add bpap_attenuation as a multitrace feature

efel/pyfeatures/multitrace.py

@@ -0,0 +1,24 @@
+"""Contains the features that are computed using multiple traces."""
+
+
+import numpy as np
+
+import efel
+
+
+def bpap_attenuation(soma_trace: dict, dendrite_trace: dict) -> float:
+    """Computes the attenuation of backpropagating action potential.
+
+    Backpropagating action potential is the action potential that is initiated
+    in the soma and propagates to the dendrite. The attenuation is the ratio
+    of the amplitude of the action potential in the soma and the dendrite.
+    The attenuation is computed by first subtracting the resting potential
+    from the voltage traces.
+    """
+    f_values = efel.getFeatureValues([soma_trace, dendrite_trace], ["voltage_base"])
+    vb_soma = f_values[0]["voltage_base"][0]
+    vb_dend = f_values[1]["voltage_base"][0]
+    v_soma = soma_trace["V"]
+    v_dend = dendrite_trace["V"]
+    res = (np.max(v_soma) - vb_soma) / (np.max(v_dend) - vb_dend)
+    return res

tests/test_multitrace.py

@@ -0,0 +1,39 @@
+"""Unit tests for the multitrace module."""
+
+from pathlib import Path
+import efel
+from efel.io import load_ascii_input
+from efel.pyfeatures.multitrace import bpap_attenuation
+
+
+testdata_dir = Path(__file__).parent / "testdata"
+meanfrequency1_url = testdata_dir / "basic" / "mean_frequency_1.txt"
+
+
+def test_bpap_attenuation():
+    efel.reset()
+    stim_start, stim_end = 1.0, 2.0  # dummy values not used in this feature
+
+    time, voltage = load_ascii_input(meanfrequency1_url)
+    soma_trace = dendrite_trace = {
+        "T": time,
+        "V": voltage,
+        "stim_start": [stim_start],
+        "stim_end": [stim_end],
+    }
+    assert bpap_attenuation(soma_trace, dendrite_trace) == 1.0
+
+    # test voltage base subtraction
+    soma_trace = {
+        "T": time,
+        "V": voltage,
+        "stim_start": [stim_start],
+        "stim_end": [stim_end],
+    }
+    # subtract 10 mv from V of soma_trace
+    soma_trace["V"] = soma_trace["V"] - 10
+    assert bpap_attenuation(soma_trace, dendrite_trace) == 1.0
+
+    # divide by 2
+    soma_trace["V"] = voltage / 2
+    assert bpap_attenuation(soma_trace, dendrite_trace) == 0.5