new example: settings

docs/examples_to_rst.sh

@@ -11,6 +11,8 @@ rm docs/source/extrafeats_example.rst
 rm docs/source/multiprocessing_example.rst
 rm docs/source/voltage_clamp.rst
 rm -rf docs/source/voltage_clamp_files
+rm docs/source/settings.rst
+rm -rf docs/source/settings_notebook_files
 
 # convert
 jupyter nbconvert --to rst examples/sonata-network/sonata-network.ipynb
@@ -19,6 +21,7 @@ jupyter nbconvert --to rst examples/neo/load_nwb.ipynb
 jupyter nbconvert --to rst examples/extracellular/extrafeats_example.ipynb
 jupyter nbconvert --to rst examples/parallel/multiprocessing_example.ipynb
 jupyter nbconvert --to rst examples/voltage_clamp/voltage_clamp.ipynb
+jupyter nbconvert --to rst examples/settings/settings_notebook.ipynb
 
 # move
 mv examples/sonata-network/sonata-network.rst docs/source/
@@ -30,4 +33,6 @@ mv examples/neo/load_nwb_files docs/source/
 mv examples/extracellular/extrafeats_example.rst docs/source/
 mv examples/parallel/multiprocessing_example.rst docs/source/
 mv examples/voltage_clamp/voltage_clamp.rst docs/source/
-mv examples/voltage_clamp/voltage_clamp_files docs/source/
+mv examples/voltage_clamp/voltage_clamp_files docs/source/
+mv examples/settings/settings_notebook.rst docs/source/settings.rst
+mv examples/settings/settings_notebook_files docs/source/

docs/source/eFeatures.rst

@@ -393,7 +393,7 @@ The first spike is ignored by default. This can be changed by setting ignore_fir
 The burst detection can be fine-tuned by changing the setting strict_burst_factor. Default value is 2.0.
 
 - **Required features**: all_ISI_values
-- **Units**: Hz
+- **Units**: constant
 - **Pseudocode**: ::
 
     burst_begin_indices = [1]
@@ -433,7 +433,7 @@ The first spike is ignored by default. This can be changed by setting ignore_fir
 The burst detection can be fine-tuned by changing the setting strict_burst_factor. Default value is 2.0.
 
 - **Required features**: all_ISI_values
-- **Units**: Hz
+- **Units**: constant
 - **Pseudocode**: ::
 
     burst_begin_indices = [1]
@@ -1370,7 +1370,7 @@ min_AHP_indices
 - **Pseudocode**: ::
 
     peak_indices_plus = peak_indices
-    peak_indices_plus.append(len(voltage))
+    peak_indices_plus.append(len(voltage) - 1)
     for i in range(peak_indices):
         min_AHP_indices.append(numpy.argmin(v[i:i + 1]) + i)
 
@@ -1570,6 +1570,32 @@ min_voltage_between_spikes
     for peak1, peak2 in zip(peak_indices[:-1], peak_indices[1:]):
         min_voltage_between_spikes.append(numpy.min(voltage[peak1:peak2]))
 
+min_between_peaks_indices
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+`SpikeShape`_ : Indices of the minimal voltage between consecutive spikes
+
+The last value of min_between_peaks_values is the minimum between last spike and stimulus end
+if strict stiminterval is True, or minimum between last spike and last voltage value
+if strict stiminterval is False
+
+Attention! This feature represents indices of the interpolated time series.
+If you want to use it on time or voltage, make sure that you are using the interpolated output time or voltage feature,
+and not the time or voltage variable you gave as input.
+
+- **Required features**: peak_indices
+- **Units**: constant
+- **Pseudocode**: ::
+
+    if strict_stiminterval:
+        end_idx = numpy.argmin(t >= stim_end)[0][0]
+    else:
+        end_idx = len(time) - 1
+    peak_indices_plus = peak_indices
+    peak_indices_plus.append(end_idx)
+    for i in range(peak_indices):
+        min_between_peaks_indices.append(numpy.argmin(v[i:i + 1]) + i)
+
 min_between_peaks_values
 ~~~~~~~~~~~~~~~~~~~~~~~~
 

docs/source/examples.rst

@@ -4,6 +4,7 @@ Examples
 .. toctree::
 
    python_example1
+   settings
    multiprocessing_example
    deap_optimisation
    neoIO_example

efel/settings.py

@@ -35,11 +35,11 @@ class Settings:
     Attributes:
         Threshold (float): Spike detection threshold (default: -20.0).
         DerivativeThreshold (float): Threshold value for derivative calculations
-        (default: 10.0).
+            (default: 10.0).
         DownDerivativeThreshold (float): Threshold value for downward derivative
-        calculations (default: -12.0).
+            calculations (default: -12.0).
         dependencyfile_path (str): Path to the dependency file
-        (default: 'DependencyV5.txt').
+            (default: 'DependencyV5.txt').
         spike_skipf (float): Fraction of spikes to skip (default: 0.1).
         max_spike_skip (int): Maximum number of spikes to skip (default: 2).
         interp_step (float): Interpolation step (default: 0.1).
@@ -55,7 +55,7 @@ class Settings:
         min_spike_height (float): Minimum spike height (default: 20.0).
         strict_stiminterval (bool): Strict stimulus interval (default: False).
         initburst_freq_threshold (int): Initial burst frequency threshold
-        (default: 50)
+            (default: 50).
         initburst_sahp_start (int): Initial burst SAHP start (default: 5).
         initburst_sahp_end (int): Initial burst SAHP end (default: 100).
         DerivativeWindow (int): Derivative window (default: 3).
@@ -66,7 +66,7 @@ class Settings:
         ignore_first_ISI (bool): Ignore first ISI (default: True).
         impedance_max_freq (float): Impedance maximum frequency (default: 50.0).
         inactivation_tc_end_skip (int): number of data points to skip before
-            stim end for inactivation_time_constant feature
+            stim end for inactivation_time_constant feature (default: 10).
     """
 
     Threshold: float = -20.0

efel/units/units.json

@@ -161,5 +161,27 @@
     "deactivation_time_constant": "ms",
     "inactivation_time_constant": "ms",
     "check_ais_initiation": "constant",
-    "bpap_attenuation": "constant"
+    "bpap_attenuation": "constant",
+    "peak_indices": "constant",
+    "AP_rise_indices": "constant",
+    "AP_end_indices": "constant",
+    "AP_fall_indices": "constant",
+    "min_AHP_indices": "constant",
+    "AP_begin_indices": "constant",
+    "min_between_peaks_indices": "constant",
+    "burst_begin_indices": "constant",
+    "burst_end_indices": "constant",
+    "ADP_peak_indices": "constant",
+    "interburst_min_indices": "constant",
+    "postburst_min_indices": "constant",
+    "postburst_slow_ahp_indices": "constant",
+    "postburst_fast_ahp_indices": "constant",
+    "postburst_adp_peak_indices": "constant",
+    "interburst_15percent_indices": "constant",
+    "interburst_20percent_indices": "constant",
+    "interburst_25percent_indices": "constant",
+    "interburst_30percent_indices": "constant",
+    "interburst_40percent_indices": "constant",
+    "interburst_60percent_indices": "constant",
+    "burst_ISI_indices": "constant"
 }