Merge pull request #352 from AurelienJaquier/dend-validation-features

New feature: phaseslope_max

CHANGELOG.md

@@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [5.5.4] - 2024-01
+
+- New feature: phaseslope_max
+
 ## [5.5.3] - 2024-01
 
 - Add type stub for cppcore module to make Python recognise the C++ functions' arguments and return values.

docs/source/eFeatures.rst

@@ -1926,6 +1926,19 @@ with impedance_max_freq being a setting with 50.0 as a default value.
     else:
         return None
 
+`Python efeature`_ : phaseslope_max
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Computes the maximum of the phase slope.
+Attention, this feature is sensitive to interpolation timestep.
+
+- **Required features**: time, voltage
+- **Units**: V/s
+- **Pseudocode**: ::
+
+    phaseslope = numpy.diff(voltage) / numpy.diff(time)
+    phaseslope_max = numpy.array([numpy.max(phaseslope)])
+
 
 
 .. _LibV1: https://github.com/BlueBrain/eFEL/blob/master/efel/cppcore/LibV1.cpp

efel/pyfeatures/pyfeatures.py

@@ -54,7 +54,8 @@
     'impedance',
     'burst_number',
     'strict_burst_number',
-    'trace_check'
+    'trace_check',
+    'phaseslope_max',
 ]
 
 
@@ -424,6 +425,22 @@ def spikes_in_burst1_burstlast_diff():
     ])
 
 
+def phaseslope_max():
+    """Calculate the maximum phase slope"""
+
+    voltage = get_cpp_feature("voltage")
+    time = get_cpp_feature("time")
+    time = time[:len(voltage)]
+
+    from numpy import diff
+
+    phaseslope = diff(voltage) / diff(time)
+    try:
+        return numpy.array([numpy.max(phaseslope)])
+    except ValueError:
+        return None
+
+
 def get_cpp_feature(featureName, raise_warnings=None):
     """Return value of feature implemented in cpp"""
     cppcoreFeatureValues = list()

efel/units/units.json

@@ -136,5 +136,6 @@
     "initburst_sahp_ssse": "mV",
     "initburst_sahp_vb": "mV",
     "depol_block_bool": "constant",
-    "impedance": "Hz"
+    "impedance": "Hz",
+    "phaseslope_max": "V/s"
 }

tests/featurenames.json

@@ -147,5 +147,6 @@
     "postburst_min_indices",
     "postburst_min_values",
     "time_to_interburst_min",
-    "AHP_depth_slow"
+    "AHP_depth_slow",
+    "phaseslope_max"
 ]

tests/test_allfeatures.py

@@ -177,7 +177,7 @@ def test_allfeatures_on_constant_voltage():
         "voltage_deflection", "voltage_deflection_begin", "voltage_deflection_vb_ssse",
         "depol_block", "depol_block_bool", "voltage_base", "Spikecount",
         "Spikecount_stimint", "burst_number", "strict_burst_number", "trace_check",
-        "spike_count", "spike_count_stimint"
+        "spike_count", "spike_count_stimint", "phaseslope_max"
     ]
 
     for field in array_fields:

tests/test_pyfeatures.py

@@ -326,3 +326,13 @@ def test_trace_check():
     mf1_trace["V"] = [0] * len(mf1_trace["V"])
     feature_values = efel.getFeatureValues([mf1_trace], ['trace_check'])
     assert feature_values[0]['trace_check'][0] == 0
+
+
+def test_phaseslope_max():
+    """Unit test for phaseslope_max."""
+    expected_values = {
+        "mean_frequency1": 574.86769012,
+        "depol_block_spiking": 93.51242208,
+        "depol_block_db": 180.7325033,
+    }
+    _test_expected_value("phaseslope_max", expected_values)

tests/testdata/allfeatures/expectedresults.json

@@ -60639,5 +60639,6 @@
         32.02907786238346,
         32.65404519917785,
         33.435288866699345
-    ]
+    ],
+    "phaseslope_max": [111.6276337625179]
 }