Merge pull request BlueBrain#274 from AurelienJaquier/new-features

new features comparing number of spikes across bursts

docs/source/eFeatures.rst

@@ -1820,3 +1820,41 @@ The first spike is ignored by default. This can be changed by setting ignore_fir
     for idx_begin, idx_end in zip(burst_begin_indices, burst_end_indices):
         spike_per_bursts.append(idx_end - idx_begin + 1)
 
+Python efeature: spikes_per_burst_diff
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Difference of number of spikes between each burst and the next one.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+- **Required features**: spikes_per_burst
+- **Units**: constant
+- **Pseudocode**: ::
+
+    spikes_per_burst[:-1] - spikes_per_burst[1:]
+
+Python efeature: spikes_in_burst1_burst2_diff
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Difference of number of spikes between the first burst and the second one.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+- **Required features**: spikes_per_burst_diff
+- **Units**: constant
+- **Pseudocode**: ::
+
+    numpy.array([spikes_per_burst_diff[0]])
+
+Python efeature: spikes_in_burst1_burstlast_diff
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Difference of number of spikes between the first burst and the last one.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+- **Required features**: spikes_per_burst
+- **Units**: constant
+- **Pseudocode**: ::
+
+    numpy.array([spikes_per_burst[0] - spikes_per_burst[-1]])

efel/pyfeatures/pyfeatures.py

@@ -40,7 +40,10 @@
     'initburst_sahp_ssse',
     'depol_block',
     'depol_block_bool',
-    'spikes_per_burst'
+    'spikes_per_burst',
+    'spikes_per_burst_diff',
+    'spikes_in_burst1_burst2_diff',
+    'spikes_in_burst1_burstlast_diff'
 ]
 
 
@@ -272,6 +275,37 @@ def spikes_per_burst():
     return numpy.array(ap_per_bursts)
 
 
+def spikes_per_burst_diff():
+    """Calculate the diff between the spikes in each burst and the next one"""
+    spikes_per_burst_values = spikes_per_burst()
+    if spikes_per_burst_values is None:
+        return None
+
+    return spikes_per_burst_values[:-1] - spikes_per_burst_values[1:]
+
+
+def spikes_in_burst1_burst2_diff():
+    """Calculate the diff between the spikes in 1st and 2nd bursts"""
+    spikes_per_burst_diff_values = spikes_per_burst_diff()
+    if spikes_per_burst_diff_values is None or len(
+        spikes_per_burst_diff_values
+    ) < 1:
+        return None
+
+    return numpy.array([spikes_per_burst_diff_values[0]])
+
+
+def spikes_in_burst1_burstlast_diff():
+    """Calculate the diff between the spikes in 1st and last bursts"""
+    spikes_per_burst_values = spikes_per_burst()
+    if spikes_per_burst_values is None or len(spikes_per_burst_values) < 2:
+        return None
+
+    return numpy.array([
+        spikes_per_burst_values[0] - spikes_per_burst_values[-1]
+    ])
+
+
 def _get_cpp_feature(feature_name):
     """Get cpp feature"""
     cppcoreFeatureValues = list()

efel/tests/featurenames.json

@@ -150,6 +150,9 @@
     "spike_half_width",
     "spike_width2",
     "spikes_per_burst",
+    "spikes_per_burst_diff",
+    "spikes_in_burst1_burst2_diff",
+    "spikes_in_burst1_burstlast_diff",
     "steady_state_hyper",
     "steady_state_voltage",
     "steady_state_voltage_stimend",
@@ -180,4 +183,4 @@
     "interburst_min_values",
     "time_to_interburst_min",
     "AHP_depth_slow"
-]
+]

efel/tests/test_basic.py

@@ -3646,3 +3646,85 @@ def test_time_to_interburst_min():
         numpy.testing.assert_allclose(
             time_to_interburst_min_py, time_to_interburst_min
         )
+
+
+def test_spikes_per_burst_diff():
+    """basic: Test spikes_per_burst_diff"""
+    import efel
+    efel.reset()
+
+    time = efel.io.load_fragment('%s#col=1' % burst1_url)
+    voltage = efel.io.load_fragment('%s#col=2' % burst1_url)
+    time, voltage = interpolate(time, voltage, 0.1)
+
+    trace = {}
+    trace['T'] = time
+    trace['V'] = voltage
+    trace['stim_start'] = [250]
+    trace['stim_end'] = [1600]
+
+    features = ['spikes_per_burst_diff']
+
+    feature_values = \
+        efel.getFeatureValues(
+            [trace],
+            features, raise_warnings=False)
+
+    spikes_per_burst_diff = feature_values[0]['spikes_per_burst_diff']
+    assert list(spikes_per_burst_diff) == [1]
+
+
+def test_spikes_in_burst1_burst2_diff():
+    """basic: Test spikes_in_burst1_burst2_diff"""
+    import efel
+    efel.reset()
+
+    time = efel.io.load_fragment('%s#col=1' % burst1_url)
+    voltage = efel.io.load_fragment('%s#col=2' % burst1_url)
+    time, voltage = interpolate(time, voltage, 0.1)
+
+    trace = {}
+    trace['T'] = time
+    trace['V'] = voltage
+    trace['stim_start'] = [250]
+    trace['stim_end'] = [1600]
+
+    features = ['spikes_in_burst1_burst2_diff']
+
+    feature_values = \
+        efel.getFeatureValues(
+            [trace],
+            features, raise_warnings=False)
+
+    spikes_in_burst1_burst2_diff = feature_values[0][
+        'spikes_in_burst1_burst2_diff'
+    ]
+    assert list(spikes_in_burst1_burst2_diff) == [1]
+
+
+def test_spikes_in_burst1_burstlast_diff():
+    """basic: Test spikes_in_burst1_burstlast_diff"""
+    import efel
+    efel.reset()
+
+    time = efel.io.load_fragment('%s#col=1' % burst1_url)
+    voltage = efel.io.load_fragment('%s#col=2' % burst1_url)
+    time, voltage = interpolate(time, voltage, 0.1)
+
+    trace = {}
+    trace['T'] = time
+    trace['V'] = voltage
+    trace['stim_start'] = [250]
+    trace['stim_end'] = [1600]
+
+    features = ['spikes_in_burst1_burstlast_diff']
+
+    feature_values = \
+        efel.getFeatureValues(
+            [trace],
+            features, raise_warnings=False)
+
+    spikes_in_burst1_burstlast_diff = feature_values[0][
+        'spikes_in_burst1_burstlast_diff'
+    ]
+    assert list(spikes_in_burst1_burstlast_diff) == [1]

efel/tests/testdata/allfeatures/expectedresults.json

@@ -540,7 +540,12 @@
         2.6602184713542556,
         2.8238770245407068
     ],
-    "spikes_per_burst": [2],
+    "spikes_per_burst": [
+        2
+    ],
+    "spikes_per_burst_diff": [],
+    "spikes_in_burst1_burst2_diff": null,
+    "spikes_in_burst1_burstlast_diff": null,
     "steady_state_hyper": [
         -39.7063975216648
     ],
@@ -60675,10 +60680,10 @@
     "interburst_min_indices": [],
     "interburst_min_values": [],
     "time_to_interburst_min": [],
-    "AHP_depth_slow":[
+    "AHP_depth_slow": [
         28.81047723194662,
         32.02907786238346,
         32.65404519917785,
         33.435288866699345
     ]
-}
+}