slim.simulation.farm module

A Farm is a fundamental agent in this simulation. It has a number of functions:

controlling individual cages
managing its own finances
choose whether to cooperate with other farms belonging to the same organisation

class slim.simulation.farm.Farm(id_: int, cfg: Config, initial_lice_pop: Optional[Dict[str, int]] = None)

Bases: slim.log.LoggableMixin

Define a salmon farm containing salmon cages. Over time the salmon in the cages grow and are subjected to external infestation pressure from sea lice.

Create a farm.

Parameters

id – the id of the farm.
cfg – the farm configuration
initial_lice_pop – if provided, overrides default generated lice population

add_treatment(treatment_type: Treatment, day: datetime.datetime, force=False) → bool

Ask to add a treatment. If a treatment was applied too early or if too many treatments have been applied so far the request is rejected.

Note that if at least one cage is eligible for treatment and the conditions above are still respected this method will still return True.

Eligibility depends on the following conditions:

the cage should have started by the day treatment is applied
the cage should not be fallowing
the cage should not be treated by that day with that same type of treatment
the lice count should be greater than 1.0 (to prevent spamming)

If force is True, the last three constraints will be ignored.

Parameters

treatment_type – the treatment type to apply
day – the day when to start applying the treatment
force – if True, ignore some eligibility requirement.

Returns

whether the treatment has been added to at least one cage or not.

apply_action(cur_date: datetime.datetime, action: int)

Apply an action

Parameters

cur_date – the date when the action was issued
action – the action identifier as defined in slim.types.Treatments

disperse_offspring(eggs_by_hatch_date: Dict[datetime.datetime, GenoDistrib], cur_date: datetime.datetime) → List[Tuple[List[Dict[datetime.datetime, GenoDistrib]], datetime.datetime]]

DEPRECATED: it shouldn’t be within a farm’s responbility to calculate cage arrivals within other farms.

Allocate new offspring between the farms and cages.

Assumes the lice can float freely across a given farm so that they are not bound to a single cage while not attached to a fish.

Parameters

eggs_by_hatch_date – Dictionary of genotype distributions based on hatch date
cur_date – Current date of the simulation

disperse_offspring_v2(eggs_by_hatch_date: Dict[datetime.datetime, GenoDistrib], cur_date: datetime.datetime) → Tuple[List[Dict[datetime.datetime, GenoDistrib]], datetime.datetime]

Allocate new offspring within the farm

Assumes the lice can float freely across a given farm so that they are not bound to a single cage while not attached to a fish.

Parameters

eggs_by_hatch_date – Dictionary of genotype distributions based on hatch date
cur_date – Current date of the simulation

distribute_cage_offspring(cage_allocations: List[Dict[datetime.datetime, GenoDistrib]], arrival_time: datetime.datetime)

fallow()

generate_sampling_events()

generate_treatment_event(treatment_type: Treatment, cur_date: datetime.datetime) → TreatmentEvent

Generate a new treatment event with the correct efficacy based on the given day and type.

Parameters

treatment_type – the type of treatment
cur_date – the current date

Returns

the treatment event

get_cage_allocation(ncages: int, eggs_by_hatch_date: Dict[datetime.datetime, GenoDistrib]) → List[Dict[datetime.datetime, GenoDistrib]]

Return allocation of eggs for given number of cages.

Parameters

ncages – Number of bins to allocate to
eggs_by_hatch_date – Dictionary of genotype distributions based on hatch date

Returns

List of dictionaries of genotype distributions based on hatch date per bin

get_cage_arrivals_stats(cage_arrivals: List[Dict[datetime.datetime, GenoDistrib]]) → Tuple[int, List[int], List[GenoDistrib]]

Get stats about the cage arrivals for logging

Parameters: cage_arrivals – List of Dictionaries of genotype distributions based on hatch date.
Returns: Tuple representing total number of arrivals, arrival, distribution and genotype distribution by cage

get_cage_pressures(external_inflow: int) → List[int]

Get external pressure divided into cages

Parameters: external_inflow – the total external pressure
Returns: List of values of external pressure for each cage

get_farm_allocation(target_farm: int, eggs_by_hatch_date: Dict[datetime.datetime, GenoDistrib]) → Dict[datetime.datetime, GenoDistrib]

Return farm allocation of arrivals, that is a dictionary of genotype distributions based on hatch date updated to take into account probability of making it to the target farm.

The probability accounts for interfarm water movement (currents) as well as lice egg survival.

Note: for efficiency reasons this class modifies eggs_by_hatch_date in-place.

Parameters

target_farm_id – Farm the eggs are travelling to
eggs_by_hatch_date – Dictionary of genotype distributions based on hatch date

Returns

Updated dictionary of genotype distributions based on hatch date

get_gym_space() → ObservationSpace

Returns: a Gym space for the agent that controls this farm.

get_profit(cur_date: datetime.datetime) → float

Get the current mass of fish that can be resold.

Parameters: cur_date – the current day
Returns: the total profit that can be earned from this farm at the current time

property is_treating

Returns: a list of applied treatments as binary indices

property lice_genomics: Return the overall lice population indexed by geno distribution and stage.

property lice_population: Return the overall lice population in a farm

property num_fish: Return the number of fish across all cages

to_json_dict(**kwargs)

update(cur_date: datetime.datetime, ext_influx: int, ext_pressure_ratios: numpy.ndarray) → Tuple[Dict[datetime.datetime, GenoDistrib], float]

Update the status of the farm given the growth of fish and change in population of parasites. Also distribute the offspring across cages.

Parameters

cur_date – Current date
ext_influx – the amount of lice that enter a cage
ext_pressure_ratios – the ratio to use for the external pressure

Returns

a pair of (dictionary of genotype distributions based on hatch date, cost of the update)

update_arrivals(arrivals: Tuple[List[Dict[datetime.datetime, GenoDistrib]], datetime.datetime])