histopath_bim_des.model module

The histopathology simulation model.

Note that while Model class instances are constructed using Config instances, which are JSON serialisable, Model instances are themselves not serialisable.

class histopath_bim_des.model.Resources(env: Model)[source]

Bases: object

Dataclass for tracking the resources of a Model.

booking_in_staff: Resource

bms: Resource

cut_up_assistant: Resource

processing_room_staff: Resource

microtomy_staff: Resource

staining_staff: Resource

scanning_staff: Resource

qc_staff: Resource

histopathologist: Resource

bone_station: Resource

processing_machine: Resource

staining_machine: Resource

coverslip_machine: Resource

scanning_machine_regular: Resource

scanning_machine_megas: Resource

class histopath_bim_des.model.TaskDurations(*, receive_and_sort: Constant | Tri | PERT, pre_booking_in_investigation: Constant | Tri | PERT, booking_in_internal: Constant | Tri | PERT, booking_in_external: Constant | Tri | PERT, booking_in_investigation_internal_easy: Constant | Tri | PERT, booking_in_investigation_internal_hard: Constant | Tri | PERT, booking_in_investigation_external: Constant | Tri | PERT, cut_up_bms: Constant | Tri | PERT, cut_up_pool: Constant | Tri | PERT, cut_up_large_specimens: Constant | Tri | PERT, load_bone_station: Constant | Tri | PERT, decalc: Constant | Tri | PERT, unload_bone_station: Constant | Tri | PERT, load_into_decalc_oven: Constant | Tri | PERT, unload_from_decalc_oven: Constant | Tri | PERT, load_processing_machine: Constant | Tri | PERT, unload_processing_machine: Constant | Tri | PERT, processing_urgent: Constant | Tri | PERT, processing_small_surgicals: Constant | Tri | PERT, processing_large_surgicals: Constant | Tri | PERT, processing_megas: Constant | Tri | PERT, embedding: Constant | Tri | PERT, embedding_cooldown: Constant | Tri | PERT, block_trimming: Constant | Tri | PERT, microtomy_serials: Constant | Tri | PERT, microtomy_levels: Constant | Tri | PERT, microtomy_larges: Constant | Tri | PERT, microtomy_megas: Constant | Tri | PERT, load_staining_machine_regular: Constant | Tri | PERT, load_staining_machine_megas: Constant | Tri | PERT, staining_regular: Constant | Tri | PERT, staining_megas: Constant | Tri | PERT, unload_staining_machine_regular: Constant | Tri | PERT, unload_staining_machine_megas: Constant | Tri | PERT, load_coverslip_machine_regular: Constant | Tri | PERT, coverslip_regular: Constant | Tri | PERT, coverslip_megas: Constant | Tri | PERT, unload_coverslip_machine_regular: Constant | Tri | PERT, labelling: Constant | Tri | PERT, load_scanning_machine_regular: Constant | Tri | PERT, load_scanning_machine_megas: Constant | Tri | PERT, scanning_regular: Constant | Tri | PERT, scanning_megas: Constant | Tri | PERT, unload_scanning_machine_regular: Constant | Tri | PERT, unload_scanning_machine_megas: Constant | Tri | PERT, block_and_quality_check: Constant | Tri | PERT, assign_histopathologist: Constant | Tri | PERT, write_report: Constant | Tri | PERT)[source]

Bases: object

Dataclass for tracking task durations in a Model.

receive_and_sort: Constant | Tri | PERT

pre_booking_in_investigation: Constant | Tri | PERT

booking_in_internal: Constant | Tri | PERT

booking_in_external: Constant | Tri | PERT

booking_in_investigation_internal_easy: Constant | Tri | PERT

booking_in_investigation_internal_hard: Constant | Tri | PERT

booking_in_investigation_external: Constant | Tri | PERT

cut_up_bms: Constant | Tri | PERT

cut_up_pool: Constant | Tri | PERT

cut_up_large_specimens: Constant | Tri | PERT

load_bone_station: Constant | Tri | PERT

decalc: Constant | Tri | PERT

unload_bone_station: Constant | Tri | PERT

load_into_decalc_oven: Constant | Tri | PERT

unload_from_decalc_oven: Constant | Tri | PERT

load_processing_machine: Constant | Tri | PERT

unload_processing_machine: Constant | Tri | PERT

processing_urgent: Constant | Tri | PERT

processing_small_surgicals: Constant | Tri | PERT

processing_large_surgicals: Constant | Tri | PERT

processing_megas: Constant | Tri | PERT

embedding: Constant | Tri | PERT

embedding_cooldown: Constant | Tri | PERT

block_trimming: Constant | Tri | PERT

microtomy_serials: Constant | Tri | PERT

microtomy_levels: Constant | Tri | PERT

microtomy_larges: Constant | Tri | PERT

microtomy_megas: Constant | Tri | PERT

load_staining_machine_regular: Constant | Tri | PERT

load_staining_machine_megas: Constant | Tri | PERT

staining_regular: Constant | Tri | PERT

staining_megas: Constant | Tri | PERT

unload_staining_machine_regular: Constant | Tri | PERT

unload_staining_machine_megas: Constant | Tri | PERT

load_coverslip_machine_regular: Constant | Tri | PERT

coverslip_regular: Constant | Tri | PERT

coverslip_megas: Constant | Tri | PERT

unload_coverslip_machine_regular: Constant | Tri | PERT

labelling: Constant | Tri | PERT

load_scanning_machine_regular: Constant | Tri | PERT

load_scanning_machine_megas: Constant | Tri | PERT

scanning_regular: Constant | Tri | PERT

scanning_megas: Constant | Tri | PERT

unload_scanning_machine_regular: Constant | Tri | PERT

unload_scanning_machine_megas: Constant | Tri | PERT

block_and_quality_check: Constant | Tri | PERT

assign_histopathologist: Constant | Tri | PERT

write_report: Constant | Tri | PERT

class histopath_bim_des.model.Wips(env: Model)[source]

Bases: object

Dataclass for tracking work-in-progress counters for the Model simulation.

total: Monitor

in_reception: Monitor

in_cut_up: Monitor

in_processing: Monitor

in_microtomy: Monitor

in_staining: Monitor

in_labelling: Monitor

in_scanning: Monitor

in_qc: Monitor

in_reporting: Monitor

class histopath_bim_des.model.Globals(prob_internal: float, prob_urgent_cancer: float, prob_urgent_non_cancer: float, prob_priority_cancer: float, prob_priority_non_cancer: float, prob_prebook: float, prob_invest_easy: float, prob_invest_hard: float, prob_invest_external: float, prob_bms_cutup: float, prob_bms_cutup_urgent: float, prob_large_cutup: float, prob_large_cutup_urgent: float, prob_pool_cutup: float, prob_pool_cutup_urgent: float, prob_mega_blocks: float, prob_decalc_bone: float, prob_decalc_oven: float, prob_microtomy_levels: float, num_blocks_large_surgical: IntConstant | IntTri | IntPERT, num_blocks_mega: IntConstant | IntTri | IntPERT, num_slides_larges: IntConstant | IntTri | IntPERT, num_slides_levels: IntConstant | IntTri | IntPERT, num_slides_megas: IntConstant | IntTri | IntPERT, num_slides_serials: IntConstant | IntTri | IntPERT)[source]

Bases: object

Dataclass for global model variables.

prob_internal: float

prob_urgent_cancer: float

prob_urgent_non_cancer: float

prob_priority_cancer: float

prob_priority_non_cancer: float

prob_prebook: float

prob_invest_easy: float

prob_invest_hard: float

prob_invest_external: float

prob_bms_cutup: float

prob_bms_cutup_urgent: float

prob_large_cutup: float

prob_large_cutup_urgent: float

prob_pool_cutup: float

prob_pool_cutup_urgent: float

prob_mega_blocks: float

prob_decalc_bone: float

prob_decalc_oven: float

prob_microtomy_levels: float

num_blocks_large_surgical: IntConstant | IntTri | IntPERT

num_blocks_mega: IntConstant | IntTri | IntPERT

num_slides_larges: IntConstant | IntTri | IntPERT

num_slides_levels: IntConstant | IntTri | IntPERT

num_slides_megas: IntConstant | IntTri | IntPERT

num_slides_serials: IntConstant | IntTri | IntPERT

class histopath_bim_des.model.RunnerTimes(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: object

Dataclass for runner times.

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

class histopath_bim_des.model.Model(config: Config, **kwargs)[source]

Bases: Environment

The histopathology simulation model class.

num_reps

The number of simulation replications to run the model.

Type:: int

sim_length

The duration of each simulation replication.

Type:: float

resources

The resources associated with this model, as a dataclass instance.

Type:: Resources

task_durations

Dataclass instance containing the task durations for the model.

Type:: TaskDurations

batch_sizes

Dataclass instance containing the batch sizes for various tasks in the model.

Type:: config.batching.BatchSizes

globals

Dataclass instance containing global variables for the model.

Type:: Globals

specimen_data

Dict containing specimen attributes for all specimens in the simulation model (in-progress or completed).

Type:: dict[str,Any]

wips

Dataclass instance containing work-in-progress counters for the model.

Type:: Wips

processes

Dict mapping strings to the processes of the simulation model.

Type:: list[process.core.BaseProcess]

setup(config: Config) → None[source]: Set up the component, called immediately after initialisation.

run() → None[source]

start execution of the simulation

Parameters:

duration (float or distribution) –
schedule with a delay of duration

if 0, now is used

if distribution, the distribution is sampled
till (float or distribution) –
schedule time

if omitted, inf is assumed. See also note below

if distribution, the distribution is sampled
priority (float) –
priority

default: inf

if a component has the same time on the event list, main is sorted accoring to the priority. The default value of inf makes that all components will finish before the run is ended
urgent (bool) –
urgency indicator

if False (default), main will be scheduled behind all other components scheduled with the same time and priority

if True, main will be scheduled in front of all components scheduled for the same time and priority
cap_now (bool) – indicator whether times (till, duration) in the past are allowed. If, so now() will be used. default: sys.default_cap_now(), usualy False

Note

if neither till nor duration is specified, the main component will be reactivated at the time there are no more events on the eventlist, i.e. possibly not at inf.

if you want to run till inf (particularly when animating), issue run(sim.inf)

only issue run() from the main level