def test_optimize_imports(self):
from neurolib.optimize.evolution import Evolution
evolution = Evolution(evalFunction=(lambda f: f), parameterSpace=self.pars)
from neurolib.optimize.exploration import BoxSearch
search = BoxSearch(evalFunction=(lambda f: f), parameterSpace=self.pars)
def setUpClass(cls):
ds = Dataset("hcp")
model = FHNModel(Cmat=ds.Cmat, Dmat=ds.Dmat)
model.params.duration = 10 * 1000 # ms
model.params.dt = 0.05
model.params.bold = True
parameters = ParameterSpace(
{
"x_ext": [
np.ones((model.params["N"], )) * a
for a in np.linspace(0, 2, 2)
],
"K_gl":
np.linspace(0, 2, 2),
"coupling": ["additive", "diffusive"],
},
kind="grid",
)
search = BoxSearch(
model=model,
parameterSpace=parameters,
filename=f"test_exploration_utils_{randomString(20)}.hdf")
search.run(chunkwise=True, bold=True)
search.loadResults()
# flatten x_ext parameter
search.dfResults.x_ext = [a[0] for a in list(search.dfResults.x_ext)]
cls.model = model
cls.search = search
cls.ds = ds
def setUpClass(cls):
# def test_brain_network_postprocessing(self):
ds = Dataset("hcp")
model = ALNModel(Cmat=ds.Cmat, Dmat=ds.Dmat)
# Resting state fits
model.params["mue_ext_mean"] = 1.57
model.params["mui_ext_mean"] = 1.6
model.params["sigma_ou"] = 0.09
model.params["b"] = 5.0
model.params["signalV"] = 2
model.params["dt"] = 0.2
model.params["duration"] = 0.2 * 60 * 1000
# multi stage evaluation function
def evaluateSimulation(traj):
model = search.getModelFromTraj(traj)
model.randomICs()
model.params["dt"] = 0.2
model.params["duration"] = 4 * 1000.0
model.run(bold=True)
result_dict = {"outputs": model.outputs}
search.saveToPypet(result_dict, traj)
# define and run exploration
parameters = ParameterSpace({
"mue_ext_mean": np.linspace(0, 3, 2),
"mui_ext_mean": np.linspace(0, 3, 2)
})
search = BoxSearch(
evalFunction=evaluateSimulation,
model=model,
parameterSpace=parameters,
filename=f"test_brain_postprocessing_{randomString(20)}.hdf",
)
search.run()
cls.model = model
cls.search = search
cls.ds = ds
def setUpClass(cls):
ds = Dataset("hcp")
model = ALNModel(Cmat=ds.Cmat, Dmat=ds.Dmat)
model.params.duration = 11 * 1000 # ms
model.params.dt = 0.2
parameters = ParameterSpace(
{
"mue_ext_mean": np.linspace(0, 3, 2),
"mui_ext_mean": np.linspace(0, 3, 2),
"b": [0.0, 10.0],
},
kind="grid",
)
search = BoxSearch(
model=model,
parameterSpace=parameters,
filename=f"test_exploration_utils_{randomString(20)}.hdf")
search.run(chunkwise=True, bold=True)
search.loadResults()
cls.model = model
cls.search = search
cls.ds = ds
def test_multimodel_explore(self):
start = time.time()
DELAY = 13.0
fhn_net = FitzHughNagumoNetwork(np.random.rand(2, 2), np.array([[0.0, DELAY], [DELAY, 0.0]]))
model = MultiModel(fhn_net)
parameters = ParameterSpace({"*noise*sigma": [0.0, 0.05], "*epsilon*": [0.5, 0.6]}, allow_star_notation=True)
search = BoxSearch(model, parameters, filename="test_multimodel.hdf")
search.run()
search.loadResults()
dataarray = search.xr()
self.assertTrue(isinstance(dataarray, xr.DataArray))
self.assertTrue(isinstance(dataarray.attrs, dict))
self.assertListEqual(list(dataarray.attrs.keys()), list(parameters.dict().keys()))
end = time.time()
logging.info("\t > Done in {:.2f} s".format(end - start))
def test_single_node(self):
logging.info("\t > BoxSearch: Testing ALN single node ...")
start = time.time()
aln = ALNModel()
parameters = {
"mue_ext_mean": np.linspace(0, 3, 2).tolist(),
"mui_ext_mean": np.linspace(0, 3, 2).tolist()
}
search = BoxSearch(aln, parameters)
search.initializeExploration()
search.run()
search.loadResults()
for i in search.dfResults.index:
search.dfResults.loc[i, "max_r"] = np.max(
search.results[i]["rates_exc"][:,
-int(1000 / aln.params["dt"]):])
end = time.time()
logging.info("\t > Done in {:.2f} s".format(end - start))
def test_single_node(self):
start = time.time()
model = ALNModel()
parameters = ParameterSpace({"mue_ext_mean": np.linspace(0, 3, 2), "mui_ext_mean": np.linspace(0, 3, 2)})
search = BoxSearch(model, parameters, filename="test_single_nodes.hdf")
search.run()
search.loadResults()
dataarray = search.xr()
self.assertTrue(isinstance(dataarray, xr.DataArray))
self.assertFalse(dataarray.attrs)
for i in search.dfResults.index:
search.dfResults.loc[i, "max_r"] = np.max(
search.results[i]["rates_exc"][:, -int(1000 / model.params["dt"]) :]
)
end = time.time()
logging.info("\t > Done in {:.2f} s".format(end - start))
def test_circle_exploration(self):
def explore_me(traj):
pars = search.getParametersFromTraj(traj)
# let's calculate the distance to a circle
computation_result = abs((pars["x"] ** 2 + pars["y"] ** 2) - 1)
result_dict = {"distance": computation_result}
search.saveOutputsToPypet(result_dict, traj)
parameters = ParameterSpace({"x": np.linspace(-2, 2, 2), "y": np.linspace(-2, 2, 2)})
search = BoxSearch(evalFunction=explore_me, parameterSpace=parameters, filename="test_circle_exploration.hdf")
search.run()
search.loadResults(pypetShortNames=False)
for i in search.dfResults.index:
search.dfResults.loc[i, "distance"] = search.results[i]["distance"]
search.dfResults
def test_circle_exploration(self):
def explore_me(traj):
pars = search.getParametersFromTraj(traj)
# let's calculate the distance to a circle
computation_result = abs((pars["x"] ** 2 + pars["y"] ** 2) - 1)
result_dict = {"scalar_result": computation_result, "list_result": [1, 2, 3, 4], "array_result": np.ones(3)}
search.saveToPypet(result_dict, traj)
parameters = ParameterSpace({"x": np.linspace(-2, 2, 2), "y": np.linspace(-2, 2, 2)})
search = BoxSearch(evalFunction=explore_me, parameterSpace=parameters, filename="test_circle_exploration.hdf")
search.run()
search.loadResults(pypetShortNames=False)
# call the result dataframe
search.dfResults
# test integrity of dataframe
for i in search.dfResults.index:
self.assertEqual(search.dfResults.loc[i, "scalar_result"], search.results[i]["scalar_result"])
self.assertListEqual(search.dfResults.loc[i, "list_result"], search.results[i]["list_result"])
np.testing.assert_array_equal(search.dfResults.loc[i, "array_result"], search.results[i]["array_result"])
def test_fhn_brain_network_exploration(self):
ds = Dataset("hcp")
model = FHNModel(Cmat=ds.Cmat, Dmat=ds.Dmat)
model.params.duration = 10 * 1000 # ms
model.params.dt = 0.2
model.params.bold = True
parameters = ParameterSpace(
{
"x_ext": [np.ones((model.params["N"],)) * a for a in np.linspace(0, 2, 2)],
"K_gl": np.linspace(0, 2, 2),
"coupling": ["additive", "diffusive"],
},
kind="grid",
)
search = BoxSearch(model=model, parameterSpace=parameters, filename="test_fhn_brain_network_exploration.hdf")
search.run(chunkwise=True, bold=True)
pu.getTrajectorynamesInFile(os.path.join(paths.HDF_DIR, "test_fhn_brain_network_exploration.hdf"))
search.loadDfResults()
search.getRun(0, pypetShortNames=True)
search.getRun(0, pypetShortNames=False)
search.loadResults()
def test_brain_network(self):
from neurolib.utils.loadData import Dataset
ds = Dataset("hcp")
aln = ALNModel(Cmat=ds.Cmat, Dmat=ds.Dmat, bold=True)
# Resting state fits
aln.params["mue_ext_mean"] = 1.57
aln.params["mui_ext_mean"] = 1.6
aln.params["sigma_ou"] = 0.09
aln.params["b"] = 5.0
aln.params["signalV"] = 2
aln.params["dt"] = 0.2
aln.params["duration"] = 0.2 * 60 * 1000
# multi stage evaluation function
def evaluateSimulation(traj):
model = search.getModelFromTraj(traj)
defaultDuration = model.params["duration"]
invalid_result = {"fc": [0] * len(ds.BOLDs)}
# -------- stage wise simulation --------
# Stage 1 : simulate for a few seconds to see if there is any activity
# ---------------------------------------
model.params["dt"] = 0.1
model.params["duration"] = 3 * 1000.0
model.run()
# check if stage 1 was successful
if np.max(model.rates_exc[:, model.t > 500]) > 300 or np.max(
model.rates_exc[:, model.t > 500]) < 10:
search.saveOutputsToPypet(invalid_result, traj)
return invalid_result, {}
# Stage 2: simulate BOLD for a few seconds to see if it moves
# ---------------------------------------
model.params["dt"] = 0.2
model.params["duration"] = 20 * 1000.0
model.run(bold=True)
if np.std(model.BOLD.BOLD[:, 5:10]) < 0.001:
search.saveOutputsToPypet(invalid_result, traj)
return invalid_result, {}
# Stage 3: full and final simulation
# ---------------------------------------
model.params["dt"] = 0.2
model.params["duration"] = defaultDuration
model.run()
# -------- evaluation here --------
scores = []
for i, fc in enumerate(ds.FCs): # range(len(ds.FCs)):
fc_score = func.matrix_correlation(
func.fc(model.BOLD.BOLD[:, 5:]), fc)
scores.append(fc_score)
meanScore = np.mean(scores)
result_dict = {"fc": meanScore}
search.saveOutputsToPypet(result_dict, traj)
# define and run exploration
parameters = ParameterSpace({
"mue_ext_mean": np.linspace(0, 3, 2),
"mui_ext_mean": np.linspace(0, 3, 2)
})
search = BoxSearch(evalFunction=evaluateSimulation,
model=aln,
parameterSpace=parameters)
search.run()
def param_search(model, parameters, fname='scz_sleep.hdf', run=True):
def evaluateSimulation(traj):
model = search.getModelFromTraj(traj)
# initiate the model with random initial contitions
model.randomICs()
if hasattr(model, "model.j_values_list"):
jei = model.params["Jei_max"]
jie = model.params["Jie_max"]
jii = model.params["Jii_max"]
if [jie, jei, jii] not in model.j_values_list:
result = {
"max_output": np.nan,
"max_amp_output": np.nan,
"domfr": np.nan,
"up_down_difference": np.nan,
"normalized_down_lengths": np.nan,
"normalized_down_lengths_mean": np.nan,
"normalized_up_lengths_mean": np.nan,
"n_local_waves": np.nan,
"perc_local_waves": np.nan,
"n_global_waves": np.nan,
"all_SWS": np.nan,
"SWS_per_min": np.nan,
"local_waves_isi": np.nan,
"global_waves_isi": np.nan,
"frontal_normalized_down_lengths": np.nan,
"frontal_normalized_down_lengths_mean": np.nan,
"frontalnormalized_up_lengths_mean": np.nan,
"frontal_n_local_waves": np.nan,
"frontal_perc_local_waves": np.nan,
"frontal_all_SWS": np.nan,
"frontal_SWS_per_min": np.nan,
"frontal_n_global_waves": np.nan,
"frontal_local_waves_isi": np.nan,
"frontal_global_waves_isi": np.nan
}
search.saveToPypet(result, traj)
return
defaultDuration = model.params['duration']
# -------- stage wise simulation --------
# Stage 3: full and final simulation
# ---------------------------------------
model.params['duration'] = defaultDuration
rect_stimulus = construct_stimulus(stim="rect",
duration=model.params.duration,
dt=model.params.dt)
model.params['ext_exc_current'] = rect_stimulus * 5.0
model.run()
# up down difference
state_length = 2000
# last_state = (model.t > defaultDuration - state_length)
# time period in ms where we expect the down-state
down_window = ((defaultDuration / 2 - state_length < model.t)
& (model.t < defaultDuration / 2))
# and up state
up_window = ((defaultDuration - state_length < model.t)
& (model.t < defaultDuration))
up_state_rate = np.mean(model.output[:, up_window], axis=1)
down_state_rate = np.mean(model.output[:, down_window], axis=1)
up_down_difference = np.max(up_state_rate - down_state_rate)
# check rates!
max_amp_output = np.max(
np.max(model.output[:, up_window], axis=1) -
np.min(model.output[:, up_window], axis=1))
max_output = np.max(model.output[:, up_window])
model_frs, model_pwrs = func.getMeanPowerSpectrum(
model.output, dt=model.params.dt, maxfr=40, spectrum_windowsize=10)
model_frs, model_pwrs = func.getMeanPowerSpectrum(
model.output[:, up_window],
dt=model.params.dt,
maxfr=40,
spectrum_windowsize=5)
domfr = model_frs[np.argmax(model_pwrs)]
# -------- SWS analysis all nodes --------
(normalized_down_lengths, n_local_waves, n_global_waves,
loca_waves_isi, global_waves_isi) = sws_analysis(model.output, model)
# -------- SWS analysis frontal nodes --------
frontal_lobe_nodes = [i - 1 for i in CORTICAL_REGIONS["frontal_lobe"]]
(frontal_normalized_down_lengths, frontal_n_local_waves,
frontal_n_global_waves, frontal_loca_waves_isi,
frontal_global_waves_isi) = sws_analysis(
model.output[frontal_lobe_nodes, :], model)
result = {
"max_output":
max_output,
"max_amp_output":
max_amp_output,
"domfr":
domfr,
"up_down_difference":
up_down_difference,
"normalized_down_lengths":
normalized_down_lengths,
"normalized_down_lengths_mean":
np.mean(normalized_down_lengths),
"normalized_up_lengths_mean":
100 - np.mean(normalized_down_lengths),
"n_local_waves":
n_local_waves,
"perc_local_waves":
(n_local_waves * 100 / (n_local_waves + n_global_waves + 1)),
"n_global_waves":
n_global_waves,
"all_SWS":
n_local_waves + n_global_waves,
"SWS_per_min": (n_local_waves + n_global_waves) * 3,
"local_waves_isi":
np.mean(loca_waves_isi),
"global_waves_isi":
np.mean(global_waves_isi),
"frontal_normalized_down_lengths":
frontal_normalized_down_lengths,
"frontal_normalized_down_lengths_mean":
np.mean(frontal_normalized_down_lengths),
"frontalnormalized_up_lengths_mean":
100 - np.mean(frontal_normalized_down_lengths),
"frontal_n_local_waves":
frontal_n_local_waves,
"frontal_perc_local_waves":
(frontal_n_local_waves * 100 /
(frontal_n_local_waves + frontal_n_global_waves + 1)),
"frontal_all_SWS":
frontal_n_local_waves + frontal_n_global_waves,
"frontal_SWS_per_min":
(frontal_n_local_waves + frontal_n_global_waves) * 3,
"frontal_n_global_waves":
frontal_n_global_waves,
"frontal_local_waves_isi":
np.mean(frontal_loca_waves_isi),
"frontal_global_waves_isi":
np.mean(frontal_global_waves_isi)
}
search.saveToPypet(result, traj)
return
search = BoxSearch(evalFunction=evaluateSimulation,
model=model,
parameterSpace=parameters,
filename=fname)
if run:
search.run()
return search
