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ophth_ds_types

Types for ophthalmology data sources.

Classes​

DICOMImage​

class DICOMImage(    AcquisitionDeviceTypeCodeSequence: collections.abc.Sequence[bitfount.data.datasources.ophthalmology.ophth_ds_types._AcquisitionDeviceTypeCodeSequenceElement],    PatientName: str,    PatientBirthDate: str,    AcquisitionDateTime: str,    ImageLaterality: str,    NumberOfFrames: int,):

Named tuple for a DICOM image.

Variables​

  • AcquisitionDateTime : str - Alias for field number 3
  • AcquisitionDeviceTypeCodeSequence : collections.abc.Sequence[bitfount.data.datasources.ophthalmology.ophth_ds_types._AcquisitionDeviceTypeCodeSequenceElement] - Alias for field number 0
  • ImageLaterality : str - Alias for field number 4
  • NumberOfFrames : int - Alias for field number 5
  • PatientBirthDate : str - Alias for field number 2
  • PatientName : str - Alias for field number 1

FunctionalGroupsSequenceField​

class FunctionalGroupsSequenceField(    name: Literal['Shared Functional Groups Sequence', 'Per-Frame Functional Groups Sequence'],    value: list[bitfount.data.datasources.ophthalmology.ophth_ds_types._FunctionalGroupsSequenceFieldElement],):

Named tuple for Functional Groups Sequence Fields.

Applies to Shared Functional Groups Sequence (5200, 9229) and Per-Frame Functional Groups Sequence (0028, 9230).

Arguments

  • name: The name of the sequence field.
  • value: The value of the sequence field.

Variables​

  • name : Literal['Shared Functional Groups Sequence', 'Per-Frame Functional Groups Sequence'] - Alias for field number 0
  • value : list[bitfount.data.datasources.ophthalmology.ophth_ds_types._FunctionalGroupsSequenceFieldElement] - Alias for field number 1

FunctionalGroupsSequenceProcessingOutput​

class FunctionalGroupsSequenceProcessingOutput(*args, **kwargs):

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list. For example: dict(one=1, two=2)

Variables​

  • static Pixel Spacing Column : float
  • static Pixel Spacing Row : float
  • static Slice Thickness : float

Metadata​

class Metadata(*args, **kwargs):

The initial JSON output of from parsing a single ophthalmology file.

Variables​

  • static exam : bitfount.data.datasources.ophthalmology.ophth_ds_types._ExamInfo
  • static images : bitfount.data.datasources.ophthalmology.ophth_ds_types._ImagesInfo
  • static patient : bitfount.data.datasources.ophthalmology.ophth_ds_types._PatientInfo
  • static series : bitfount.data.datasources.ophthalmology.ophth_ds_types._SeriesInfo

ProcessedDICOMImage​

class ProcessedDICOMImage(    file_name: str,    modality: Literal['OCT', 'SLO', None],    patient_key: str,    acquisition_datetime: Optional[datetime.datetime],):

Named tuple for a processed DICOM image.

Variables​

  • file_name : str - Alias for field number 0
  • modality : Literal['OCT', 'SLO', None] - Alias for field number 1
  • patient_key : str - Alias for field number 2

ProcessedDataRequiredTypes​

class ProcessedDataRequiredTypes(*args, **kwargs):

The final output of the processing from a single ophthalmology file.

Variables​

  • static Columns : int
  • static Manufacturer : str
  • static Manufacturer's Model Name : str
  • static Number of Frames : int
  • static Patient ID : str
  • static Patient's Name : str
  • static Patient's Sex : str
  • static Pixel Spacing Column : float
  • static Pixel Spacing Row : float
  • static Rows : int
  • static Scan Laterality : str
  • static Slice Thickness : float
  • static date_of_birth : str
  • static dimensions_mm_depth : float
  • static dimensions_mm_height : float
  • static dimensions_mm_width : float
  • static first_name : str
  • static fixation : str
  • static gender : str
  • static group_id : int
  • static images : list[str]
  • static last_name : str
  • static laterality : str
  • static num_bscans : int
  • static num_modalities : int
  • static patient_key : str
  • static photo_locations_end_x : list[float]
  • static photo_locations_end_y : list[float]
  • static photo_locations_start_x : list[float]
  • static photo_locations_start_y : list[float]
  • static protocol : str
  • static resolutions_mm_depth : float
  • static resolutions_mm_height : float
  • static resolutions_mm_width : float
  • static scan_datetime : str
  • static scanner_model : str
  • static size_height : int
  • static size_width : int
  • static slo_dimensions_mm_height : float
  • static slo_dimensions_mm_width : float
  • static slo_images : list[str]
  • static slo_size_height : int
  • static slo_size_width : int
  • static source_info : str

ProcessedDataRequiredTypesDICOM​

class ProcessedDataRequiredTypesDICOM(*args, **kwargs):

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list. For example: dict(one=1, two=2)

Variables​

  • static Columns : int
  • static Manufacturer : str
  • static Manufacturer's Model Name : str
  • static Number of Frames : int
  • static Patient ID : str
  • static Patient's Name : str
  • static Patient's Sex : str
  • static Pixel Spacing Column : float
  • static Pixel Spacing Row : float
  • static Rows : int
  • static Scan Laterality : str
  • static Slice Thickness : float