Recorder Updates for Neuro and NG911

Simulator/Connections/Connections.h

@@ -65,6 +65,9 @@ class Connections {
    ///  Registered to OperationManager as Operation::printParameters
    virtual void printParameters() const = 0;
 
+   /// Registers history variables for recording during simulation
+   virtual void registerHistoryVariables() = 0;
+
    ///  Update the connections status in every epoch.
    ///
    ///  @param  vertices  The vertex list to search from.

Simulator/Connections/NG911/Connections911.cpp

@@ -73,7 +73,7 @@ bool Connections911::updateConnections(AllVertices &vertices)
    // Record old type map
    int numVertices = Simulator::getInstance().getTotalVertices();
    Layout &layout = Simulator::getInstance().getModel().getLayout();
-   oldTypeMap_ = layout.vertexTypeMap_;
+   // oldTypeMap_ = layout.vertexTypeMap_;
 
    // Erase PSAPs
    for (int i = 0; i < psapsToErase_; i++) {
@@ -183,7 +183,7 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
          erasedEdge.srcV = srcVertex;
          erasedEdge.destV = destVertex;
          erasedEdge.eType = layout.edgType(srcVertex, destVertex);
-         edgesErased.push_back(erasedEdge);
+         edgesErased_.push_back(erasedEdge);
 
          changesMade = true;
          edges_->eraseEdge(destVertex, iEdg);
@@ -204,7 +204,7 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
 
    if (changesMade) {
       // This is here so that we don't delete the vertex if we can't find any edges
-      verticesErased.push_back(randPSAP);
+      verticesErased_.push_back(randPSAP);
       layout.vertexTypeMap_[randPSAP] = vertexType::VTYPE_UNDEF;
    }
 
@@ -238,7 +238,7 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
       addedEdge.srcV = srcVertex;
       addedEdge.destV = closestPSAP;
       addedEdge.eType = edgeType::CP;
-      edgesAdded.push_back(addedEdge);
+      edgesAdded_.push_back(addedEdge);
    }
 
    // For each psap-less responder, find closest match
@@ -266,7 +266,7 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
       addedEdge.srcV = closestPSAP;
       addedEdge.destV = destVertex;
       addedEdge.eType = edgeType::PR;
-      edgesAdded.push_back(addedEdge);
+      edgesAdded_.push_back(addedEdge);
    }
 
    return changesMade;
@@ -317,7 +317,7 @@ bool Connections911::eraseRESP(AllVertices &vertices, Layout &layout)
          erasedEdge.srcV = srcVertex;
          erasedEdge.destV = destVertex;
          erasedEdge.eType = layout.edgType(srcVertex, destVertex);
-         edgesErased.push_back(erasedEdge);
+         edgesErased_.push_back(erasedEdge);
 
          changesMade = true;
          edges_->eraseEdge(destVertex, iEdg);
@@ -326,7 +326,7 @@ bool Connections911::eraseRESP(AllVertices &vertices, Layout &layout)
 
    if (changesMade) {
       // This is here so that we don't delete the vertex if we can't find any edges
-      verticesErased.push_back(randRESP);
+      verticesErased_.push_back(randRESP);
       layout.vertexTypeMap_[randRESP] = vertexType::VTYPE_UNDEF;
    }
 
@@ -370,16 +370,23 @@ string Connections911::ChangedEdge::toString()
    return os.str();
 }
 
+/// Registers variable to be recorded
+void Connections911::registerHistoryVariables()
+{
+   Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
+   recorder.registerVariable("verticesDeleted", verticesErased_, Recorder::UpdatedType::DYNAMIC);
+}
+
 ///  Returns the complete list of all deleted or added edges as a string.
 string Connections911::changedEdgesToXML(bool added)
 {
    stringstream os;
 
-   vector<ChangedEdge> changed = edgesErased;
+   vector<ChangedEdge> changed = edgesErased_;
    string name = "edgesDeleted";
 
    if (added) {
-      changed = edgesAdded;
+      changed = edgesAdded_;
       name = "edgesAdded";
    }
 
@@ -394,22 +401,24 @@ string Connections911::changedEdgesToXML(bool added)
    return os.str();
 }
 
+/*
 ///  Returns the complete list of deleted vertices as a string.
 string Connections911::erasedVerticesToXML()
 {
    stringstream os;
 
    os << "<Matrix name=\"verticesDeleted\" type=\"complete\" rows=\"1\" columns=\""
-      << verticesErased.size() << "\" multiplier=\"1.0\">" << endl;
+      << verticesErased_.size() << "\" multiplier=\"1.0\">" << endl;
    os << "   ";
 
-   sort(verticesErased.begin(), verticesErased.end());
-   for (int i = 0; i < verticesErased.size(); i++) {
-      os << verticesErased[i] << " ";
+   sort(verticesErased_.begin(), verticesErased_.end());
+   for (int i = 0; i < verticesErased_.size(); i++) {
+      os << verticesErased_[i] << " ";
    }
 
    os << endl << "</Matrix>";
    return os.str();
 }
+*/
 
 #endif

Simulator/Connections/NG911/Connections911.h

@@ -15,6 +15,7 @@
 
 #include "Connections.h"
 #include "InputEvent.h"
+#include "RecordableVector.h"
 #include <vector>
 
 using namespace std;
@@ -33,7 +34,7 @@ class Connections911 : public Connections {
       return new Connections911();
    }
    /// Records typeMap history for recorders
-   vector<vertexType> oldTypeMap_;
+   /// vector<vertexType> oldTypeMap_;
 
    ///  Setup the internal structure of the class (allocate memories and initialize them).
    ///  Initialize the network characterized by parameters:
@@ -48,6 +49,9 @@ class Connections911 : public Connections {
    ///  Registered to OperationManager as Operation::printParameters
    virtual void printParameters() const override;
 
+   /// Registers history variables for recording during simulation
+   virtual void registerHistoryVariables() override;
+
 private:
    /// number of psaps to erase at the end of 1 epoch
    int psapsToErase_;
@@ -58,13 +62,13 @@ class Connections911 : public Connections {
    struct ChangedEdge;
 
    // Edges that were added but later removed are still here
-   vector<ChangedEdge> edgesAdded;
+   vector<ChangedEdge> edgesAdded_;
 
    // New edges = (old edges + edgesAdded) - edgesErased  <-- works
    // New edges = (old edges - edgesErased) + edgesAdded  <-- does not work
-   vector<ChangedEdge> edgesErased;
+   vector<ChangedEdge> edgesErased_;
 
-   vector<int> verticesErased;
+   RecordableVector<int> verticesErased_;
 
 #if !defined(USE_GPU)
 

Simulator/Connections/Neuro/ConnGrowth.cpp

@@ -328,3 +328,7 @@ void ConnGrowth::printRadii() const
       cout << "radii[" << i << "] = " << radii_[i] << endl;
    }
 }
+
+void ConnGrowth::registerHistoryVariables()
+{
+}

Simulator/Connections/Neuro/ConnGrowth.h

@@ -97,6 +97,9 @@ class ConnGrowth : public Connections {
    /// Registered to OperationManager as Operations::op::loadParameters
    virtual void loadParameters() override;
 
+   /// Registers history variables for recording during simulation
+   virtual void registerHistoryVariables() override;
+
    ///  Prints out all parameters to logging file.
    ///  Registered to OperationManager as Operation::printParameters
    virtual void printParameters() const override;

Simulator/Connections/Neuro/ConnStatic.cpp

@@ -89,3 +89,15 @@ void ConnStatic::loadParameters()
 void ConnStatic::printParameters() const
 {
 }
+
+void ConnStatic::registerHistoryVariables()
+{
+   // Register the following variables to be recorded
+   // Note: There may be potential duplicate weight, source, destination vertices
+   Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
+   recorder.registerVariable("weight", WCurrentEpoch_, Recorder::UpdatedType::DYNAMIC);
+   recorder.registerVariable("sourceVertex", sourceVertexIndexCurrentEpoch_,
+                             Recorder::UpdatedType::DYNAMIC);
+   recorder.registerVariable("destinationVertex", destVertexIndexCurrentEpoch_,
+                             Recorder::UpdatedType::DYNAMIC);
+}

Simulator/Connections/Neuro/ConnStatic.h

@@ -61,6 +61,9 @@ class ConnStatic : public Connections {
    ///  Registered to OperationManager as Operation::printParameters
    virtual void printParameters() const override;
 
+   /// Registers history variables for recording during simulation
+   virtual void registerHistoryVariables() override;
+
    /// Get array of vertex weights
    const vector<BGFLOAT> &getWCurrentEpoch() const
    {
@@ -71,24 +74,24 @@ class ConnStatic : public Connections {
    /// Get all edge source vertex indices
    const vector<int> &getSourceVertexIndexCurrentEpoch() const
    {
-      return sourceVertexIndexCurrentEpoch_;
+      return sourceVertexIndexCurrentEpoch_.getVector();
    }
 
    /// Get all edge destination vertex indices
    const vector<int> &getDestVertexIndexCurrentEpoch() const
    {
-      return destVertexIndexCurrentEpoch_;
+      return destVertexIndexCurrentEpoch_.getVector();
    }
 
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive);
 
 private:
    /// Indices of the source vertex for each edge
-   vector<int> sourceVertexIndexCurrentEpoch_;
+   RecordableVector<int> sourceVertexIndexCurrentEpoch_;
 
    /// Indices of the destination vertex for each edge
-   vector<int> destVertexIndexCurrentEpoch_;
+   RecordableVector<int> destVertexIndexCurrentEpoch_;
 
    /// The weight (scaling factor, strength, maximal amplitude) of each vertex for the current epoch.
    // vector<BGFLOAT> changes to RecordableVector for recording purpose

Simulator/Core/Core.cpp

@@ -207,6 +207,7 @@ int Core::runSimulation(string executableName, string cmdLineArguments)
 
    // Helper function for recorder to register spike history variables for all neurons.
    simulator.getModel().getLayout().getVertices().registerHistoryVariables();
+   simulator.getModel().getConnections().registerHistoryVariables();
 
    // Run simulation
    LOG4CPLUS_TRACE(consoleLogger, "Starting Simulation");

Simulator/Layouts/Layout.cpp

@@ -117,13 +117,13 @@ void Layout::setup()
    // Finally take the square root to get the distances
    dist_ = sqrt(dist2_);
 
-   // Register variable: vertex locations if need
-   //Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
-   //string baseName = "Location";
-   //string xLocation = "x_" + baseName;
-   //string yLocation = "y_" + baseName;
-   //recorder.registerVariable(xLocation, xloc_, Recorder::UpdatedType::CONSTANT);
-   //recorder.registerVariable(yLocation, yloc_, Recorder::UpdatedType::CONSTANT);
+   //Register variable: vertex locations
+   Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
+   string baseName = "Location";
+   string xLocation = "x_" + baseName;
+   string yLocation = "y_" + baseName;
+   recorder.registerVariable(xLocation, xloc_, Recorder::UpdatedType::CONSTANT);
+   recorder.registerVariable(yLocation, yloc_, Recorder::UpdatedType::CONSTANT);
 
    // test purpose
    // cout << "xloc_: " << &xloc_ << endl;

Simulator/Layouts/Layout.h

@@ -14,6 +14,7 @@
 #pragma once
 
 #include "AllVertices.h"
+#include "RecordableVector.h"
 #include "Utils/Global.h"
 #include <iostream>
 #include <log4cplus/loggingmacros.h>
@@ -78,7 +79,7 @@ class Layout {
    vector<int>
       probedNeuronList_;   ///< Probed neurons list. // ToDo: Move this to Hdf5 recorder once its implemented in project -chris
 
-   vector<vertexType> vertexTypeMap_;   ///< The vertex type mao, (INH, EXC).
+   RecordableVector<vertexType> vertexTypeMap_;   ///< The vertex type mao, (INH, EXC).
 
    vector<bool> starterMap_;   ///< The starter existence map (T/F).
 

Simulator/Layouts/NG911/Layout911.cpp

@@ -102,6 +102,10 @@ void Layout911::generateVertexTypeMap()
       vTypeCount[gm[*vi].type] += 1;
    }
 
+   // Register vertexTypes with recorder
+   Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
+   recorder.registerVariable("vertexTypeMap", vertexTypeMap_, Recorder::UpdatedType::CONSTANT);
+
    LOG4CPLUS_DEBUG(fileLogger_, "\nVERTEX TYPE MAP"
                                    << endl
                                    << "\tTotal vertices: " << numVertices_ << endl

Simulator/Layouts/Neuro/LayoutNeuro.cpp

@@ -67,6 +67,10 @@ void LayoutNeuro::generateVertexTypeMap()
       }
    }
 
+   // Register vertexTypeMap to be recorded
+   Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
+   recorder.registerVariable("vertexTypeMap", vertexTypeMap_, Recorder::UpdatedType::CONSTANT);
+
    numExcititoryNeurons = numVertices_ - numInhibitoryNeurons;
 
    LOG4CPLUS_DEBUG(fileLogger_, "\nVERTEX TYPE MAP"

Simulator/Recorders/Hdf5Recorder.cpp

@@ -215,17 +215,32 @@ void Hdf5Recorder::compileHistories()
                   }
                   variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,
                                                   memSpace, fileSpace);
+               } else if (variableInfo.hdf5Datatype_ == PredType::NATIVE_DOUBLE) {
+                  vector<double> dataBuffer(variableInfo.variableLocation_.getNumElements());
+                  for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {
+                     dataBuffer[i] = get<double>(variableInfo.variableLocation_.getElement(i));
+                  }
+                  variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,
+                                                  memSpace, fileSpace);
+               } else if (variableInfo.hdf5Datatype_ == PredType::NATIVE_UCHAR) {
+                  vector<unsigned char> dataBuffer(variableInfo.variableLocation_.getNumElements());
+                  for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {
+                     dataBuffer[i]
+                        = get<unsigned char>(variableInfo.variableLocation_.getElement(i));
+                  }
+                  variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,
+                                                  memSpace, fileSpace);
                } else {
                   // Throw an exception if the data type is unsupported
                   throw runtime_error("Unsupported data type for variable: "
                                       + variableInfo.variableName_);
                }
             }
          }
+         // Call startNewEpoch() to prepare for new data input
+         // Only done for dynamic variables since constant variables are only captured at end
+         variableInfo.variableLocation_.startNewEpoch();
       }
-
-      // Call startNewEpoch() to prepare for new data input
-      variableInfo.variableLocation_.startNewEpoch();
    }
 }
 

Simulator/Recorders/Hdf5Recorder.h

@@ -116,6 +116,8 @@ class Hdf5Recorder : public Recorder {
             hdf5Datatype_ = PredType::NATIVE_DOUBLE;
          } else if (dataType_ == typeid(vertexType).name()) {
             hdf5Datatype_ = PredType::NATIVE_INT;
+         } else if (dataType_ == typeid(unsigned char).name()) {
+            hdf5Datatype_ = PredType::NATIVE_UCHAR;
          } else {
             throw runtime_error("Unsupported data type");
          }
@@ -163,6 +165,19 @@ class Hdf5Recorder : public Recorder {
                }
                hdf5DataSet_.write(dataBuffer.data(), hdf5Datatype_);
 
+            } else if (hdf5Datatype_ == PredType::NATIVE_DOUBLE) {
+               vector<double> dataBuffer(variableLocation_.getNumElements());
+               for (int i = 0; i < variableLocation_.getNumElements(); ++i) {
+                  dataBuffer[i] = get<double>(variableLocation_.getElement(i));
+               }
+               hdf5DataSet_.write(dataBuffer.data(), hdf5Datatype_);
+
+            } else if (hdf5Datatype_ == PredType::NATIVE_UCHAR) {
+               vector<unsigned char> dataBuffer(variableLocation_.getNumElements());
+               for (int i = 0; i < variableLocation_.getNumElements(); ++i) {
+                  dataBuffer[i] = get<unsigned char>(variableLocation_.getElement(i));
+               }
+               hdf5DataSet_.write(dataBuffer.data(), hdf5Datatype_);
             } else {
                // Throw an error if the data type is unsupported
                throw runtime_error("Unsupported data type");

Simulator/Recorders/NG911/Xml911Recorder.cpp

@@ -27,6 +27,7 @@ void Xml911Recorder::compileHistories()
 /// @param  vertices the Vertex list to search from.
 void Xml911Recorder::saveSimData()
 {
+   /*
    auto &conns = Simulator::getInstance().getModel().getConnections();
    Connections911 &conns911 = dynamic_cast<Connections911 &>(conns);
    All911Vertices &all911Vertices = dynamic_cast<All911Vertices &>(
@@ -104,6 +105,7 @@ void Xml911Recorder::saveSimData()
    resultOut_ << "   " << g_simulationStep * Simulator::getInstance().getDeltaT() << endl;
    resultOut_ << "</Matrix>" << endl;
    resultOut_ << "</SimState>" << endl;
+   */
 }
 
 ///  Prints out all parameters to logging file.