Merge pull request #823 from UWB-Biocomputing/recorder-updates-neuro-ng911

Recorder Updates for Neuro and NG911

Author: stiber

.gitignore

@@ -41,6 +41,7 @@ ThirdParty/log4cplus-2.0.7/src/liblog4cplus.so.2.0.7
 graphitti
 ggraphitti
 cgraphitti
+compare_matrices
 tests
 serialFullTest
 serialFirstHalfTest

Simulator/Connections/Connections.cpp

@@ -44,6 +44,10 @@ Connections::Connections()
    function<void()> regGraphPropsFunc = bind(&Connections::registerGraphProperties, this);
    opsManager.registerOperation(Operations::registerGraphProperties, regGraphPropsFunc);
 
+   // Register registerHistoryVariables function as a registerHistoryVariables operation in the OperationManager
+   function<void()> registerHistoryVarsFunc = bind(&Connections::registerHistoryVariables, this);
+   opsManager.registerOperation(Operations::registerHistoryVariables, registerHistoryVarsFunc);
+
    // Get a copy of the file logger to use log4cplus macros
    fileLogger_ = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("file"));
    edgeLogger_ = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("edge"));

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.
    ///
    ///  @return true if successful, false otherwise.

Simulator/Connections/NG911/Connections911.cpp

@@ -74,7 +74,6 @@ bool Connections911::updateConnections()
    int numVertices = Simulator::getInstance().getTotalVertices();
    Layout &layout = Simulator::getInstance().getModel().getLayout();
    AllVertices &vertices = layout.getVertices();
-   oldTypeMap_ = layout.vertexTypeMap_;
 
    // Erase PSAPs
    for (int i = 0; i < psapsToErase_; i++) {
@@ -184,7 +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);
@@ -205,7 +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;
    }
 
@@ -239,7 +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
@@ -267,7 +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;
@@ -318,7 +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);
@@ -327,7 +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;
    }
 
@@ -371,16 +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";
    }
 
@@ -395,22 +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

@@ -330,3 +330,7 @@ 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

@@ -90,13 +90,14 @@ void ConnStatic::printParameters() const
 {
 }
 
-///  Output the weights matrix after every epoch.
-///
-///  @return true if successful, false otherwise.
-bool ConnStatic::updateConnections()
+void ConnStatic::registerHistoryVariables()
 {
-   AllNeuroEdges &synapses = dynamic_cast<AllNeuroEdges &>(*edges_);
-   synapses.outputWeights(Simulator::getInstance().getCurrentStep());
-
-   return true;
+   // 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
    {
@@ -71,29 +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();
    }
 
-   ///  Output the weights matrix after every epoch.
-   ///
-   ///  @return true if successful, false otherwise.
-   virtual bool updateConnections() override;
-
    ///  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/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;