Merge pull request #318 from AurelienJaquier/interpolate-current

interpolate current if present
BlueBrain · Sep 28, 2023 · 1a24079 · 1a24079
2 parents b2ee3df + e7565d8
commit 1a24079
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Showing 3 changed files with 28 additions and 23 deletions.
diff --git a/efel/DependencyV5.txt b/efel/DependencyV5.txt
@@ -150,7 +150,7 @@ LibV5:current #LibV1:interpolate
 LibV5:time #LibV1:interpolate 
 LibV5:steady_state_voltage_stimend #LibV1:interpolate 
 LibV5:voltage_base #LibV1:interpolate
-LibV5:current_base 
+LibV5:current_base #LibV1:interpolate
 LibV5:decay_time_constant_after_stim #LibV1:interpolate 
 LibV5:sag_time_constant #LibV1:minimum_voltage #LibV5:steady_state_voltage_stimend #LibV5:sag_amplitude #LibV1:interpolate
 LibV5:multiple_decay_time_constant_after_stim #LibV5:decay_time_constant_after_stim #LibV1:interpolate
@@ -172,7 +172,7 @@ LibV5:ADP_peak_indices    #LibV5:min_AHP_indices #LibV5:min_between_peaks_indice
 LibV5:ADP_peak_values     #LibV5:ADP_peak_indices #LibV1:interpolate
 LibV5:ADP_peak_amplitude  #LibV5:ADP_peak_values #LibV5:min_AHP_values #LibV1:interpolate
 LibV5:interburst_min_indices     #LibV5:peak_indices #LibV5:burst_end_indices #LibV1:interpolate
-LibV5:interburst_min_values      #LibV5:interburst_min_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:time_to_interburst_min     #LibV5:interburst_min_indices #LibV1:peak_time #LibV5:burst_end_indices #LibV1:interpolate
diff --git a/efel/cppcore/LibV1.cpp b/efel/cppcore/LibV1.cpp
@@ -73,6 +73,15 @@ int LibV1::interpolate(mapStr2intVec& IntFeatureData,
   setVec(DoubleFeatureData, StringData, "V", VIntrpol);
   setVec(DoubleFeatureData, StringData, "T", TIntrpol);
   setVec(IntFeatureData, StringData, "interpolate", intrpolte);
+
+  // also interpolate current if present
+  vector<double> I, IIntrpol, TIntrpolI;
+  int retValI;
+  retValI = getVec(DoubleFeatureData, StringData, "I", I);
+  if (retValI > 0){
+    LinearInterpolation(InterpStep, T, I, TIntrpolI, IIntrpol);
+    setVec(DoubleFeatureData, StringData, "I", IIntrpol);
+  }
   return retVal;
 }
 

diff --git a/tests/test_pyfeatures.py b/tests/test_pyfeatures.py
@@ -152,6 +152,9 @@ def _load_trace(trace_name):
         'stim_end': [trace_data['stim_end']],
     }
 
+    if trace_name == "current":
+        trace['T'] = trace['T'] * 1000.0  # s -> ms
+
     if 'i_col' in trace_data:
         trace['I'] = efel.io.load_fragment('%s#col=%d' %
                                            (url, trace_data['i_col']))
@@ -331,18 +334,6 @@ def test_pydistance_featurefail():
         trace_check=True), 250.0)
 
 
-def test_current():
-    """pyfeatures: Test current feature"""
-
-    feature_name = 'current'
-    data = numpy.loadtxt(os.path.join(os.path.abspath(testdata_dir),
-                                      'basic',
-                                      'current.txt'))
-    current = data[:, 1]
-    expected_values = {'current': current}
-    _test_expected_value(feature_name, expected_values)
-
-
 def test_interpolate_current():
     """pyfeatures: Test interpolation of current"""
 
@@ -357,16 +348,21 @@ def interpolate(time, voltage, new_dt):
     data = numpy.loadtxt(os.path.join(os.path.abspath(testdata_dir),
                                       'basic',
                                       'current.txt'))
-    time = data[:, 0]
+    time = data[:, 0] * 1000.0  # -> ms
     current = data[:, 1]
     voltage = data[:, 2]
 
     feature_name = ['time', 'current', 'voltage']
     trace = _load_trace('current')
-    feature_values = efel.getFeatureValues([trace], ['current'])
-    interp_time, interp_current = interpolate(time, current, new_dt=0.00025)
-
-    assert len(interp_time) == len(time)
-    assert len(interp_current) == len(current)
-    assert len(voltage) == len(current)
-    assert numpy.allclose(interp_current, current)
+    feature_values = efel.getFeatureValues([trace], feature_name)
+    feature_time = feature_values[0]["time"]
+    feature_current = feature_values[0]["current"]
+    feature_voltage = feature_values[0]["voltage"]
+    interp_time, interp_current = interpolate(time, current, new_dt=0.1)
+    _, interp_voltage = interpolate(time, voltage, new_dt=0.1)
+
+    assert len(interp_time) == len(feature_time)
+    assert len(interp_current) == len(feature_current)
+    assert len(interp_voltage) == len(feature_voltage)
+    assert len(feature_voltage) == len(feature_current)
+    assert numpy.allclose(interp_current, feature_current, atol=1e-6)