Add extra_features_utils tests with test data

Author: Jaquier Aurélien Tristan

bluepyopt/tests/test_ephys/test_extra_features_utils.py

@@ -0,0 +1,106 @@
+"""Tests for ephys.extra_features_utils"""
+
+import os
+
+import numpy
+import pytest
+
+from bluepyopt import ephys
+
+
+testdata_dir = os.path.join(
+    os.path.dirname(os.path.abspath(__file__)), 'testdata'
+)
+waveforms_fpath = os.path.join(testdata_dir, 'mean_waveforms.dat')
+waveforms = numpy.loadtxt(waveforms_fpath)
+waveform = numpy.array([waveforms[0]])
+sampling_freq = 10000
+
+def test_peak_to_valley():
+    """ephys.extra_features_utils: Test peak_to_valley"""
+    ptv = ephys.extra_features_utils.peak_to_valley(waveform, sampling_freq)
+    assert len(ptv) == 1
+    assert ptv[0] == pytest.approx(0.0013)
+
+
+def test_peak_trough_ratio():
+    """ephys.extra_features_utils: Test peak_trough_ratio"""
+    ptratio = ephys.extra_features_utils.peak_trough_ratio(waveform)
+    assert len(ptratio) == 1
+    print(ptratio)
+    assert ptratio[0] == pytest.approx(0.53804035)
+
+
+def test_halfwidth():
+    """ephys.extra_features_utils: Test halfwidth"""
+    ret = ephys.extra_features_utils.halfwidth(waveform, sampling_freq, True)
+    assert len(ret) == 3
+
+    hw = ephys.extra_features_utils.halfwidth(waveform, sampling_freq)
+    assert len(hw) == 1
+    assert hw[0] == pytest.approx(0.0015)
+
+
+def test_repolarization_slope():
+    """ephys.extra_features_utils: Test repolarization_slope"""
+    ret = ephys.extra_features_utils.repolarization_slope(waveform, sampling_freq, True)
+    assert len(ret) == 2
+
+    rslope = ephys.extra_features_utils.repolarization_slope(waveform, sampling_freq)
+    assert len(rslope) == 1
+    assert rslope[0] == pytest.approx(73.12572131)
+
+
+def test_recovery_slope():
+    """ephys.extra_features_utils: Test recovery_slope"""
+    window=0.7
+    rslope = ephys.extra_features_utils.recovery_slope(waveform, sampling_freq, window=window)
+    assert len(rslope) == 1
+    assert rslope[0] == pytest.approx(-3.63355521)
+
+
+def test_peak_image():
+    """ephys.extra_features_utils: Test peak_image"""
+    rel_peaks = ephys.extra_features_utils.peak_image(waveforms, sign="negative")
+    assert len(rel_peaks) == 209
+    assert rel_peaks[0] == pytest.approx(0.06084468)
+
+    rel_peaks = ephys.extra_features_utils.peak_image(waveforms, sign="positive")
+    assert len(rel_peaks) == 209
+    assert rel_peaks[0] == pytest.approx(0.10850117)
+
+
+def test_relative_amplitude():
+    """ephys.extra_features_utils: Test relative_amplitude"""
+    rel_amp = ephys.extra_features_utils.relative_amplitude(waveforms, sign="negative")
+    assert len(rel_amp) == 209
+    assert rel_amp[0] == pytest.approx(0.09513392)
+
+    rel_amp = ephys.extra_features_utils.relative_amplitude(waveforms, sign="positive")
+    assert len(rel_amp) == 209
+    assert rel_amp[0] == pytest.approx(0.2135929)
+
+
+def test_peak_time_diff():
+    """ephys.extra_features_utils: Test peak_time_diff"""
+    peak_t = ephys.extra_features_utils.peak_time_diff(waveforms, sampling_freq, sign="negative")
+    assert len(peak_t) == 209
+    assert peak_t[0] == pytest.approx(0.0009)
+
+    peak_t = ephys.extra_features_utils.peak_time_diff(waveforms, sampling_freq, sign="positive")
+    assert len(peak_t) == 209
+    assert peak_t[0] == pytest.approx(0.0007)
+
+
+def test__get_trough_and_peak_idx():
+    """ephys.extra_features_utils: Test _get_trough_and_peak_idx"""
+    t_idx, p_idx = ephys.extra_features_utils._get_trough_and_peak_idx(waveform)
+    assert t_idx == 102
+    assert p_idx == 115
+
+
+def test_calculate_features():
+    """ephys.extra_features_utils: Test calculate_features"""
+    feats = ephys.extra_features_utils.calculate_features(waveforms, sampling_freq)
+    for feature_name in ephys.extra_features_utils.all_1D_features:
+        assert feature_name in feats