add current_precision to the emodel_settings

Change-Id: I37bc2ba549d707b8a719e3c90c6eccf73bed761b
BlueBrain · Jul 9, 2024 · 7c4ece3 · 7c4ece3
1 parent 77237a8
commit 7c4ece3
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Showing 4 changed files with 18 additions and 1 deletion.
diff --git a/bluepyemodel/emodel_pipeline/emodel_settings.py b/bluepyemodel/emodel_pipeline/emodel_settings.py
@@ -79,6 +79,7 @@ def __init__(
         neuron_dt=None,
         cvode_minstep=0.0,
         use_params_for_seed=True,
+        current_precision=1e-2,
         max_threshold_voltage=-30,
         strict_holding_bounds=True,
         max_depth_holding_search=7,
@@ -268,6 +269,8 @@ def __init__(
             cvode_minstep (float): minimum time step allowed when using cvode.
             use_params_for_seed (bool): use a hashed version of the parameter
                 dictionary as a seed for the simulator
+            current_precision (float): size of search interval in current to stop the search
+                in SearchThresholdProtocol
             max_threshold_voltage (float): upper bound for the voltage during the
                 search for the threshold or rheobase current (see SearchThresholdProtocol).
             strict_holding_bounds (bool): if True, the minimum and maximum values for the current
@@ -305,6 +308,7 @@ def __init__(
         self.minimum_protocol_delay = minimum_protocol_delay
 
         # Settings related to the evaluator
+        self.current_precision = current_precision
         self.max_threshold_voltage = max_threshold_voltage
         self.threshold_efeature_std = threshold_efeature_std
         self.max_depth_holding_search = max_depth_holding_search

diff --git a/bluepyemodel/evaluation/evaluator.py b/bluepyemodel/evaluation/evaluator.py
@@ -464,6 +464,7 @@ def define_holding_protocol(
 
 def define_threshold_protocol(
     efeatures,
+    current_precision=1e-2,
     max_threshold_voltage=-30,
     step_delay=500.0,
     step_duration=2000.0,
@@ -497,6 +498,7 @@ def define_threshold_protocol(
         name=thres_prot_name,
         location=location,
         target_threshold=target_current[0],
+        current_precision=current_precision,
         max_threshold_voltage=max_threshold_voltage,
         stimulus_delay=step_delay,
         stimulus_duration=step_duration,
@@ -626,6 +628,7 @@ def define_preprotocols(
     fitness_calculator_configuration,
     strict_holding_bounds=False,
     max_depth_holding_search=7,
+    current_precision=1e-2,
     max_threshold_voltage=-30,
     spikecount_timeout=50,
     max_depth_threshold_search=10,
@@ -685,6 +688,7 @@ def define_preprotocols(
     )
     threshold_prot = define_threshold_protocol(
         efeatures,
+        current_precision,
         max_threshold_voltage,
         fitness_calculator_configuration.search_threshold_step_delay,
         fitness_calculator_configuration.search_threshold_step_duration,
@@ -717,6 +721,7 @@ def define_threshold_based_optimisation_protocol(
     stochasticity=True,
     ais_recording=False,
     efel_settings=None,
+    current_precision=1e-2,
     max_threshold_voltage=-30,
     strict_holding_bounds=True,
     use_fixed_dt_recordings=False,
@@ -740,6 +745,7 @@ def define_threshold_based_optimisation_protocol(
             deterministic
         ais_recording (bool): if True all the soma recording will be at the first axonal section.
         efel_settings (dict): eFEl settings.
+        current_precision (float): size of search interval in current to stop the search
         max_threshold_voltage (float): maximum voltage at which the SearchThresholdProtocol
             will search for the rheobase.
         strict_holding_bounds (bool): to adaptively enlarge bounds if holding current is outside
@@ -789,6 +795,7 @@ def define_threshold_based_optimisation_protocol(
                             fitness_calculator_configuration=fitness_calculator_configuration,
                             strict_holding_bounds=strict_holding_bounds,
                             max_depth_holding_search=max_depth_holding_search,
+                            current_precision=current_precision,
                             max_threshold_voltage=max_threshold_voltage,
                             spikecount_timeout=spikecount_timeout,
                             max_depth_threshold_search=max_depth_threshold_search,
@@ -820,6 +827,7 @@ def define_threshold_based_optimisation_protocol(
                             fitness_calculator_configuration=fitness_calculator_configuration,
                             strict_holding_bounds=strict_holding_bounds,
                             max_depth_holding_search=max_depth_holding_search,
+                            current_precision=current_precision,
                             max_threshold_voltage=max_threshold_voltage,
                             spikecount_timeout=spikecount_timeout,
                             max_depth_threshold_search=max_depth_threshold_search,
@@ -847,6 +855,7 @@ def define_threshold_based_optimisation_protocol(
                         fitness_calculator_configuration=fitness_calculator_configuration,
                         strict_holding_bounds=strict_holding_bounds,
                         max_depth_holding_search=max_depth_holding_search,
+                        current_precision=current_precision,
                         max_threshold_voltage=max_threshold_voltage,
                         spikecount_timeout=spikecount_timeout,
                         max_depth_threshold_search=max_depth_threshold_search,
@@ -976,6 +985,7 @@ def create_evaluator(
             include_validation_protocols,
             stochasticity=stochasticity,
             efel_settings=pipeline_settings.efel_settings,
+            current_precision=pipeline_settings.current_precision,
             max_threshold_voltage=pipeline_settings.max_threshold_voltage,
             strict_holding_bounds=pipeline_settings.strict_holding_bounds,
             use_fixed_dt_recordings=use_fixed_dt_recordings,

diff --git a/bluepyemodel/evaluation/protocols.py b/bluepyemodel/evaluation/protocols.py
@@ -686,7 +686,7 @@ def __init__(
         name,
         location,
         target_threshold=None,
-        current_precision=2e-3,
+        current_precision=1e-2,
         stimulus_delay=500.0,
         stimulus_duration=2000.0,
         stimulus_totduration=3000.0,

diff --git a/examples/memodel/memodel.py b/examples/memodel/memodel.py
@@ -452,6 +452,9 @@ def update_memodel(
         access_token=access_token,
     )
 
+    # update settings for better threshold precision
+    access_point.pipeline_settings.current_precision = 2e-3
+
     # get cell evaluator with 'new' morphology
     cell_evaluator = get_cell_evaluator(access_point, morph_name, morph_format, morph_id)