamespaceEntityID
issuer_of_parent_specimen_identitier_item = TextContentItem(
name=codes.DCM.IssuerOfParentSpecimenIdentifier,
value=entity_id
)
self.append(issuer_of_parent_specimen_identitier_item)
# CID 8103
parent_specimen_type_item = CodeContentItem(
name=codes.DCM.ParentSpecimenType,
value=parent_specimen_type
)
self.append(parent_specimen_type_item)
def test_text_item_construction(self):
name = codes.DCM.TrackingIdentifier
value = '1234'
i = TextContentItem(name=name, value=value)
assert i.ValueType == 'TEXT'
assert i.ConceptNameCodeSequence[0] == name
assert i.TextValue == value
with pytest.raises(AttributeError):
assert i.RelationshipType
def __init__(self,
specimen_id: str,
specimen_uid: str,
specimen_location: Optional[Union[str, Tuple[float, float,
float]]] = None,
specimen_preparation_steps: Optional[
Sequence[SpecimenPreparationStep]] = None,
issuer_of_specimen_id: Optional[IssuerOfIdentifier] = None):
"""
Parameters
----------
specimen_id: str
Identifier of the examined specimen
specimen_uid: str
Unique identifier of the examined specimen
specimen_location: Union[str, Tuple[float, float, float]], optional
Location of the examined specimen relative to the container
provided either in form of text or in form of spatial x, y, z
coordinates specifying the position (offset) relative to the
three-dimensional slide coordinate system
specimen_preparation_steps: Sequence[highdicom.content.SpecimenPreparationStep], optional
Steps that were applied during the preparation of the examined
specimen in the laboratory prior to image acquisition
issuer_of_specimen_id: highdicom.content.IssuerOfIdentifier, optional
Description of the issuer of the specimen identifier
""" # noqa
super().__init__()
self.SpecimenIdentifier = specimen_id
self.SpecimenUID = specimen_uid
self.SpecimenPreparationSequence: List[Dataset] = []
if specimen_preparation_steps is not None:
for step in specimen_preparation_steps:
if not isinstance(step, ContentSequence):
raise TypeError(
'Each specimen preparation step must be provided as '
'a sequence of content items.')
step_item = Dataset()
step_item.SpecimenPreparationStepContentItemSequence = step
self.SpecimenPreparationSequence.append(step_item)
if specimen_location is not None:
loc_seq = []
if isinstance(specimen_location, str):
loc_item = TextContentItem(name=codes.DCM.LocationOfSpecimen,
value=specimen_location)
loc_seq.append(loc_item)
elif isinstance(specimen_location, tuple):
names = (
codes.DCM.LocationOfSpecimenXOffset,
codes.DCM.LocationOfSpecimenYOffset,
codes.DCM.LocationOfSpecimenZOffset,
)
for i, coordinate in enumerate(specimen_location):
loc_item = NumContentItem(
name=names[i],
value=coordinate,
)
loc_seq.append(loc_item)
self.SpecimenLocalizationContentItemSequence = loc_seq
self.IssuerOfTheSpecimenIdentifierSequence: List[Dataset] = []
if issuer_of_specimen_id is not None:
self.IssuerOfTheSpecimenIdentifierSequence.append(
issuer_of_specimen_id)
def __init__(self,
specimen_id: str,
processing_type: Union[Code, CodedConcept],
processing_procedure: Union[SpecimenCollection,
SpecimenSampling,
SpecimenStaining, ],
processing_description: Optional[Union[str, Code,
CodedConcept]] = None,
processing_datetime: Optional[datetime.datetime] = None,
issuer_of_specimen_id: Optional[IssuerOfIdentifier] = None,
fixative: Optional[Union[Code, CodedConcept]] = None,
embedding_medium: Optional[Union[Code, CodedConcept]] = None):
"""
Parameters
----------
specimen_id: str
Identifier of the processed specimen
processing_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
Type of processing
processing_procedure: Union[highdicom.content.SpecimenCollection, highdicom.content.SpecimenSampling, highdicom.content.SpecimenStaining]
Procedure used during processing
processing_datetime: datetime.datetime, optional
Datetime of processing
processing_description: Union[str, pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional
Description of processing
issuer_of_specimen_id: highdicom.content.IssuerOfIdentifier, optional
fixative: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional
Fixative used during processing
embedding_medium: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional
Embedding medium used during processing
""" # noqa
super().__init__()
specimen_identifier_item = TextContentItem(
name=codes.DCM.SpecimenIdentifier, value=specimen_id)
self.append(specimen_identifier_item)
if issuer_of_specimen_id is not None:
self.append(issuer_of_specimen_id)
# CID 8111
processing_type_item = CodeContentItem(name=codes.DCM.ProcessingType,
value=processing_type)
self.append(processing_type_item)
if processing_datetime is not None:
processing_datetime_item = DateTimeContentItem(
name=codes.DCM.DateTimeOfProcessing, value=processing_datetime)
self.append(processing_datetime_item)
if processing_description is not None:
if isinstance(processing_description, str):
processing_description_item = TextContentItem(
name=codes.DCM.ProcessingStepDescription,
value=processing_description)
else:
processing_description_item = CodeContentItem(
name=codes.DCM.ProcessingStepDescription,
value=processing_description)
self.append(processing_description_item)
accepted_procedure_types = (
SpecimenCollection,
SpecimenSampling,
SpecimenStaining,
)
if not isinstance(processing_procedure, accepted_procedure_types):
raise TypeError('Unknown procedure of specimen preparation step.')
self.extend(processing_procedure)
if fixative is not None:
tissue_fixative_item = CodeContentItem(
name=codes.SCT.TissueFixative, value=fixative)
self.append(tissue_fixative_item)
if embedding_medium is not None:
embedding_medium_item = CodeContentItem(
name=codes.SCT.EmbeddingMedium, value=embedding_medium)
self.append(embedding_medium_item)