def generate_model_sample(n_runs, model_params, seed=[None]):
""" function for generating stationsim model runs to test
Parameters
------
n_runs : int
`n_runs`number of stationsim runs to generate.
Must be positive intiger.
model_params : dict
`model_params` dictionary of model parameters required for
stationsim to run. See stationsim_model.py for more details.
seed : list
`seed` seeding for stationsim. Can a single seed for every run
or a list of n_runs seeds.
"""
models = []
if len(seed) == 1:
seed *= n_runs
elif len(seed) != n_runs:
print("not enough seeds specificed. Either provide precisely 1 or " +
f"{n_runs} seeds")
for _ in range(n_runs):
model = Model(**model_params)
while model.status == 1:
model.step()
models.append(model)
return models
def generate_Model_Sample(self,
n_runs,
model_params,
single_process=False):
""" function for generating stationsim model runs to test
Parameters
------
n_runs : int
`n_runs`number of stationsim runs to generate.
Must be positive intiger.
model_params : dict
`model_params` dictionary of model parameters required for
stationsim to run. See stationsim_model.py for more details.
single_process : bool (default False)
whether to run the models as a single process or using
multiple processes simultaneously.
Returns
------
models : list
a list of completed stationsim `models` given the required
width, height, pop_total, and gate_speed.
"""
#placeholder list
models = []
if n_runs > 1 and model_params["random_seed"] != None:
raise Exception("Error: the 'random_seed' parameter is not None\
which means that all models generate the same results, which\
I'm sure isn't what you want!")
elif n_runs < 1:
raise Exception(
"Error: need one or more 'n_runs', not {}".format(n_runs))
#supress excessive printing
with HiddenPrints():
if single_process or n_runs == 1:
for _ in range(n_runs):
#generate model and run til status goes back to 0 (finished)
model = Model(**model_params)
while model.status == 1:
model.step()
models.append(model)
else:
pool = multiprocessing.Pool()
try:
numcores = multiprocessing.cpu_count()
models = pool.map(stationsim_RipleysK.run_model,
[model_params for _ in range(n_runs)])
finally:
pool.close(
) # Make sure whatever happens the processes are killed
return models
def assign_agents(cls, particle_num: int, state: np.array, model: Model):
"""
Assign the state of the particles to the
locations of the agents.
:param particle_num
:param state: The state of the particle to be assigned
:param model: The model to assign the state to
:type model: Return the model after having the agents assigned according to the state.
"""
model.set_state(state, sensor='location')
return model
def make_truth_data(model_params):
"""
Run StationSim to generate synthetic truth data.
Returns a list of the states of each agent;
Each list entry is the state of the agents at a timestep.
"""
# Run model with provided params
model = Model(model_params)
model.batch()
# Extract agent tracks
return model.state_history
def test_StationSim_seeding(self):
""" Test stationsim seeding by running two models with same seed
and comparing positions.
Parameters
------
model_params : dict
`model_params` dictionary of stationsim model_parameters.
seed : int
`seed` for fixing numpy random outputs. must be 0<int<2**32-1.
see stationsim_model for model parameter defintions"""
model_params = {
'pop_total':5,
'width': 200,
'height': 100,
'gates_in': 3,
'gates_out': 2,
'gates_space': 1,
'gates_speed': 1,
'speed_min': .2,
'speed_mean': 1,
'speed_std': 1,
'speed_steps': 3,
'separation': 5,
'max_wiggle': 1,
'step_limit': 3600,
'do_history': True,
'do_print': True,
"random_seed" : 8**8
}
model1 = Model(**model_params)
model1 = model_Run(model1)
array1 = np.hstack(model1.history_state)
model2 = Model(**model_params)
model2 = model_Run(model2)
array2 = np.hstack(model2.history_state)
self.assertAlmostEqual(np.nansum(array1-array2), 0)
def aggregate_params(n, bin_size, model_params, ukf_params):
"""update ukf_params with fx/hx and their parameters for experiment 2
Parameters
------
ukf_params : dict
Returns
------
ukf_params : dict
"""
model_params["pop_total"] = n
base_model = Model(**model_params)
ukf_params["bin_size"] = bin_size
ukf_params["poly_list"] = grid_poly(model_params["width"],
model_params["height"],
ukf_params["bin_size"])
ukf_params["p"] = np.eye(2 * n) #inital guess at state covariance
ukf_params["q"] = np.eye(2 * n)
ukf_params["r"] = np.eye(len(ukf_params["poly_list"])) #sensor noise
ukf_params["fx"] = fx
ukf_params["fx_kwargs"] = {"base_model": base_model}
ukf_params["hx"] = hx2
ukf_params["hx_kwargs"] = {"poly_list": ukf_params["poly_list"]}
ukf_params["obs_key_func"] = obs_key_func
ukf_params["obs_key_kwargs"] = {"pop_total": n}
ukf_params["file_name"] = ex2_pickle_name(n, bin_size)
return model_params, ukf_params, base_model
def omission_params(n, prop, model_params, ukf_params):
"""update ukf_params with fx/hx and their parameters for experiment 1
- assign population size and proportion observed.
- randomly select agents to observed for index/index2
- assign initial covariance p as well as sensor and process noise (q,r)
- assign transition and measurement functions (fx,hx)
- assign observation key function and numpy file name for saving later.
Parameters
------
n, prop : float
`n` population and proportion observed 0<=`prop`<=1
model_params, ukf_params : dict
dictionaries of model `model_params` and ukf `ukf_params` parameters
Returns
------
model_params, ukf_params : dict
updated dictionaries of model `model_params` and ukf `ukf_params`
parameters ready to use in ukf_ss
"""
model_params["pop_total"] = n
model_params["station"] = None
base_model = Model(**model_params)
ukf_params["prop"] = prop
ukf_params["sample_size"]= floor(n * prop)
ukf_params["index"], ukf_params["index2"] = omission_index(n, ukf_params["sample_size"])
ukf_params["p"] = np.eye(2 * n) #inital guess at state covariance
ukf_params["q"] = np.eye(2 * n)
ukf_params["r"] = np.eye(2 * ukf_params["sample_size"])#sensor noise
ukf_params["fx"] = fx
ukf_params["fx_kwargs"] = {"base_model" : base_model}
ukf_params["fx_kwargs_update"] = None
ukf_params["hx"] = hx1
ukf_params["hx_kwargs"] = {"index2" : ukf_params["index2"],
"n" : n,
"index" : ukf_params["index"],}
ukf_params["obs_key_func"] = obs_key_func
ukf_params["file_name"] = ex1_pickle_name(n, prop)
ukf_params["light"] = True
ukf_params["record"] = True
return model_params, ukf_params, base_model
def run_model(model_params):
"""
Create a new stationsim model using `model_params` and step it
until it has finished.
Parameters
------
model_params : dict
`model_params` dictionary of model parameters required for
stationsim to run. See stationsim_model.py for more details.
Returns
------
model : StaionSim object
the finished model
"""
model = Model(**model_params)
while model.status == 1:
model.step()
return model
def cone_params(n, cameras, model_params, ukf_params):
"""update ukf_params with fx/hx and their parameters for experiment 4
-add ground truth stationsim model base_model
Parameters
------
n : int
`n` population total
cameras: list
list of camera_Sensor objects. Each camera has a polygon it observes.
model_params, ukf_params : `dict`
default stationsim `model_params` and ukf `ukf_params` parameter
dictionaries to be updated for the experiment to run.
Returns
------
model_params, ukf_params : `dict`
updated default stationsim `model_params` and ukf `ukf_params`
dictionaries
base_model : `class`
initiated stationsim model `base_model` used as the ground truth.
"""
#stationsim truth model
model_params["pop_total"] = n
base_model = Model(**model_params)
#cameras
ukf_params["cameras"] = cameras
#noise structures
ukf_params["p"] = 0.1 * np.eye(2 * n) #inital guess at state covariance
ukf_params["q"] = 0.01 * np.eye(2 * n) #process noise
"sensor noise here dynamically updated depending on how many agents in the cameras."
ukf_params["r"] = 0.01 * np.eye(2 * n) #sensor noise
#kalman functions
ukf_params["fx"] = fx
ukf_params["fx_kwargs"] = {"base_model": base_model}
ukf_params["hx"] = hx4
ukf_params["hx_kwargs"] = {
"cameras": cameras,
"n": n,
}
ukf_params["obs_key_func"] = obs_key_func
ukf_params["hx_kwargs_update_function"] = hx4_kwargs_updater
#pickle file name
ukf_params["file_name"] = ex4_pickle_name(n)
return model_params, ukf_params, base_model
def ex0_params(n, noise, sample_rate, model_params, ukf_params):
"""update ukf_params with fx/hx and their parameters for experiment 1
- assign population size, observation noise, and sampling/assimilation rate
- assign initial covariance p as well as sensor and process noise (q,r)
- assign transition and measurement functions (fx,hx)
- assign observation key function and numpy file name for saving later.
Parameters
------
n, noise, sample_rate : float
`n` population, additive `noise`, and `sample_rate` sampling rate
model_params, ukf_params : dict
dictionaries of model `model_params` and ukf `ukf_params` parameters
Returns
------
model_params, ukf_params : dict
updated dictionaries of model `model_params` and ukf `ukf_params`
parameters ready to use in ukf_ss
"""
model_params["pop_total"] = n
ukf_params["noise"] = noise
ukf_params["sample_rate"] = sample_rate
base_model = Model(**model_params)
ukf_params["p"] = np.eye(2 * n) #inital guess at state covariance
ukf_params["q"] = np.eye(2 * n)
ukf_params["r"] = np.eye(2 * n) #sensor noise
ukf_params["fx"] = fx
ukf_params["fx_kwargs"] = {"base_model": base_model}
ukf_params["hx"] = hx0
ukf_params["hx_kwargs"] = {}
ukf_params["obs_key_func"] = None
ukf_params[
"file_name"] = f"config_agents_{n}_rate_{sample_rate}_noise_{noise}"
return model_params, ukf_params, base_model
def cone_params(n, cameras, model_params, ukf_params):
"""update ukf_params with fx/hx and their parameters for experiment 2
Parameters
------
n : int
`n` population total
cameras: list
list of camera_Sensor sensor objects.
model_params, ukf_params : dict
Returns
------
model_params, ukf_params : dict
"""
model_params["pop_total"] = n
base_model = Model(**model_params)
ukf_params["cameras"] = cameras
ukf_params["p"] = np.eye(2 * n) #inital guess at state covariance
ukf_params["q"] = np.eye(2 * n) #process noise
"sensor noise here dynamically updated depending on how many agents in the cameras."
ukf_params["r"] = np.eye(2 * n) #sensor noise
ukf_params["fx"] = fx
ukf_params["fx_kwargs"] = {"base_model": base_model}
ukf_params["hx"] = hx4
ukf_params["hx_kwargs"] = {"cameras": cameras}
ukf_params["obs_key_func"] = obs_key_func
ukf_params["obs_key_kwargs"] = {"pop_total": n}
ukf_params["file_name"] = """ex4_pickle_name(n, cameras) """
return model_params, ukf_params, base_model
def setUpClass(cls):
"""unittest.TestCase's special __init__
"""
# init params for a SEEDED stationsim
cls.model_params = {
'width': 200,
'height': 50,
'pop_total': 2,
'gates_speed': 1,
'gates_in': 3,
'gates_out': 2,
'gates_space': 1,
'speed_min': .2,
'speed_mean': 1,
'speed_std': 1,
'speed_steps': 3,
'separation': 5,
'max_wiggle': 1,
'step_limit': 3600,
'do_history' : True,
'do_print' : True,
'random_seed' : 8,
}
cls.ukf_params = configs.ukf_params
cls.base_model = Model(**cls.model_params)
pool = multiprocessing.Pool(processes = multiprocessing.cpu_count())
cls.rjmcmc_ukf = rjmcmc_ukf(cls.model_params, cls.ukf_params,
cls.base_model, pool)
def step_particle(cls, particle_num: int, model: Model, num_iter: int, particle_std: float, particle_shape: tuple):
"""
Step a particle, assign the locations of the
agents to the particle state with some noise, and
then use the new particle state to set the location
of the agents.
:param particle_num: The particle number to step
:param model: A pointer to the model object associated with the particle that needs to be stepped
:param num_iter: The number of iterations to step
:param particle_std: the particle noise standard deviation
:param particle_shape: the shape of the particle array
"""
# Force the model to re-seed its random number generator (otherwise each child process
# has the same generator https://stackoverflow.com/questions/14504866/python-multiprocessing-numpy-random
model.set_random_seed()
for i in range(num_iter):
model.step()
noise = np.random.normal(0, particle_std ** 2, size=particle_shape)
state = model.get_state(sensor='location') + noise
model.set_state(state, sensor='location')
return model, state
'gates_in': 3,
'gates_out': 2,
'gates_space': 1,
'gates_speed': 1,
'speed_min': .2,
'speed_mean': 1,
'speed_std': 1,
'speed_steps': 3,
'separation': 5,
'max_wiggle': 1,
'step_limit': 3600,
'do_history': True,
'do_print': True,
}
model = Model(**model_params)
while model.status != 0:
model.step()
marker_attributes = {
"markers": {
-1: "o"
},
"colours": {
-1: "black"
},
"labels": {
-1: "Pseudo-Truths"
}
}
def ex3_params(n, model_params, ukf_params):
"""update ukf_params with fx/hx and their parameters for experiment 1
- assign population size and proportion observed.
- randomly select agents to observed for index/index2
- assign initial covariance p as well as sensor and process noise (q,r)
- assign transition and measurement functions (fx,hx)
- assign observation key function and numpy file name for saving later.
Parameters
------
n, prop : float
`n` population and proportion observed 0<=`prop`<=1
model_params, ukf_params : dict
dictionaries of model `model_params` and ukf `ukf_params` parameters
Returns
------
model_params, ukf_params : dict
updated dictionaries of model `model_params` and ukf `ukf_params`
parameters ready to use in ukf_ss
"""
model_params["pop_total"] = n
model_params["station"] = None
base_model = Model(**model_params)
model_params["exit_gates"] = base_model.gates_locations[
-model_params["gates_out"]:]
model_params["get_gates_dict"], model_params[
"set_gates_dict"] = gates_dict(base_model)
width = model_params["width"]
height = model_params["height"]
ukf_params["boundary"] = generate_Camera_Rect(np.array([0, 0]),
np.array([0, height]),
np.array([width, height]),
np.array([width, 0]))
ukf_params["p"] = np.eye(1 * 2 * n) #inital guess at state covariance
ukf_params["q"] = 0.05 * np.eye(1 * 2 * n)
ukf_params["r"] = 0.01 * np.eye(1 * 2 * n) #sensor noise
ukf_params["x0"] = base_model.get_state("location")
ukf_params["fx"] = fx3
ukf_params["fx_kwargs"] = {
"state": ukf_params["x0"],
"boundary": ukf_params["boundary"],
"get_gates_dict": model_params["get_gates_dict"],
"set_gates_dict": model_params["set_gates_dict"],
"set_gates": set_gates,
"exit_gates": model_params["exit_gates"]
}
ukf_params["fx_kwargs_update"] = fx3_kwargs_updater
ukf_params["hx"] = hx3_1
ukf_params["hx_kwargs"] = {}
ukf_params["obs_key_func"] = obs_key_func
ukf_params["file_name"] = ex3_pickle_name(n)
return model_params, ukf_params, base_model
"""
a - alpha between 1 and 1e-4 typically determines spread of sigma points.
however for large dimensions may need to be even higher
b - beta set to 2 for gaussian. determines trust in prior distribution.
k - kappa usually 0 for state estimation and 3-dim(state) for parameters.
not 100% sure what kappa does. think its a bias parameter.
!! might be worth making an interactive notebook that varies these. for fun
"""
ukf_params = {
"a": 1,
"b": 2,
"k": 0,
}
base_model = Model(**model_params)
u = ukf_ss(model_params, filter_params, ukf_params, base_model)
u.init_ukf(ukf_params)
#%%
def state_test(u):
"""Make sure the ukf state is still in tact.
"""
"check an array of correct size"
assert type(u.ukf.x) == np.ndarray
assert np.shape(u.ukf.x) == (model_params["pop_total"] * 2, )
"check all agents within boundaries"
"""
def __init__(self):
pass
def test_Sigmas(self):
pass
def test_Unscented_Mean(self):
pass
def test_Covariance(self):
pass
class Test_ex1(object):
"""tests for 1st ukf experiment module
"""
def __init__(self, model):
pass
if __name__ == "__main__":
start_model = Model(**model_params)
macros = Test_macros(start_model, 8**8, default_model_params,
default_ukf_params)