def pse_from_hypothesis(hypothesis,
model_connectivity,
region_labels,
n_samples,
param_range=0.1,
global_coupling=[],
healthy_regions_parameters=[],
save_flag=False,
folder_res=OutputConfig().FOLDER_RES,
filename=None,
**kwargs):
logger = initialize_logger(__name__)
logger.info("Running hypothesis: " + hypothesis.name)
# Compute lsa for this hypothesis before the parameter search:
model_configuration_builder, model_configuration, lsa_service, lsa_hypothesis = \
start_lsa_run(hypothesis, model_connectivity)
pse_results, pse_params_list = pse_from_lsa_hypothesis(
lsa_hypothesis,
model_connectivity,
region_labels,
n_samples,
param_range,
global_coupling,
healthy_regions_parameters,
model_configuration_builder,
lsa_service,
save_flag,
folder_res=folder_res,
filename=filename,
logger=logger,
**kwargs)
return model_configuration, lsa_service, lsa_hypothesis, pse_results, pse_params_list
def main_pse(config=Config()):
# -------------------------------Reading data-----------------------------------
reader = Reader()
writer = H5Writer()
head = reader.read_head(config.input.HEAD)
logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
# --------------------------Manual Hypothesis definition-----------------------------------
n_samples = 100
x0_indices = [20]
x0_values = [0.9]
e_indices = [70]
e_values = [0.9]
disease_indices = x0_indices + e_indices
n_disease = len(disease_indices)
n_x0 = len(x0_indices)
n_e = len(e_indices)
all_regions_indices = np.array(range(head.number_of_regions))
healthy_indices = np.delete(all_regions_indices, disease_indices).tolist()
n_healthy = len(healthy_indices)
# This is an example of x0_values mixed Excitability and Epileptogenicity Hypothesis:
hyp_x0_E = HypothesisBuilder(
head.connectivity.number_of_regions).set_x0_hypothesis(
x0_indices,
x0_values).set_e_hypothesis(e_indices,
e_values).build_hypothesis()
# Now running the parameter search analysis:
logger.info("running PSE LSA...")
model_config, lsa_service, lsa_hypothesis, pse_res = pse_from_hypothesis(
hyp_x0_E,
head.connectivity.normalized_weights,
head.connectivity.region_labels,
n_samples,
param_range=0.1,
global_coupling=[{
"indices": all_regions_indices
}],
healthy_regions_parameters=[{
"name": "x0_values",
"indices": healthy_indices
}],
save_services=True)[:4]
logger.info("Plotting LSA...")
Plotter(config).plot_lsa(lsa_hypothesis,
model_config,
lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number,
region_labels=head.connectivity.region_labels,
pse_results=pse_res,
lsa_service=lsa_service)
logger.info("Saving LSA results ...")
writer.write_dictionary(
pse_res,
os.path.join(config.out.FOLDER_RES,
lsa_hypothesis.name + "_PSE_LSA_results.h5"))
def parse_csv(fname, merge=True):
if '*' in fname:
import glob
return parse_csv(glob.glob(fname), merge=merge)
if isinstance(fname, (list, tuple)):
csv = [parse_csv(_) for _ in fname]
if merge:
csv = merge_csv_data(*csv)
return csv
lines = []
with open(fname, 'r') as fd:
for line in fd.readlines():
if not line.startswith('#'):
lines.append(line.strip().split(','))
names = [field.split('.') for field in lines[0]]
data = []
for id_line, line in enumerate(lines[1:]):
append_data = True
for iline in range(len(line)):
try:
line[iline] = float(line[iline])
except:
logger = initialize_logger(__name__)
logger.warn("Failed to convert string " + line[iline] +
" to float!" + "\nSkipping line " + str(id_line) +
": " + str(line) + "!")
append_data = False
break
if append_data:
data.append(line)
data = np.array(data)
namemap = {}
maxdims = {}
for i, name in enumerate(names):
if name[0] not in namemap:
namemap[name[0]] = []
namemap[name[0]].append(i)
if len(name) > 1:
maxdims[name[0]] = name[1:]
for name in maxdims.keys():
dims = []
for dim in maxdims[name]:
dims.append(int(dim))
maxdims[name] = tuple(reversed(dims))
# data in linear order per Stan, e.g. mat is col maj
# TODO array is row maj, how to distinguish matrix vs array[,]?
data_ = {}
for name, idx in namemap.items():
new_shape = (-1, ) + maxdims.get(name, ())
data_[name] = data[:, idx].reshape(new_shape)
return data_
def read_edf(path,
sensors,
rois_selection=None,
label_strip_fun=None,
time_units="ms"):
logger = initialize_logger(__name__)
logger.info("Reading empirical dataset from mne file...")
raw_data = read_raw_edf(path, preload=True)
if not callable(label_strip_fun):
label_strip_fun = lambda label: label
rois = []
rois_inds = []
rois_lbls = []
if len(rois_selection) == 0:
rois_selection = sensors.labels
logger.info("Selecting target signals from dataset...")
for iR, s in enumerate(raw_data.ch_names):
this_label = label_strip_fun(s)
this_index = sensors.get_sensors_inds_by_sensors_labels(this_label)
if this_label in rois_selection or (len(this_index) == 1 and
this_index[0] in rois_selection):
rois.append(iR)
rois_inds.append(this_index[0])
rois_lbls.append(this_label)
data, times = raw_data[:, :]
data = data[rois].T
# Assuming that edf file time units is "sec"
if ensure_string(time_units).find("ms") == 0:
times = 1000 * times
sort_inds = np.argsort(rois_lbls)
rois = np.array(rois)[sort_inds]
rois_inds = np.array(rois_inds)[sort_inds]
rois_lbls = np.array(rois_lbls)[sort_inds]
data = data[:, sort_inds]
return data, times, rois, rois_inds, rois_lbls
def sensitivity_analysis_pse_from_hypothesis(n_samples,
hypothesis,
connectivity_matrix,
region_labels,
method="sobol",
half_range=0.1,
global_coupling=[],
healthy_regions_parameters=[],
save_services=False,
config=Config(),
model_config_kwargs={},
**kwargs):
logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
# Compute lsa for this hypothesis before sensitivity analysis:
logger.info("Running hypothesis: " + hypothesis.name)
model_configuration_builder, model_configuration, lsa_service, lsa_hypothesis = \
start_lsa_run(hypothesis, connectivity_matrix, config, **model_config_kwargs)
results, pse_results = sensitivity_analysis_pse_from_lsa_hypothesis(
n_samples, lsa_hypothesis, connectivity_matrix,
model_configuration_builder, lsa_service, region_labels, method,
half_range, global_coupling, healthy_regions_parameters, save_services,
config, **kwargs)
return model_configuration_builder, model_configuration, lsa_service, lsa_hypothesis, results, pse_results
def __init__(self, number_of_regions=0, config=Config()):
self.config = config
self.logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
self.number_of_regions = number_of_regions
self.diseased_regions_values = numpy.zeros((self.number_of_regions,))
class ModelInversionService(object):
logger = initialize_logger(__name__)
active_regions_selection_methods = ["E", "LSA"]
active_e_th = 0.1
active_x0_th = 0.1
active_lsa_th = None
def __init__(self):
self.logger.info("Model Inversion Service instance created!")
def _repr(self, d=OrderedDict()):
for ikey, (key, val) in enumerate(self.__dict__.iteritems()):
d.update({key: val})
return d
def __repr__(self, d=OrderedDict()):
return formal_repr(self, self._repr(d))
def __str__(self):
return self.__repr__()
def update_active_regions_e_values(self,
probabilistic_model,
e_values,
reset=False):
if reset:
probabilistic_model.update_active_regions([])
if len(e_values) > 0:
probabilistic_model.update_active_regions(
probabilistic_model.active_regions +
select_greater_values_array_inds(e_values,
self.active_e_th).tolist())
else:
warning(
"Skipping active regions setting by E values because no such values were provided!"
)
return probabilistic_model
def update_active_regions_x0_values(self,
probabilistic_model,
x0_values,
reset=False):
if reset:
probabilistic_model.update_active_regions([])
if len(x0_values) > 0:
probabilistic_model.update_active_regions(
probabilistic_model.active_regions +
select_greater_values_array_inds(x0_values,
self.active_x0_th).tolist())
else:
warning(
"Skipping active regions setting by x0 values because no such values were provided!"
)
return probabilistic_model
def update_active_regions_lsa(self,
probabilistic_model,
lsa_propagation_strengths,
reset=False):
if reset:
probabilistic_model.update_active_regions([])
if len(lsa_propagation_strengths) > 0:
ps_strengths = lsa_propagation_strengths / np.max(
lsa_propagation_strengths)
probabilistic_model.update_active_regions(
probabilistic_model.active_regions +
select_greater_values_array_inds(ps_strengths,
self.active_lsa_th).tolist())
else:
self.logger.warning(
"No LSA results found (empty propagations_strengths vector)!" +
"\nSkipping of setting active regions according to LSA!")
return probabilistic_model
def update_active_regions(self,
probabilistic_model,
e_values=[],
x0_values=[],
lsa_propagation_strengths=[],
reset=False):
if reset:
probabilistic_model.update_active_regions([])
for m in ensure_list(self.active_regions_selection_methods):
if isequal_string(m, "E"):
probabilistic_model = self.update_active_regions_e_values(
probabilistic_model, e_values, reset=False)
elif isequal_string(m, "x0"):
probabilistic_model = self.update_active_regions_x0_values(
probabilistic_model, x0_values, reset=False)
elif isequal_string(m, "LSA"):
probabilistic_model = self.update_active_regions_lsa(
probabilistic_model,
lsa_propagation_strengths,
reset=False)
return probabilistic_model
class SimulatorBuilder(object):
logger = initialize_logger(__name__)
simulator = "tvb"
model_name = "EpileptorDP"
simulated_period = 2000
fs = 16384.0
fs_monitor = 1024.0
def __init__(self, simulator="tvb"):
self.simulator = simulator
def set_model_name(self, model_name):
# TODO: check that model_name is one of the available ones
if model_name not in AVAILABLE_DYNAMICAL_MODELS_NAMES:
raise_value_error(model_name +
" is not one of the available models: \n" +
str(AVAILABLE_DYNAMICAL_MODELS_NAMES) + " !")
self.model_name = model_name
return self
def set_simulated_period(self, simulated_period):
self.simulated_period = simulated_period
return self
def set_fs(self, fs):
self.fs = fs
return self
def set_fs_monitor(self, fs_monitor):
self.fs_monitor = fs_monitor
return self
def set_time_scales(self):
scale_fsavg = int(numpy.round(self.fs / self.fs_monitor))
dt = 1000.0 / self.fs
monitor_period = scale_fsavg * dt
return dt, monitor_period
def generate_model(self, model_configuration):
if isequal_string(self.model_name,
EpileptorModel._ui_name) and not isequal_string(
self.simulator, "java"):
raise_value_error(
"Custom EpileptorModel can be used only with java simulator!")
elif not isequal_string(self.model_name,
EpileptorModel._ui_name) and isequal_string(
self.simulator, "java"):
raise_value_error(
"Only java EpileptorModel can be used with java simulator!")
return model_build_dict[self.model_name](model_configuration)
def _check_noise_intesity_size(self, noise_intensity):
nn = len(ensure_list(noise_intensity))
if nn != 1 and nn != EPILEPTOR_MODEL_NVARS[self.model_name]:
raise_value_error(
"Noise intensity is neither of size 1 nor of size equal to the number of model variables, "
"\n but of size: " + str(nn) + "!")
def generate_white_noise(self, noise_intensity):
self._check_noise_intesity_size(noise_intensity)
noise_instance = noise.Additive(
nsig=noise_intensity,
random_stream=numpy.random.RandomState(seed=NOISE_SEED))
noise_instance.configure_white(dt=1.0 / self.fs)
return noise_instance
def generate_colored_noise(self, noise_intensity, ntau, **kwargs):
self._check_noise_intesity_size(noise_intensity)
eq = equations.Linear(parameters=kwargs.get("parameters", {
"a": 1.0,
"b": 0.0
}))
noise_instance = noise.Multiplicative(
ntau=ntau,
nsig=noise_intensity,
b=eq,
random_stream=numpy.random.RandomState(seed=NOISE_SEED))
noise_shape = noise_instance.nsig.shape
noise_instance.configure_coloured(dt=1.0 / self.fs, shape=noise_shape)
return noise_instance
def build_sim_settings(self):
dt, monitor_period = self.set_time_scales()
return SimulationSettings(
simulated_period=self.simulated_period,
integration_step=dt,
noise_type=WHITE_NOISE,
noise_ntau=0.0,
noise_seed=NOISE_SEED,
noise_intensity=model_noise_intensity_dict[self.model_name],
monitor_sampling_period=monitor_period,
monitor_expressions=VOIS[self.model_name])
def set_noise(self, sim_settings, **kwargs):
# Check if the user provides a preconfigured noise instance to override
noise = kwargs.get("noise", None)
if isinstance(noise, Noise):
self._check_noise_intesity_size(noise.nsig)
sim_settings.noise_intensity = noise.nsig
if isinstance(noise, Additive):
sim_settings.noise_type = WHITE_NOISE
elif isinstance(noise, Multiplicative):
sim_settings.noise_type = COLORED_NOISE
sim_settings.noise_ntau = noise.ntau
else:
if isequal_string(sim_settings.noise_type, COLORED_NOISE):
noise = self.generate_colored_noise(
sim_settings.noise_intensity, sim_settings.noise_ntau,
**kwargs)
else:
noise = self.generate_white_noise(sim_settings.noise_intensity)
sim_settings.noise_ntau = noise.ntau
return noise, sim_settings
def generate_temporal_average_monitor(self, monitor_sampling_period):
monitor = TemporalAverage()
monitor.period = monitor_sampling_period
return monitor
def set_monitor(self, model, sim_settings, monitors=None):
model.variables_of_interest = [
me.replace('lfp', 'x2 - x1')
for me in sim_settings.monitor_expressions
]
# Check if the user provides a preconfigured set of monitor instances to override
if isinstance(monitors, Monitor):
monitors = (monitors, )
sim_settings.monitor_sampling_period = monitors.period
elif isinstance(monitors, tuple) or isinstance(monitors, list):
what_to_watch = []
sim_settings.monitor_sampling_period = []
for monitor in monitors:
if isinstance(monitor, Monitor):
what_to_watch.append(monitor)
sim_settings.monitor_sampling_period.append(monitor.period)
what_to_watch = tuple(what_to_watch)
monitors = what_to_watch
else:
monitors = (self.generate_temporal_average_monitor(
sim_settings.monitor_sampling_period), )
return model, monitors, sim_settings
def build_simulator_TVB_from_model_sim_settings(self, model_configuration,
connectivity, model,
sim_settings, **kwargs):
model, monitors, sim_settings = self.set_monitor(
model, sim_settings, kwargs.get("monitors", None))
noise, sim_settings = self.set_noise(sim_settings, **kwargs)
simulator_instance = SimulatorTVB(connectivity, model_configuration,
model, sim_settings)
simulator_instance.config_simulation(noise,
monitors,
initial_conditions=None)
return simulator_instance, sim_settings, model
def build_simulator_TVB(self, model_configuration, connectivity, **kwargs):
model = self.generate_model(model_configuration)
sim_settings = self.build_sim_settings()
return self.build_simulator_TVB_from_model_sim_settings(
model_configuration, connectivity, model, sim_settings, **kwargs)
def build_simulator_java_from_model_configuration(self,
model_configuration,
connectivity, **kwargs):
self.set_model_name("EpileptorModel")
model = java_model_builder(model_configuration)
sim_settings = self.build_sim_settings()
sim_settings.noise_intensity = kwargs.get("noise_intensity", 1e-6)
simulator_instance = SimulatorJava(connectivity, model_configuration,
model, sim_settings)
return simulator_instance, sim_settings, model
def build_simulator(self, model_configuration, connectivity, **kwargs):
if isequal_string(self.simulator, "java"):
return self.build_simulator_java_from_model_configuration(
model_configuration, connectivity, **kwargs)
else:
return self.build_simulator_TVB(model_configuration, connectivity,
**kwargs)
class ABCPSEService(object):
__metaclass__ = ABCMeta
logger = initialize_logger(__name__)
def __init__(self):
self.params_vals = []
self.params_paths = []
self.params_indices = []
self.params_names = []
self.n_params_vals = []
self.n_params = 0
def run_pse(self, conn_matrix, grid_mode=False, *kwargs):
results = []
execution_status = []
loop_tenth = 1
for iloop in range(self.n_loops):
params = self.params_vals[iloop]
if iloop == 0 or iloop + 1 >= loop_tenth * self.n_loops / 10.0:
print "\nExecuting loop " + str(iloop + 1) + " of " + str(
self.n_loops)
if iloop > 0:
loop_tenth += 1
status = False
output = None
# try:
status, output = self.run(params, conn_matrix, *kwargs)
# except:
# pass
# if not status:
# self.logger.warning("\nExecution of loop " + str(iloop) + " failed!")
results.append(output)
execution_status.append(status)
if grid_mode:
results = np.reshape(np.array(results, dtype="O"),
tuple(self.n_params_vals))
execution_status = np.reshape(np.array(execution_status),
tuple(self.n_params_vals))
return results, execution_status
@abstractmethod
def run_pse_parallel(self):
# TODO: start each loop on a separate process, gather results and return them
pass
@abstractmethod
def run(self, *kwargs):
pass
@abstractmethod
def prepare_run_results(self, *kwargs):
pass
def prepare_params(self, params_pse):
if isinstance(params_pse, list):
temp = []
for param in params_pse:
self.params_paths.append(param["path"])
temp2 = param["samples"].flatten()
temp.append(temp2)
self.n_params_vals.append(temp2.size)
indices = param.get("indices", [])
self.params_indices.append(indices)
self.params_names.append(
param.get("name",
param["path"].rsplit('.', 1)[-1] + str(indices)))
self.n_params_vals = np.array(self.n_params_vals)
self.n_params = len(self.params_paths)
if not (np.all(self.n_params_vals == self.n_params_vals[0])):
raise_value_error(
"\nNot all parameters have the same number of samples!: " +
"\n" + str(self.params_paths) + " = " +
str(self.n_params_vals))
else:
self.n_params_vals = self.n_params_vals[0]
self.params_vals = np.vstack(temp).T
self.params_paths = np.array(self.params_paths)
self.params_indices = np.array(self.params_indices)
self.n_loops = self.params_vals.shape[0]
print "\nGenerated a parameter search exploration for " + str(
"lsa/sim task") + ","
print "with " + str(self.n_params) + " parameters of " + str(
self.n_params_vals) + " values each,"
print "leading to " + str(self.n_loops) + " total execution loops"
else:
self.logger.warning("\nparams_pse is not a list of tuples!")
def update_hypo_model_config(
self,
hypothesis,
params,
conn_matrix,
model_config_service_input=None,
yc=YC_DEF,
Iext1=I_EXT1_DEF,
K=K_DEF,
a=A_DEF,
b=B_DEF,
tau1=TAU1_DEF,
tau0=TAU0_DEF,
x1eq_mode="optimize",
):
# Copy and update hypothesis
hypo_copy = deepcopy(hypothesis)
hypo_copy.update_for_pse(params, self.params_paths,
self.params_indices)
# Create a ModelConfigService and update it
if isinstance(model_config_service_input, ModelConfigurationBuilder):
model_configuration_builder = deepcopy(model_config_service_input)
else:
model_configuration_builder = ModelConfigurationBuilder(
hypo_copy.number_of_regions,
yc=yc,
Iext1=Iext1,
K=K,
a=a,
b=b,
tau1=tau1,
tau0=tau0,
x1eq_mode=x1eq_mode)
model_configuration_builder.set_attributes_from_pse(
params, self.params_paths, self.params_indices)
# Obtain Modelconfiguration
if hypo_copy.type == "Epileptogenicity":
model_configuration = model_configuration_builder.build_model_from_E_hypothesis(
hypo_copy, conn_matrix)
else:
model_configuration = model_configuration_builder.build_model_from_hypothesis(
hypo_copy, conn_matrix)
return hypo_copy, model_configuration
def set_object_attribute_recursively(self, object, values, path, indices):
# If there is more than one levels...
if len(path) > 1:
# ...call the function recursively
self.set_object_attribute_recursively(getattr(object, path[0]),
values, path[1:], indices)
else:
# ...else, set the parameter values for the specified indices
temp = getattr(object, path[0])
if len(indices) > 0:
temp[indices] = values # index has to be linear... i.e., 1D...
else:
temp = values
setattr(object, path[0], temp)
def update_object(self, object, params, object_type=None):
if not (isinstance(object_type, basestring)):
object_type = object.__class__.__name__
for i, path in enumerate(self.params_paths):
path = path.split(".")
if path[0] == object_type:
self.set_object_attribute_recursively(object, params[i],
path[1:],
self.params_indices[i])
class SimulatorTVB(ABCSimulator):
"""
This class is used as a Wrapper over the TVB Simulator.
It keeps attributes needed in order to create and configure a TVB Simulator object.
"""
logger = initialize_logger(__name__)
def __init__(self, connectivity, model_configuration, model,
simulation_settings):
self.model = model
self.simulation_settings = simulation_settings
self.model_configuration = model_configuration
self.connectivity = connectivity
@staticmethod
def _vep2tvb_connectivity(vep_conn, model_connectivity=None):
if model_connectivity is None:
model_connectivity = vep_conn.normalized_weights
return connectivity.Connectivity(use_storage=False,
weights=model_connectivity,
tract_lengths=TIME_DELAYS_FLAG *
vep_conn.tract_lengths,
region_labels=vep_conn.region_labels,
centres=vep_conn.centres,
hemispheres=vep_conn.hemispheres,
orientations=vep_conn.orientations,
areas=vep_conn.areas)
def get_vois(self):
# TODO: change 'lfp' for 'source'
return [
me.replace('x2 - x1', 'source')
for me in self.simulation_settings.monitor_expressions
]
def config_simulation(self,
noise,
monitors,
initial_conditions=None,
**kwargs):
if isinstance(self.model_configuration.model_connectivity,
numpy.ndarray):
tvb_connectivity = self._vep2tvb_connectivity(
self.connectivity, self.model_configuration.model_connectivity)
else:
tvb_connectivity = self._vep2tvb_connectivity(self.connectivity)
tvb_coupling = coupling.Difference(a=1.)
integrator = getattr(integrators,
kwargs.get("integrator", "HeunStochastic"))(
dt=self.simulation_settings.integration_step,
noise=noise)
self.simTVB = simulator.Simulator(
model=self.model,
connectivity=tvb_connectivity,
coupling=tvb_coupling,
integrator=integrator,
monitors=monitors,
simulation_length=self.simulation_settings.simulated_period)
self.simTVB.configure()
self.configure_initial_conditions(
initial_conditions=initial_conditions)
def launch_simulation(self, report_every_n_monitor_steps=None):
if report_every_n_monitor_steps >= 1:
time_length_avg = numpy.round(
self.simulation_settings.simulated_period /
self.simTVB.monitors[0].period)
n_report_blocks = max(
report_every_n_monitor_steps *
numpy.round(time_length_avg / 100), 1.0)
else:
n_report_blocks = 1
self.simTVB._configure_history(
initial_conditions=self.simTVB.initial_conditions)
status = True
if n_report_blocks < 2:
try:
tavg_time, tavg_data = self.simTVB.run()[0]
except Exception, error_message:
status = False
self.logger.warning(
"Something went wrong with this simulation...:" + "\n" +
error_message)
return None, None, status
return tavg_time, tavg_data, status
else:
def __init__(self, config=None):
self.config = config or Config()
self.logger = initialize_logger(self.__class__.__name__, self.config.out.FOLDER_LOGS)
class H5Writer(object):
logger = initialize_logger(__name__)
H5_TYPE_ATTRIBUTE = "EPI_Type"
H5_SUBTYPE_ATTRIBUTE = "EPI_Subtype"
# TODO: write variants.
def write_connectivity(self, connectivity, path):
"""
:param connectivity: Connectivity object to be written in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
h5_file.create_dataset(ConnectivityH5Field.WEIGHTS,
data=connectivity.weights)
h5_file.create_dataset(ConnectivityH5Field.TRACTS,
data=connectivity.tract_lengths)
h5_file.create_dataset(ConnectivityH5Field.CENTERS,
data=connectivity.centres)
h5_file.create_dataset(ConnectivityH5Field.REGION_LABELS,
data=connectivity.region_labels)
h5_file.create_dataset(ConnectivityH5Field.ORIENTATIONS,
data=connectivity.orientations)
h5_file.create_dataset(ConnectivityH5Field.HEMISPHERES,
data=connectivity.hemispheres)
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "Connectivity")
h5_file.attrs.create("Number_of_regions",
str(connectivity.number_of_regions))
if connectivity.normalized_weights.size > 0:
dataset = h5_file.create_dataset(
"normalized_weights/" + ConnectivityH5Field.WEIGHTS,
data=connectivity.normalized_weights)
dataset.attrs.create(
"Operations",
"Removing diagonal, normalizing with 95th percentile, and ceiling to it"
)
self.logger.info("Connectivity has been written to file: %s" % path)
h5_file.close()
def write_sensors(self, sensors, path):
"""
:param sensors: Sensors object to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
h5_file.create_dataset(SensorsH5Field.LABELS, data=sensors.labels)
h5_file.create_dataset(SensorsH5Field.LOCATIONS,
data=sensors.locations)
h5_file.create_dataset(SensorsH5Field.NEEDLES, data=sensors.needles)
gain_dataset = h5_file.create_dataset(SensorsH5Field.GAIN_MATRIX,
data=sensors.gain_matrix)
gain_dataset.attrs.create("Max", str(sensors.gain_matrix.max()))
gain_dataset.attrs.create("Min", str(sensors.gain_matrix.min()))
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "Sensors")
h5_file.attrs.create("Number_of_sensors",
str(sensors.number_of_sensors))
h5_file.attrs.create("Sensors_subtype", sensors.s_type)
self.logger.info("Sensors have been written to file: %s" % path)
h5_file.close()
def write_surface(self, surface, path):
"""
:param surface: Surface object to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
h5_file.create_dataset(SurfaceH5Field.VERTICES, data=surface.vertices)
h5_file.create_dataset(SurfaceH5Field.TRIANGLES,
data=surface.triangles)
h5_file.create_dataset(SurfaceH5Field.VERTEX_NORMALS,
data=surface.vertex_normals)
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "Surface")
h5_file.attrs.create("Surface_subtype", surface.surface_subtype)
h5_file.attrs.create("Number_of_triangles", surface.triangles.shape[0])
h5_file.attrs.create("Number_of_vertices", surface.vertices.shape[0])
h5_file.attrs.create(
"Voxel_to_ras_matrix",
str(surface.vox2ras.flatten().tolist())[1:-1].replace(",", ""))
self.logger.info("Surface has been written to file: %s" % path)
h5_file.close()
def write_head(self, head, path):
"""
:param head: Head object to be written
:param path: path to head folder
"""
self.logger.info("Starting to write Head folder: %s" % head)
if not (os.path.isdir(path)):
os.mkdir(path)
self.write_connectivity(head.connectivity,
os.path.join(path, "Connectivity.h5"))
self.write_surface(head.cortical_surface,
os.path.join(path, "CorticalSurface.h5"))
for sensor_list in (head.sensorsSEEG, head.sensorsEEG,
head.sensorsMEG):
for sensors in sensor_list:
self.write_sensors(
sensors,
os.path.join(
path, "Sensors%s_%s.h5" %
(sensors.s_type, sensors.number_of_sensors)))
self.logger.info("Successfully wrote Head folder at: %s" % path)
def write_hypothesis(self, hypothesis, path):
"""
:param hypothesis: DiseaseHypothesis object to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
h5_file.create_dataset("x0_values", data=hypothesis.x0_values)
h5_file.create_dataset("e_values", data=hypothesis.e_values)
h5_file.create_dataset("w_values", data=hypothesis.w_values)
h5_file.create_dataset("lsa_propagation_strengths",
data=hypothesis.lsa_propagation_strengths)
# TODO: change HypothesisModel to GenericModel here and inside Epi
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "HypothesisModel")
h5_file.attrs.create(self.H5_SUBTYPE_ATTRIBUTE,
hypothesis.__class__.__name__)
h5_file.attrs.create("number_of_regions", hypothesis.number_of_regions)
h5_file.attrs.create("type", hypothesis.type)
h5_file.attrs.create("x0_indices", hypothesis.x0_indices)
h5_file.attrs.create("e_indices", hypothesis.e_indices)
h5_file.attrs.create("w_indices", hypothesis.w_indices)
h5_file.attrs.create("lsa_propagation_indices",
hypothesis.lsa_propagation_indices)
h5_file.close()
def write_model_configuration(self, model_configuration, path):
"""
:param model_configuration: ModelConfiguration object to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
datasets_dict, metadata_dict = self._determine_datasets_and_attributes(
model_configuration)
for key, value in datasets_dict.iteritems():
h5_file.create_dataset(key, data=value)
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "HypothesisModel")
h5_file.attrs.create(self.H5_SUBTYPE_ATTRIBUTE,
model_configuration.__class__.__name__)
for key, value in metadata_dict.iteritems():
h5_file.attrs.create(key, value)
h5_file.close()
def write_model_configuration_builder(self, model_configuration_builder,
path):
"""
:param model_configuration_builder: ModelConfigurationService object to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
datasets_dict, metadata_dict = self._determine_datasets_and_attributes(
model_configuration_builder)
for key, value in datasets_dict.iteritems():
h5_file.create_dataset(key, data=value)
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "HypothesisModel")
h5_file.attrs.create(self.H5_SUBTYPE_ATTRIBUTE,
model_configuration_builder.__class__.__name__)
for key, value in metadata_dict.iteritems():
h5_file.attrs.create(key, value)
h5_file.close()
def write_lsa_service(self, lsa_service, path):
"""
:param lsa_service: LSAService object to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
datasets_dict, metadata_dict = self._determine_datasets_and_attributes(
lsa_service)
for key, value in datasets_dict.iteritems():
h5_file.create_dataset(key, data=value)
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "HypothesisModel")
h5_file.attrs.create(self.H5_SUBTYPE_ATTRIBUTE,
lsa_service.__class__.__name__)
for key, value in metadata_dict.iteritems():
h5_file.attrs.create(key, value)
h5_file.close()
def write_model_inversion_service(self, model_inversion_service, path):
"""
:param model_inversion_service: ModelInversionService object to write in H5
:param path: H5 path to be written
"""
if getattr(model_inversion_service, "signals_inds", None) is not None:
model_inversion_service.signals_inds = numpy.array(
model_inversion_service.signals_inds)
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
datasets_dict, metadata_dict = self._determine_datasets_and_attributes(
model_inversion_service)
for key, value in datasets_dict.iteritems():
h5_file.create_dataset(key, data=value)
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "HypothesisModel")
h5_file.attrs.create(self.H5_SUBTYPE_ATTRIBUTE,
model_inversion_service.__class__.__name__)
for key, value in metadata_dict.iteritems():
h5_file.attrs.create(key, value)
h5_file.close()
def write_pse_service(self, pse_service, path):
"""
:param pse_service: PSEService object to write in H5
:param path: H5 path to be written
"""
if "params_vals" not in dir(pse_service):
params_samples = pse_service.pse_params.T
else:
params_samples = pse_service.params_vals
pse_dict = {
"task":
pse_service.task,
"params_names":
pse_service.params_names,
"params_paths":
pse_service.params_paths,
"params_indices":
numpy.array([str(inds) for inds in pse_service.params_indices],
dtype="S"),
"params_samples":
params_samples
}
self.write_dictionary(pse_dict, path)
def write_sensitivity_analysis_service(self, sensitivity_service, path):
"""
:param sensitivity_service: SensitivityAnalysisService object to write in H5
:param path: H5 path to be written
"""
sensitivity_service_dict = {
"method": sensitivity_service.method,
"calc_second_order": sensitivity_service.calc_second_order,
"conf_level": sensitivity_service.conf_level,
"n_inputs": sensitivity_service.n_inputs,
"n_outputs": sensitivity_service.n_outputs,
"input_names": sensitivity_service.input_names,
"output_names": sensitivity_service.output_names,
"input_bounds": sensitivity_service.input_bounds,
}
self.write_dictionary(sensitivity_service_dict, path)
def write_dictionary(self, dictionary, path):
"""
:param dictionary: dictionary to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
for key, value in dictionary.iteritems():
try:
if isinstance(value, numpy.ndarray) and value.size > 0:
h5_file.create_dataset(key, data=value)
else:
if isinstance(value, list) and len(value) > 0:
h5_file.create_dataset(key, data=value)
else:
h5_file.attrs.create(key, value)
except:
self.logger.warning("Did not manage to write " + key +
" to h5 file " + path + " !")
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "HypothesisModel")
h5_file.attrs.create(self.H5_SUBTYPE_ATTRIBUTE,
dictionary.__class__.__name__)
h5_file.close()
# TODO: can this be visualized? should we keep groups?
def write_simulation_settings(self, simulation_settings, path):
"""
:param simulation_settings: SimulationSettings object to write in H5
:param path: H5 path to be written
"""
h5_file = h5py.File(change_filename_or_overwrite(path),
'a',
libver='latest')
datasets_dict, metadata_dict = self._determine_datasets_and_attributes(
simulation_settings)
for key, value in datasets_dict.iteritems():
h5_file.create_dataset(key, data=value)
h5_file.attrs.create(self.H5_TYPE_ATTRIBUTE, "HypothesisModel")
h5_file.attrs.create(self.H5_SUBTYPE_ATTRIBUTE,
simulation_settings.__class__.__name__)
for key, value in metadata_dict.iteritems():
h5_file.attrs.create(key, value)
h5_file.close()
def write_ts_seeg_epi(self, seeg_data, sampling_period, path):
if not os.path.exists(path):
raise_error(
"TS file %s does not exist. First define the raw data!" + path,
self.logger)
return
sensors_name = "SeegSensors-" + str(seeg_data.shape[1])
self.logger.info("Writing a TS at:\n" + path + ", " + sensors_name)
try:
h5_file = h5py.File(path, 'a', libver='latest')
h5_file.create_dataset("/" + sensors_name, data=seeg_data)
write_metadata(
{
KEY_MAX: seeg_data.max(),
KEY_MIN: seeg_data.min(),
KEY_STEPS: seeg_data.shape[0],
KEY_CHANNELS: seeg_data.shape[1],
KEY_SV: 1,
KEY_SAMPLING: sampling_period,
KEY_START: 0.0
}, h5_file, KEY_DATE, KEY_VERSION, "/" + sensors_name)
h5_file.close()
except Exception, e:
raise_error(
e + "\nSeeg dataset already written as " + sensors_name,
self.logger)
class HeadService(object):
logger = initialize_logger(__name__)
def compute_nearest_regions_to_sensors(self, head, sensors=None, target_contacts=None, s_type=Sensors.TYPE_SEEG,
sensors_id=0, n_regions=None, gain_matrix_th=None):
if not (isinstance(sensors, Sensors)):
sensors = head.get_sensors_id(s_type=s_type, sensor_ids=sensors_id)
n_contacts = sensors.labels.shape[0]
if isinstance(target_contacts, (list, tuple, np.ndarray)):
target_contacts = ensure_list(target_contacts)
for itc, tc in enumerate(target_contacts):
if isinstance(tc, int):
continue
elif isinstance(tc, basestring):
target_contacts[itc] = sensors.contact_label_to_index([tc])
else:
raise_value_error("target_contacts[" + str(itc) + "] = " + str(tc) +
"is neither an integer nor a string!")
else:
target_contacts = range(n_contacts)
auto_flag = False
if n_regions is "all":
n_regions = head.connectivity.number_of_regions
elif not (isinstance(n_regions, int)):
auto_flag = True
nearest_regions = []
for tc in target_contacts:
projs = sensors.gain_matrix[tc]
inds = np.argsort(projs)[::-1]
if auto_flag:
n_regions = select_greater_values_array_inds(projs[inds], threshold=gain_matrix_th)
inds = inds[:n_regions]
nearest_regions.append((inds, head.connectivity.region_labels[inds], projs[inds]))
return nearest_regions
def select_sensors_power(self, sensors, power, selection=[], power_th=0.5):
if len(selection) == 0:
selection = range(sensors.number_of_sensors)
return (np.array(selection)[select_greater_values_array_inds(power, power_th)]).tolist()
def select_sensors_rois(self, sensors, rois=None, initial_selection=[], gain_matrix_th=0.5):
if len(initial_selection) == 0:
initial_selection = range(sensors.number_of_sensors)
selection = []
if sensors.gain_matrix is None:
raise_value_error("Projection matrix is not set!")
else:
for proj in sensors.gain_matrix[initial_selection].T[rois]:
selection += (
np.array(initial_selection)[select_greater_values_array_inds(proj, gain_matrix_th)]).tolist()
return np.unique(selection).tolist()
def sensors_in_electrodes_disconnectivity(self, sensors, sensors_labels=[]):
if len(sensors_labels) < 2:
sensors_labels = sensors.labels
n_sensors = len(sensors_labels)
elec_labels, elec_inds = sensors.group_sensors_to_electrodes(sensors_labels)
if len(elec_labels) >= 2:
disconnectivity = np.ones((n_sensors, n_sensors))
for ch in elec_inds:
disconnectivity[np.meshgrid(ch, ch)] = 0.0
return disconnectivity
def select_sensors_corr(self, sensors, distance, initial_selection=[], n_electrodes=10, sensors_per_electrode=1,
power=None, group_electrodes=False):
if len(initial_selection) == 0:
initial_selection = range(sensors.number_of_sensors)
n_sensors = len(initial_selection)
if n_sensors > 2:
initial_selection = np.array(initial_selection)
distance = 1.0 - distance
if group_electrodes:
disconnectivity = self.sensors_in_electrodes_disconnectivity(sensors, sensors.labels[initial_selection])
selection = \
select_by_hierarchical_group_metric_clustering(distance, disconnectivity, metric=power,
n_groups=n_electrodes,
members_per_group=sensors_per_electrode)
return np.unique(np.hstack(initial_selection[selection])).tolist()
else:
self.logger.warning("Number of sensors' left < 2!\n" + "Skipping clustering and returning all of them!")
return initial_selection
class StanService(object):
__metaclass__ = ABCMeta
logger = initialize_logger(__name__)
def __init__(self, model_name="", model=None, model_code=None, model_code_path="",
model_data_path="", fitmethod="sampling", config=None):
self.fitmethod = fitmethod
self.model_name = model_name
self.model = model
self.config = config or Config()
model_dir = config.out.FOLDER_RES
if not (os.path.isdir(model_dir)):
os.mkdir(model_dir)
self.model_path = os.path.join(model_dir, self.model_name)
self.model_code = model_code
if os.path.isfile(model_code_path):
self.model_code_path = model_code_path
else:
self.model_code_path = self.model_path + ".stan"
if model_data_path == "":
self.model_data_path = os.path.join(model_dir, "ModelData.h5")
self.compilation_time = 0.0
@abstractmethod
def compile_stan_model(self, save_model=True, **kwargs):
pass
@abstractmethod
def set_model_from_file(self, **kwargs):
pass
@abstractmethod
def fit(self, model_data, **kwargs):
pass
def write_model_data_to_file(self, model_data, reset_path=False, **kwargs):
model_data_path = kwargs.get("model_data_path", self.model_data_path)
if reset_path:
self.model_data_path = model_data_path
extension = model_data_path.split(".", -1)[-1]
if isequal_string(extension, "npy"):
np.save(model_data_path, model_data)
elif isequal_string(extension, "mat"):
savemat(model_data_path, model_data)
elif isequal_string(extension, "pkl"):
with open(model_data_path, 'wb') as f:
pickle.dump(model_data, f)
elif isequal_string(extension, "R"):
rdump(model_data_path, model_data)
else:
H5Writer().write_dictionary(model_data, os.path.join(os.path.dirname(model_data_path),
os.path.basename(model_data_path)))
def load_model_data_from_file(self, reset_path=False, **kwargs):
model_data_path = kwargs.get("model_data_path", self.model_data_path)
if reset_path:
self.model_data_path = model_data_path
extension = model_data_path.split(".", -1)[-1]
if isequal_string(extension, "R"):
model_data = rload(model_data_path)
elif isequal_string(extension, "npy"):
model_data = np.load(model_data_path).item()
elif isequal_string(extension, "mat"):
model_data = loadmat(model_data_path)
elif isequal_string(extension, "pkl"):
with open(model_data_path, 'wb') as f:
model_data = pickle.load(f)
elif isequal_string(extension, "h5"):
model_data = H5Reader().read_dictionary(model_data_path)
else:
raise_not_implemented_error("model_data file (" + model_data_path +
") that are not one of (.R, .npy, .mat, .pkl) cannot be read!")
for key in model_data.keys():
if key[:3] == "EPI":
del model_data[key]
return model_data
def set_model_data(self, debug=0, simulate=0, **kwargs):
self.model_data_path = kwargs.get("model_data_path", self.model_data_path)
model_data = kwargs.pop("model_data", None)
if not(isinstance(model_data, dict)):
model_data = self.load_model_data_from_file(self.model_data_path)
# -1 for no debugging at all
# 0 for printing only scalar parameters
# 1 for printing scalar and vector parameters
# 2 for printing all (scalar, vector and matrix) parameters
model_data["DEBUG"] = debug
# > 0 for simulating without using the input observation data:
model_data["SIMULATE"] = simulate
model_data = sort_dict(model_data)
return model_data
def set_or_compile_model(self, **kwargs):
try:
self.set_model_from_file(**kwargs)
except:
self.logger.info("Trying to compile model from file: " + str(self.model_code_path) + str("!"))
self.compile_stan_model(save_model=kwargs.get("save_model", True), **kwargs)
copyfile(self.model_code_path, os.path.join(os.path.dirname(self.model_path),
os.path.basename(self.model_code_path)))
def read_output_samples(self, output_filepath, **kwargs):
samples = ensure_list(parse_csv(output_filepath.replace(".csv", "*"), merge=kwargs.pop("merge_outputs", False)))
if len(samples) == 1:
return samples[0]
return samples
def compute_estimates_from_samples(self, samples):
ests = []
for chain_or_run_samples in ensure_list(samples):
est = {}
for pkey, pval in chain_or_run_samples.items():
try:
est[pkey + "_low"], est[pkey], est[pkey + "_std"] = describe(chain_or_run_samples[pkey])[1:4]
est[pkey + "_high"] = est[pkey + "_low"][1]
est[pkey + "_low"] = est[pkey + "_low"][0]
est[pkey + "_std"] = np.sqrt(est[pkey + "_std"])
for skey in [pkey, pkey + "_low", pkey + "_high", pkey + "_std"]:
est[skey] = np.squeeze(est[skey])
except:
est[pkey] = chain_or_run_samples[pkey]
ests.append(sort_dict(est))
if len(ests) == 1:
return ests[0]
else:
return ests
def compute_information_criteria(self, samples, nparams=None, nsamples=None, ndata=None, parameters=[],
skip_samples=0, merge_chains_or_runs_flag=False, log_like_str='log_likelihood'):
"""
:param samples: a dictionary of stan outputs or a list of dictionaries for multiple runs/chains
:param nparams: number of model parameters, it can be inferred from parameters if None
:param nsamples: number of samples, it can be inferred from loglikelihood if None
:param ndata: number of data points, it can be inferred from loglikelihood if None
:param parameters: a list of parameter names, necessary for dic metric computations and in case nparams is None,
as well as for aicc, aic and bic computation
:param merge_chains_or_runs_flag: logical flag for merging seperate chains/runs, default is True
:param log_like_str: the name of the log likelihood output of stan, default ''log_likelihood
:return:
"""
import sys
sys.path.insert(0, self.config.generic.MODEL_COMPARISON_PATH)
from information_criteria.ComputeIC import maxlike, aicc, aic, bic, dic, waic
from information_criteria.ComputePSIS import psisloo
# if self.fitmethod.find("opt") >= 0:
# warning("No model comparison can be computed for optimization method!")
# return None
samples = ensure_list(samples)
if merge_chains_or_runs_flag and len(samples) > 1:
samples = ensure_list(merge_samples(samples, skip_samples, flatten=True))
skip_samples = 0
results = []
for sample in samples:
log_likelihood = -1 * sample[log_like_str][skip_samples:]
log_lik_shape = log_likelihood.shape
if len(log_lik_shape) > 1:
target_shape = log_lik_shape[1:]
else:
target_shape = (1,)
if nsamples is None:
nsamples = log_lik_shape[0]
elif nsamples != log_likelihood.shape[0]:
warning("nsamples (" + str(nsamples) +
") is not equal to likelihood.shape[0] (" + str(log_lik_shape[0]) + ")!")
log_likelihood = np.reshape(log_likelihood, (log_lik_shape[0], -1))
if log_likelihood.shape > 1:
ndata_real = np.maximum(log_likelihood.shape[1], 1)
else:
ndata_real = 1
if ndata is None:
ndata = ndata_real
elif ndata != ndata_real:
warning("ndata (" + str(ndata) + ") is not equal to likelihood.shape[1] (" + str(ndata_real) + ")!")
result = maxlike(log_likelihood)
if len(parameters) == 0:
parameters = [param for param in sample.keys() if param.find("_star") >= 0]
if len(parameters) > 0:
nparams_real = 0
zscore_params = []
for p in parameters:
pval = sample[p][skip_samples:]
pzscore = np.array((pval - np.mean(pval, axis=0)) / np.std(pval, axis=0))
if len(pzscore.shape) > 2:
pzscore = np.reshape(pzscore, (pzscore.shape[0], -1))
zscore_params.append(pzscore)
if len(pzscore.shape) > 1:
nparams_real += np.maximum(pzscore.shape[1], 1)
else:
nparams_real += 1
if nparams is None:
nparams = nparams_real
elif nparams != nparams_real:
warning("nparams (" + str(nparams) +
") is not equal to number of parameters included in the dic computation (" +
str(nparams_real) + ")!")
# TODO: find out how to reduce dic to 1 value, from 1 value per parameter. mean(.) for the moment:
result['dic'] = np.mean(dic(log_likelihood, zscore_params))
else:
warning("Parameters' names' list is empty and we found no _star parameters! No computation of dic!")
if nparams is not None:
result['aicc'] = aicc(log_likelihood, nparams, ndata)
result['aic'] = aic(log_likelihood, nparams)
result['bic'] = bic(log_likelihood, nparams, ndata)
else:
warning("Unknown number of parameters! No computation of aic, aaic, bic!")
result.update(waic(log_likelihood))
if nsamples > 1:
result.update(psisloo(log_likelihood))
result["loos"] = np.reshape(result["loos"], target_shape)
result["ks"] = np.reshape(result["ks"], target_shape)
else:
result.pop('p_waic', None)
for metric, value in result.items():
result[metric] = value * np.ones(1,)
results.append(result)
if len(results) == 1:
return results[0]
else:
return list_of_dicts_to_dicts_of_ndarrays(results)
def compare_models(self, samples, nparams=None, nsamples=None, ndata=None, parameters=[],
skip_samples=0, merge_chains_or_runs_flag=False, log_like_str='log_likelihood'):
"""
:param samples: a dictionary of model's names and samples
:param nparams: a number or list of numbers of parameters,
it can be inferred from parameters list or from _star parameters
:param nsamples: a number or lists of numbers of samples, it can be inferred from loglikelihood if None
:param ndata: a number or lists of numbers of data point, it can be inferred from loglikelihood if None
:param parameters: a list (or list of lists) of parameter names,
it can be inferred from parameters list or from _star parameters
:param merge_chains_or_runs_flag: logical flag for merging seperate chains/runs, default is True
:param log_like_str: the name of the log likelihood output of stan, default ''log_likelihood
:return:
"""
def check_number_of_inputs(nmodels, input, input_str):
input = ensure_list(input)
ninput = len(input)
if ninput != nmodels:
if ninput == 1:
input *= nmodels
else:
raise_value_error("The size of input " + input_str + " (" + str(ninput) +
") is neither equal to the number of models (" + str(nmodels) +
") nor equal to 1!")
return input
nmodels = len(samples)
n_parameters = parameters
if n_parameters > 0:
if isinstance(parameters[0], (list, tuple)):
parameters = check_number_of_inputs(nmodels, parameters, "number of parameters")
else:
parameters = nmodels*[parameters]
nparams = check_number_of_inputs(nmodels, nparams, "number of parameters")
nsamples = check_number_of_inputs(nmodels, nsamples, "number of samples")
ndata = check_number_of_inputs(nmodels, ndata, "number of data points")
skip_samples = check_number_of_inputs(nmodels, skip_samples, "skip_samples")
log_like_str = check_number_of_inputs(nmodels, log_like_str, "log_like_str")
results = {}
for i_model, (model_name, model_samples) in enumerate(samples.items()):
results[model_name] = \
self.compute_information_criteria(model_samples, nparams[i_model], nsamples[i_model], ndata[i_model],
parameters[i_model], skip_samples[i_model], merge_chains_or_runs_flag,
log_like_str[i_model])
# Return result into a dictionary with metrics at the upper level and models at the lower one
return switch_levels_of_dicts_of_dicts(results)
class Head(object):
"""
One patient virtualization. Fully configured for defining hypothesis on it.
"""
logger = initialize_logger(__name__)
def __init__(self,
connectivity,
cortical_surface,
rm={},
vm={},
t1={},
name='',
**kwargs):
self.connectivity = connectivity
self.cortical_surface = cortical_surface
self.region_mapping = rm
self.volume_mapping = vm
self.t1_background = t1
self.sensorsSEEG = []
self.sensorsEEG = []
self.sensorsMEG = []
for s_type in Sensors.SENSORS_TYPES:
self.set_sensors(kwargs.get("sensors" + s_type), s_type=s_type)
if len(name) == 0:
self.name = 'Head' + str(self.number_of_regions)
else:
self.name = name
@property
def number_of_regions(self):
return self.connectivity.number_of_regions
def filter_regions(self, filter_arr):
return self.connectivity.region_labels[filter_arr]
def __repr__(self):
d = {
"1. name": self.name,
"2. connectivity": self.connectivity,
"3. RM": reg_dict(self.region_mapping,
self.connectivity.region_labels),
"4. VM": reg_dict(self.volume_mapping,
self.connectivity.region_labels),
"5. surface": self.cortical_surface,
"6. T1": self.t1_background,
"7. SEEG": self.sensorsSEEG,
"8. EEG": self.sensorsEEG,
"9. MEG": self.sensorsMEG
}
return formal_repr(self, sort_dict(d))
def __str__(self):
return self.__repr__()
def get_sensors(self, s_type=Sensors.TYPE_SEEG):
if np.in1d(s_type.upper(), Sensors.SENSORS_TYPES):
return getattr(self, "sensors" + s_type)
else:
raise_value_error("Invalid input sensor type " + str(s_type))
def set_sensors(self,
input_sensors,
s_type=Sensors.TYPE_SEEG,
reset=False):
if input_sensors is None:
return
sensors = ensure_list(self.get_sensors(s_type))
if reset is False or len(sensors) == 0:
sensors = []
for s in ensure_list(input_sensors):
if isinstance(s, Sensors) and (s.s_type == s_type):
if s.gain_matrix is None or s.gain_matrix.shape != (
s.number_of_sensors, self.number_of_regions):
self.logger.warning(
"No correctly sized gain matrix found in sensors! Computing and adding gain matrix!"
)
s.gain_matrix = s.compute_gain_matrix(self.connectivity)
# if s.orientations == None or s.orientations.shape != (s.number_of_sensors, 3):
# self.logger.warning("No orientations found in sensors!")
sensors.append(s)
else:
if s is not None:
raise_value_error(
"Input sensors:\n" + str(s) +
"\nis not a valid Sensors object of type " +
str(s_type) + "!")
if len(sensors) == 0:
setattr(self, "sensors" + s_type, [])
else:
setattr(self, "sensors" + s_type, sensors)
def get_sensors_id(self, s_type=Sensors.TYPE_SEEG, sensor_ids=0):
sensors = self.get_sensors(s_type)
if sensors is None:
return sensors
else:
out_sensors = []
sensors = ensure_list(sensors)
for iS, s in enumerate(sensors):
if np.in1d(iS, sensor_ids):
out_sensors.append(sensors[iS])
if len(out_sensors) == 0:
return None
elif len(out_sensors) == 1:
return out_sensors[0]
else:
return out_sensors
class ProbabilisticSamplingService(SamplingService):
logger = initialize_logger(__name__)
def __init__(self, n_samples=10, sampling_module="scipy", random_seed=None):
super(ProbabilisticSamplingService, self).__init__(n_samples)
self.random_seed = random_seed
self.sampling_module = sampling_module.lower()
def __repr__(self):
d = {"01. Sampling module": self.sampling_module,
"02. Sampler": self.sampler,
"03. Number of samples": self.n_samples,
"04. Samples' p_shape": self.shape,
"05. Random seed": self.random_seed,
}
return formal_repr(self, d) + "\n06. Resulting statistics: " + dict_str(self.stats)
def __str__(self):
return self.__repr__()
def _truncated_distribution_sampling(self, trunc_limits, size):
# Following: https://stackoverflow.com/questions/25141250/
# how-to-truncate-a-numpy-scipy-exponential-distribution-in-an-efficient-way
# TODO: to have distributions parameters valid for the truncated distributions instead for the original one
# pystan might be needed for that...
rnd_cdf = nr.uniform(self.sampler.cdf(x=trunc_limits.get("low", -np.inf)),
self.sampler.cdf(x=trunc_limits.get("high", np.inf)),
size=size)
return self.sampler.ppf(q=rnd_cdf)
def sample(self, parameter=(), loc=0.0, scale=1.0, **kwargs):
nr.seed(self.random_seed)
if isinstance(parameter, (ProbabilisticParameterBase, TransformedProbabilisticParameterBase)):
parameter_shape = parameter.p_shape
low = parameter.low
high = parameter.high
prob_distr = parameter
loc = parameter.loc
scale = parameter.scale
else:
parameter_shape = kwargs.pop("shape", (1,))
low = kwargs.pop("low", -CalculusConfig.MAX_SINGLE_VALUE)
high = kwargs.pop("high", CalculusConfig.MAX_SINGLE_VALUE)
prob_distr = kwargs.pop("probability_distribution", "uniform")
low, high = self.check_for_infinite_bounds(low, high)
low, high, n_outputs, parameter_shape = self.check_size(low, high, parameter_shape)
self.adjust_shape(parameter_shape)
out_shape = tuple([self.n_samples] + list(self.shape)[:-1])
if np.any(low > -CalculusConfig.MAX_SINGLE_VALUE) or np.any(high < CalculusConfig.MAX_SINGLE_VALUE):
if not(isequal_string(self.sampling_module, "scipy")):
self.logger.warning("Switching to scipy for truncated distributions' sampling!")
self.sampling_module = "scipy"
if isinstance(prob_distr, basestring):
self.sampler = getattr(ss, prob_distr)(*parameter, **kwargs)
samples = self._truncated_distribution_sampling({"low": low, "high": high}, out_shape) * scale + loc
elif isinstance(prob_distr, (ProbabilisticParameterBase, TransformedProbabilisticParameterBase)):
self.sampler = prob_distr.scipy()
samples = self._truncated_distribution_sampling({"low": low, "high": high}, out_shape)
elif self.sampling_module.find("scipy") >= 0:
if isinstance(prob_distr, basestring):
self.sampler = getattr(ss, prob_distr)(*parameter, **kwargs)
samples = self.sampler.rvs(size=out_shape) * scale + loc
elif isinstance(prob_distr, ProbabilisticParameterBase):
self.sampler = prob_distr._scipy(**kwargs)
samples = self.sampler.rvs(size=out_shape)
elif self.sampling_module.find("numpy") >= 0:
if isinstance(prob_distr, basestring):
self.sampler = lambda size: getattr(nr, prob_distr)(*parameter, size=size, **kwargs)
samples = self.sampler(out_shape) * scale + loc
elif isinstance(prob_distr, (ProbabilisticParameterBase, TransformedProbabilisticParameterBase)):
self.sampler = lambda size: prob_distr.numpy(size=size)
samples = self.sampler(out_shape)
return samples.T
import os
from tvb_epilepsy.base.constants.config import Config
from tvb_epilepsy.base.utils.log_error_utils import initialize_logger
from tvb_epilepsy.io.tvb_data_reader import TVBReader
from tvb_epilepsy.io.h5_reader import H5Reader
from tvb_epilepsy.io.h5_writer import H5Writer
from tvb_epilepsy.plot.plotter import Plotter
# input_folder = os.path.join(os.path.expanduser("~"), 'Dropbox', 'Work', 'VBtech', 'VEP', "results", "CC", "TVB3", "tvb")
# head_folder = os.path.join(os.path.expanduser("~"), 'Dropbox', 'Work', 'VBtech', 'VEP', "results", "CC", "TVB3", "Head")
input_folder = os.path.join(os.path.expanduser("~"), 'Dropbox', 'Work',
'VBtech', 'VEP', "results", "INS", "JUNCH", "tvb")
head_folder = os.path.join(os.path.expanduser("~"), 'Dropbox', 'Work',
'VBtech', 'VEP', "results", "INS", "JUNCH", "Head")
output_folder = os.path.join(os.path.expanduser("~"), 'Dropbox', 'Work',
'VBtech', 'VEP', "results", "tests")
config = Config(head_folder=input_folder,
output_base=output_folder,
data_mode="tvb") #, data_mode="java"
config.hypothesis.head_folder = head_folder
config.figures.MATPLOTLIB_BACKEND = "inline"
config.figures.SHOW_FLAG = True
logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
reader = TVBReader() if config.input.IS_TVB_MODE else H5Reader()
writer = H5Writer()
plotter = Plotter(config)
logger.info("Reading from: " + config.input.HEAD)
head = reader.read_head(config.input.HEAD,
seeg_sensors_files=[("seeg_xyz.txt", )])
print("OK!")
def main_vep(config=Config(), sim_type="default", test_write_read=False,
pse_flag=PSE_FLAG, sa_pse_flag=SA_PSE_FLAG, sim_flag=SIM_FLAG):
logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
# -------------------------------Reading data-----------------------------------
reader = TVBReader() if config.input.IS_TVB_MODE else H5Reader()
writer = H5Writer()
logger.info("Reading from: " + config.input.HEAD)
head = reader.read_head(config.input.HEAD)
plotter = Plotter(config)
plotter.plot_head(head)
if test_write_read:
writer.write_head(head, os.path.join(config.out.FOLDER_RES, "Head"))
# --------------------------Hypothesis definition-----------------------------------
n_samples = 100
# # Manual definition of hypothesis...:
# x0_indices = [20]
# x0_values = [0.9]
# e_indices = [70]
# e_values = [0.9]
# disease_values = x0_values + e_values
# disease_indices = x0_indices + e_indices
# ...or reading a custom file:
hypo_builder = HypothesisBuilder(head.connectivity.number_of_regions, config=config).set_normalize(0.95)
# This is an example of Epileptogenicity Hypothesis: you give as ep all indices for values > 0
hyp_E = hypo_builder.build_hypothesis_from_file(EP_NAME, e_indices=[1, 3, 16, 25])
# print(hyp_E.string_regions_disease(head.connectivity.region_labels))
# This is an example of Excitability Hypothesis:
hyp_x0 = hypo_builder.build_hypothesis_from_file(EP_NAME)
# # This is an example of Mixed Hypothesis set manually by the user:
# x0_indices = [hyp_x0.x0_indices[-1]]
# x0_values = [hyp_x0.x0_values[-1]]
# e_indices = hyp_x0.x0_indices[0:-1].tolist()
# e_values = hyp_x0.x0_values[0:-1].tolist()
# hyp_x0_E = hypo_builder.set_x0_hypothesis(x0_indices, x0_values). \
# set_e_hypothesis(e_indices, e_values).build_hypothesis()
# This is an example of x0_values mixed Excitability and Epileptogenicity Hypothesis set from file:
all_regions_indices = np.array(range(head.number_of_regions))
healthy_indices = np.delete(all_regions_indices, hyp_E.x0_indices + hyp_E.e_indices).tolist()
hyp_x0_E = hypo_builder.build_hypothesis_from_file(EP_NAME, e_indices=[16, 25])
hypotheses = (hyp_x0_E, hyp_x0, hyp_E)
# --------------------------Simulation preparations-----------------------------------
# If you choose model...
# Available models beyond the TVB Epileptor (they all encompass optional variations from the different papers):
# EpileptorDP: similar to the TVB Epileptor + optional variations,
# EpileptorDP2D: reduced 2D model, following Proix et all 2014 +optional variations,
# EpleptorDPrealistic: starting from the TVB Epileptor + optional variations, but:
# -x0, Iext1, Iext2, slope and K become noisy state variables,
# -Iext2 and slope are coupled to z, g, or z*g in order for spikes to appear before seizure,
# -multiplicative correlated noise is also used
# We don't want any time delays for the moment
head.connectivity.tract_lengths *= config.simulator.USE_TIME_DELAYS_FLAG
sim_builder = SimulatorBuilder(config.simulator.MODE)
if isequal_string(sim_type, "realistic"):
sim_settings = sim_builder.set_model_name("EpileptorDPrealistic").set_simulated_period(50000).build_sim_settings()
sim_settings.noise_type = COLORED_NOISE
sim_settings.noise_ntau = 10
elif isequal_string(sim_type, "fitting"):
sim_settings = sim_builder.set_model_name("EpileptorDP2D").build_sim_settings()
sim_settings.noise_intensity = 1e-3
elif isequal_string(sim_type, "paper"):
sim_builder.set_model_name("Epileptor")
sim_settings = sim_builder.build_sim_settings()
else:
sim_settings = sim_builder.build_sim_settings()
# --------------------------Hypothesis and LSA-----------------------------------
for hyp in hypotheses:
logger.info("\n\nRunning hypothesis: " + hyp.name)
logger.info("\n\nCreating model configuration...")
builder = ModelConfigurationBuilder(hyp.number_of_regions)
mcs_file = os.path.join(config.out.FOLDER_RES, hyp.name + "_model_config_service.h5")
writer.write_model_configuration_builder(builder, mcs_file)
if test_write_read:
logger.info("Written and read model configuration services are identical?: " +
str(assert_equal_objects(builder, reader.read_model_configuration_builder(mcs_file),
logger=logger)))
if hyp.type == "Epileptogenicity":
model_configuration = builder.build_model_from_E_hypothesis(hyp, head.connectivity.normalized_weights)
else:
model_configuration = builder.build_model_from_hypothesis(hyp, head.connectivity.normalized_weights)
mc_path = os.path.join(config.out.FOLDER_RES, hyp.name + "_ModelConfig.h5")
writer.write_model_configuration(model_configuration, mc_path)
if test_write_read:
logger.info("Written and read model configuration are identical?: " +
str(assert_equal_objects(model_configuration, reader.read_model_configuration(mc_path),
logger=logger)))
# Plot nullclines and equilibria of model configuration
plotter.plot_state_space(model_configuration, "6d", head.connectivity.region_labels,
special_idx=hyp_x0.x0_indices + hyp_E.e_indices, zmode="lin",
figure_name=hyp.name + "_StateSpace")
logger.info("\n\nRunning LSA...")
lsa_service = LSAService(eigen_vectors_number=None, weighted_eigenvector_sum=True)
lsa_hypothesis = lsa_service.run_lsa(hyp, model_configuration)
lsa_path = os.path.join(config.out.FOLDER_RES, lsa_hypothesis.name + "_LSA.h5")
lsa_config_path = os.path.join(config.out.FOLDER_RES, lsa_hypothesis.name + "_LSAConfig.h5")
writer.write_hypothesis(lsa_hypothesis, lsa_path)
writer.write_lsa_service(lsa_service, lsa_config_path)
if test_write_read:
logger.info("Written and read LSA services are identical?: " +
str(assert_equal_objects(lsa_service, reader.read_lsa_service(lsa_config_path), logger=logger)))
logger.info("Written and read LSA hypotheses are identical (no input check)?: " +
str(assert_equal_objects(lsa_hypothesis, reader.read_hypothesis(lsa_path), logger=logger)))
plotter.plot_lsa(lsa_hypothesis, model_configuration, lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number, head.connectivity.region_labels, None)
if pse_flag:
# --------------Parameter Search Exploration (PSE)-------------------------------
logger.info("\n\nRunning PSE LSA...")
pse_results = pse_from_lsa_hypothesis(lsa_hypothesis,
head.connectivity.normalized_weights,
head.connectivity.region_labels,
n_samples, param_range=0.1,
global_coupling=[{"indices": all_regions_indices}],
healthy_regions_parameters=[
{"name": "x0_values", "indices": healthy_indices}],
model_configuration_builder=builder,
lsa_service=lsa_service, logger=logger, save_flag=True)[0]
plotter.plot_lsa(lsa_hypothesis, model_configuration, lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number, head.connectivity.region_labels, pse_results)
pse_lsa_path = os.path.join(config.out.FOLDER_RES, lsa_hypothesis.name + "_PSE_LSA_results.h5")
writer.write_dictionary(pse_results, pse_lsa_path)
if test_write_read:
logger.info("Written and read sensitivity analysis parameter search results are identical?: " +
str(assert_equal_objects(pse_results, reader.read_dictionary(pse_lsa_path), logger=logger)))
if sa_pse_flag:
# --------------Sensitivity Analysis Parameter Search Exploration (PSE)-------------------------------
logger.info("\n\nrunning sensitivity analysis PSE LSA...")
sa_results, pse_sa_results = \
sensitivity_analysis_pse_from_lsa_hypothesis(lsa_hypothesis,
head.connectivity.normalized_weights,
head.connectivity.region_labels,
n_samples, method="sobol", param_range=0.1,
global_coupling=[{"indices": all_regions_indices,
"bounds": [0.0, 2 *
builder.K_unscaled[
0]]}],
healthy_regions_parameters=[
{"name": "x0_values", "indices": healthy_indices}],
model_configuration_builder=builder,
lsa_service=lsa_service, config=config)
plotter.plot_lsa(lsa_hypothesis, model_configuration, lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number, head.connectivity.region_labels, pse_sa_results,
title="SA PSE Hypothesis Overview")
sa_pse_path = os.path.join(config.out.FOLDER_RES, lsa_hypothesis.name + "_SA_PSE_LSA_results.h5")
sa_lsa_path = os.path.join(config.out.FOLDER_RES, lsa_hypothesis.name + "_SA_LSA_results.h5")
writer.write_dictionary(pse_sa_results, sa_pse_path)
writer.write_dictionary(sa_results, sa_lsa_path)
if test_write_read:
logger.info("Written and read sensitivity analysis results are identical?: " +
str(assert_equal_objects(sa_results, reader.read_dictionary(sa_lsa_path), logger=logger)))
logger.info("Written and read sensitivity analysis parameter search results are identical?: " +
str(assert_equal_objects(pse_sa_results, reader.read_dictionary(sa_pse_path),
logger=logger)))
if sim_flag:
# ------------------------------Simulation--------------------------------------
logger.info("\n\nConfiguring simulation from model_configuration...")
model = sim_builder.generate_model(model_configuration)
if isequal_string(sim_type, "realistic"):
model.tau0 = 30000.0
model.tau1 = 0.2
model.slope = 0.25
elif isequal_string(sim_type, "fitting"):
model.tau0 = 10.0
model.tau1 = 0.5
sim, sim_settings, model = sim_builder.build_simulator_TVB_from_model_sim_settings(model_configuration,
head.connectivity, model, sim_settings)
# Integrator and initial conditions initialization.
# By default initial condition is set right on the equilibrium point.
writer.write_generic(sim.model, config.out.FOLDER_RES, lsa_hypothesis.name + "_sim_model.h5")
logger.info("\n\nSimulating...")
ttavg, tavg_data, status = sim.launch_simulation(report_every_n_monitor_steps=100)
sim_path = os.path.join(config.out.FOLDER_RES, lsa_hypothesis.name + "_sim_settings.h5")
writer.write_simulation_settings(sim.simulation_settings, sim_path)
if test_write_read:
# TODO: find out why it cannot set monitor expressions
logger.info("Written and read simulation settings are identical?: " +
str(assert_equal_objects(sim.simulation_settings,
reader.read_simulation_settings(sim_path), logger=logger)))
if not status:
logger.warning("\nSimulation failed!")
else:
time = np.array(ttavg, dtype='float32')
output_sampling_time = np.mean(np.diff(time))
tavg_data = tavg_data[:, :, :, 0]
logger.info("\n\nSimulated signal return shape: %s", tavg_data.shape)
logger.info("Time: %s - %s", time[0], time[-1])
logger.info("Values: %s - %s", tavg_data.min(), tavg_data.max())
# Variables of interest in a dictionary:
res_ts = prepare_vois_ts_dict(sim_settings.monitor_expressions, tavg_data)
res_ts['time'] = time
res_ts['time_units'] = 'msec'
res_ts = compute_seeg_and_write_ts_h5_file(config.out.FOLDER_RES, lsa_hypothesis.name + "_ts.h5",
sim.model, res_ts, output_sampling_time,
sim_settings.simulated_period,
hpf_flag=True, hpf_low=10.0, hpf_high=512.0,
sensors_list=head.sensorsSEEG)
# Plot results
if model._ui_name is "EpileptorDP2D":
spectral_raster_plot = False
trajectories_plot = True
else:
spectral_raster_plot = "lfp"
trajectories_plot = False
#TODO: plotting fails when spectral_raster_plot="lfp". Denis will fix this
plotter.plot_sim_results(sim.model, lsa_hypothesis.lsa_propagation_indices, res_ts,
head.sensorsSEEG, hpf_flag=True, trajectories_plot=trajectories_plot,
spectral_raster_plot=False, log_scale=True)
class LSAService(object):
logger = initialize_logger(__name__)
def __init__(
self,
eigen_vectors_number_selection=CalculusConfig.
EIGENVECTORS_NUMBER_SELECTION,
eigen_vectors_number=None,
weighted_eigenvector_sum=CalculusConfig.WEIGHTED_EIGENVECTOR_SUM,
normalize_propagation_strength=False):
self.eigen_vectors_number_selection = eigen_vectors_number_selection
self.eigen_values = []
self.eigen_vectors = []
self.eigen_vectors_number = eigen_vectors_number
self.weighted_eigenvector_sum = weighted_eigenvector_sum
self.normalize_propagation_strength = normalize_propagation_strength
def __repr__(self):
d = {
"01. Eigenvectors' number selection mode":
self.eigen_vectors_number_selection,
"02. Eigenvectors' number":
self.eigen_vectors_number_selection,
"03. Eigen values":
self.eigen_values,
"04. Eigenvectors":
self.eigen_vectors,
"05. Eigenvectors' number":
self.eigen_vectors_number,
"06. Weighted eigenvector's sum flag":
str(self.weighted_eigenvector_sum)
}
return formal_repr(self, d)
def __str__(self):
return self.__repr__()
def set_attribute(self, attr_name, data):
setattr(self, attr_name, data)
def get_curve_elbow_point(self, values_array):
return curve_elbow_point(values_array)
def _ensure_eigen_vectors_number(self, eigen_values, e_values, x0_values,
disease_indices):
if self.eigen_vectors_number is None:
if self.eigen_vectors_number_selection is "auto_eigenvals":
self.eigen_vectors_number = self.get_curve_elbow_point(
numpy.abs(eigen_values)) + 1
elif self.eigen_vectors_number_selection is "auto_disease":
self.eigen_vectors_number = len(disease_indices)
elif self.eigen_vectors_number_selection is "auto_epileptogenicity":
self.eigen_vectors_number = self.get_curve_elbow_point(
e_values) + 1
elif self.eigen_vectors_number_selection is "auto_excitability":
self.eigen_vectors_number = self.get_curve_elbow_point(
x0_values) + 1
else:
raise_value_error(
"\n" + self.eigen_vectors_number_selection +
"is not a valid option when for automatic computation of self.eigen_vectors_number"
)
else:
self.eigen_vectors_number_selection = "user_defined"
def _compute_jacobian(self, model_configuration):
# Check if any of the equilibria are in the supercritical regime (beyond the separatrix) and set it right before
# the bifurcation.
zEQ = model_configuration.zEQ
temp = model_configuration.x1EQ > X1_EQ_CR_DEF - 10**(-3)
if temp.any():
correction_value = X1_EQ_CR_DEF - 10**(-3)
self.logger.warning(
"Equilibria x1EQ[" + str(numpy.where(temp)[0]) + "] = " +
str(model_configuration.x1EQ[temp]) +
"\nwere corrected for LSA to value: X1_EQ_CR_DEF - 10 ** (-3) = "
+ str(correction_value) + " to be sub-critical!")
model_configuration.x1EQ[temp] = correction_value
i_temp = numpy.ones(model_configuration.x1EQ.shape)
zEQ[temp] = calc_eq_z(model_configuration.x1EQ[temp],
model_configuration.yc * i_temp[temp],
model_configuration.Iext1 * i_temp[temp],
"2d", 0.0,
model_configuration.slope * i_temp[temp],
model_configuration.a * i_temp[temp],
model_configuration.b * i_temp[temp],
model_configuration.d * i_temp[temp])
fz_jacobian = calc_fz_jac_square_taylor(
model_configuration.zEQ, model_configuration.yc,
model_configuration.Iext1, model_configuration.K,
model_configuration.model_connectivity, model_configuration.a,
model_configuration.b, model_configuration.d)
if numpy.any([
numpy.any(numpy.isnan(fz_jacobian.flatten())),
numpy.any(numpy.isinf(fz_jacobian.flatten()))
]):
raise_value_error("nan or inf values in dfz")
return fz_jacobian
def run_lsa(self, disease_hypothesis, model_configuration):
jacobian = self._compute_jacobian(model_configuration)
# Perform eigenvalue decomposition
eigen_values, eigen_vectors = numpy.linalg.eig(jacobian)
sorted_indices = numpy.argsort(eigen_values, kind='mergesort')
self.eigen_values = eigen_values[sorted_indices]
self.eigen_vectors = eigen_vectors[:, sorted_indices]
self._ensure_eigen_vectors_number(
self.eigen_values, model_configuration.e_values,
model_configuration.x0_values,
disease_hypothesis.get_all_disease_indices())
if self.eigen_vectors_number == disease_hypothesis.number_of_regions:
# Calculate the propagation strength index by summing all eigenvectors
lsa_propagation_strength = numpy.abs(
numpy.sum(self.eigen_vectors, axis=1))
else:
sorted_indices = max(self.eigen_vectors_number, 1)
# Calculate the propagation strength index by summing the first n eigenvectors (minimum 1)
if self.weighted_eigenvector_sum:
lsa_propagation_strength = numpy.abs(
weighted_vector_sum(self.eigen_values[:sorted_indices],
self.eigen_vectors[:, :sorted_indices],
normalize=True))
else:
lsa_propagation_strength = numpy.abs(
numpy.sum(self.eigen_vectors[:, :sorted_indices], axis=1))
if self.normalize_propagation_strength:
# Normalize by the maximum
lsa_propagation_strength /= numpy.max(lsa_propagation_strength)
# # TODO: this has to be corrected
# if self.eigen_vectors_number < 0.2 * disease_hypothesis.number_of_regions:
# propagation_strength_elbow = numpy.max([self.get_curve_elbow_point(lsa_propagation_strength),
# self.eigen_vectors_number])
# else:
propagation_strength_elbow = self.get_curve_elbow_point(
lsa_propagation_strength)
propagation_indices = lsa_propagation_strength.argsort(
)[-propagation_strength_elbow:]
hypothesis_builder = HypothesisBuilder(disease_hypothesis.number_of_regions).\
set_attributes_based_on_hypothesis(disease_hypothesis). \
set_lsa_propagation(propagation_indices, lsa_propagation_strength)
return hypothesis_builder.build_lsa_hypothesis()
def update_for_pse(self, values, paths, indices):
for i, val in enumerate(paths):
vals = val.split(".")
if vals[0] == "lsa_service":
getattr(self, vals[1])[indices[i]] = values[i]
def test_computations(self):
logger = initialize_logger(__name__, self.config.out.FOLDER_LOGS)
# ------------------------------------------------------------------------------------------------------------------
x1 = numpy.array([-4.1 / 3, -4.9 / 3, -5.0 / 3], dtype="float32")
w = numpy.array([[0, 0.1, 0.9], [0.1, 0, 0.0], [0.9, 0.0, 0]])
n = x1.size
K = 0.0 * K_DEF * numpy.ones(x1.shape, dtype=x1.dtype)
yc = YC_DEF * numpy.ones(x1.shape, dtype=x1.dtype)
Iext1 = I_EXT1_DEF * numpy.ones(x1.shape, dtype=x1.dtype)
slope = SLOPE_DEF * numpy.ones(x1.shape, dtype=x1.dtype)
Iext2 = I_EXT2_DEF * numpy.ones(x1.shape, dtype=x1.dtype)
a = A_DEF
b = B_DEF
d = D_DEF
s = S_DEF
gamma = GAMMA_DEF
tau1 = TAU1_DEF
tau2 = TAU2_DEF
tau0 = TAU0_DEF
x1, K = assert_arrays([x1, K])
w = assert_arrays([w]) # , (x1.size, x1.size)
zmode = numpy.array("lin")
pmode = numpy.array("const")
model = "EpileptorDPrealistic"
x1eq = x1
z = calc_eq_z(x1,
yc,
Iext1,
"2d",
x2=0.0,
slope=slope,
a=a,
b=b,
d=d,
x1_neg=True)
zeq = z
x0cr, r = calc_x0cr_r(yc,
Iext1,
zmode=zmode,
x1_rest=X1_DEF,
x1_cr=X1EQ_CR_DEF,
x0def=X0_DEF,
x0cr_def=X0_CR_DEF)
x0 = calc_x0(x1, z, K, w, zmode=zmode, z_pos=True)
calc_model_x0_to_x0_val(x0,
yc,
Iext1,
a,
b,
d,
zmode=numpy.array("lin"))
if model == "EpileptorDP2D":
eq = numpy.c_[x1eq, zeq].T.astype('float32')
model_vars = 2
dfun = calc_dfun(eq[0].T,
eq[1].T,
yc,
Iext1,
x0,
K,
w,
model_vars,
zmode=zmode,
pmode=pmode,
x0_var=x0,
slope_var=slope,
Iext1_var=Iext1,
Iext2_var=Iext2,
K_var=K,
slope=slope,
a=a,
b=b,
d=d,
s=s,
Iext2=Iext2,
gamma=gamma,
tau1=tau1,
tau0=tau0,
tau2=tau2,
output_mode="array")
jac = calc_jac(eq[0].T,
eq[1].T,
yc,
Iext1,
x0,
K,
w,
model_vars,
zmode=zmode,
pmode=pmode,
x1_neg=True,
z_pos=True,
x2_neg=False,
x0_var=x0,
slope_var=slope,
Iext1_var=Iext1,
Iext2_var=Iext2,
K_var=K,
slope=slope,
a=a,
b=b,
d=d,
s=s,
Iext2=Iext2,
gamma=gamma,
tau1=tau1,
tau0=tau0,
tau2=tau2)
else:
if model == "EpileptorDPrealistic":
# the 11D "realistic" simulations model
eq, slope_eq, Iext2_eq = calc_eq_11d(
x0,
K,
w,
yc,
Iext1,
Iext2,
slope,
EpileptorDPrealistic.fun_slope_Iext2,
x1,
a=a,
b=b,
d=d,
zmode=zmode,
pmode=pmode)
model_vars = 11
dfun = calc_dfun(eq[0].T,
eq[2].T,
yc,
Iext1,
x0,
K,
w,
model_vars,
zmode,
pmode,
y1=eq[1].T,
x2=eq[3].T,
y2=eq[4].T,
g=eq[5].T,
x0_var=eq[6].T,
slope_var=eq[7].T,
Iext1_var=eq[8].T,
Iext2_var=eq[9].T,
K_var=eq[10].T,
slope=slope,
a=a,
b=b,
d=d,
s=s,
Iext2=Iext2,
gamma=gamma,
tau1=tau1,
tau0=tau0,
tau2=tau2,
output_mode="array")
jac = calc_jac(eq[0].T,
eq[2].T,
yc,
Iext1,
x0,
K,
w,
model_vars,
zmode,
pmode,
x1_neg=True,
z_pos=True,
x2_neg=False,
y1=eq[1].T,
x2=eq[3].T,
y2=eq[4].T,
g=eq[5].T,
x0_var=eq[6].T,
slope_var=eq[7].T,
Iext1_var=eq[8].T,
Iext2_var=eq[9].T,
K_var=eq[10].T,
slope=slope,
a=a,
b=b,
d=d,
s=s,
Iext2=Iext2,
gamma=gamma,
tau1=tau1,
tau0=tau0,
tau2=tau2)
else:
# all >=6D models
eq = calc_eq_6d(x0,
K,
w,
yc,
Iext1,
Iext2,
x1,
a=a,
b=b,
d=d,
zmode=zmode)
model_vars = 6
dfun = calc_dfun(eq[0].T,
eq[2].T,
yc,
Iext1,
x0,
K,
w,
model_vars,
zmode,
y1=eq[1].T,
x2=eq[3].T,
y2=eq[4].T,
g=eq[5].T,
slope=slope,
a=a,
b=b,
d=d,
s=s,
Iext2=Iext2,
gamma=gamma,
tau1=tau1,
tau0=tau0,
tau2=tau2,
output_mode="array")
jac = calc_jac(eq[0].T,
eq[2].T,
yc,
Iext1,
r,
K,
w,
model_vars,
zmode,
x1_neg=True,
z_pos=True,
x2_neg=False,
y1=eq[1].T,
x2=eq[3].T,
y2=eq[4].T,
g=eq[5].T,
slope=slope,
a=a,
b=b,
d=d,
s=s,
Iext2=Iext2,
gamma=gamma,
tau1=tau1,
tau0=tau0,
tau2=tau2)
model = str(model_vars) + "d"
sx1, sy1, sz, sx2, sy2, sg, sx0, sx0_val, sK, syc, sIext1, sIext2, sslope, sa, sb, sd, stau1, stau0, stau2, v = \
symbol_vars(n, ["x1", "y1", "z", "x2", "y2", "g", "x0", "x0_val", "K", "yc", "Iext1", "Iext2",
"slope", "a", "b", "d", "tau1", "tau0", "tau2"], shape=(3,))
sw, vw = symbol_vars(n, ["w"], dims=2, output_flag="numpy_array")
v.update(vw)
del vw
numpy.fill_diagonal(sw, 0.0)
sw = numpy.array(sw)
a = numpy.ones((n, ))
b = 3.0 * a
d = 5.0 * a
s = 6.0 * a
tau1 = a
tau0 = a
tau2 = a
x1sq = -4.0 / 3 * a
if model == "2d":
y1 = yc
else:
y1 = eq[1].T
x2 = eq[3].T
y2 = eq[4].T
g = eq[5].T
if model == "11d":
x0_var = eq[6].T
slope_var = eq[7].T
Iext1_var = eq[8].T
Iext2_var = eq[9].T
K_var = eq[10].T
# -------------------------------------------- Test symbolic x0cr, r calculation ----------------------------------
logger.info("\n\nTest symbolic x0cr, r calculation...")
x0cr2, r2 = calc_x0cr_r(syc,
sIext1,
zmode=zmode,
x1_rest=X1_DEF,
x1_cr=X1EQ_CR_DEF,
x0def=X0_DEF,
x0cr_def=X0_CR_DEF) # test=True
lx0cr_r, sx0cr_r, v = symbol_eqtn_x0cr_r(
n, zmode=zmode,
shape=(n, )) # symbol_calc_x0cr_r(n, zmode=zmode, shape=(3, ))
sx0cr_r = list(sx0cr_r)
for ii in range(2):
sx0cr_r[ii] = Matrix(sx0cr_r[ii])
for iv in range(n):
sx0cr_r[ii][iv] = sx0cr_r[ii][iv].subs([
(v["a"][iv], a[iv]), (v["b"][iv], b[iv]),
(v["d"][iv], d[iv]), (v["x1_rest"][iv], X1_DEF),
(v["x0_rest"][iv], X0_DEF), (v["x1_cr"][iv], X1EQ_CR_DEF),
(v["x0_cr"][iv], X0_CR_DEF)
])
assert list(x0cr2) == list(sx0cr_r[0])
assert list(r2) == list(sx0cr_r[1])
# -------------------------------------------- Test coupling ------------------------------------------------------
coupling = calc_coupling(sx1, sK, sw)
scoupling = symbol_eqtn_coupling(n, shape=(n, ))[:2]
assert list(coupling) == list(scoupling[1])
assert list(calc_coupling(x1, K, w)) == list(scoupling[0](x1, K, w))
assert coupling.shape == scoupling[1].shape
# ---------------------------------------- Test coupling derivative to x1 ------------------------------------------
coupling_diff = calc_coupling_diff(sK, sw)
scoupling_diff = symbol_calc_coupling_diff(n, ix=None, jx=None,
K="K")[:2]
assert coupling_diff.shape == scoupling_diff[1].shape
# ------------------------------------- Test the fz with substitution of z via fx1 ----------------------------------
fx1z = calc_fx1z(sx1,
sx0,
sK,
sw,
syc,
sIext1,
sa,
sb,
sd,
stau1,
stau0,
zmode=zmode)
sfx1z = symbol_eqtn_fx1z(n, model, zmode, shape=(n, ))[:2]
# if model == "2d":
# fx1z = calc_fx1z(x1, x0, K, w, yc, Iext1, a=a, b=b, d=d, tau1=tau1, tau0=tau0, model=model, zmode=zmode)
# s_fx1z = sfx1z[0](x1, x0, K, w, yc, Iext1, a, b, d, tau1, tau0)
# assert list(fx1z) == list(s_fx1z)
# else:
# fx1z = calc_fx1z(x1, x0, K, w, yc, Iext1, a=a, b=b, d=d, tau1=tau1, tau0=tau0, model=model, zmode=zmode)
# s_fx1z = sfx1z[0](x1, x0, K, w, yc, Iext1, a, b, d, tau1, tau0)
# assert list(fx1z) == list(s_fx1z)
# ------------------------------- Test the derivative to x1 of fz with substitution of z via fx1 ---------------------
fx1z_diff = calc_fx1z_diff(sx1,
sK,
sw,
sa,
sb,
sd,
stau1,
stau0,
model=model,
zmode=zmode)
sfx1z_diff = symbol_eqtn_fx1z_diff(n, model, zmode)[:2]
# for ii in range(n):
# assert list(fx1z_diff[ii]) == list(sfx1z_diff[1][ii, :])
# -------------------------------- Test symbolic fx2 with substitution of y2 via fy2 ----------------------------------
if model != "2d":
sfx2y2 = symbol_eqtn_fx2y2(n, x2_neg=False, shape=(n, ))[:2]
# ----------------------------------------------- Test calc_fx1_2d_taylor ---------------------------------------------
x_taylor = symbol_vars(n, ["x1lin"],
shape=(n, ))[0] # x_taylor = -4.5/3 (=x1lin)
fx1lin = calc_fx1_2d_taylor(sx1,
x_taylor,
sz,
syc,
sIext1,
sslope,
sa,
sb,
stau1,
x1_neg=True,
order=2,
shape=(n, ))
sfx1lin = symbol_calc_2d_taylor(n,
"x1lin",
order=2,
x1_neg=True,
slope="slope",
Iext1="Iext1",
shape=(n, ))[:2]
# for ii in range(3):
# assert numpy.array(fx1lin[ii].expand(sx1[ii]).collect(sx1[ii])) == numpy.array(
# sfx1lin[1][ii].expand(sx1[ii]).collect(sx1[ii]))
calc_fx1_2d_taylor(x1,
-1.5,
z,
yc,
Iext1,
slope,
a=a,
b=b,
d=d,
tau1=tau1,
x1_neg=True,
order=2,
shape=(n, ))
# ----------------------------------------- Test calc_fx1y1_6d_diff_x1 -------------------------------------------------
fx1y1_6d_diff_x1 = calc_fx1y1_6d_diff_x1(sx1, syc, sIext1, sa, sb, sd,
stau1, stau0)
sfx1y1_6d_diff_x1 = symbol_calc_fx1y1_6d_diff_x1(n, shape=(n, ))[:2]
# for ii in range(n):
# assert fx1y1_6d_diff_x1[ii].expand(sx1[ii]).collect(sx1[ii]) == sfx1y1_6d_diff_x1[1][ii].expand(sx1[ii]).collect(sx1[ii])
# ------------------------------- Test eq_x1_hypo_x0_optimize_fun & eq_x1_hypo_x0_optimize_jac --------------------------
ix0 = numpy.array([1, 2])
iE = numpy.array([0])
x = numpy.empty_like(sx1).flatten()
x[ix0] = sx1[ix0]
x[iE] = sx0[iE]
eq_x1_hypo_x0_optimize(ix0,
iE,
x1eq,
zeq,
x0[ix0],
K,
w,
yc,
Iext1,
a=A_DEF,
b=B_DEF,
d=D_DEF,
slope=SLOPE_DEF)
eq_x1_hypo_x0_optimize_fun(x, ix0, iE, sx1, numpy.array(sz), sx0[ix0],
sK, sw, syc, sIext1)
eq_x1_hypo_x0_optimize_jac(x, ix0, iE, sx1, numpy.array(sz), sx0[ix0],
sK, sw, sy1, sIext1)
eq_x1_hypo_x0_optimize(ix0, iE, x1eq, zeq, x0[ix0], K, w, yc, Iext1)
eq_x1_hypo_x0_linTaylor(ix0, iE, x1eq, zeq, x0[ix0], K, w, yc, Iext1)
# ------------------------------------------ Test calc_fz_jac_square_taylor ----------------------------------------------
calc_fz_jac_square_taylor(numpy.array(sz),
syc,
sIext1,
sK,
sw,
tau1=tau1,
tau0=tau0)
lfz_jac_square_taylor, sfz_jac_square_taylor, v = symbol_calc_fz_jac_square_taylor(
n)
sfz_jac_square_taylor = Matrix(sfz_jac_square_taylor).reshape(n, n)
for iv in range(n):
for jv in range(n):
sfz_jac_square_taylor[iv,
jv] = sfz_jac_square_taylor[iv, jv].subs(
[(v["x_taylor"][jv], x1sq[jv]),
(v["a"][jv], a[jv]),
(v["b"][jv], b[jv]),
(v["d"][jv], d[jv]),
(v["tau1"][iv], tau1[iv]),
(v["tau0"][iv], tau2[iv])])
assert list(
calc_fz_jac_square_taylor(
z, yc, Iext1, K, w, tau1=tau1, tau0=tau0)[0]) == list(
lfz_jac_square_taylor(zeq, yc, Iext1, K, w, a, b, d, tau1,
tau0, x1sq)[0])
class SimulatorJava(ABCSimulator):
"""
From a VEP Hypothesis, write a custom JSON simulation configuration.
To run a simulation, we can also open a GUI and import the resulted JSON file.
"""
logger = initialize_logger(__name__)
reader = H5Reader()
json_custom_config_file = "SimulationConfiguration.json"
def __init__(self, connectivity, model_configuration, simulation_settings):
self.model = None
self.simulation_settings = simulation_settings
self.model_configuration = model_configuration
self.connectivity = connectivity
self.head_path = os.path.dirname(self.connectivity.file_path)
self.json_config_path = os.path.join(self.head_path,
self.json_custom_config_file)
self.configure_model()
def get_vois(self):
return self.model.vois
@staticmethod
def _save_serialized(ep_full_config, result_path):
json_text = json.dumps(obj_to_dict(ep_full_config), indent=2)
result_file = open(result_path, 'w')
result_file.write(json_text)
result_file.close()
def config_simulation(self):
ep_settings = Settings(
integration_step=self.simulation_settings.integration_step,
noise_seed=self.simulation_settings.noise_seed,
simulated_period=self.simulation_settings.simulated_period,
downsampling_period=self.simulation_settings.
monitor_sampling_period)
if isinstance(self.simulation_settings.noise_intensity, (float, int)):
self.logger.info("Using uniform noise %s" %
self.simulation_settings.noise_intensity)
ep_settings.noise_intensity = self.simulation_settings.noise_intensity
elif len(self.simulation_settings.noise_intensity
) == JavaEpileptor._nvar:
self.logger.info("Using noise/voi %s" %
self.simulation_settings.noise_intensity)
ep_settings.set_voi_noise_dispersions(
self.simulation_settings.noise_intensity,
self.connectivity.number_of_regions)
elif len(
self.simulation_settings.noise_intensity
) == JavaEpileptor._nvar * self.connectivity.number_of_regions:
self.logger.info("Using node noise %s" %
self.simulation_settings.noise_intensity)
ep_settings.set_node_noise_dispersions(
self.simulation_settings.noise_intensity)
else:
self.logger.warning("Could not set noise %s" %
self.simulation_settings.noise_intensity)
json_model = self.prepare_epileptor_model_for_json(
self.connectivity.number_of_regions)
# TODO: history length has to be computed given the time delays (i.e., the tract lengths...)
# TODO: when dfun is implemented for JavaEpileptor, we can use commented lines with initial_conditions
# initial_conditions = self.prepare_initial_conditions(history_length=1)
# custom_config = FullConfiguration(connectivity_path=os.path.abspath(self.connectivity.file_path),
# epileptor_params=json_model, settings=ep_settings,
# initial_states=initial_conditions.flatten(),
# initial_states_shape=numpy.array(initial_conditions.shape))
custom_config = FullConfiguration(connectivity_path=os.path.abspath(
self.connectivity.file_path),
epileptor_params=json_model,
settings=ep_settings,
initial_states=None,
initial_states_shape=None)
self._save_serialized(custom_config, self.json_config_path)
def launch_simulation(self):
opts = "java -Dncsa.hdf.hdf5lib.H5.hdf5lib=" + os.path.join(GenericConfig.LIB_PATH, GenericConfig.HDF5_LIB) + \
" " + "-Djava.library.path=" + GenericConfig.LIB_PATH + " " + "-cp" + " " + GenericConfig.JAR_PATH + \
" " + GenericConfig.JAVA_MAIN_SIM + " " + os.path.abspath(self.json_config_path) + " " + \
os.path.abspath(self.head_path)
try:
status = subprocess.call(opts, shell=True)
print(status)
except:
status = False
self.logger.warning("Something went wrong with this simulation...")
time, data = self.reader.read_ts(
os.path.join(self.head_path, "full-configuration", "ts.h5"))
return time, data, status
def prepare_epileptor_model_for_json(self, no_regions=88):
epileptor_params_list = []
self.logger.warning("No of regions is " + str(no_regions))
for idx in xrange(no_regions):
epileptor_params_list.append(
EpileptorParams(self.model.a[idx], self.model.b[idx],
self.model.c[idx], self.model.d[idx],
self.model.aa[idx], self.model.r[idx],
self.model.Kvf[idx], self.model.Kf[idx],
self.model.Ks[idx], self.model.tau[idx],
self.model.Iext[idx], self.model.Iext2[idx],
self.model.slope[idx], self.model.x0[idx],
self.model.tt[idx]))
return epileptor_params_list
def configure_model(self):
x0 = calc_x0_val_to_model_x0(
self.model_configuration.x0_values, self.model_configuration.yc,
self.model_configuration.Iext1, self.model_configuration.a,
self.model_configuration.b - self.model_configuration.d)
self.model = JavaEpileptor(a=self.model_configuration.a,
b=self.model_configuration.b,
d=self.model_configuration.d,
x0=x0,
iext=self.model_configuration.Iext1,
ks=self.model_configuration.K,
c=self.model_configuration.yc,
tt=self.model_configuration.tau1,
r=1.0 / self.model_configuration.tau0)
def configure_initial_conditions(self, initial_conditions=None):
if isinstance(initial_conditions, numpy.ndarray):
self.initial_conditions = initial_conditions
else:
# TODO: have a function to calculate the correct history length when we have time delays
self.initial_conditions = self.prepare_initial_conditions(
history_length=1)
class TimeseriesService(object):
logger = initialize_logger(__name__)
def __init__(self, logger=initialize_logger(__name__)):
self.logger = logger
def decimate(self, timeseries, decim_ratio):
if decim_ratio > 1:
return Timeseries(timeseries.data[0:timeseries.time_length:decim_ratio], timeseries.dimension_labels,
timeseries.time_start, decim_ratio*timeseries.time_step, timeseries.time_unit)
else:
return timeseries
def decimate_by_filtering(self, timeseries, decim_ratio):
if decim_ratio > 1:
decim_data, decim_time, decim_dt, decim_n_times = decimate_signals(timeseries.squeezed,
timeseries.time_line, decim_ratio)
return Timeseries(decim_data, timeseries.dimension_labels,
decim_time[0], decim_dt, timeseries.time_unit)
else:
return timeseries
def convolve(self, timeseries, win_len=None, kernel=None):
if kernel is None:
kernel = np.ones((np.int(np.round(win_len)), 1, 1, 1))
else:
kernel = kernel * np.ones((np.int(np.round(win_len)), 1, 1, 1))
return Timeseries(convolve(timeseries.data, kernel, mode='same'), timeseries.dimension_labels,
timeseries.time_start, timeseries.time_step, timeseries.time_unit)
def hilbert_envelope(self, timeseries):
return Timeseries(np.abs(hilbert(timeseries.data, axis=0)), timeseries.dimension_labels,
timeseries.time_start, timeseries.time_step, timeseries.time_unit)
def detrend(self, timeseries, type='linear'):
return Timeseries(detrend(timeseries.data, axis=0, type=type), timeseries.dimension_labels,
timeseries.time_start, timeseries.time_step, timeseries.time_unit)
def normalize(self, timeseries, normalization=None):
return Timeseries(normalize_signals(timeseries.data, normalization), timeseries.dimension_labels,
timeseries.time_start, timeseries.time_step, timeseries.time_unit)
def filter(self, timeseries, lowcut=None, highcut=None, mode='bandpass', order=3):
return Timeseries(filter_data(timeseries.data, timeseries.sampling_frequency, lowcut, highcut, mode, order),
timeseries.dimension_labels, timeseries.time_start, timeseries.time_step, timeseries.time_unit)
def log(self, timeseries):
return Timeseries(np.log(timeseries.data), timeseries.dimension_labels,
timeseries.time_start, timeseries.time_step, timeseries.time_unit)
def power(self, timeseries):
return np.sum(self.square(timeseries).squeezed, axis=0)
def square(self, timeseries):
return Timeseries(timeseries.data ** 2, timeseries.dimension_labels,
timeseries.time_start, timeseries.time_step, timeseries.time_unit)
def correlation(self, timeseries):
return np.corrcoef(timeseries.squeezed.T)
def select_by_metric(self, timeseries, metric, metric_th=None):
return timeseries.get_subspace_by_index(select_greater_values_array_inds(metric, metric_th))
def select_by_power(self, timeseries, power=np.array([]), power_th=None):
if len(power) != timeseries.number_of_labels:
power = self.power(timeseries)
return self.select_by_metric(timeseries, power, power_th)
def select_by_hierarchical_group_metric_clustering(self, timeseries, distance, disconnectivity=np.array([]),
metric=None, n_groups=10, members_per_group=1):
selection = select_by_hierarchical_group_metric_clustering(distance, disconnectivity, metric,
n_groups, members_per_group)
return timeseries.get_subspace_by_index(selection)
def select_by_correlation_power(self, timeseries, correlation=np.array([]), disconnectivity=np.array([]),
power=np.array([]), n_groups=10, members_per_group=1):
if correlation.shape[0] != timeseries.number_of_labels:
correlation = self.correlation(timeseries)
if len(power) != timeseries.number_of_labels:
power = self.power(timeseries)
return self.select_by_hierarchical_group_metric_clustering(timeseries, 1-correlation,
disconnectivity, power, n_groups, members_per_group)
def select_by_rois_proximity(self, timeseries, proximity, proximity_th=None):
initial_selection = range(timeseries.number_of_labels)
selection = []
for prox in proximity:
selection += (
np.array(initial_selection)[select_greater_values_array_inds(prox, proximity_th)]).tolist()
return timeseries.get_subspace_by_index(np.unique(selection).tolist())
def select_by_rois(self, timeseries, rois, all_labels):
for ir, roi in rois:
if not(isinstance(roi, basestring)):
rois[ir] = all_labels[roi]
return timeseries.get_subspace_by_labels(rois)
def compute_seeg(self, source_timeseries, sensors, sum_mode="lin"):
if sum_mode == "exp":
seeg_fun = lambda source, gain_matrix: np.log(np.exp(source.squeezed).dot(gain_matrix.T))
else:
seeg_fun = lambda source, gain_matrix: source.squeezed.dot(gain_matrix.T)
seeg = []
for sensor in ensure_list(sensors):
seeg.append(Timeseries(seeg_fun(source_timeseries, sensor.gain_matrix),
{TimeseriesDimensions.SPACE.value: sensor.labels,
TimeseriesDimensions.VARIABLES.value:
PossibleVariables.SEEG.value + str(sensor.labels)},
source_timeseries.time_start, source_timeseries.time_step,
source_timeseries.time_unit))
return seeg
class ModelConfigurationBuilder(object):
logger = initialize_logger(__name__)
x1EQcr = X1_EQ_CR_DEF
def __init__(self, number_of_regions=1, x0_values=X0_DEF, e_values=E_DEF, yc=YC_DEF, Iext1=I_EXT1_DEF,
Iext2=I_EXT2_DEF, K=K_DEF, a=A_DEF, b=B_DEF, d=D_DEF, slope=SLOPE_DEF, s=S_DEF, gamma=GAMMA_DEF,
zmode=np.array("lin"), x1eq_mode="optimize"):
self.number_of_regions = number_of_regions
self.x0_values = x0_values * np.ones((self.number_of_regions,), dtype=np.float32)
self.yc = yc
self.Iext1 = Iext1
self.Iext2 = Iext2
self.a = a
self.b = b
self.d = d
self.slope = slope
self.s = s
self.gamma = gamma
self.zmode = zmode
self.x1eq_mode = x1eq_mode
if len(ensure_list(K)) == 1:
self.K_unscaled = np.array(K) * np.ones((self.number_of_regions,), dtype=np.float32)
elif len(ensure_list(K)) == self.number_of_regions:
self.K_unscaled = np.array(K)
else:
self.logger.warning(
"The length of input global coupling K is neither 1 nor equal to the number of regions!" +
"\nSetting model_configuration_builder.K_unscaled = K_DEF for all regions")
self.K = None
self._normalize_global_coupling()
self.e_values = e_values * np.ones((self.number_of_regions,), dtype=np.float32)
self.x0cr = 0.0
self.rx0 = 0.0
self._compute_critical_x0_scaling()
def __repr__(self):
d = {"01. Number of regions": self.number_of_regions,
"02. x0_values": self.x0_values,
"03. e_values": self.e_values,
"04. K_unscaled": self.K_unscaled,
"05. K": self.K,
"06. yc": self.yc,
"07. Iext1": self.Iext1,
"08. Iext2": self.Iext2,
"09. K": self.K,
"10. a": self.a,
"11. b": self.b,
"12. d": self.d,
"13. s": self.s,
"14. slope": self.slope,
"15. gamma": self.gamma,
"16. zmode": self.zmode,
"07. x1eq_mode": self.x1eq_mode
}
return formal_repr(self, d)
def __str__(self):
return self.__repr__()
def set_attribute(self, attr_name, data):
setattr(self, attr_name, data)
def _compute_model_x0(self, x0_values):
return calc_x0_val_to_model_x0(x0_values, self.yc, self.Iext1, self.a, self.b, self.d, self.zmode)
def _ensure_equilibrum(self, x1EQ, zEQ):
temp = x1EQ > self.x1EQcr - 10 ** (-3)
if temp.any():
x1EQ[temp] = self.x1EQcr - 10 ** (-3)
zEQ = self._compute_z_equilibrium(x1EQ)
return x1EQ, zEQ
def _compute_x1_equilibrium_from_E(self, e_values):
array_ones = np.ones((self.number_of_regions,), dtype=np.float32)
return ((e_values - 5.0) / 3.0) * array_ones
def _compute_z_equilibrium(self, x1EQ):
return calc_eq_z(x1EQ, self.yc, self.Iext1, "2d", slope=self.slope, a=self.a, b=self.b, d=self.d)
def _compute_critical_x0_scaling(self):
(self.x0cr, self.rx0) = calc_x0cr_r(self.yc, self.Iext1, a=self.a, b=self.b, d=self.d, zmode=self.zmode)
def _compute_coupling_at_equilibrium(self, x1EQ, model_connectivity):
return calc_coupling(x1EQ, self.K, model_connectivity)
def _compute_x0_values_from_x0_model(self, x0):
return calc_model_x0_to_x0_val(x0, self.yc, self.Iext1, self.a, self.b, self.d, self.zmode)
def _compute_x0_values(self, x1EQ, zEQ, model_connectivity):
x0 = calc_x0(x1EQ, zEQ, self.K, model_connectivity)
return self._compute_x0_values_from_x0_model(x0)
def _compute_e_values(self, x1EQ):
return 3.0 * x1EQ + 5.0
def _compute_params_after_equilibration(self, x1EQ, zEQ, model_connectivity):
self._compute_critical_x0_scaling()
Ceq = self._compute_coupling_at_equilibrium(x1EQ, model_connectivity)
x0_values = self._compute_x0_values(x1EQ, zEQ, model_connectivity)
e_values = self._compute_e_values(x1EQ)
x0 = self._compute_model_x0(x0_values)
return x0, Ceq, x0_values, e_values
def _compute_x1_and_z_equilibrium_from_E(self, e_values):
x1EQ = self._compute_x1_equilibrium_from_E(e_values)
zEQ = self._compute_z_equilibrium(x1EQ)
return x1EQ, zEQ
def _compute_x1_equilibrium(self, e_indices, x1EQ, zEQ, x0_values, model_connectivity):
self._compute_critical_x0_scaling()
x0 = self._compute_model_x0(x0_values)
x0_indices = np.delete(np.array(range(model_connectivity.shape[0])), e_indices)
if self.x1eq_mode == "linTaylor":
x1EQ = \
eq_x1_hypo_x0_linTaylor(x0_indices, e_indices, x1EQ, zEQ, x0, self.K,
model_connectivity, self.yc, self.Iext1, self.a, self.b, self.d)[0]
else:
x1EQ = \
eq_x1_hypo_x0_optimize(x0_indices, e_indices, x1EQ, zEQ, x0, self.K,
model_connectivity, self.yc, self.Iext1, self.a, self.b, self.d)[0]
return x1EQ
def _normalize_global_coupling(self):
self.K = self.K_unscaled / self.number_of_regions
def _configure_model_from_equilibrium(self, x1EQ, zEQ, model_connectivity):
# x1EQ, zEQ = self._ensure_equilibrum(x1EQ, zEQ) # We don't this by default anymore
x0, Ceq, x0_values, e_values = self._compute_params_after_equilibration(x1EQ, zEQ, model_connectivity)
return ModelConfiguration(self.yc, self.Iext1, self.Iext2, self.K, self.a, self.b, self.d,
self.slope, self.s, self.gamma, x1EQ, zEQ, Ceq, x0, x0_values,
e_values, self.zmode, model_connectivity)
def build_model_from_E_hypothesis(self, disease_hypothesis, model_connectivity):
# Always normalize K first
self._normalize_global_coupling()
# Then apply connectivity disease hypothesis scaling if any:
if len(disease_hypothesis.w_indices) > 0:
model_connectivity *= disease_hypothesis.get_connectivity_disease()
# All nodes except for the diseased ones will get the default epileptogenicity:
e_values = np.array(self.e_values)
e_values[disease_hypothesis.e_indices] = disease_hypothesis.e_values
# Compute equilibrium from epileptogenicity:
x1EQ, zEQ = self._compute_x1_and_z_equilibrium_from_E(e_values)
return self._configure_model_from_equilibrium(x1EQ, zEQ, model_connectivity)
def build_model_from_hypothesis(self, disease_hypothesis, model_connectivity):
# Always normalize K first
self._normalize_global_coupling()
# Then apply connectivity disease hypothesis scaling if any:
if len(disease_hypothesis.w_indices) > 0:
model_connectivity *= disease_hypothesis.get_connectivity_disease()
# We assume that all nodes have the default (healthy) excitability:
x0_values = np.array(self.x0_values)
# ...and some excitability-diseased ones:
x0_values[disease_hypothesis.x0_indices] = disease_hypothesis.x0_values
# x0_values values must have size of len(x0_indices):
x0_values = np.delete(x0_values, disease_hypothesis.e_indices)
# There might be some epileptogenicity-diseased regions as well:
# Initialize with the default e_values
e_values = np.array(self.e_values)
# and assign any diseased E_values if any
e_values[disease_hypothesis.e_indices] = disease_hypothesis.e_values
# Compute equilibrium from epileptogenicity:
x1EQ_temp, zEQ_temp = self._compute_x1_and_z_equilibrium_from_E(e_values)
# Now, solve the system in order to compute equilibrium:
x1EQ = self._compute_x1_equilibrium(disease_hypothesis.e_indices, x1EQ_temp, zEQ_temp, x0_values,
model_connectivity)
zEQ = self._compute_z_equilibrium(x1EQ)
return self._configure_model_from_equilibrium(x1EQ, zEQ, model_connectivity)
# TODO: This is used from PSE for varying an attribute's value. We should find a better way, not hardcoded strings.
def set_attributes_from_pse(self, values, paths, indices):
for i, val in enumerate(paths):
vals = val.split(".")
if vals[0] == "model_configuration_builder":
getattr(self, vals[1])[indices[i]] = values[i]
def __init__(self, logger=initialize_logger(__name__)):
self.logger = logger
def main_vep(config=Config(),
ep_name=EP_NAME,
K_unscaled=K_DEF,
ep_indices=[],
hyp_norm=0.99,
manual_hypos=[],
sim_type="paper",
pse_flag=PSE_FLAG,
sa_pse_flag=SA_PSE_FLAG,
sim_flag=SIM_FLAG,
n_samples=1000,
test_write_read=False):
logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
# -------------------------------Reading data-----------------------------------
reader = TVBReader() if config.input.IS_TVB_MODE else H5Reader()
writer = H5Writer()
logger.info("Reading from: " + config.input.HEAD)
head = reader.read_head(config.input.HEAD)
plotter = Plotter(config)
plotter.plot_head(head)
if test_write_read:
writer.write_head(head, os.path.join(config.out.FOLDER_RES, "Head"))
# --------------------------Hypothesis definition-----------------------------------
hypotheses = []
# Reading a h5 file:
if len(ep_name) > 0:
# For an Excitability Hypothesis you leave e_indices empty
# For a Mixed Hypothesis: you give as e_indices some indices for values > 0
# For an Epileptogenicity Hypothesis: you give as e_indices all indices for values > 0
hyp_file = HypothesisBuilder(head.connectivity.number_of_regions, config=config).set_normalize(hyp_norm). \
build_hypothesis_from_file(ep_name, e_indices=ep_indices)
hyp_file.name += ep_name
# print(hyp_file.string_regions_disease(head.connectivity.region_labels))
hypotheses.append(hyp_file)
hypotheses += manual_hypos
# --------------------------Hypothesis and LSA-----------------------------------
for hyp in hypotheses:
logger.info("\n\nRunning hypothesis: " + hyp.name)
all_regions_indices = np.array(range(head.number_of_regions))
healthy_indices = np.delete(all_regions_indices,
hyp.regions_disease_indices).tolist()
logger.info("\n\nCreating model configuration...")
model_config_builder = ModelConfigurationBuilder(hyp.number_of_regions,
K=K_unscaled,
tau1=TAU1_DEF,
tau0=TAU0_DEF)
mcs_file = os.path.join(config.out.FOLDER_RES,
hyp.name + "_model_config_builder.h5")
writer.write_model_configuration_builder(model_config_builder,
mcs_file)
if test_write_read:
logger.info(
"Written and read model configuration services are identical?: "
+ str(
assert_equal_objects(
model_config_builder,
reader.read_model_configuration_builder(mcs_file),
logger=logger)))
# Fix healthy regions to default equilibria:
# model_configuration = \
# model_config_builder.build_model_from_E_hypothesis(hyp, head.connectivity.normalized_weights)
# Fix healthy regions to default x0s:
model_configuration = \
model_config_builder.build_model_from_hypothesis(hyp, head.connectivity.normalized_weights)
mc_path = os.path.join(config.out.FOLDER_RES,
hyp.name + "_ModelConfig.h5")
writer.write_model_configuration(model_configuration, mc_path)
if test_write_read:
logger.info(
"Written and read model configuration are identical?: " + str(
assert_equal_objects(model_configuration,
reader.read_model_configuration(
mc_path),
logger=logger)))
# Plot nullclines and equilibria of model configuration
plotter.plot_state_space(model_configuration,
"6d",
head.connectivity.region_labels,
special_idx=hyp.regions_disease_indices,
zmode="lin",
figure_name=hyp.name + "_StateSpace")
logger.info("\n\nRunning LSA...")
lsa_service = LSAService(eigen_vectors_number=1)
lsa_hypothesis = lsa_service.run_lsa(hyp, model_configuration)
lsa_path = os.path.join(config.out.FOLDER_RES,
lsa_hypothesis.name + "_LSA.h5")
lsa_config_path = os.path.join(config.out.FOLDER_RES,
lsa_hypothesis.name + "_LSAConfig.h5")
writer.write_hypothesis(lsa_hypothesis, lsa_path)
writer.write_lsa_service(lsa_service, lsa_config_path)
if test_write_read:
logger.info("Written and read LSA services are identical?: " + str(
assert_equal_objects(lsa_service,
reader.read_lsa_service(lsa_config_path),
logger=logger)))
logger.info(
"Written and read LSA hypotheses are identical (no input check)?: "
+ str(
assert_equal_objects(lsa_hypothesis,
reader.read_hypothesis(lsa_path),
logger=logger)))
plotter.plot_lsa(lsa_hypothesis,
model_configuration,
lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number,
head.connectivity.region_labels,
None,
lsa_service=lsa_service)
if pse_flag:
# --------------Parameter Search Exploration (PSE)-------------------------------
logger.info("\n\nRunning PSE LSA...")
pse_results = pse_from_lsa_hypothesis(
n_samples,
lsa_hypothesis,
head.connectivity.normalized_weights,
model_config_builder,
lsa_service,
head.connectivity.region_labels,
param_range=0.1,
global_coupling=[{
"indices": all_regions_indices
}],
healthy_regions_parameters=[{
"name": "x0_values",
"indices": healthy_indices
}],
logger=logger,
save_flag=True)[0]
plotter.plot_lsa(lsa_hypothesis, model_configuration,
lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number,
head.connectivity.region_labels, pse_results)
pse_lsa_path = os.path.join(
config.out.FOLDER_RES,
lsa_hypothesis.name + "_PSE_LSA_results.h5")
writer.write_dictionary(pse_results, pse_lsa_path)
if test_write_read:
logger.info(
"Written and read sensitivity analysis parameter search results are identical?: "
+ str(
assert_equal_objects(pse_results,
reader.read_dictionary(
pse_lsa_path),
logger=logger)))
if sa_pse_flag:
# --------------Sensitivity Analysis Parameter Search Exploration (PSE)-------------------------------
logger.info("\n\nrunning sensitivity analysis PSE LSA...")
sa_results, pse_sa_results = \
sensitivity_analysis_pse_from_lsa_hypothesis(n_samples, lsa_hypothesis,
head.connectivity.normalized_weights,
model_config_builder, lsa_service,
head.connectivity.region_labels,
method="sobol", param_range=0.1,
global_coupling=[{"indices": all_regions_indices,
"bounds": [0.0, 2 *
model_config_builder.K_unscaled[
0]]}],
healthy_regions_parameters=[
{"name": "x0_values", "indices": healthy_indices}],
config=config)
plotter.plot_lsa(lsa_hypothesis,
model_configuration,
lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number,
head.connectivity.region_labels,
pse_sa_results,
title="SA PSE Hypothesis Overview")
sa_pse_path = os.path.join(
config.out.FOLDER_RES,
lsa_hypothesis.name + "_SA_PSE_LSA_results.h5")
sa_lsa_path = os.path.join(
config.out.FOLDER_RES,
lsa_hypothesis.name + "_SA_LSA_results.h5")
writer.write_dictionary(pse_sa_results, sa_pse_path)
writer.write_dictionary(sa_results, sa_lsa_path)
if test_write_read:
logger.info(
"Written and read sensitivity analysis results are identical?: "
+ str(
assert_equal_objects(sa_results,
reader.read_dictionary(
sa_lsa_path),
logger=logger)))
logger.info(
"Written and read sensitivity analysis parameter search results are identical?: "
+ str(
assert_equal_objects(pse_sa_results,
reader.read_dictionary(
sa_pse_path),
logger=logger)))
if sim_flag:
# --------------------------Simulation preparations-----------------------------------
# If you choose model...
# Available models beyond the TVB Epileptor (they all encompass optional variations from the different papers):
# EpileptorDP: similar to the TVB Epileptor + optional variations,
# EpileptorDP2D: reduced 2D model, following Proix et all 2014 +optional variations,
# EpleptorDPrealistic: starting from the TVB Epileptor + optional variations, but:
# -x0, Iext1, Iext2, slope and K become noisy state variables,
# -Iext2 and slope are coupled to z, g, or z*g in order for spikes to appear before seizure,
# -correlated noise is also used
# We don't want any time delays for the moment
head.connectivity.tract_lengths *= config.simulator.USE_TIME_DELAYS_FLAG
sim_types = ensure_list(sim_type)
integrator = "HeunStochastic"
for sim_type in sim_types:
# ------------------------------Simulation--------------------------------------
logger.info(
"\n\nConfiguring simulation from model_configuration...")
sim_builder = SimulatorBuilder(config.simulator.MODE)
if isequal_string(sim_type, "realistic"):
model.tau0 = 60000.0
model.tau1 = 0.2
model.slope = 0.25
model.Iext2 = 0.45
model.pmode = np.array(
"z") # np.array("None") to opt out for feedback
sim_settings = \
sim_builder.set_fs(2048.0).set_fs_monitor(1024.0).set_simulated_period(60000).build_sim_settings()
sim_settings.noise_type = COLORED_NOISE
sim_settings.noise_ntau = 20
integrator = "Dop853Stochastic"
elif isequal_string(sim_type, "fitting"):
sim_settings = sim_builder.set_model_name("EpileptorDP2D").set_fs(2048.0).set_fs_monitor(2048.0).\
set_simulated_period(2000).build_sim_settings()
sim_settings.noise_intensity = 1e-5
model = sim_builder.generate_model_tvb(model_configuration)
model.tau0 = 300.0
model.tau1 = 0.5
elif isequal_string(sim_type, "reduced"):
sim_settings = sim_builder.set_model_name("EpileptorDP2D").set_fs(4096.0). \
set_simulated_period(1000).build_sim_settings()
model = sim_builder.generate_model_tvb(model_configuration)
elif isequal_string(sim_type, "paper"):
sim_builder.set_model_name("Epileptor")
sim_settings = sim_builder.build_sim_settings()
model = sim_builder.generate_model_tvb(model_configuration)
else:
sim_settings = sim_builder.build_sim_settings()
model = sim_builder.generate_model_tvb(model_configuration)
sim, sim_settings, model = \
sim_builder.build_simulator_TVB_from_model_sim_settings(model_configuration,head.connectivity,
model, sim_settings, integrator=integrator)
# Integrator and initial conditions initialization.
# By default initial condition is set right on the equilibrium point.
writer.write_simulator_model(
sim.model, sim.connectivity.number_of_regions,
os.path.join(config.out.FOLDER_RES,
lsa_hypothesis.name + "_sim_model.h5"))
logger.info("\n\nSimulating...")
sim_output, status = sim.launch_simulation(
report_every_n_monitor_steps=100)
sim_path = os.path.join(
config.out.FOLDER_RES,
lsa_hypothesis.name + "_sim_settings.h5")
writer.write_simulation_settings(sim.simulation_settings,
sim_path)
if test_write_read:
# TODO: find out why it cannot set monitor expressions
logger.info(
"Written and read simulation settings are identical?: "
+ str(
assert_equal_objects(
sim.simulation_settings,
reader.read_simulation_settings(sim_path),
logger=logger)))
if not status:
logger.warning("\nSimulation failed!")
else:
time = np.array(sim_output.time_line).astype("f")
logger.info("\n\nSimulated signal return shape: %s",
sim_output.shape)
logger.info("Time: %s - %s", time[0], time[-1])
logger.info("Values: %s - %s", sim_output.data.min(),
sim_output.data.max())
if not status:
logger.warning("\nSimulation failed!")
else:
sim_output, seeg = compute_seeg_and_write_ts_to_h5(
sim_output,
sim.model,
head.sensorsSEEG,
os.path.join(config.out.FOLDER_RES,
model._ui_name + "_ts.h5"),
seeg_gain_mode="lin",
hpf_flag=True,
hpf_low=10.0,
hpf_high=512.0)
# Plot results
plotter.plot_simulated_timeseries(
sim_output,
sim.model,
lsa_hypothesis.lsa_propagation_indices,
seeg_list=seeg,
spectral_raster_plot=False,
title_prefix=hyp.name,
spectral_options={"log_scale": True})
def main_sampling_service(config=Config()):
logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
n_samples = 100
logger.info("\nDeterministic numpy.linspace sampling:")
sampler = DeterministicSamplingService(n_samples=n_samples, grid_mode=True)
samples, stats = sampler.generate_samples(low=1.0,
high=2.0,
shape=(2, ),
stats=True)
for key, value in stats.iteritems():
logger.info("\n" + key + ": " + str(value))
logger.info(sampler.__repr__())
writer = H5Writer()
writer.write_generic(sampler, config.out.FOLDER_RES,
"test_Stochastic_Sampler.h5")
logger.info("\nStochastic uniform sampling with numpy:")
sampler = StochasticSamplingService(n_samples=n_samples,
sampling_module="numpy")
# a (low), b (high)
samples, stats = sampler.generate_samples(
parameter=(1.0, 2.0),
probability_distribution=ProbabilityDistributionTypes.UNIFORM,
shape=(2, ),
stats=True)
for key, value in stats.iteritems():
logger.info("\n" + key + ": " + str(value))
logger.info(sampler.__repr__())
writer.write_generic(sampler, config.out.FOLDER_RES,
"test1_Stochastic_Sampler.h5")
logger.info("\nStochastic truncated normal sampling with scipy:")
sampler = StochasticSamplingService(n_samples=n_samples)
# loc (mean), scale (sigma)
samples, stats = sampler.generate_samples(parameter=(1.5, 1.0),
probability_distribution="norm",
low=1,
high=2,
shape=(2, ),
stats=True)
for key, value in stats.iteritems():
logger.info("\n" + key + ": " + str(value))
logger.info(sampler.__repr__())
writer.write_generic(sampler, config.out.FOLDER_RES,
"test2_Stochastic_Sampler.h5")
logger.info("\nSensitivity analysis sampling:")
sampler = SalibSamplingService(n_samples=n_samples, sampler="latin")
samples, stats = sampler.generate_samples(low=1,
high=2,
shape=(2, ),
stats=True)
for key, value in stats.iteritems():
logger.info("\n" + key + ": " + str(value))
logger.info(sampler.__repr__())
writer.write_generic(sampler, config.out.FOLDER_RES,
"test3_Stochastic_Sampler.h5")
logger.info("\nTesting distribution class and conversions...")
sampler = StochasticSamplingService(n_samples=n_samples)
for distrib_name in ProbabilityDistributionTypes.available_distributions:
logger.info("\n" + distrib_name)
logger.info("\nmode/mean, std to distribution " + distrib_name + ":")
if np.in1d(distrib_name, [
ProbabilityDistributionTypes.EXPONENTIAL,
ProbabilityDistributionTypes.CHISQUARE
]):
target_stats = {"mean": 1.0}
stats_m = "mean"
elif np.in1d(distrib_name, [
ProbabilityDistributionTypes.BERNOULLI,
ProbabilityDistributionTypes.POISSON
]):
target_stats = {"mean": np.ones((2, ))}
stats_m = "mean"
elif isequal_string(distrib_name,
ProbabilityDistributionTypes.BINOMIAL):
target_stats = {"mean": 1.0, "std": 2.0}
stats_m = "mean"
else:
if isequal_string(distrib_name,
ProbabilityDistributionTypes.UNIFORM):
target_stats = {"mean": 1.0, "std": 2.0}
stats_m = "mean"
else:
target_stats = {"mean": 1.0, "std": 2.0}
stats_m = "mean"
parameter1 = generate_stochastic_parameter(
name="test1_" + distrib_name,
low=0.0,
high=2.0,
p_shape=(2, 2),
probability_distribution=distrib_name,
optimize_pdf=True,
use="manual",
**target_stats)
name2 = "test2_" + distrib_name
defaults = set_parameter_defaults(name2,
_pdf=distrib_name,
_shape=(2, 2),
_lo=0.0,
_hi=2.0,
**(deepcopy(target_stats)))
parameter2 = set_parameter(name=name2, use="manual", **defaults)
for parameter in (parameter1, parameter2):
logger.info(str(parameter))
samples = sampler.generate_samples(parameter=parameter, stats=True)
for key, value in stats.iteritems():
logger.info("\n" + key + ": " + str(value))
diff = target_stats[stats_m] - stats[stats_m]
if np.any(np.abs(diff.flatten()) > 0.001):
logger.warning(
"Large difference between target and resulting samples' " +
stats_m + "!: " + str(diff))
del parameter
class H5Reader(object):
logger = initialize_logger(__name__)
connectivity_filename = "Connectivity.h5"
cortical_surface_filename = "CorticalSurface.h5"
region_mapping_filename = "RegionMapping.h5"
volume_mapping_filename = "VolumeMapping.h5"
structural_mri_filename = "StructuralMRI.h5"
sensors_filename_prefix = "Sensors"
sensors_filename_separator = "_"
def read_connectivity(self, path):
"""
:param path: Path towards a custom Connectivity H5 file
:return: Connectivity object
"""
self.logger.info("Starting to read a Connectivity from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
weights = h5_file['/' + ConnectivityH5Field.WEIGHTS][()]
tract_lengths = h5_file['/' + ConnectivityH5Field.TRACTS][()]
region_centres = h5_file['/' + ConnectivityH5Field.CENTERS][()]
region_labels = h5_file['/' + ConnectivityH5Field.REGION_LABELS][()]
orientations = h5_file['/' + ConnectivityH5Field.ORIENTATIONS][()]
hemispheres = h5_file['/' + ConnectivityH5Field.HEMISPHERES][()]
h5_file.close()
conn = Connectivity(path, weights, tract_lengths, region_labels, region_centres, hemispheres, orientations)
self.logger.info("Successfully read connectvity from: %s" % path)
return conn
def read_surface(self, path):
"""
:param path: Path towards a custom Surface H5 file
:return: Surface object
"""
if not os.path.isfile(path):
self.logger.warning("Surface file %s does not exist" % path)
return None
self.logger.info("Starting to read Surface from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
vertices = h5_file['/' + SurfaceH5Field.VERTICES][()]
triangles = h5_file['/' + SurfaceH5Field.TRIANGLES][()]
vertex_normals = h5_file['/' + SurfaceH5Field.VERTEX_NORMALS][()]
h5_file.close()
surface = Surface(vertices, triangles, vertex_normals)
self.logger.info("Successfully read surface from: %s" % path)
return surface
def read_sensors(self, path):
"""
:param path: Path towards a custom head folder
:return: 3 lists with all sensors from Path by type
"""
sensors_seeg = []
sensors_eeg = []
sensors_meg = []
self.logger.info("Starting to read all Sensors from: %s" % path)
all_head_files = os.listdir(path)
for head_file in all_head_files:
str_head_file = str(head_file)
if not str_head_file.startswith(self.sensors_filename_prefix):
continue
type = str_head_file[len(self.sensors_filename_prefix):str_head_file.index(self.sensors_filename_separator)]
if type == Sensors.TYPE_SEEG:
sensors_seeg.append(self.read_sensors_of_type(os.path.join(path, head_file), Sensors.TYPE_SEEG))
if type == Sensors.TYPE_EEG:
sensors_eeg.append(self.read_sensors_of_type(os.path.join(path, head_file), Sensors.TYPE_EEG))
if type == Sensors.TYPE_MEG:
sensors_meg.append(self.read_sensors_of_type(os.path.join(path, head_file), Sensors.TYPE_MEG))
self.logger.info("Successfuly read all sensors from: %s" % path)
return sensors_seeg, sensors_eeg, sensors_meg
def read_sensors_of_type(self, sensors_file, type):
"""
:param
sensors_file: Path towards a custom Sensors H5 file
type: Senors type
:return: Sensors object
"""
if not os.path.exists(sensors_file):
self.logger.warning("Senors file %s does not exist!" % sensors_file)
return None
self.logger.info("Starting to read sensors of type %s from: %s" % (type, sensors_file))
h5_file = h5py.File(sensors_file, 'r', libver='latest')
labels = h5_file['/' + SensorsH5Field.LABELS][()]
locations = h5_file['/' + SensorsH5Field.LOCATIONS][()]
if '/orientations' in h5_file:
orientations = h5_file['/orientations'][()]
else:
orientations = None
if '/' + SensorsH5Field.GAIN_MATRIX in h5_file:
gain_matrix = h5_file['/' + SensorsH5Field.GAIN_MATRIX][()]
else:
gain_matrix = None
h5_file.close()
sensors = Sensors(labels, locations, orientations=orientations, gain_matrix=gain_matrix, s_type=type)
self.logger.info("Successfully read sensors from: %s" % sensors_file)
return sensors
def read_volume_mapping(self, path):
"""
:param path: Path towards a custom VolumeMapping H5 file
:return: volume mapping in a numpy array
"""
if not os.path.isfile(path):
self.logger.warning("VolumeMapping file %s does not exist" % path)
return numpy.array([])
self.logger.info("Starting to read VolumeMapping from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
data = h5_file['/data'][()]
h5_file.close()
self.logger.info("Successfully read volume mapping!") #: %s" % data)
return data
def read_region_mapping(self, path):
"""
:param path: Path towards a custom RegionMapping H5 file
:return: region mapping in a numpy array
"""
if not os.path.isfile(path):
self.logger.warning("RegionMapping file %s does not exist" % path)
return numpy.array([])
self.logger.info("Starting to read RegionMapping from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
data = h5_file['/data'][()]
h5_file.close()
self.logger.info("Successfully read region mapping!") #: %s" % data)
return data
def read_t1(self, path):
"""
:param path: Path towards a custom StructuralMRI H5 file
:return: structural MRI in a numpy array
"""
if not os.path.isfile(path):
self.logger.warning("StructuralMRI file %s does not exist" % path)
return numpy.array([])
self.logger.info("Starting to read StructuralMRI from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
data = h5_file['/data'][()]
h5_file.close()
self.logger.info("Successfully read structural MRI from: %s" % path)
return data
def read_head(self, path):
"""
:param path: Path towards a custom head folder
:return: Head object
"""
self.logger.info("Starting to read Head from: %s" % path)
conn = self.read_connectivity(os.path.join(path, self.connectivity_filename))
srf = self.read_surface(os.path.join(path, self.cortical_surface_filename))
rm = self.read_region_mapping(os.path.join(path, self.region_mapping_filename))
vm = self.read_volume_mapping(os.path.join(path, self.volume_mapping_filename))
t1 = self.read_t1(os.path.join(path, self.structural_mri_filename))
sensorsSEEG, sensorsEEG, sensorsMEG = self.read_sensors(path)
head = Head(conn, srf, rm, vm, t1, path, sensorsSEEG=sensorsSEEG, sensorsEEG=sensorsEEG, sensorsMEG=sensorsMEG)
self.logger.info("Successfully read Head from: %s" % path)
return head
def read_epileptogenicity(self, root_folder, name="ep"):
"""
:param
root_folder: Path towards a valid custom Epileptogenicity H5 file
name: the name of the hypothesis
:return: Timeseries in a numpy array
"""
path = os.path.join(root_folder, name, name + ".h5")
self.logger.info("Starting to read Epileptogenicity from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
values = h5_file['/values'][()]
h5_file.close()
self.logger.info("Successfully read epileptogenicity values!") #: %s" % values)
return values
def read_timeseries(self, path):
"""
:param path: Path towards a valid TimeSeries H5 file
:return: Timeseries data and time in 2 numpy arrays
"""
self.logger.info("Starting to read TimeSeries from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
data = h5_file['/data'][()]
total_time = int(h5_file["/"].attrs["Simulated_period"][0])
nr_of_steps = int(h5_file["/data"].attrs["Number_of_steps"][0])
start_time = float(h5_file["/data"].attrs["Start_time"][0])
time = numpy.linspace(start_time, total_time, nr_of_steps)
self.logger.info("First Channel sv sum: " + str(numpy.sum(data[:, 0])))
self.logger.info("Successfully read Timeseries!") #: %s" % data)
h5_file.close()
return time, data
def read_hypothesis(self, path):
"""
:param path: Path towards a Hypothesis H5 file
:return: DiseaseHypothesis object
"""
self.logger.info("Starting to read Hypothesis from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
if h5_file.attrs["EPI_Subtype"] != "DiseaseHypothesis":
self.logger.warning("This file does not seem to holds a DiseaseHypothesis!")
hypothesis = DiseaseHypothesis()
for dataset in h5_file.keys():
hypothesis.set_attribute(dataset, h5_file["/" + dataset][()])
for attr in h5_file.attrs.keys():
if attr in ["x0_indices", "e_indices", "w_indices"]:
hypothesis.set_attribute(attr, h5_file.attrs[attr].tolist())
else:
hypothesis.set_attribute(attr, h5_file.attrs[attr])
h5_file.close()
return hypothesis
def read_model_configuration(self, path):
"""
:param path: Path towards a ModelConfiguration H5 file
:return: ModelConfiguration object
"""
self.logger.info("Starting to read ModelConfiguration from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
if h5_file.attrs["EPI_Subtype"] != "ModelConfiguration":
self.logger.warning("This file does not seem to hold a ModelConfiguration")
model_configuration = ModelConfiguration()
for dataset in h5_file.keys():
model_configuration.set_attribute(dataset, h5_file["/" + dataset][()])
for attr in h5_file.attrs.keys():
model_configuration.set_attribute(attr, h5_file.attrs[attr])
h5_file.close()
return model_configuration
def read_lsa_service(self, path):
"""
:param path: Path towards a LSAService H5 file
:return: LSAService object
"""
self.logger.info("Starting to read LSAService from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
from tvb_epilepsy.service.lsa_service import LSAService
lsa_service = LSAService()
for dataset in h5_file.keys():
lsa_service.set_attribute(dataset, h5_file["/" + dataset][()])
for attr in h5_file.attrs.keys():
lsa_service.set_attribute(attr, h5_file.attrs[attr])
h5_file.close()
return lsa_service
def read_model_configuration_builder(self, path):
"""
:param path: Path towards a ModelConfigurationService H5 file
:return: ModelConfigurationService object
"""
self.logger.info("Starting to read ModelConfigurationService from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
from tvb_epilepsy.service.model_configuration_builder import ModelConfigurationBuilder
mc_service = ModelConfigurationBuilder()
for dataset in h5_file.keys():
mc_service.set_attribute(dataset, h5_file["/" + dataset][()])
for attr in h5_file.attrs.keys():
mc_service.set_attribute(attr, h5_file.attrs[attr])
h5_file.close()
return mc_service
def read_model_inversions_service(self, path):
"""
:param path: Path towards a ModelConfigurationService H5 file
:return: ModelInversionService object
"""
# TODO: add a specialized reader function
model_inversions_service = self.read_dictionary(path, "OrderedDictDot")
if model_inversions_service.dict.get("signals_inds", None) is not None:
model_inversions_service.dict["signals_inds"] = model_inversions_service.dict["signals_inds"].tolist()
return model_inversions_service
def read_dictionary(self, path, type="dict"):
"""
:param path: Path towards a dictionary H5 file
:return: dict
"""
self.logger.info("Starting to read a dictionary from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
dictionary = dict()
for dataset in h5_file.keys():
dictionary.update({dataset: h5_file["/" + dataset][()]})
for attr in h5_file.attrs.keys():
dictionary.update({attr: h5_file.attrs[attr]})
h5_file.close()
if isequal_string(type, "DictDot"):
return DictDot(dictionary)
elif isequal_string(type, "OrderedDictDot"):
return OrderedDictDot(dictionary)
else:
return dictionary
def read_simulation_settings(self, path):
"""
:param path: Path towards a SimulationSettings H5 file
:return: SimulationSettings
"""
self.logger.info("Starting to read SimulationSettings from: %s" % path)
h5_file = h5py.File(path, 'r', libver='latest')
sim_settings = SimulationSettings()
for dataset in h5_file.keys():
sim_settings.set_attribute(dataset, h5_file["/" + dataset][()])
for attr in h5_file.attrs.keys():
sim_settings.set_attribute(attr, h5_file.attrs[attr])
h5_file.close()
return sim_settings
def read_generic(self, path, obj=None, output_shape=None):
return read_h5_model(path).convert_from_h5_model(obj, output_shape)
def main_cc_vep(config,
head_folder,
ep_name="clinical_hypothesis",
x0_indices=[],
pse_flag=False,
sim_flag=True):
if not (os.path.isdir(config.out.FOLDER_RES)):
os.mkdir(config.out.FOLDER_RES)
logger = initialize_logger(__name__, config.out.FOLDER_LOGS)
# -------------------------------Reading data-----------------------------------
reader = TVBReader() if config.input.IS_TVB_MODE else H5Reader()
writer = H5Writer()
logger.info("Reading from: %s", head_folder)
head = reader.read_head(head_folder)
plotter = Plotter(config)
plotter.plot_head(head)
# --------------------------Hypothesis definition-----------------------------------
hypo_builder = HypothesisBuilder(head.connectivity.number_of_regions)
all_regions_indices = np.array(range(head.number_of_regions))
# This is an example of Epileptogenicity Hypothesis:
hyp_E = hypo_builder.build_hypothesis_from_file(ep_name, x0_indices)
# This is an example of Excitability Hypothesis:
hyp_x0 = hypo_builder.build_hypothesis_from_file(ep_name)
disease_indices = hyp_E.e_indices + hyp_x0.x0_indices
healthy_indices = np.delete(all_regions_indices, disease_indices).tolist()
if len(x0_indices) > 0:
# This is an example of x0_values mixed Excitability and Epileptogenicity Hypothesis:
disease_values = reader.read_epileptogenicity(head_folder,
name=ep_name)
disease_values = disease_values.tolist()
x0_values = []
for ix0 in x0_indices:
ind = disease_indices.index(ix0)
del disease_indices[ind]
x0_values.append(disease_values.pop(ind))
e_indices = disease_indices
e_values = np.array(disease_values)
x0_values = np.array(x0_values)
hyp_x0_E = hypo_builder.set_x0_hypothesis(
x0_indices,
x0_values).set_e_hypothesis(e_indices,
e_values).build_hypothesis()
hypotheses = (hyp_E, hyp_x0, hyp_x0_E)
else:
hypotheses = (
hyp_E,
hyp_x0,
)
# --------------------------Hypothesis and LSA-----------------------------------
for hyp in hypotheses:
logger.info("Running hypothesis: %s", hyp.name)
logger.info("Creating model configuration...")
builder = ModelConfigurationBuilder(hyp.number_of_regions)
writer.write_model_configuration_builder(
builder,
os.path.join(config.out.FOLDER_RES, "model_config_service.h5"))
if hyp.type == "Epileptogenicity":
model_configuration = builder.build_model_from_E_hypothesis(
hyp, head.connectivity.normalized_weights)
else:
model_configuration = builder.build_model_from_hypothesis(
hyp, head.connectivity.normalized_weights)
writer.write_model_configuration(
model_configuration,
os.path.join(config.out.FOLDER_RES, "ModelConfiguration.h5"))
# Plot nullclines and equilibria of model configuration
plotter.plot_state_space(model_configuration,
region_labels=head.connectivity.region_labels,
special_idx=disease_indices,
model="2d",
zmode="lin",
figure_name=hyp.name + "_StateSpace")
logger.info("Running LSA...")
lsa_service = LSAService(eigen_vectors_number=None,
weighted_eigenvector_sum=True)
lsa_hypothesis = lsa_service.run_lsa(hyp, model_configuration)
writer.write_hypothesis(
lsa_hypothesis,
os.path.join(config.out.FOLDER_RES, lsa_hypothesis.name + ".h5"))
writer.write_lsa_service(
lsa_service,
os.path.join(config.out.FOLDER_RES, "lsa_config_service.h5"))
plotter.plot_lsa(lsa_hypothesis, model_configuration,
lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number,
head.connectivity.region_labels, None)
if pse_flag:
n_samples = 100
# --------------Parameter Search Exploration (PSE)-------------------------------
logger.info("Running PSE LSA...")
pse_results = pse_from_lsa_hypothesis(
lsa_hypothesis,
head.connectivity.normalized_weights,
head.connectivity.region_labels,
n_samples,
param_range=0.1,
global_coupling=[{
"indices": all_regions_indices
}],
healthy_regions_parameters=[{
"name": "x0_values",
"indices": healthy_indices
}],
model_configuration_builder=builder,
lsa_service=lsa_service,
save_flag=True,
folder_res=config.out.FOLDER_RES,
filename="PSE_LSA",
logger=logger)[0]
plotter.plot_lsa(lsa_hypothesis,
model_configuration,
lsa_service.weighted_eigenvector_sum,
lsa_service.eigen_vectors_number,
head.connectivity.region_labels,
pse_results,
title="Hypothesis PSE LSA Overview")
if sim_flag:
config.out.subfolder = "simulations"
for folder in (config.out.FOLDER_RES, config.out.FOLDER_FIGURES):
if not (os.path.isdir(folder)):
os.mkdir(folder)
dynamical_models = ["EpileptorDP2D", "EpileptorDPrealistic"]
for dynamical_model, sim_type in zip(dynamical_models,
["fitting", "realistic"]):
ts_file = None # os.path.join(sim_folder_res, dynamical_model + "_ts.h5")
vois_ts_dict = \
from_model_configuration_to_simulation(model_configuration, head, lsa_hypothesis,
sim_type=sim_type, dynamical_model=dynamical_model,
ts_file=ts_file, plot_flag=True, config=config)
import os
import numpy as np
from tvb_epilepsy.base.constants.config import Config
from tvb_epilepsy.base.utils.log_error_utils import initialize_logger
from tvb_epilepsy.base.utils.data_structures_utils import isequal_string
from tvb_epilepsy.base.model.vep.sensors import Sensors
from tvb_epilepsy.io.h5_reader import H5Reader
from tvb_epilepsy.io.h5_writer import H5Writer
from tvb_epilepsy.plot.plotter import Plotter
from tvb_epilepsy.base.epileptor_models import EpileptorDP2D
from tvb_epilepsy.service.simulator.simulator_builder import build_simulator_TVB_realistic, \
build_simulator_TVB_fitting, build_simulator_TVB_default, build_simulator_TVB_paper
from tvb_epilepsy.service.timeseries_service import TimeseriesService
logger = initialize_logger(__name__)
def _compute_and_write_seeg(source_timeseries,
sensors_list,
filename,
hpf_flag=False,
hpf_low=10.0,
hpf_high=256.0,
seeg_gain_mode="lin",
h5_writer=H5Writer()):
ts_service = TimeseriesService()
fsAVG = 1000.0 / source_timeseries.time_step
if hpf_flag:
hpf_low = max(
hpf_low, 1000.0 /
class SensitivityAnalysisService(object):
logger = initialize_logger(__name__)
def __init__(self,
inputs,
outputs,
method="delta",
calc_second_order=True,
conf_level=0.95):
self._set_method(method)
self._set_calc_second_order(calc_second_order)
self._set_conf_level(conf_level)
self.n_samples = []
self.input_names = []
self.input_bounds = []
self.input_samples = []
self.n_inputs = len(inputs)
for input in inputs:
self.input_names.append(input["name"])
samples = np.array(input["samples"]).flatten()
self.n_samples.append(samples.size)
self.input_samples.append(samples)
self.input_bounds.append(
input.get("bounds",
[samples.min(), samples.max()]))
if len(self.n_samples) > 0:
if np.all(np.array(self.n_samples) == self.n_samples[0]):
self.n_samples = self.n_samples[0]
else:
raise_value_error(
"Not all input parameters have equal number of samples!: "
+ str(self.n_samples))
self.input_samples = np.array(self.input_samples).T
self.n_outputs = 0
self.output_values = []
self.output_names = []
for output in outputs:
if output["values"].size == self.n_samples:
n_outputs = 1
self.output_values.append(output["values"].flatten())
else:
if output["values"].shape[0] == self.n_samples:
self.output_values.append(output["values"])
n_outputs = output["values"].shape[1]
elif output["values"].shape[1] == self.n_samples:
self.output_values.append(output["values"].T)
n_outputs = output["values"].shape[0]
else:
raise_value_error(
"None of the dimensions of output samples: " +
str(output["values"].shape) + " matches n_samples = " +
str(self.n_samples) + " !")
self.n_outputs += n_outputs
if n_outputs > 1 and len(output["names"]) == 1:
self.output_names += np.array([
"%s[%d]" % l
for l in zip(np.repeat(output["names"][0], n_outputs),
range(n_outputs))
]).tolist()
else:
self.output_names += output["names"]
if len(self.output_values) > 0:
self.output_values = np.vstack(self.output_values)
self.problem = {}
self.other_parameters = {}
def __repr__(self):
d = {
"01. Method": self.method,
"02. Second order calculation flag": self.calc_second_order,
"03. Confidence level": self.conf_level,
"05. Number of inputs": self.n_inputs,
"06. Number of outputs": self.n_outputs,
"07. Input names": self.input_names,
"08. Output names": self.output_names,
"09. Input bounds": self.input_bounds,
"10. Problem": dict_str(self.problem),
"11. Other parameters": dict_str(self.other_parameters),
}
return formal_repr(self, d)
def __str__(self):
return self.__repr__()
def _set_method(self, method):
method = method.lower()
if np.in1d(method, METHODS):
self.method = method
else:
raise_value_error("Method " + str(method) +
" is not one of the available methods " +
str(METHODS) + " !")
def _set_calc_second_order(self, calc_second_order):
if isinstance(calc_second_order, bool):
self.calc_second_order = calc_second_order
else:
raise_value_error("calc_second_order = " + str(calc_second_order) +
"is not a boolean as it should!")
def _set_conf_level(self, conf_level):
if isinstance(conf_level,
float) and conf_level > 0.0 and conf_level < 1.0:
self.conf_level = conf_level
else:
raise_value_error(
"conf_level = " + str(conf_level) +
"is not a float in the (0.0, 1.0) interval as it should!")
def _update_parameters(self,
method=None,
calc_second_order=None,
conf_level=None):
if method is not None:
self._set_method(method)
if calc_second_order is not None:
self._calc_set_second_order(calc_second_order)
if conf_level is not None:
self._set_conf_level(conf_level)
def run(self,
input_ids=None,
output_ids=None,
method=None,
calc_second_order=None,
conf_level=None,
**kwargs):
self._update_parameters(method, calc_second_order, conf_level)
self.other_parameters = kwargs
if input_ids is None:
input_ids = range(self.n_inputs)
self.problem = {
"num_vars": len(input_ids),
"names": np.array(self.input_names)[input_ids].tolist(),
"bounds": np.array(self.input_bounds)[input_ids].tolist()
}
if output_ids is None:
output_ids = range(self.n_outputs)
n_outputs = len(output_ids)
if self.method.lower() == "sobol":
self.logger.warning(
"'sobol' method requires 'saltelli' sampling scheme!")
# Additional keyword parameters and their defaults:
# calc_second_order (bool): Calculate second-order sensitivities (default True)
# num_resamples (int): The number of resamples used to compute the confidence intervals (default 1000)
# conf_level (float): The confidence interval level (default 0.95)
# print_to_console (bool): Print results directly to console (default False)
# parallel: False,
# n_processors: None
self.analyzer = lambda output: sobol.analyze(
self.problem,
output,
calc_second_order=self.calc_second_order,
conf_level=self.conf_level,
num_resamples=self.other_parameters.get("num_resamples", 1000),
parallel=self.other_parameters.get("parallel", False),
n_processors=self.other_parameters.get("n_processors", None),
print_to_console=self.other_parameters.get(
"print_to_console", False))
elif np.in1d(self.method.lower(), ["latin", "delta"]):
self.logger.warning(
"'latin' sampling scheme is recommended for 'delta' method!")
# Additional keyword parameters and their defaults:
# num_resamples (int): The number of resamples used to compute the confidence intervals (default 1000)
# conf_level (float): The confidence interval level (default 0.95)
# print_to_console (bool): Print results directly to console (default False)
self.analyzer = lambda output: delta.analyze(
self.problem,
self.input_samples[:, input_ids],
output,
conf_level=self.conf_level,
num_resamples=self.other_parameters.get("num_resamples", 1000),
print_to_console=self.other_parameters.get(
"print_to_console", False))
elif np.in1d(self.method.lower(), ["fast", "fast_sampler"]):
self.logger.warning(
"'fast' method requires 'fast_sampler' sampling scheme!")
# Additional keyword parameters and their defaults:
# M (int): The interference parameter,
# i.e., the number of harmonics to sum in the Fourier series decomposition (default 4)
# print_to_console (bool): Print results directly to console (default False)
self.analyzer = lambda output: fast.analyze(
self.problem,
output,
M=self.other_parameters.get("M", 4),
print_to_console=self.other_parameters.get(
"print_to_console", False))
elif np.in1d(self.method.lower(), ["ff", "fractional_factorial"]):
# Additional keyword parameters and their defaults:
# second_order (bool, default=False): Include interaction effects
# print_to_console (bool, default=False): Print results directly to console
self.logger.warning(
"'fractional_factorial' method requires 'fractional_factorial' sampling scheme!"
)
self.analyzer = lambda output: ff.analyze(
self.problem,
self.input_samples[:, input_ids],
output,
calc_second_order=self.calc_second_order,
conf_level=self.conf_level,
num_resamples=self.other_parameters.get("num_resamples", 1000),
print_to_console=self.other_parameters.get(
"print_to_console", False))
elif self.method.lower().lower() == "morris":
self.logger.warning(
"'morris' method requires 'morris' sampling scheme!")
# Additional keyword parameters and their defaults:
# num_resamples (int): The number of resamples used to compute the confidence intervals (default 1000)
# conf_level (float): The confidence interval level (default 0.95)
# print_to_console (bool): Print results directly to console (default False)
# grid_jump (int): The grid jump size, must be identical to the value passed to
# SALib.sample.morris.sample() (default 2)
# num_levels (int): The number of grid levels, must be identical to the value passed to
# SALib.sample.morris (default 4)
self.analyzer = lambda output: morris.analyze(
self.problem,
self.input_samples[:, input_ids],
output,
conf_level=self.conf_level,
grid_jump=self.other_parameters.get("grid_jump", 2),
num_levels=self.other_parameters.get("num_levels", 4),
num_resamples=self.other_parameters.get("num_resamples", 1000),
print_to_console=self.other_parameters.get(
"print_to_console", False))
elif self.method.lower() == "dgsm":
# num_resamples (int): The number of resamples used to compute the confidence intervals (default 1000)
# conf_level (float): The confidence interval level (default 0.95)
# print_to_console (bool): Print results directly to console (default False)
self.analyzer = lambda output: dgsm.analyze(
self.problem,
self.input_samples[:, input_ids],
output,
conf_level=self.conf_level,
num_resamples=self.other_parameters.get("num_resamples", 1000),
print_to_console=self.other_parameters.get(
"print_to_console", False))
else:
raise_value_error("Method " + str(self.method) +
" is not one of the available methods " +
str(METHODS) + " !")
output_names = []
results = []
for io in output_ids:
output_names.append(self.output_names[io])
results.append(self.analyzer(self.output_values[:, io]))
# TODO: Adjust list_of_dicts_to_dicts_of_ndarrays to handle ndarray concatenation
results = list_of_dicts_to_dicts_of_ndarrays(results)
results.update({"output_names": output_names})
return results