histopath_bim_des.config.runners module

Runner-related configuration module for the histopath simulation model.

Bases: BaseModel

A mapping of process stages to door names. Each door name corresponds to a room where the the process takes place.

Note that some processes (e.g., cutup) may take place in multiple rooms.

reception: str | Sequence[str]

cutup: str | Sequence[str]

processing: str | Sequence[str]

microtomy: str | Sequence[str]

staining: str | Sequence[str]

labelling: str | Sequence[str]

scanning: str | Sequence[str]

qc: str | Sequence[str]

class histopath_bim_des.config.runners.PathDefinition(*, path: tuple[str, str], duration_seconds: float)[source]

Bases: BaseModel

Defines a direct path between two doors, with a travel duration.

path: tuple[str, str]

duration_seconds: float

class histopath_bim_des.config.runners.RunnerExtraDurations(*, loading_time: float | str, unloading_time: float | str)[source]

Bases: BaseModel

Defines runner durations independent of the travel distance, i.e. loading and unloading times.

loading_time: float | str

unloading_time: float | str

class histopath_bim_des.config.runners.RunnerConfig(*, door_map: ProcessDoorMap, runner_speed: float, cutup_dist: Sequence[float], extra_paths: Sequence[PathDefinition], extra_durations: RunnerExtraDurations)[source]

Bases: BaseModel

Configuration dataclass for runner-related parameters.

door_map: ProcessDoorMap

runner_speed: float

cutup_dist: Sequence[float]

extra_paths: Sequence[PathDefinition]

extra_durations: RunnerExtraDurations

static from_excel(wbook: Workbook) → Self[source]

Generate a RunnerConfig from an Excel file.

Parameters:: wbook (Workbook) – The Excel file to parse.
Returns:: the parsed RunnerConfig.
Return type:: RunnerConfig

class histopath_bim_des.config.runners.RunnerTimesConfig(*, reception_cutup: float, cutup_processing: float, processing_microtomy: float, microtomy_staining: float, staining_labelling: float, labelling_scanning: float, scanning_qc: float, extra_loading: float, extra_unloading: float)[source]

Bases: BaseModel

Configuration dataclass containing runner times between process stages.

reception_cutup: float

cutup_processing: float

processing_microtomy: float

microtomy_staining: float

staining_labelling: float

labelling_scanning: float

scanning_qc: float

extra_loading: float

extra_unloading: float

static from_workbook(wbook: Workbook, speed: float | None = None) → RunnerTimesConfig[source]

Construct a dataclass instance from an Excel workbook.

Parameters:: wbook (Workbook) – The Excel workbook to parse.
Returns:: The parsed dataclass instance.
Return type:: RunnerTimesConfig