move Spikecount implementation to Python

BlueBrain · Dec 21, 2023 · 241a2d7 · 241a2d7
1 parent 9e9286f
commit 241a2d7
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Showing 11 changed files with 25 additions and 30 deletions.
diff --git a/efel/DependencyV5.txt b/efel/DependencyV5.txt
@@ -28,8 +28,7 @@ LibV1:maximum_voltage #LibV1:interpolate
 LibV1:minimum_voltage #LibV1:interpolate 
 LibV1:steady_state_voltage #LibV1:interpolate 
 LibV3:depolarized_base #LibV5:AP_end_indices #LibV5:AP_begin_indices #LibV1:interpolate
-LibV1:ISI_CV	#LibV1:ISI_values #LibV1:interpolate 
-LibV1:Spikecount	#LibV5:peak_indices #LibV1:interpolate 
+LibV1:ISI_CV	#LibV1:ISI_values #LibV1:interpolate
 LibV5:Spikecount_stimint	#LibV1:peak_time #LibV1:interpolate 
 LibV1:AHP_depth	#LibV5:voltage_base	#LibV5:min_AHP_values #LibV1:interpolate 
 LibV1:AHP_depth_slow    #LibV5:voltage_base	#LibV1:AHP_depth_abs_slow #LibV1:interpolate

diff --git a/efel/cppcore/FillFptrTable.cpp b/efel/cppcore/FillFptrTable.cpp
@@ -48,7 +48,6 @@ int FillFptrTable() {
   FptrTableV1["ISI_CV"] = &LibV1::ISI_CV;
   FptrTableV1["AHP_depth_abs_slow"] = &LibV1::AHP_depth_abs_slow;
   FptrTableV1["AHP_slow_time"] = &LibV1::AHP_slow_time;
-  FptrTableV1["Spikecount"] = &LibV1::Spikecount;
   FptrTableV1["AHP_depth"] = &LibV1::AHP_depth;
   FptrTableV1["AHP_depth_slow"] = &LibV1::AHP_depth_slow;
   FptrTableV1["burst_number"] = &LibV1::burst_number;

diff --git a/efel/cppcore/LibV1.cpp b/efel/cppcore/LibV1.cpp
@@ -76,17 +76,6 @@ int LibV1::interpolate(mapStr2intVec& IntFeatureData,
   return 1;
 }
 
-// *** Spikecount ***
-int LibV1::Spikecount(mapStr2intVec& IntFeatureData,
-                      mapStr2doubleVec& DoubleFeatureData,
-                      mapStr2Str& StringData) {
-  size_t spikecount_value = getFeature(IntFeatureData, {"peak_indices"}).size();
-  vector<int> spikecount(1, spikecount_value);
-  setVec(IntFeatureData, StringData, "Spikecount", spikecount);
-  return spikecount_value;
-}
-// end of Spikecount
-
 int LibV1::ISI_values(mapStr2intVec& IntFeatureData,
                       mapStr2doubleVec& DoubleFeatureData,
                       mapStr2Str& StringData) {

diff --git a/efel/cppcore/LibV1.h b/efel/cppcore/LibV1.h
@@ -116,8 +116,6 @@ int AHP_depth_abs_slow(mapStr2intVec& IntFeatureData,
                        mapStr2Str& StringData);
 int AHP_slow_time(mapStr2intVec& IntFeatureData,
                   mapStr2doubleVec& DoubleFeatureData, mapStr2Str& StringData);
-int Spikecount(mapStr2intVec& IntFeatureData,
-               mapStr2doubleVec& DoubleFeatureData, mapStr2Str& StringData);
 int AHP_depth(mapStr2intVec& IntFeatureData,
               mapStr2doubleVec& DoubleFeatureData, mapStr2Str& StringData);
 int AHP_depth_slow(mapStr2intVec& IntFeatureData,

diff --git a/efel/cppcore/cfeature.cpp b/efel/cppcore/cfeature.cpp
@@ -128,7 +128,6 @@ void cFeature::fillfeaturetypes() {
   featuretypes["ISI_CV"] = "double";
   featuretypes["AHP_depth_abs_slow"] = "double";
   featuretypes["AHP_slow_time"] = "double";
-  featuretypes["Spikecount"] = "int";
   featuretypes["Spikecount_stimint"] = "int";
   featuretypes["AHP_depth"] = "double";
   featuretypes["AHP_depth_slow"] = "double";

diff --git a/efel/pyfeatures/pyfeatures.py b/efel/pyfeatures/pyfeatures.py
@@ -25,6 +25,7 @@
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
 
+from typing_extensions import deprecated
 
 import numpy
 import efel.cppcore
@@ -41,6 +42,7 @@
     'initburst_sahp_ssse',
     'depol_block',
     'depol_block_bool',
+    'Spikecount',
     'spikes_per_burst',
     'spikes_per_burst_diff',
     'spikes_in_burst1_burst2_diff',
@@ -59,6 +61,19 @@ def time():
     return _get_cpp_feature("time")
 
 
+@deprecated("Use spike_count instead.")
+def Spikecount() -> numpy.ndarray:
+    return spike_count()
+
+
+def spike_count() -> numpy.ndarray:
+    """Get spike count."""
+    peak_indices = _get_cpp_feature("peak_indices")
+    if peak_indices is None:
+        return numpy.array([0])
+    return numpy.array([peak_indices.size])
+
+
 def impedance():
     from scipy.ndimage.filters import gaussian_filter1d
 
@@ -71,10 +86,10 @@ def impedance():
     if current_trace is not None:
         holding_current = _get_cpp_feature("current_base")
         normalized_current = current_trace - holding_current
-        spike_count = _get_cpp_feature("Spikecount")
-        if spike_count is None:
-            spike_count = 0
-        if spike_count < 1:  # if there is no spikes in ZAP
+        n_spikes = spike_count()
+        if n_spikes is None:
+            n_spikes = 0
+        if n_spikes < 1:  # if there is no spikes in ZAP
             fft_volt = numpy.fft.fft(normalized_voltage)
             fft_cur = numpy.fft.fft(normalized_current)
             if any(fft_cur) == 0:

diff --git a/examples/deap/GranuleCell1/GranuleCellDeap1.ipynb b/examples/deap/GranuleCell1/GranuleCellDeap1.ipynb
@@ -111,7 +111,6 @@
     "        times.append(time)\n",
     "        voltages.append(voltage)\n",
     "\n",
-    "    feature_values[0][\"Spikecount\"] = 0.0  # replace None with 0.0     \n",
     "    return feature_values, times, voltages\n",
     "\n",
     "orig_features, orig_times, orig_voltages = get_features(orig_conductances)"
@@ -406,7 +405,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/setup.py b/setup.py
@@ -78,7 +78,7 @@
     name="efel",
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    install_requires=['numpy>=1.6', 'neo>=0.5.2'],
+    install_requires=['numpy>=1.6', 'neo>=0.5.2', 'typing-extensions>=4.8.0'],
     packages=['efel', 'efel.pyfeatures', 'efel.units'],
     author="BlueBrain Project, EPFL",
     maintainer="Werner Van Geit",

diff --git a/tests/DependencyV5_LibV5peakindices.txt b/tests/DependencyV5_LibV5peakindices.txt
@@ -27,7 +27,6 @@ LibV1:interpolate
 LibV1:steady_state_voltage
 LibV3:depolarized_base
 LibV1:ISI_CV	#LibV1:ISI_values
-LibV1:Spikecount	#LibV5:peak_indices
 LibV1:AHP_depth	#LibV5:voltage_base	#LibV5:min_AHP_values
 LibV2:AP_rise_indices       #LibV5:peak_indices     #LibV5:AP_begin_indices
 LibV2:AP_end_indices        #LibV5:peak_indices

diff --git a/tests/test_allfeatures.py b/tests/test_allfeatures.py
@@ -173,7 +173,7 @@ def test_allfeatures_on_constant_voltage():
         "sag_amplitude", "voltage_after_stim", "steady_state_hyper",
         "steady_state_voltage", "steady_state_voltage_stimend",
         "voltage_deflection", "voltage_deflection_begin", "voltage_deflection_vb_ssse",
-        "depol_block", "depol_block_bool", "voltage_base"
+        "depol_block", "depol_block_bool", "voltage_base", "Spikecount"
     ]
 
     for field in array_fields:

diff --git a/tests/test_basic.py b/tests/test_basic.py
@@ -626,7 +626,6 @@ def test_strict_stiminterval():
         peak_indices = feature_values[0]['peak_indices']
         peak_time = feature_values[0]['peak_time']
         spikecount = feature_values[0]['Spikecount']
-
         assert len(peak_indices) == n_of_spikes
         assert len(peak_time) == n_of_spikes
         assert spikecount == n_of_spikes
@@ -1132,7 +1131,6 @@ def test_getDistance_trace_check():
     trace['stim_start'] = [10]
     trace['stim_end'] = [70]
     traces.append(trace)
-
     numpy.testing.assert_allclose(
         efel.getDistance(trace, 'Spikecount', 0, 1), 3.0
     )
@@ -1638,8 +1636,8 @@ def test_spikecount2():
             [trace],
             features)
 
-    spikecount = feature_values[0]['Spikecount']
-    assert spikecount is None
+    spikecount = feature_values[0]['Spikecount'][0]
+    assert spikecount == 0
 
 
 def test_min_voltage_between_spikes1():