diff --git a/emodel_generalisation/adaptation.py b/emodel_generalisation/adaptation.py index 58f5f60..0d032cc 100644 --- a/emodel_generalisation/adaptation.py +++ b/emodel_generalisation/adaptation.py @@ -201,7 +201,7 @@ def __adapt_single_soma_ais( def _adapt_single_soma_ais(*args, **kwargs): - timeout = kwargs.pop("timeout", 5 * 60) + timeout = kwargs.pop("timeout", 30 * 60) res = isolate(__adapt_single_soma_ais, timeout=timeout)(*args, **kwargs) if res is None: print("timeout", args, kwargs) diff --git a/emodel_generalisation/bluecellulab_evaluator.py b/emodel_generalisation/bluecellulab_evaluator.py index 24aac2b..2f118c2 100644 --- a/emodel_generalisation/bluecellulab_evaluator.py +++ b/emodel_generalisation/bluecellulab_evaluator.py @@ -57,7 +57,7 @@ def calculate_threshold_current(cell, config, holding_current): def binsearch_threshold_current(cell, config, holding_current, min_current, max_current): """Binary search for threshold currents""" mid_current = (min_current + max_current) / 2 - if abs(max_current - min_current) < config["threshold_current_precision"]: + if abs(max_current - min_current) < config.get("threshold_current_precision", 0.001): spike_count = run_spike_sim( cell, config, diff --git a/emodel_generalisation/cli.py b/emodel_generalisation/cli.py index e65167a..5f1584d 100644 --- a/emodel_generalisation/cli.py +++ b/emodel_generalisation/cli.py @@ -206,12 +206,15 @@ def compute_currents( ) failed_cells = unique_cells_df[ - unique_cells_df["input_resistance"].isna() | (unique_cells_df["input_resistance"] < 0) + unique_cells_df["input_resistance"].isna() | (unique_cells_df["input_resistance"] <= 0) ].index if len(failed_cells) > 0: - L.info("still %s failed cells (we drop):", len(failed_cells)) + L.info("still %s failed cells (we set default values):", len(failed_cells)) L.info(unique_cells_df.loc[failed_cells]) - unique_cells_df.loc[failed_cells, "mtype"] = None + unique_cells_df.loc[failed_cells, "@dynamics:holding_current"] = 0.0 + unique_cells_df.loc[failed_cells, "@dynamics:threshold_current"] = 0.0 + unique_cells_df.loc[failed_cells, "@dynamics:input_resistance"] = 0.0 + unique_cells_df.loc[failed_cells, "@dynamics:resting_potential"] = -80.0 cols = ["resting_potential", "input_resistance", "exception"] if not only_rin: