encourage use of spike_count instead of Spikecount

docs/source/eFeatures.rst

@@ -150,20 +150,20 @@ time from stimulus start to last spike
     else:
         time_to_last_spike = 0
 
-`Python efeature`_ : Spikecount
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+`Python efeature`_ : spike_count
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 number of spikes in the trace, including outside of stimulus interval
 
 - **Required features**: LibV1:peak_indices
 - **Units**: constant
 - **Pseudocode**: ::
 
-    Spikecount = len(peak_indices)
+    spike_count = len(peak_indices)
 
 **Note**: In the future this feature will be called "spike_count".
 
-`Python efeature`_ : Spikecount_stimint
+`Python efeature`_ : spike_count_stimint
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 number of spikes inside the stimulus interval
@@ -173,7 +173,7 @@ number of spikes inside the stimulus interval
 - **Pseudocode**: ::
 
     peaktimes_stimint = numpy.where((peak_time >= stim_start) & (peak_time <= stim_end)) 
-    Spikecount_stimint = len(peaktimes_stimint)
+    spike_count_stimint = len(peaktimes_stimint)
 
 **Note**: In the future this feature will be called "spike_count_stimint".
 
@@ -1902,7 +1902,7 @@ Computes the impedance given a ZAP current input and its voltage response.
 It will return the frequency at which the impedance is maximal, in the range (0, impedance_max_freq] Hz,
 with impedance_max_freq being a setting with 50.0 as a default value.
 
-- **Required features**: current, LibV1:Spikecount, LibV5:voltage_base, LibV5:current_base
+- **Required features**: current, spike_count, LibV5:voltage_base, LibV5:current_base
 - **Units**: Hz
 - **Pseudocode**: ::
 

docs/source/tex/efeatures.tex

@@ -858,16 +858,16 @@ \section{Elementary features}
 \end{efeature}
 
 \begin{efeature}
-  {Spikecount}
-  {LibV1}
-  {Spikecount}
+  {spike_count}
+  {Python efeature}
+  {spike_count}
   {none}
   {peak indices\\&trace check}
   {none}
   {none}
   {The number of peaks during stimulus}
   {
-  APPEND length of peak\_indices TO Spikecount
+  APPEND length of peak\_indices TO spike_count
   }
   Yield the length of \myid{peak indices}.
 

efel/units/units.json

@@ -55,8 +55,8 @@
     "ISI_log_slope_skip": "ms",
     "ISI_semilog_slope": "ms",
     "ISI_values": "ms",
-    "Spikecount": "constant",
-    "Spikecount_stimint": "constant",
+    "spike_count": "constant",
+    "spike_count_stimint": "constant",
     "adaptation_index": "constant",
     "adaptation_index_2": "constant",
     "all_ISI_values": "ms",

examples/deap/GranuleCell1/GranuleCellDeap1-scoop.py

@@ -39,7 +39,7 @@
 from deap import tools
 
 FEATURES = ['voltage_base',
-            'Spikecount',
+            'spike_count',
             'min_voltage_between_spikes',
             'steady_state_voltage_stimend']
 

examples/deap/GranuleCell1/GranuleCellDeap1.ipynb

@@ -99,7 +99,7 @@
     "\n",
     "        result = efel.getFeatureValues(\n",
     "            traces, [\n",
-    "                'voltage_base', 'Spikecount', 'min_voltage_between_spikes', 'AP_height', 'steady_state_voltage_stimend'])\n",
+    "                'voltage_base', 'spike_count', 'min_voltage_between_spikes', 'AP_height', 'steady_state_voltage_stimend'])\n",
     "\n",
     "        for feature_name, feature_list in result[0].items():\n",
     "            if feature_list is not None and len(feature_list) > 0:\n",

tests/featurenames.json

@@ -55,8 +55,8 @@
     "ISI_semilog_slope",
     "ISI_values",
     "ISIs",
-    "Spikecount",
-    "Spikecount_stimint",
+    "spike_count",
+    "spike_count_stimint",
     "adaptation_index",
     "adaptation_index2",
     "all_ISI_values",

tests/test_allfeatures.py

@@ -126,10 +126,9 @@ def test_allfeatures():
     """allfeatures: Regression testing all features on a trace"""
 
     feature_values = get_allfeature_values()
-    # drop spike_count and spike_count_stimint from feature values since they
-    # are the same as deprecated Spikecount and Spikecount_stimint
-    feature_values.pop('spike_count')
-    feature_values.pop('spike_count_stimint')
+    # drop Spikecount and Spikecount_stimint deprecated features
+    feature_values.pop('Spikecount')
+    feature_values.pop('Spikecount_stimint')
     test_data_path = os.path.join(testdata_dir, 'expectedresults.json')
     with open(test_data_path, 'r') as expected_json:
         expected_results = json.load(expected_json)

tests/test_basic.py

@@ -616,7 +616,7 @@ def test_strict_stiminterval():
         trace['stim_start'] = [stim_start]
         trace['stim_end'] = [stim_end]
 
-        features = ['peak_indices', 'peak_time', 'Spikecount']
+        features = ['peak_indices', 'peak_time', 'spike_count']
 
         feature_values = \
             efel.getFeatureValues(
@@ -625,7 +625,7 @@ def test_strict_stiminterval():
 
         peak_indices = feature_values[0]['peak_indices']
         peak_time = feature_values[0]['peak_time']
-        spikecount = feature_values[0]['Spikecount']
+        spikecount = feature_values[0]['spike_count']
         assert len(peak_indices) == n_of_spikes
         assert len(peak_time) == n_of_spikes
         assert spikecount == n_of_spikes
@@ -1132,7 +1132,7 @@ def test_getDistance_trace_check():
     trace['stim_end'] = [70]
     traces.append(trace)
     numpy.testing.assert_allclose(
-        efel.getDistance(trace, 'Spikecount', 0, 1), 3.0
+        efel.getDistance(trace, 'spike_count', 0, 1), 3.0
     )
 
     trace['stim_end'] = [50]
@@ -1141,15 +1141,15 @@ def test_getDistance_trace_check():
     numpy.testing.assert_allclose(
         efel.getDistance(
             trace,
-            'Spikecount',
+            'spike_count',
             0,
             1,
             trace_check=False),
         3.0)
 
     efel.reset()
     numpy.testing.assert_allclose(
-        efel.getDistance(trace, 'Spikecount', 0, 1), 250.0
+        efel.getDistance(trace, 'spike_count', 0, 1), 250.0
     )
 
 
@@ -1261,8 +1261,8 @@ def test_derivwindow1():
     numpy.testing.assert_allclose(AP_begin_voltage, -45.505521563640386)
 
 
-def test_spikecount1():
-    """basic: Test Spikecount 1"""
+def test_spike_count1():
+    """basic: Test spike_count 1"""
 
     import efel
     efel.reset()
@@ -1279,20 +1279,20 @@ def test_spikecount1():
     trace['stim_start'] = [stim_start]
     trace['stim_end'] = [stim_end]
 
-    features = ['peak_indices', 'Spikecount']
+    features = ['peak_indices', 'spike_count']
 
     feature_values = \
         efel.getFeatureValues(
             [trace],
             features)
 
     peak_indices = feature_values[0]['peak_indices']
-    spikecount = feature_values[0]['Spikecount'][0]
+    spikecount = feature_values[0]['spike_count'][0]
     assert len(peak_indices) == spikecount
 
 
-def test_spikecount_stimint1():
-    """basic: Test Spikecount_stimint 1."""
+def test_spike_count_stimint1():
+    """basic: Test spike_count_stimint 1."""
     import efel
     efel.reset()
 
@@ -1307,16 +1307,16 @@ def test_spikecount_stimint1():
     trace['stim_start'] = [stim_start]
     trace['stim_end'] = [stim_end]
 
-    features = ['peak_time', 'Spikecount_stimint', 'Spikecount']
+    features = ['peak_time', 'spike_count_stimint', 'spike_count']
 
     feature_values = \
         efel.getFeatureValues(
             [trace],
             features)
 
     peak_times = feature_values[0]['peak_time']
-    spikecount = feature_values[0]['Spikecount'][0]
-    spikecount_stimint = feature_values[0]['Spikecount_stimint'][0]
+    spikecount = feature_values[0]['spike_count'][0]
+    spikecount_stimint = feature_values[0]['spike_count_stimint'][0]
 
     interval_peaktimes, = \
         numpy.where((peak_times >= stim_start) & (peak_times <= stim_end))
@@ -1610,8 +1610,8 @@ def test_ohmic_input_resistance_vb_ssse_zero_stimulus_current():
     assert ohmic_input_resistance is None
 
 
-def test_spikecount2():
-    """basic: Test Spikecount 2: test empty trace"""
+def test_spike_count2():
+    """basic: Test spike_count 2: test empty trace"""
 
     import efel
     efel.reset()
@@ -1629,14 +1629,14 @@ def test_spikecount2():
     trace['stim_start'] = [stim_start]
     trace['stim_end'] = [stim_end]
 
-    features = ['Spikecount']
+    features = ['spike_count']
 
     feature_values = \
         efel.getFeatureValues(
             [trace],
             features)
 
-    spikecount = feature_values[0]['Spikecount'][0]
+    spikecount = feature_values[0]['spike_count'][0]
     assert spikecount == 0
 
 
@@ -1712,7 +1712,7 @@ def test_getFeatureNames():
     with open(test_data_path, 'r') as featurenames_json:
         expected_featurenames = json.load(featurenames_json)
     # add the new names for the deprecated ones
-    expected_featurenames += ["spike_count", "spike_count_stimint"]
+    expected_featurenames += ["Spikecount", "Spikecount_stimint"]
     assert set(efel.getFeatureNames()) == set(expected_featurenames)
 
 
@@ -2038,7 +2038,7 @@ def test_mean_AP_amplitude():
 
 
 def test_unfinished_peak():
-    """basic: Test if unfinished peak doesn't break Spikecount"""
+    """basic: Test if unfinished peak doesn't break spike_count"""
 
     import efel
     efel.setIntSetting('strict_stiminterval', True)
@@ -2055,17 +2055,17 @@ def test_unfinished_peak():
     trace['stim_start'] = [10]
     trace['stim_end'] = [70]
 
-    traces_results = efel.getFeatureValues([trace], ['Spikecount'])
-    spikecount = traces_results[0]['Spikecount'][0]
+    traces_results = efel.getFeatureValues([trace], ['spike_count'])
+    spikecount = traces_results[0]['spike_count'][0]
 
     assert spikecount == 3
 
     # When the signal at the end of the trace is larger than the threshold,
-    # Spikecount and possibly other features cannont be estimated.
+    # spike_count and possibly other features cannont be estimated.
     v[int(80 / dt):] = -19
 
-    traces_results = efel.getFeatureValues([trace], ['Spikecount'])
-    spikecount = traces_results[0]['Spikecount'][0]
+    traces_results = efel.getFeatureValues([trace], ['spike_count'])
+    spikecount = traces_results[0]['spike_count'][0]
 
     assert spikecount == 3
 

tests/test_cppcore.py

@@ -98,7 +98,7 @@ def test_getFeatureNames(self):  # pylint: disable=R0201
         with open(test_data_path, 'r') as featurenames_json:
             expected_featurenames = json.load(featurenames_json)
         # add the new names for the deprecated ones
-        expected_featurenames += ["spike_count", "spike_count_stimint"]
+        expected_featurenames += ["Spikecount", "Spikecount_stimint"]
         assert set(feature_names) == set(expected_featurenames)
 
     def test_getFeatureDouble_failure(self):  # pylint: disable=R0201

tests/testdata/allfeatures/expectedresults.json

@@ -314,10 +314,10 @@
         675.4999999993856,
         250.29999999977235
     ],
-    "Spikecount": [
+    "spike_count": [
         6
     ],
-    "Spikecount_stimint": [
+    "spike_count_stimint": [
         6
     ],
     "adaptation_index": [