new features: postburst_slow_ahp_values, time_to_postburst_slow_ahp (#…

…289)

* new features: postburst_slow_ahp_values, time_to_postburst_slow_ahp

* remove std::cout in LibV1

* fix edge case when index is stim_end_index or end_index

* new feature: postburst_fast_ahp_values

* new feature: postburst_adp_peak_values

* add new features: interburst_XX_percent_values for 20, 40, 60%

* adding test, docs for postburst_fast_ahp_values, postburst_adp_peak_values

* fix time_to_postburst_adp_peak for edge case when there are less adp peaks than bursts

* add test and doc for feature time_to_postburst_fast_ahp

* add test and doc for feature time_to_postburst_adp_peak

* add test and docs to interburst 20%, 40%, 60% features

* turn 40%, 60% into 25%, 30% for interburst voltage

* add interburst 10% and 15% voltage values features

* interburst features: removed 10%, restored 40% and 60%

* new feature: interburst_duration

* update docs and tests with new features

* update memoization of new features

* fix docs, units and tests for latest new features

* create interburst_percent_indices function to reduce code duplication

* remove deprecated bind2nd

* refactor interburst_XXpercent_indices

* merging all interburst_XXpercent_values in the docs

---------

Co-authored-by: Jaquier Aurélien Tristan <[email protected]>

docs/source/eFeatures.rst

@@ -534,7 +534,7 @@ The burst detection can be fine-tuned by changing the setting strict_burst_facto
 - **Units**: mV
 - **Pseudocode**: ::
 
-    interburst_min = [
+    postburst_min = [
         numpy.min(
             v[peak_indices[i]:peak_indices[i + 1]]
         ) for i in burst_end_indices if i + 1 < len(peak_indices)
@@ -551,6 +551,36 @@ The burst detection can be fine-tuned by changing the setting strict_burst_facto
                 v[peak_indices[burst_end_indices[-1]]:]
             ))
 
+`LibV5`_ : postburst_slow_ahp_values
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The slow AHP voltage after the end of a burst.
+
+The number of ms to skip after the spike to skip fast AHP and look for slow AHP can be set with sahp_start.
+Default is 5.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: peak_indices, burst_end_indices
+- **Units**: mV
+- **Pseudocode**: ::
+
+    postburst_slow_ahp = []
+    for i in burst_end_indices:
+        i_start = numpy.where(t >= t[peak_indices[i]] + sahp_start)[0][0]
+        if i + 1 < len(peak_indices):
+            postburst_slow_ahp.append(numpy.min(v[i_start:peak_indices[i + 1]]))
+        else:
+            if t[burst_end_indices[-1]] < stim_end:
+                end_idx = numpy.where(t >= stim_end)[0][0]
+                postburst_slow_ahp.append(numpy.min(v[i_start:end_idx]))
+            else:
+                postburst_slow_ahp.append(numpy.min(v[i_start:]))
+
 `LibV5`_ : time_to_interburst_min
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -573,6 +603,181 @@ The burst detection can be fine-tuned by changing the setting strict_burst_facto
         for i in burst_end_indices if i + 1 < len(peak_indices)
     ]
 
+`LibV5`_ : time_to_postburst_slow_ahp
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The time between the last spike of a burst and the slow ahp afterwards.
+
+The number of ms to skip after the spike to skip fast AHP and look for slow AHP can be set with sahp_start.
+Default is 5.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: postburst_slow_ahp_indices, burst_end_indices, peak_time
+- **Units**: ms
+- **Pseudocode**: ::
+
+    time_to_postburst_slow_ahp_py = t[postburst_slow_ahp_indices] - peak_time[burst_end_indices]
+
+`LibV5`_ : postburst_fast_ahp_values
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The fast AHP voltage after the end of a burst.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: peak_indices, burst_end_indices
+- **Units**: mV
+- **Pseudocode**: ::
+
+    postburst_fahp = []
+    for i in burst_end_indices:
+        if i + 1 < len(peak_indices):
+            stop_i = peak_indices[i + 1]
+        elif i + 1 < stim_end_index:
+            stop_i = stim_end_index
+        else:
+            stop_i = len(v) - 1
+        
+        v_crop = v[peak_indices[i]:stop_i]
+        # get where the voltage is going up
+        crop_args = numpy.argwhere(numpy.diff(v_crop) >= 0)[:,0]
+        # the voltage should go up for at least two consecutive points
+        crop_arg_arg = numpy.argwhere(numpy.diff(crop_args) == 1)[0][0]
+        crop_arg = crop_args[crop_arg_arg]
+        end_i = peak_indices[i] + crop_arg + 1
+        # the fast ahp is between last peak of burst and the point where voltage is going back up
+        postburst_fahp.append(numpy.min(v[peak_indices[i]:end_i]))
+
+    return postburst_fahp
+
+`LibV5`_ : postburst_adp_peak_values
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The small ADP peak after the fast AHP after the end of a burst.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: postburst_fast_ahp_indices, postburst_slow_ahp_indices
+- **Units**: mV
+- **Pseudocode**: ::
+
+    adp_peak_values = []
+    for i, sahpi in enumerate(postburst_sahpi):
+        if sahpi < postburst_fahpi[i]:
+            continue
+        adppeaki = numpy.argmax(v[postburst_fahpi[i]:sahpi]) + postburst_fahpi[i]
+        if adppeaki != sahpi - 1:
+            adp_peak_values.append(v[adppeaki])
+
+    if len(adp_peak_values) == 0:
+        return None
+    return adp_peak_values
+
+`LibV5`_ : time_to_postburst_fast_ahp
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Time to the fast AHP after the end of a burst.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: postburst_fast_ahp_indices, burst_end_indices, peak_time
+- **Units**: ms
+- **Pseudocode**: ::
+
+    [t[fahpi] - peak_time[burst_endi[i]] for i, fahpi in enumerate(postburst_fahpi)]
+
+`LibV5`_ : time_to_postburst_adp_peak
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Time to the small ADP peak after the fast AHP after the end of a burst.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: postburst_adp_peak_indices, burst_end_indices, peak_time
+- **Units**: ms
+- **Pseudocode**: ::
+
+    time_to_postburst_adp_peaks = []
+    n_peaks = len(peak_time)
+    for i, adppeaki in enumerate(postburst_adppeaki):
+        # there are not always an adp peak after each burst
+        # so make sure that the burst and adp peak indices are consistent
+        k = 0
+        while (
+            burst_endi[i] + k + 1 < n_peaks and peak_time[burst_endi[i] + k + 1] < t[adppeaki]
+        ):
+            k += 1
+
+        time_to_postburst_adp_peaks.append(t[adppeaki] - peak_time[burst_endi[i] + k])
+
+    return time_to_postburst_adp_peaks
+
+
+`LibV5`_ : interburst_15percent_values, interburst_20percent_values, interburst_25percent_values, interburst_30percent_values, interburst_40percent_values, interburst_60percent_values 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Voltage value after a given percentage (15%, 20%, 25%, 30%, 40% or 60%) of the interburst duration after the fast AHP.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: postburst_fast_ahp_indices, burst_end_indices, peak_indices
+- **Units**: mV
+- **Pseudocode**: ::
+
+    interburst_XXpercent_values = []
+    for i, postburst_fahp_i in enumerate(postburst_fahpi):
+        if i < len(burst_endi) and burst_endi[i] + 1 < len(peaki):
+            time_interval = t[peaki[burst_endi[i] + 1]] - t[postburst_fahp_i]
+            time_at_XXpercent = t[postburst_fahp_i] + time_interval * percentage / 100.
+            index_at_XXpercent = numpy.argwhere(t >= time_at_XXpercent)[0][0]
+            interburst_XXpercent_values.append(v[index_at_XXpercent])
+
+`LibV5`_ : interburst_duration
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Duration between the last spike of each burst and the next spike.
+
+This implementation does not assume that every spike belongs to a burst.
+
+The first spike is ignored by default. This can be changed by setting ignore_first_ISI to 0.
+
+The burst detection can be fine-tuned by changing the setting strict_burst_factor. Defalt value is 2.0.
+
+- **Required features**: burst_end_indices, peak_time
+- **Units**: ms
+- **Pseudocode**: ::
+
+    interburst_duration = [
+        peak_time[idx + 1] - peak_time[idx]
+        for idx in burst_end_indices
+        if idx + 1 < len(peak_time)
+    ]
+
 `Python efeature`_ : single_burst_ratio
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

efel/DependencyV5.txt

@@ -114,5 +114,27 @@ LibV5:ADP_peak_amplitude  #LibV5:ADP_peak_values #LibV5:min_AHP_values #LibV1:in
 LibV5:interburst_min_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV1:interpolate
 LibV5:interburst_min_values      #LibV5:interburst_min_indices #LibV1:interpolate
 LibV5:postburst_min_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV1:interpolate
-LibV5:postburst_min_values      #LibV5:postburst_min_indices #LibV1:interpolate
+LibV5:postburst_min_values      #LibV5:postburst_min_indices #LibV1: interpolate
+LibV5:postburst_slow_ahp_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV1:interpolate
+LibV5:postburst_slow_ahp_values      #LibV5:postburst_slow_ahp_indices #LibV1:interpolate
 LibV5:time_to_interburst_min     #LibV5:interburst_min_indices #LibV1:peak_time #LibV5:burst_end_indices #LibV1:interpolate
+LibV5:time_to_postburst_slow_ahp     #LibV5:postburst_slow_ahp_indices #LibV1:peak_time #LibV5:burst_end_indices #LibV1:interpolate
+LibV5:postburst_fast_ahp_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV1:interpolate
+LibV5:postburst_fast_ahp_values      #LibV5:postburst_fast_ahp_indices #LibV1:interpolate
+LibV5:postburst_adp_peak_indices     #LibV5:postburst_fast_ahp_indices #LibV5:postburst_slow_ahp_indices #LibV1:interpolate
+LibV5:postburst_adp_peak_values      #LibV5:postburst_adp_peak_indices #LibV1:interpolate
+LibV5:time_to_postburst_fast_ahp     #LibV5:postburst_fast_ahp_indices #LibV1:peak_time #LibV5:burst_end_indices #LibV1:interpolate
+LibV5:time_to_postburst_adp_peak     #LibV5:postburst_adp_peak_indices #LibV1:peak_time #LibV5:burst_end_indices #LibV1:interpolate
+LibV5:interburst_15percent_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV5:postburst_fast_ahp_indices #LibV1:interpolate
+LibV5:interburst_15percent_values      #LibV5:interburst_15percent_indices #LibV1:interpolate
+LibV5:interburst_20percent_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV5:postburst_fast_ahp_indices #LibV1:interpolate
+LibV5:interburst_20percent_values      #LibV5:interburst_20percent_indices #LibV1:interpolate
+LibV5:interburst_25percent_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV5:postburst_fast_ahp_indices #LibV1:interpolate
+LibV5:interburst_25percent_values      #LibV5:interburst_25percent_indices #LibV1:interpolate
+LibV5:interburst_30percent_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV5:postburst_fast_ahp_indices #LibV1:interpolate
+LibV5:interburst_30percent_values      #LibV5:interburst_30percent_indices #LibV1:interpolate
+LibV5:interburst_40percent_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV5:postburst_fast_ahp_indices #LibV1:interpolate
+LibV5:interburst_40percent_values      #LibV5:interburst_40percent_indices #LibV1:interpolate
+LibV5:interburst_60percent_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV5:postburst_fast_ahp_indices #LibV1:interpolate
+LibV5:interburst_60percent_values      #LibV5:interburst_60percent_indices #LibV1:interpolate
+LibV5:interburst_duration              #LibV1:peak_time #LibV5:burst_end_indices #LibV1:interpolate

efel/cppcore/FillFptrTable.cpp

@@ -181,7 +181,77 @@ int FillFptrTable() {
   FptrTableV5["interburst_min_values"] = &LibV5::interburst_min_values;
   FptrTableV5["postburst_min_indices"] = &LibV5::postburst_min_indices;
   FptrTableV5["postburst_min_values"] = &LibV5::postburst_min_values;
+  FptrTableV5["postburst_slow_ahp_indices"] = &LibV5::postburst_slow_ahp_indices;
+  FptrTableV5["postburst_slow_ahp_values"] = &LibV5::postburst_slow_ahp_values;
   FptrTableV5["time_to_interburst_min"] = &LibV5::time_to_interburst_min;
+  FptrTableV5["time_to_postburst_slow_ahp"] = &LibV5::time_to_postburst_slow_ahp;
+  FptrTableV5["postburst_fast_ahp_indices"] = &LibV5::postburst_fast_ahp_indices;
+  FptrTableV5["postburst_fast_ahp_values"] = &LibV5::postburst_fast_ahp_values;
+  FptrTableV5["postburst_adp_peak_indices"] = &LibV5::postburst_adp_peak_indices;
+  FptrTableV5["postburst_adp_peak_values"] = &LibV5::postburst_adp_peak_values;
+  FptrTableV5["time_to_postburst_fast_ahp"] = &LibV5::time_to_postburst_fast_ahp;
+  FptrTableV5["time_to_postburst_adp_peak"] = &LibV5::time_to_postburst_adp_peak;
+  FptrTableV5["interburst_15percent_indices"] = [](mapStr2intVec& intData,
+                                                   mapStr2doubleVec& doubleData,
+                                                   mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 15);
+  };
+  FptrTableV5["interburst_15percent_values"] = [](mapStr2intVec& intData,
+                                                  mapStr2doubleVec& doubleData,
+                                                  mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 15);
+  };
+  FptrTableV5["interburst_20percent_indices"] = [](mapStr2intVec& intData,
+                                                   mapStr2doubleVec& doubleData,
+                                                   mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 20);
+  };
+  FptrTableV5["interburst_20percent_values"] = [](mapStr2intVec& intData,
+                                                  mapStr2doubleVec& doubleData,
+                                                  mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 20);
+  };
+  FptrTableV5["interburst_25percent_indices"] = [](mapStr2intVec& intData,
+                                                   mapStr2doubleVec& doubleData,
+                                                   mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 25);
+  };
+  FptrTableV5["interburst_25percent_values"] = [](mapStr2intVec& intData,
+                                                  mapStr2doubleVec& doubleData,
+                                                  mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 25);
+  };
+  FptrTableV5["interburst_30percent_indices"] = [](mapStr2intVec& intData,
+                                                   mapStr2doubleVec& doubleData,
+                                                   mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 30);
+  };
+  FptrTableV5["interburst_30percent_values"] = [](mapStr2intVec& intData,
+                                                  mapStr2doubleVec& doubleData,
+                                                  mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 30);
+  };
+  FptrTableV5["interburst_40percent_indices"] = [](mapStr2intVec& intData,
+                                                   mapStr2doubleVec& doubleData,
+                                                   mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 40);
+  };
+  FptrTableV5["interburst_40percent_values"] = [](mapStr2intVec& intData,
+                                                  mapStr2doubleVec& doubleData,
+                                                  mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 40);
+  };
+  FptrTableV5["interburst_60percent_indices"] = [](mapStr2intVec& intData,
+                                                   mapStr2doubleVec& doubleData,
+                                                   mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 60);
+  };
+  FptrTableV5["interburst_60percent_values"] = [](mapStr2intVec& intData,
+                                                  mapStr2doubleVec& doubleData,
+                                                  mapStr2Str& strData) {
+    return LibV5::interburst_XXpercent_indices(intData, doubleData, strData, 60);
+  };
+  FptrTableV5["interburst_duration"] = &LibV5::interburst_duration;
 
   //****************** end of FptrTableV5 *****************************