def __init__(self, graphic_type: Union[GraphicTypeValues3D,
str], graphic_data: np.ndarray,
frame_of_reference_uid: str) -> None:
"""
Parameters
----------
graphic_type: Union[highdicom.sr.enum.GraphicTypeValues3D, str]
name of the graphic type
graphic_data: numpy.ndarray
array of ordered spatial coordinates, where each row of the array
represents a (x, y, z) coordinate triplet
frame_of_reference_uid: str
UID of the frame of reference
""" # noqa
graphic_type = GraphicTypeValues3D(graphic_type)
if graphic_type == GraphicTypeValues3D.MULTIPOINT:
raise ValueError(
'Graphic type "MULTIPOINT" is not valid for region.')
if graphic_type == GraphicTypeValues3D.ELLIPSOID:
raise ValueError(
'Graphic type "ELLIPSOID" is not valid for region.')
super().__init__(name=CodedConcept(value='111030',
meaning='Image Region',
scheme_designator='DCM'),
graphic_type=graphic_type,
graphic_data=graphic_data,
frame_of_reference_uid=frame_of_reference_uid,
relationship_type=RelationshipTypeValues.CONTAINS)
def __init__(
self,
graphic_type: Union[GraphicTypeValues3D, str],
graphic_data: np.ndarray,
frame_of_reference_uid: str,
source_images: Optional[
Sequence[SourceImageForSegmentation]] = None,
source_series: Optional[SourceSeriesForSegmentation] = None
) -> None:
"""
Parameters
----------
graphic_type: Union[highdicom.sr.enum.GraphicTypeValues3D, str]
name of the graphic type
graphic_data: Sequence[Sequence[int]]
ordered set of (row, column, frame) coordinate pairs
frame_of_reference_uid: str
unique identifier of the frame of reference within which the
coordinates are defined
source_images: Sequence[highdicom.sr.content.SourceImageForSegmentation], optional
source images for segmentation
source_series: highdicom.sr.content.SourceSeriesForSegmentation, optional
source series for segmentation
Note
----
Either one or more source images or one source series must be provided.
""" # noqa
graphic_type = GraphicTypeValues3D(graphic_type)
if graphic_type != GraphicTypeValues3D.ELLIPSOID:
raise ValueError(
'Graphic type for volume surface must be "ELLIPSOID".')
super().__init__(name=CodedConcept(value='121231',
meaning='Volume Surface',
scheme_designator='DCM'),
frame_of_reference_uid=frame_of_reference_uid,
graphic_type=graphic_type,
graphic_data=graphic_data,
relationship_type=RelationshipTypeValues.CONTAINS)
self.ContentSequence = ContentSequence()
if source_images is not None:
for image in source_images:
if not isinstance(image, SourceImageForSegmentation):
raise TypeError(
'Items of argument "source_image" must have type '
'SourceImageForSegmentation.')
self.ContentSequence.append(image)
elif source_series is not None:
if not isinstance(source_series, SourceSeriesForSegmentation):
raise TypeError('Argument "source_series" must have type '
'SourceSeriesForSegmentation.')
self.ContentSequence.append(source_series)
else:
raise ValueError(
'One of the following two arguments must be provided: '
'"source_images" or "source_series".')
def __init__(
self,
name: Union[Code, CodedConcept],
graphic_type: Union[GraphicTypeValues3D, str],
graphic_data: np.ndarray,
frame_of_reference_uid: Union[str, UID],
fiducial_uid: Optional[Union[str, UID]] = None,
relationship_type: Optional[Union[str, RelationshipTypeValues]] = None
) -> None:
"""
Parameters
----------
name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code]
concept name
graphic_type: Union[highdicom.sr.enum.GraphicTypeValues3D, str]
name of the graphic type
graphic_data: numpy.ndarray[numpy.float]
array of spatial coordinates, where each row of the array
represents a (x, y, z) coordinate triplet
frame_of_reference_uid: Union[pydicom.uid.UID, str]
unique identifier of the frame of reference within which the
coordinates are defined
fiducial_uid: str, optional
unique identifier for the content item
relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional
type of relationship with parent content item
""" # noqa
super(Scoord3DContentItem, self).__init__(ValueTypeValues.SCOORD3D,
name, relationship_type)
graphic_type = GraphicTypeValues3D(graphic_type)
self.GraphicType = graphic_type.value
if graphic_type == GraphicTypeValues3D.POINT:
if graphic_data.shape[0] != 1 or not graphic_data.shape[1] == 3:
raise ValueError(
'Graphic data of a scoord 3D of graphic type "POINT" '
'must be a single point in three-dimensional patient or '
'slide coordinate space in form of a (x, y, z) triplet.')
elif graphic_type == GraphicTypeValues3D.ELLIPSE:
if graphic_data.shape[0] != 4 or not graphic_data.shape[1] == 3:
raise ValueError(
'Graphic data of a 3D scoord of graphic type "ELLIPSE" '
'must be four (x, y, z) triplets in three-dimensional '
'patient or slide coordinate space.')
elif graphic_type == GraphicTypeValues3D.ELLIPSOID:
if graphic_data.shape[0] != 6 or not graphic_data.shape[1] == 3:
raise ValueError(
'Graphic data of a 3D scoord of graphic type '
'"ELLIPSOID" must be six (x, y, z) triplets in '
'three-dimensional patient or slide coordinate space.')
else:
if not graphic_data.shape[0] > 1 or not graphic_data.shape[1] == 3:
raise ValueError(
'Graphic data of a 3D scoord must be multiple '
'(x, y, z) triplets in three-dimensional patient or '
'slide coordinate space.')
# Flatten list of coordinate triplets
self.GraphicData = graphic_data.flatten().tolist()
self.ReferencedFrameOfReferenceUID = frame_of_reference_uid
if fiducial_uid is not None:
self.FiducialUID = fiducial_uid