histopath_bim_des.specimens module

Defines specimens, blocks, and slides.

class histopath_bim_des.specimens.Priority(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Specimen priority. Lower value = higher priority.

ROUTINE = 0

CANCER = -1

PRIORITY = -2

URGENT = -3

class histopath_bim_des.specimens.Component(name: str = None, at: float | Callable = None, delay: float | Callable = None, priority: float = None, urgent: bool = None, process: str = None, suppress_trace: bool = False, suppress_pause_at_step: bool = False, skip_standby: bool = False, mode: str = '', cap_now: bool = None, env: Environment = None, **kwargs)

Bases: Component, ABC

A salabim component with additional fields.

prio: Priority

Priority of the component (Urgent, Priority, Cancer, or Routine).

parent: Component | None

The parent component, if it exists.

class histopath_bim_des.specimens.Specimen(name: str = None, at: float | Callable = None, delay: float | Callable = None, priority: float = None, urgent: bool = None, process: str = None, suppress_trace: bool = False, suppress_pause_at_step: bool = False, skip_standby: bool = False, mode: str = '', cap_now: bool = None, env: Environment = None, **kwargs)

Bases: Component

A tissue specimen.

Atrributes:

blocks:

The list of blocks produced from this specimen, empty if cut-up has not yet started.

setup(**kwargs) → None

Set up the component, called immediately after initialisation.

process()

Insert specimen into the arrive_reception in-queue.

timestamp(name: str)

Save timestamp data to self.env.specimen_data.

class histopath_bim_des.specimens.Block(name: str = None, at: float | Callable = None, delay: float | Callable = None, priority: float = None, urgent: bool = None, process: str = None, suppress_trace: bool = False, suppress_pause_at_step: bool = False, skip_standby: bool = False, mode: str = '', cap_now: bool = None, env: Environment = None, **kwargs)

Bases: Component

A wax block (or cassette to be turned into a wax block).

Atrributes:

slides:

The list of slides produced from this specimen, empty if microtomy has not yet started.

data:

A dict of additional data associated with the block.

setup(parent: Specimen, **kwargs) → None

Set up the component, called immediately after initialisation.

class histopath_bim_des.specimens.Slide(name: str = None, at: float | Callable = None, delay: float | Callable = None, priority: float = None, urgent: bool = None, process: str = None, suppress_trace: bool = False, suppress_pause_at_step: bool = False, skip_standby: bool = False, mode: str = '', cap_now: bool = None, env: Environment = None, **kwargs)

Bases: Component

A glass slide.

Atrributes:

data:

A dict of additional data associated with the slide.

setup(parent: Block, **kwargs) → None

Set up the component, called immediately after initialisation.

class histopath_bim_des.specimens.Batch(name: str = None, at: float | Callable = None, delay: float | Callable = None, priority: float = None, urgent: bool = None, process: str = None, suppress_trace: bool = False, suppress_pause_at_step: bool = False, skip_standby: bool = False, mode: str = '', cap_now: bool = None, env: Environment = None, **kwargs)

Bases: Component, Generic[C]

A batch of Component objects.

items

The list of items within the batch.

data

A dict of additional data associated with the batch.

setup(**kwargs) → None

Set up the component, called immediately after initialisation.