move burst_number and strict_burst_number to Python

BlueBrain · Jan 5, 2024 · 31b7212 · 31b7212
1 parent eebc16e
commit 31b7212
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Showing 12 changed files with 32 additions and 41 deletions.
diff --git a/docs/source/eFeatures.rst b/docs/source/eFeatures.rst
@@ -402,8 +402,8 @@ The burst detection can be fine-tuned by changing the setting strict_burst_facto
             )
         )
 
-`LibV1`_ : burst_number
-~~~~~~~~~~~~~~~~~~~~~~~
+`Python efeature`_ : burst_number
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The number of bursts
 
@@ -413,8 +413,8 @@ The number of bursts
 
     burst_number = len(burst_mean_freq)
 
-`LibV5`_ : strict_burst_number
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+`Python efeature`_ : strict_burst_number
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The number of bursts
 

diff --git a/efel/DependencyV5.txt b/efel/DependencyV5.txt
@@ -13,7 +13,6 @@ LibV1:adaptation_index2	#LibV1:peak_time #LibV1:interpolate
 LibV1:spike_width2	 	    #LibV5:min_AHP_indices #LibV1:interpolate 
 LibV1:AP_width  #LibV5:peak_indices #LibV5:min_AHP_indices #LibV1:interpolate 
 LibV1:burst_mean_freq	    #LibV1:burst_ISI_indices    #LibV1:peak_time #LibV1:interpolate 
-LibV1:burst_number	    #LibV1:burst_mean_freq #LibV1:interpolate 
 LibV1:interburst_voltage	#LibV1:burst_ISI_indices #LibV1:interpolate 
 LibV1:AP_height             #LibV1:peak_voltage #LibV1:interpolate 
 LibV1:AP_amplitude          #LibV5:AP_begin_indices #LibV1:peak_voltage #LibV1:peak_time #LibV1:interpolate 
@@ -125,7 +124,6 @@ LibV5:AP_width_between_threshold    #LibV5:min_between_peaks_indices #LibV1:inte
 LibV5:burst_begin_indices    #LibV5:all_ISI_values #LibV1:interpolate
 LibV5:burst_end_indices    #LibV5:burst_begin_indices #LibV1:interpolate
 LibV5:strict_burst_mean_freq    #LibV1:peak_time #LibV5:burst_begin_indices #LibV5:burst_end_indices #LibV1:interpolate
-LibV5:strict_burst_number    #LibV5:strict_burst_mean_freq #LibV1:interpolate
 LibV5:strict_interburst_voltage    #LibV5:peak_indices #LibV5:burst_begin_indices #LibV1:interpolate
 LibV5:ADP_peak_indices    #LibV5:min_AHP_indices #LibV5:min_between_peaks_indices #LibV1:interpolate
 LibV5:ADP_peak_values     #LibV5:ADP_peak_indices #LibV1:interpolate

diff --git a/efel/cppcore/FillFptrTable.cpp b/efel/cppcore/FillFptrTable.cpp
@@ -50,7 +50,6 @@ int FillFptrTable() {
   FptrTableV1["AHP_slow_time"] = &LibV1::AHP_slow_time;
   FptrTableV1["AHP_depth"] = &LibV1::AHP_depth;
   FptrTableV1["AHP_depth_slow"] = &LibV1::AHP_depth_slow;
-  FptrTableV1["burst_number"] = &LibV1::burst_number;
   FptrTableV1["AP_amplitude_diff"] = &LibV1::AP_amplitude_diff;
   FptrTableV1["AHP_depth_diff"] = &LibV1::AHP_depth_diff;
 
@@ -210,7 +209,6 @@ int FillFptrTable() {
   FptrTableV5["burst_begin_indices"] = &LibV5::burst_begin_indices;
   FptrTableV5["burst_end_indices"] = &LibV5::burst_end_indices;
   FptrTableV5["strict_burst_mean_freq"] = &LibV5::strict_burst_mean_freq;
-  FptrTableV5["strict_burst_number"] = &LibV5::strict_burst_number;
   FptrTableV5["strict_interburst_voltage"] = &LibV5::strict_interburst_voltage;
 
   FptrTableV5["ADP_peak_indices"] = &LibV5::ADP_peak_indices;

diff --git a/efel/cppcore/LibV1.cpp b/efel/cppcore/LibV1.cpp
@@ -405,17 +405,6 @@ int LibV1::burst_mean_freq(mapStr2intVec& IntFeatureData,
   return retVal;
 }
 
-int LibV1::burst_number(mapStr2intVec& IntFeatureData,
-                        mapStr2doubleVec& DoubleFeatureData,
-                        mapStr2Str& StringData) {
-  const auto& doubleFeatures =
-      getFeatures(DoubleFeatureData, {"burst_mean_freq"});
-  vector<int> BurstNum;
-  BurstNum.push_back(doubleFeatures.at("burst_mean_freq").size());
-  setVec(IntFeatureData, StringData, "burst_number", BurstNum);
-  return BurstNum.size();
-}
-
 // reminder: first ISI value is ignored in burst_ISI_indices if IgnoreFirstISI=1
 static int __interburst_voltage(const vector<int>& BurstIndex,
                                 const vector<int>& PeakIndex,

diff --git a/efel/cppcore/LibV1.h b/efel/cppcore/LibV1.h
@@ -121,8 +121,6 @@ int AHP_depth(mapStr2intVec& IntFeatureData,
 int AHP_depth_slow(mapStr2intVec& IntFeatureData,
                        mapStr2doubleVec& DoubleFeatureData,
                        mapStr2Str& StringData);
-int burst_number(mapStr2intVec& IntFeatureData,
-                 mapStr2doubleVec& DoubleFeatureData, mapStr2Str& StringData);
 int AP_amplitude_diff(mapStr2intVec& IntFeatureData,
                       mapStr2doubleVec& DoubleFeatureData,
                       mapStr2Str& StringData);

diff --git a/efel/cppcore/LibV5.cpp b/efel/cppcore/LibV5.cpp
@@ -2258,17 +2258,6 @@ int LibV5::strict_burst_mean_freq(mapStr2intVec& IntFeatureData,
   return retVal;
 }
 
-int LibV5::strict_burst_number(mapStr2intVec& IntFeatureData,
-                               mapStr2doubleVec& DoubleFeatureData,
-                               mapStr2Str& StringData) {
-  const auto& doubleFeatures =
-      getFeatures(DoubleFeatureData, {"strict_burst_mean_freq"});
-  vector<int> BurstNum;
-  BurstNum.push_back(doubleFeatures.at("strict_burst_mean_freq").size());
-  setVec(IntFeatureData, StringData, "strict_burst_number", BurstNum);
-  return BurstNum.size();
-}
-
 static int __strict_interburst_voltage(const vector<int>& burst_begin_indices,
                                        const vector<int>& PeakIndex,
                                        const vector<double>& T,

diff --git a/efel/cppcore/LibV5.h b/efel/cppcore/LibV5.h
@@ -247,9 +247,6 @@ int burst_end_indices(mapStr2intVec& IntFeatureData,
 int strict_burst_mean_freq(mapStr2intVec& IntFeatureData,
                             mapStr2doubleVec& DoubleFeatureData,
                             mapStr2Str& StringData);
-int strict_burst_number(mapStr2intVec& IntFeatureData,
-                            mapStr2doubleVec& DoubleFeatureData,
-                            mapStr2Str& StringData);
 int strict_interburst_voltage(mapStr2intVec& IntFeatureData,
                             mapStr2doubleVec& DoubleFeatureData,
                             mapStr2Str& StringData);

diff --git a/efel/cppcore/cfeature.cpp b/efel/cppcore/cfeature.cpp
@@ -135,7 +135,6 @@ void cFeature::fillfeaturetypes() {
   featuretypes["amp_drop_second_last"] = "double";
   featuretypes["max_amp_difference"] = "double";
   featuretypes["depolarized_base"] = "double";
-  featuretypes["burst_number"] = "int";
 
   // LibV5
   featuretypes["ISI_log_slope"] = "double";
@@ -212,7 +211,6 @@ void cFeature::fillfeaturetypes() {
   featuretypes["burst_begin_indices"] = "int";
   featuretypes["burst_end_indices"] = "int";
   featuretypes["strict_burst_mean_freq"] = "double";
-  featuretypes["strict_burst_number"] = "int";
   featuretypes["strict_interburst_voltage"] = "double";
 
   featuretypes["ADP_peak_indices"] = "int";

diff --git a/efel/pyfeatures/pyfeatures.py b/efel/pyfeatures/pyfeatures.py
@@ -49,6 +49,8 @@
     'spikes_in_burst1_burst2_diff',
     'spikes_in_burst1_burstlast_diff',
     'impedance',
+    'burst_number',
+    'strict_burst_number'
 ]
 
 
@@ -92,6 +94,29 @@ def spike_count_stimint() -> numpy.ndarray:
     return numpy.array([res])
 
 
+def burst_number() -> numpy.ndarray:
+    """The number of bursts."""
+    burst_mean_freq = _get_cpp_feature("burst_mean_freq")
+    if burst_mean_freq is None:
+        return numpy.array([0])
+    return numpy.array([burst_mean_freq.size])
+
+
+def strict_burst_number() -> numpy.ndarray:
+    """Calculate the strict burst number.
+
+    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. Default value is 2.0."""
+    burst_mean_freq = _get_cpp_feature("strict_burst_mean_freq")
+    if burst_mean_freq is None:
+        return numpy.array([0])
+    return numpy.array([burst_mean_freq.size])
+
+
 def impedance():
     from scipy.ndimage.filters import gaussian_filter1d
 

diff --git a/tests/DependencyV5_LibV5peakindices.txt b/tests/DependencyV5_LibV5peakindices.txt
@@ -12,7 +12,6 @@ LibV1:adaptation_index2	#LibV1:peak_time
 LibV1:spike_width2	 	    #LibV5:min_AHP_indices
 LibV1:AP_width  #LibV5:peak_indices #LibV5:min_AHP_indices
 LibV1:burst_mean_freq	    #LibV1:burst_ISI_indices    #LibV1:peak_time
-LibV1:burst_number	    #LibV1:burst_mean_freq
 LibV1:interburst_voltage	#LibV1:burst_ISI_indices
 LibV1:AP_height             #LibV1:peak_voltage
 LibV1:AP_amplitude          #LibV5:AP_begin_indices #LibV1:peak_voltage

diff --git a/tests/test_allfeatures.py b/tests/test_allfeatures.py
@@ -174,7 +174,7 @@ def test_allfeatures_on_constant_voltage():
         "steady_state_voltage", "steady_state_voltage_stimend",
         "voltage_deflection", "voltage_deflection_begin", "voltage_deflection_vb_ssse",
         "depol_block", "depol_block_bool", "voltage_base", "Spikecount",
-        "Spikecount_stimint"
+        "Spikecount_stimint", "burst_number", "strict_burst_number"
     ]
 
     for field in array_fields:

diff --git a/tests/test_basic.py b/tests/test_basic.py
@@ -201,9 +201,9 @@ def test_failing_int_feature():
 
     feature_value = efel.getFeatureValues(
         [trace],
-        ['burst_number'], raise_warnings=False)[0]['burst_number']
+        ['burst_number'], raise_warnings=False)[0]['burst_number'][0]
 
-    assert feature_value is None
+    assert feature_value == 0
 
 
 def test_empty_trace():