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v3

scan_metadata record, v3 — canonical aliases.

v3 is v2's table, which is v1's table. There is no schema change: the ORM, the record and the store are v1's, re-exported, for the reasons v2's docstring sets out.

What v3 adds is migrations.upgrade, a data migration that clears the scan_datetime values the old parse order could have written wrong, and marks their files for re-extraction. A version is the only thing the migration engine will hang that on, which is why v3 exists at all.

Module​

Submodules​

Functions​

upgrade​

def upgrade(op: Operations) ‑> None:

Delete the rows of every file holding a timestamp that may be wrong.

Idempotent: the rows it would delete are gone after the first pass, and a file it left alone holds nothing suspect, so replaying the hop by hand is safe.

Arguments

  • op: The bound Alembic operations handle; its connection is the one the caller's per-hop transaction runs in, so the deletion commits or rolls back with the version bump.

Classes​

ORM​

class ORM(**kwargs):

SQLAlchemy model for the scan_metadata cache table.

Stores vendor-normalized, header-only per-scan metadata (laterality, geometry, patient demographics, device) extracted from ophthalmology files without any pixel decode or model inference. One row per acquisition series.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance's class are allowed. These could be, for example, any mapped columns or relationships.

Ancestors​

Variables​

  • dataset_identifier : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • date_of_birth : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • dimensions_mm_depth : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • dimensions_mm_height : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • dimensions_mm_width : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • file_path : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • first_name : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • fixation : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • gender : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • last_name : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • laterality : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • manufacturer : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • num_bscans : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • patient_key : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • processed_at : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • protocol : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • reason : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • resolutions_mm_depth : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • resolutions_mm_height : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • resolutions_mm_width : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • run_id : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • scan_datetime : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • scanner_model : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • series_description : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • series_index : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • size_height : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • size_width : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • slo_dimensions_mm_height : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • slo_dimensions_mm_width : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • slo_size_height : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • slo_size_width : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • source_file_hash : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]
  • tags : Union[sqlalchemy.orm.attributes.InstrumentedAttribute[+_T_co], +_T_co]

Record​

class Record(**data: Any):

Record of a single stored row from the scan_metadata table (one per scan).

Extends NormalizedScanFields with the composite primary key (file_path, series_index) and the control/provenance columns.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Ancestors​

Variables​

  • static dataset_identifier : str | None
  • static file_path : str
  • static model_config
  • static reason : str | None
  • static run_id : str | None
  • static series_index : int
  • static source_file_hash : str | None