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Fix frequency in FI curve and add global parameters #170

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merged 3 commits into from
Sep 18, 2024
Merged

Fix frequency in FI curve and add global parameters #170

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d760b24
add global parameters
Sep 18, 2024
3a60015
turn None into nan in _get_fi_curve_from_evaluator
Sep 18, 2024
dcad6de
fix in frequencies array construction in FI curve
Sep 18, 2024
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6 changes: 4 additions & 2 deletions bluepyemodel/emodel_pipeline/plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -399,7 +399,7 @@ def thumbnail(
voltage = responses[trace_name]["voltage"]
except KeyError:
logger.warning(
"Could not find protocol %s in respsonses. Skipping thumbnail plotting.",
"Could not find protocol %s in responses. Skipping thumbnail plotting.",
trace_name,
)
return None, None
Expand Down Expand Up @@ -675,8 +675,10 @@ def _get_fi_curve_from_evaluator(
[efel_trace], ["Spikecount", "mean_frequency"], raise_warnings=False
)[0]
spike_freq_equivalent.append(1e3 * float(features["Spikecount"]) / length_step)
frequencies.append(features.get("mean_frequency", None))
mean_freq = features.get("mean_frequency", None)
frequencies.append(mean_freq[0] if mean_freq is not None else None)

frequencies = numpy.array(frequencies, dtype=float)
return amps, frequencies, spike_freq_equivalent


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2 changes: 1 addition & 1 deletion bluepyemodel/model/neuron_model_configuration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
"allact": ["apical", "basal", "somatic", "axonal"],
}

global_parameters = ["v_init", "celsius", "cm", "Ra", "ena", "ek"]
global_parameters = ["v_init", "celsius", "cm", "Ra", "ena", "ek", "eca", "eh"]


class NeuronModelConfiguration:
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