perf: reduce cppcore initialisation (#410)

Author: ilkilic

CHANGELOG.rst

@@ -5,6 +5,11 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_,
 and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
+5.7.9 - 2024-09
+---------------
+
+- Reduces redundant dependency tree initializations in cppcore, improving feature extraction performance by up to 2.5x. Ensures getFeatureValues avoids unnecessary resets; use efel.reset to reload dependencies when needed.
+
 5.6.7 - 2024-08
 ---------------
 

efel/api.py

@@ -212,8 +212,11 @@ def _initialise() -> None:
     cppcore.Initialize(_settings.dependencyfile_path, "log")
     # flush the GErrorString from previous runs by calling getgError()
     cppcore.getgError()
+    _initSettings()
 
-    # Set the settings in the cppcore
+
+def _initSettings() -> None:
+    """Init the settings in cppcore."""
     settings_attrs = vars(_settings)
     for setting_name, setting_value in settings_attrs.items():
         if isinstance(setting_value, bool):
@@ -356,7 +359,8 @@ def _get_feature_values_serial(
     else:
         raise Exception('stim_start or stim_end missing from trace')
 
-    _initialise()
+    cppcore.Clear()
+    _initSettings()
 
     # Next set time, voltage and the stimulus start and end
     for item in list(trace.keys()):

efel/cppcore.pyi

@@ -1,4 +1,5 @@
 def Initialize(depfilename: str, outfilename: str) -> int: ...
+def Clear() -> int: ...
 def getFeature(feature_name: str, values: list) -> int: ...
 def getFeatureInt(feature_name: str, values: list[int]) -> int: ...
 def getFeatureDouble(feature_name: str, values: list[float]) -> int: ...

efel/cppcore/cfeature.cpp

@@ -54,6 +54,13 @@ cFeature::cFeature(const string& strDepFile, const string& outdir)
   logger << "Using dependency file: " << strDepFile << endl;
 }
 
+void cFeature::clearMap()
+{
+    mapIntData.clear();
+    mapDoubleData.clear();
+    mapStrData.clear();
+}
+
 template <typename T>
 const vector<T> cFeature::getMapData(const string& strName,
                                      const map<string, vector<T>>& mapData) {

efel/cppcore/cfeature.h

@@ -1,21 +1,21 @@
-/* Copyright (c) 2015, EPFL/Blue Brain Project                                   
- *                                                                               
- * This file is part of eFEL <https://github.com/BlueBrain/eFEL>                 
- *                                                                               
- * This library is free software; you can redistribute it and/or modify it under 
- * the terms of the GNU Lesser General Public License version 3.0 as published   
- * by the Free Software Foundation.                                              
- *                                                                               
- * This library is distributed in the hope that it will be useful, but WITHOUT   
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
- * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more 
- * details.                                                                      
- *                                                                               
- * You should have received a copy of the GNU Lesser General Public License      
- * along with this library; if not, write to the Free Software Foundation, Inc., 
- * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.                   
+/* Copyright (c) 2015, EPFL/Blue Brain Project
+ *
+ * This file is part of eFEL <https://github.com/BlueBrain/eFEL>
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License version 3.0 as published
+ * by the Free Software Foundation.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
-      
+
 #ifndef CFEATURE_H_
 #define CFEATURE_H_
 
@@ -62,6 +62,7 @@ class cFeature {
   string featuretype(string featurename);
   string getGError();
   void get_feature_names(vector<string>& feature_names);
+  void clearMap();
 
 };
 

efel/cppcore/cppcore.cpp

@@ -54,6 +54,12 @@ int Initialize(const char* strDepFile, const char* outdir) {
   }
 }
 
+void Clear() {
+    if (pFeature != NULL) {
+        pFeature->clearMap();
+    }
+}
+
 static PyObject* CppCoreInitialize(PyObject* self, PyObject* args) {
   char *depfilename, *outfilename;
   if (!PyArg_ParseTuple(args, "ss", &depfilename, &outfilename)) {
@@ -64,6 +70,11 @@ static PyObject* CppCoreInitialize(PyObject* self, PyObject* args) {
   return Py_BuildValue("");
 }
 
+static PyObject* CppCoreClear(PyObject* self, PyObject* args) {
+  Clear();
+  return Py_BuildValue("");
+}
+
 static vector<int> PyList_to_vectorint(PyObject* input) {
   vector<int> result_vector;
   int list_size;
@@ -293,7 +304,7 @@ static PyObject* getgerrorstr(PyObject* self, PyObject* args) {
 
 static PyMethodDef CppCoreMethods[] = {
     {"Initialize", CppCoreInitialize, METH_VARARGS, "Initialise CppCore."},
-
+    {"Clear", CppCoreClear, METH_NOARGS, "Clear CppCore."},
     {"getFeature", getfeature, METH_VARARGS,
      "Get a values associated with a feature. Takes a list() to be filled."},
     {"getFeatureInt", getfeatureint, METH_VARARGS, "Get a integer feature."},

tests/test_cppcore.py

@@ -258,6 +258,21 @@ def test_caching(self, feature_name):
         # make sure Reusing computed value of text occurs twice
         assert contents.count(f"Reusing computed value of {feature_name}") == 2
 
+    def test_clear_function(self):
+        """cppcore: Testing Clear function to reset state"""
+        import efel
+        self.setup_data()
+
+        feature_values = list()
+        efel.cppcore.getFeature('AP_amplitude', feature_values)
+        assert len(feature_values) > 0  # Data should be present
+
+        efel.cppcore.Clear()
+
+        feature_values = list()
+        return_value = efel.cppcore.getFeature('AP_amplitude', feature_values)
+        assert return_value == -1  # Should return -1 since data is cleared
+
 
 def test_efel_assertion_error():
     """Testing if C++ assertion error is propagated to Python correctly."""