steps

Prefect task wrappers and pure pipeline step functions.

Module

Submodules

• bitfount.steps.biomarker_tabulation - Biomarker tabulation step.
• bitfount.steps.cache_view - Shared helpers for building a step's cache read/write view.
• bitfount.steps.config_base - Shared base behaviour for step configs.
• bitfount.steps.criteria_matching - Criteria matching step.
• bitfount.steps.criteria_matching_types - Shared, typed structures — the canonical output of criteria_matching.
• bitfount.steps.cst_calculation - CST/CRT (Central Subfield / Retinal Thickness) calculation step.
• bitfount.steps.csv_report - CSV report step.
• bitfount.steps.data_utils - Composable data utilities for steps.
• bitfount.steps.ehr_patient_lister - EHR patient lister step.
• bitfount.steps.ehr_query - EHR query step.
• bitfount.steps.eligibility_functions - Pure logic shared by the scan/ehr/patient_eligibility steps.
• bitfount.steps.filters - Trial inclusion filters for steps.
• bitfount.steps.fluid_calculation - Fluid volume calculation step.
• bitfount.steps.ga_calculation_with_fovea - GA calculation with fovea step.
• bitfount.steps.ga_calculation_without_fovea - GA calculation without fovea step.
• bitfount.steps.gcc_calculation - GCC (Ganglion Cell Complex) calculation step.
• bitfount.steps.lesion_calculation - Generic en-face lesion calculation step.
• bitfount.steps.model_inference - Model inference step.
• bitfount.steps.patient_eligibility - Patient-eligibility reduce step package.
• bitfount.steps.patient_enrichment - Patient enrichment step — externally supplied per-patient data.
• bitfount.steps.patient_identity - Deriving a BitfountPatientID from a patient's name and date of birth.
• bitfount.steps.patient_level_eligibility - Patient-level eligibility step package.
• bitfount.steps.pdf_report - PDf report step.
• bitfount.steps.protocols - Structural protocols for objects passed into step tasks.
• bitfount.steps.registry - Task registry for the YAML DAG loader.
• bitfount.steps.result_base - Shared base for step results backed by a cache partition.
• bitfount.steps.row_utils - Best-effort pd.Series row-value helpers shared across step identity building.
• bitfount.steps.scan_eligibility - Scan-eligibility step package.
• bitfount.steps.scan_filter - Scan filter step.
• bitfount.steps.staleness - Read-before-compute helper shared by the per-file calculation steps.
• bitfount.steps.tabulate_criteria_outcomes - Tabulate criteria outcomes step.
• bitfount.steps.types - Shared types and constants for steps.

---