refactoring into SpikeEvent, SpikeShape, Subthreshold

BlueBrain · May 1, 2024 · 6b3458b · 6b3458b
1 parent 5f807f7
commit 6b3458b
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Showing 19 changed files with 5,733 additions and 5,137 deletions.
diff --git a/docs/source/eFeatures.rst b/docs/source/eFeatures.rst
diff --git a/efel/DependencyV5.txt b/efel/DependencyV5.txt
diff --git a/efel/cppcore/BasicFeatures.cpp b/efel/cppcore/BasicFeatures.cpp
@@ -0,0 +1,75 @@
+/* Copyright (c) 2015-2024, 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.                   
+ */
+
+
+int BasicFeatures::interpolate(mapStr2intVec& IntFeatureData,
+                       mapStr2doubleVec& DoubleFeatureData,
+                       mapStr2Str& StringData) {
+  vector<double> V, T, VIntrpol, TIntrpol, InterpStepVec;
+  T = getFeature(DoubleFeatureData, "T");
+  // interp_step is a stimulus independent parameter
+  int retVal = getParam(DoubleFeatureData, "interp_step", InterpStepVec);
+  double InterpStep = (retVal <= 0) ? 0.1 : InterpStepVec[0];
+
+  try  // interpolate V if it's available
+  {
+    V = getFeature(DoubleFeatureData, "V");
+    LinearInterpolation(InterpStep, T, V, TIntrpol, VIntrpol);
+    setVec(DoubleFeatureData, StringData, "V", VIntrpol);
+    setVec(DoubleFeatureData, StringData, "T", TIntrpol);
+  } catch (...) {
+    return -1;  // interpolation failed
+  }
+
+  // also interpolate current if present
+  vector<double> I, IIntrpol, TIntrpolI;
+  try {
+    I = getFeature(DoubleFeatureData, "I");
+    LinearInterpolation(InterpStep, T, I, TIntrpolI, IIntrpol);
+    setVec(DoubleFeatureData, StringData, "I", IIntrpol);
+    setVec(DoubleFeatureData, StringData, "T", TIntrpol);
+  } catch (...) {
+  }  // pass, it is optional
+  return 1;
+}
+
+// return (possibly interpolate) voltage trace
+int BasicFeatures::voltage(mapStr2intVec& IntFeatureData,
+                   mapStr2doubleVec& DoubleFeatureData,
+                   mapStr2Str& StringData) {
+  const vector<double>& v = getFeature(DoubleFeatureData, "V");
+  setVec(DoubleFeatureData, StringData, "voltage", v);
+  return v.size();
+}
+
+// return (possibly interpolate) current trace
+int BasicFeatures::current(mapStr2intVec& IntFeatureData,
+                   mapStr2doubleVec& DoubleFeatureData,
+                   mapStr2Str& StringData) {
+  const vector<double>& i = getFeature(DoubleFeatureData, "I");
+  setVec(DoubleFeatureData, StringData, "current", i);
+  return i.size();
+}
+
+// return (possibly interpolate) time trace
+int BasicFeatures::time(mapStr2intVec& IntFeatureData,
+                mapStr2doubleVec& DoubleFeatureData, mapStr2Str& StringData) {
+  const vector<double>& t = getFeature(DoubleFeatureData, "T");
+  setVec(DoubleFeatureData, StringData, "time", t);
+  return t.size();
+}
diff --git a/efel/cppcore/BasicFeatures.h b/efel/cppcore/BasicFeatures.h
@@ -0,0 +1,40 @@
+/* Copyright (c) 2015-2024, 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.                   
+ */
+
+#include "mapoperations.h"
+#include "Utils.h"
+
+#include <vector>
+#include <stdexcept>
+
+using std::vector;
+
+namespace BasicFeatures {
+int interpolate(mapStr2intVec& IntFeatureData,
+                mapStr2doubleVec& DoubleFeatureData,
+                mapStr2Str& StringData);
+int voltage(mapStr2intVec& IntFeatureData,
+            mapStr2doubleVec& DoubleFeatureData,
+            mapStr2Str& StringData);
+int current(mapStr2intVec& IntFeatureData,
+            mapStr2doubleVec& DoubleFeatureData,
+            mapStr2Str& StringData);
+int time(mapStr2intVec& IntFeatureData,
+         mapStr2doubleVec& DoubleFeatureData,
+         mapStr2Str& StringData);
+}
diff --git a/efel/cppcore/CMakeLists.txt b/efel/cppcore/CMakeLists.txt
@@ -1,4 +1,4 @@
-# Copyright (c) 2015, EPFL/Blue Brain Project                                   
+# Copyright (c) 2015-2024, EPFL/Blue Brain Project                                   
 #                                                                               
 # This file is part of eFEL <https://github.com/BlueBrain/eFEL>                 
 #                                                                                
@@ -24,7 +24,7 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 
 set(CMAKE_BUILD_TYPE Debug)
 
-set(FEATURESRCS Utils.cpp LibV1.cpp LibV2.cpp LibV3.cpp LibV5.cpp
+set(FEATURESRCS Utils.cpp BasicFeatures.cpp SpikeEvent.cpp SpikeShape.cpp Subthreshold.cpp
     FillFptrTable.cpp DependencyTree.cpp cfeature.cpp
     mapoperations.cpp)
 
@@ -39,7 +39,7 @@ install(TARGETS efelStatic ARCHIVE DESTINATION lib)
 add_library(efel SHARED ${FEATURESRCS})
 install(TARGETS efel LIBRARY DESTINATION lib)
 
-install(FILES cfeature.h FillFptrTable.h LibV1.h LibV2.h LibV3.h
-    LibV5.h mapoperations.h Utils.h DependencyTree.h eFELLogger.h EfelExceptions.h
+install(FILES cfeature.h FillFptrTable.h BasicFeatures.h SpikeEvent.h SpikeShape.h
+    Subthreshold.h mapoperations.h Utils.h DependencyTree.h eFELLogger.h EfelExceptions.h
     types.h
     DESTINATION include)