def __init__(
self,
anatomic_location: Union[CodedConcept, Code],
laterality: Optional[Union[CodedConcept, Code]] = None,
topographical_modifier: Optional[Union[CodedConcept, Code]] = None
) -> None:
"""
Parameters
----------
anatomic_location: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code]
coded anatomic location (region or structure)
laterality: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional
coded laterality (see :dcm:`CID 244 <part16/sect_CID_244.html>`
"Laterality" for options)
topographical_modifier: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional
coded modifier of anatomic location
""" # noqa
super().__init__(
name=CodedConcept(
value='363698007',
meaning='Finding Site',
scheme_designator='SCT'
),
value=anatomic_location,
relationship_type=RelationshipTypeValues.HAS_CONCEPT_MOD
)
if laterality is not None or topographical_modifier is not None:
self.ContentSequence = ContentSequence()
if laterality is not None:
laterality_item = CodeContentItem(
name=CodedConcept(
value='272741003',
meaning='Laterality',
scheme_designator='SCT'
),
value=laterality,
relationship_type=RelationshipTypeValues.HAS_CONCEPT_MOD
)
self.ContentSequence.append(laterality_item)
if topographical_modifier is not None:
modifier_item = CodeContentItem(
name=CodedConcept(
value='106233006',
meaning='Topographical Modifier',
scheme_designator='SCT'
),
value=topographical_modifier,
relationship_type=RelationshipTypeValues.HAS_CONCEPT_MOD
)
self.ContentSequence.append(modifier_item)
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 __init__(
self,
value: Optional[Union[int, float]],
unit: Optional[Union[CodedConcept, Code]] = None,
event_type: Optional[Union[CodedConcept, Code]] = None) -> None:
"""
Parameters
----------
value: Union[int, float], optional
offset in time from a particular event of significance
unit: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional
unit of time, e.g., "Days" or "Seconds"
event_type: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional
type of event to which offset is relative,
e.g., "Baseline" or "Enrollment"
""" # noqa
super().__init__(
name=CodedConcept(
value='128740',
meaning='Longitudinal Temporal Offset from Event',
scheme_designator='DCM'),
value=value,
unit=unit,
relationship_type=RelationshipTypeValues.HAS_OBS_CONTEXT)
event_type_item = CodeContentItem(
name=CodedConcept(value='128741',
meaning='Longitudinal Temporal Event Type',
scheme_designator='DCM'),
value=event_type,
relationship_type=RelationshipTypeValues.HAS_CONCEPT_MOD)
self.ContentSequence = ContentSequence([event_type_item])
def test_code_item_construction(self):
name = codes.SCT.FindingSite
value = codes.SCT.Abdomen
i = CodeContentItem(name=name, value=value)
assert i.ValueType == 'CODE'
assert i.ConceptNameCodeSequence[0] == name
assert i.ConceptCodeSequence[0] == value
with pytest.raises(AttributeError):
assert i.RelationshipType
def __init__(self, procedure: Union[Code, CodedConcept]):
"""
Parameters
----------
procedure: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
Procedure used to collect the examined specimen
""" # noqa
super().__init__()
item = CodeContentItem(name=codes.SCT.SpecimenCollection,
value=procedure)
self.append(item)
def __init__(self, substances: Sequence[Union[Code, CodedConcept]]):
"""
Parameters
----------
substances: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]]
Substances used to stain examined specimen(s)
""" # noqa
super().__init__()
# CID 8112
for s in substances:
item = CodeContentItem(name=codes.SCT.UsingSubstance, value=s)
self.append(item)
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)
