diff --git a/emodel_generalisation/bluecellulab_evaluator.py b/emodel_generalisation/bluecellulab_evaluator.py index 4fbe8e8..971f879 100644 --- a/emodel_generalisation/bluecellulab_evaluator.py +++ b/emodel_generalisation/bluecellulab_evaluator.py @@ -1,4 +1,6 @@ """Compute the threshold and holding current using bluecellulab, adapted from BluePyThresh.""" + +import os import logging from copy import copy from multiprocessing.context import TimeoutError # pylint: disable=redefined-builtin @@ -325,4 +327,5 @@ def evaluate_currents( "timeout": timeout, "only_rin": only_rin, }, + progress_bar=os.environ.get("NO_PROGRESS", False), ) diff --git a/emodel_generalisation/model/bpopt.py b/emodel_generalisation/model/bpopt.py index a12ed61..93a9513 100644 --- a/emodel_generalisation/model/bpopt.py +++ b/emodel_generalisation/model/bpopt.py @@ -113,7 +113,8 @@ def calculate_bpo_score(self, responses): if feature_value is None: return self.max_score - + if self.efel_feature_name == "peak_voltage": + print(feature_value, self.exp_mean, self.exp_std) return abs(feature_value - self.exp_mean) / self.exp_std def _construct_efel_trace(self, responses): diff --git a/emodel_generalisation/model/evaluation.py b/emodel_generalisation/model/evaluation.py index dfa3481..28176a7 100644 --- a/emodel_generalisation/model/evaluation.py +++ b/emodel_generalisation/model/evaluation.py @@ -1211,9 +1211,9 @@ def _add_legacy_protocol(self, protocol_name, protocol): if "extra_recordings" in protocol: for protocol_def in protocol["extra_recordings"]: recordings.append(protocol_def) - protocol_def[ - "name" - ] = f"{protocol_name}.{protocol_def['name']}.{protocol_def['var']}" + protocol_def["name"] = ( + f"{protocol_name}.{protocol_def['name']}.{protocol_def['var']}" + ) stimulus = deepcopy(protocol["stimuli"]["step"]) if "holding" in protocol["stimuli"]: @@ -1806,11 +1806,9 @@ def _single_feature_evaluation( ]: evaluator.fitness_protocols["main_protocol"].protocols.pop(prot) - evaluator.fitness_protocols[ - "main_protocol" - ].execution_order = evaluator.fitness_protocols[ - "main_protocol" - ].compute_execution_order() + evaluator.fitness_protocols["main_protocol"].execution_order = ( + evaluator.fitness_protocols["main_protocol"].compute_execution_order() + ) evaluator.cell_model.unfreeze(params) responses = evaluator.run_protocols(evaluator.fitness_protocols.values(), params) @@ -1922,6 +1920,7 @@ def feature_evaluation( resume=resume, parallel_factory=parallel_factory, db_url=db_url, + progress_bar=os.environ.get("NO_PROGRESS", False), ) .sort_values(by="index") .set_index("index") @@ -2033,6 +2032,7 @@ def evaluate_rin_no_soma( resume=resume, parallel_factory=parallel_factory, db_url=db_url, + progress_bar=os.environ.get("NO_PROGRESS", False), ) @@ -2075,6 +2075,7 @@ def evaluate_soma_rin( resume=resume, parallel_factory=parallel_factory, db_url=db_url, + progress_bar=os.environ.get("NO_PROGRESS", False), ) @@ -2117,6 +2118,7 @@ def evaluate_ais_rin( resume=resume, parallel_factory=parallel_factory, db_url=db_url, + progress_bar=os.environ.get("NO_PROGRESS", False), ) @@ -2157,6 +2159,7 @@ def evaluate_somadend_rin( resume=resume, parallel_factory=parallel_factory, db_url=db_url, + progress_bar=os.environ.get("NO_PROGRESS", False), )