New test data and test for spontaneous firing

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### C++ changes
 - AP_end_indices, AP_rise_time, AP_fall_time, AP_rise_rate, AP_fall_rate do not take into account peaks before stim_start anymore
+- New test and test data for spontaneous firing case.
+  The data is provided by github user SzaBoglarka using cell https://modeldb.science/114047
 
 
 ## [5.4.0] - 2024-01

tests/test_basic.py

@@ -56,6 +56,7 @@
     / 'basic'
     / 'spiking_from_beginning_to_end.txt'
 )
+spontaneous_url = testdata_dir / 'basic' / 'spontaneous.txt'
 
 
 def load_data(data_name, interp=False, interp_dt=0.1):
@@ -3724,3 +3725,105 @@ def test_spikes_in_burst1_burstlast_diff():
         'spikes_in_burst1_burstlast_diff'
     ]
     assert list(spikes_in_burst1_burstlast_diff) == [1]
+
+
+def test_spontaneous_firing():
+    """basic: Test features with spontaneous firing"""
+    import efel
+    efel.reset()
+
+    time, voltage = load_ascii_input(spontaneous_url)
+    trace = {}
+    trace['T'] = time
+    trace['V'] = voltage
+    trace['stim_start'] = [200]
+    trace['stim_end'] = [400]
+
+    features = [
+        "AP_begin_indices",
+        "AP_end_indices",
+        "AP_duration",
+        "AP_rise_time",
+        "AP_fall_time",
+        "AP_rise_rate",
+        "AP_fall_rate"
+    ]
+    feature_values = \
+        efel.getFeatureValues(
+            [trace],
+            features, raise_warnings=False)
+
+    ap_begin_indices = feature_values[0]["AP_begin_indices"]
+    ap_end_indices = feature_values[0]["AP_end_indices"]
+    ap_duration = feature_values[0]["AP_duration"]
+    ap_rise_time = feature_values[0]["AP_rise_time"]
+    ap_fall_time = feature_values[0]["AP_fall_time"]
+    ap_rise_rate = feature_values[0]["AP_rise_rate"]
+    ap_fall_rate = feature_values[0]["AP_fall_rate"]
+
+    assert len(ap_begin_indices) == len(ap_end_indices) == 17
+    assert len(ap_rise_time) == len(ap_fall_time) == 17
+    assert len(ap_rise_rate) == len(ap_fall_rate) == 17
+
+    ap_duration_expected = numpy.asarray(
+        [3.4, 3.2, 3.2, 3.2, 3.2, 3.3, 3.3, 3.2, 3.2, 3.2, 3.3, 3.2, 3.2, 3.2, 3.3, 3.2, 3.2]
+    )
+    ap_rise_time_expected = numpy.asarray(
+        [1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1., 1.1]
+    )
+    ap_fall_time_expected = numpy.asarray(
+        [2.3, 2.1, 2.1, 2.1, 2.1, 2.2, 2.2, 2.1, 2.1, 2.1, 2.2, 2.1, 2.1, 2.1, 2.2, 2.2, 2.1]
+    )
+    ap_rise_rate_expected = numpy.asarray(
+        [
+            82.71999369,
+            75.10676844,
+            74.81153,
+            74.49859629,
+            74.06181713,
+            74.79034563,
+            74.81447401,
+            74.625776,
+            74.25400107,
+            73.72304677,
+            74.83236875,
+            74.72279679,
+            74.41938034,
+            73.94843724,
+            74.81475705,
+            82.5914875,
+            75.61000111
+        ]
+    )
+    ap_fall_rate_expected = numpy.asarray(
+        [
+            -50.29279717,
+            -51.47121886,
+            -51.17771356,
+            -51.17143474,
+            -51.1426409,
+            -48.8666936,
+            -49.0424941,
+            -51.14053045,
+            -51.15984648,
+            -51.0874205,
+            -48.98788642,
+            -51.10475374,
+            -51.16398341,
+            -51.12579796,
+            -48.91465101,
+            -49.87112779,
+            -52.17949364
+        ]
+    )
+    assert list(ap_begin_indices) == [
+        2018, 2156, 2291, 2426, 2561, 2695, 2830, 2965, 3100, 3235, 3369, 3504, 3639, 3774, 3908, 4564, 5352
+    ]
+    assert list(ap_end_indices) == [
+        2052, 2188, 2323, 2458, 2593, 2728, 2863, 2997, 3132, 3267, 3402, 3536, 3671, 3806, 3941, 4596, 5384
+    ]
+    numpy.testing.assert_allclose(ap_duration, ap_duration_expected)
+    numpy.testing.assert_allclose(ap_rise_time, ap_rise_time_expected)
+    numpy.testing.assert_allclose(ap_fall_time, ap_fall_time_expected)
+    numpy.testing.assert_allclose(ap_rise_rate, ap_rise_rate_expected)
+    numpy.testing.assert_allclose(ap_fall_rate, ap_fall_rate_expected)