Merge branch 'development' into issue-516-rename-summationMap

Author: d-kamath

Simulator/Connections/NG911/Connections911.cpp

@@ -35,8 +35,7 @@ void Connections911::setup()
       BGFLOAT dist = layout.dist_(srcV, destV);
       LOG4CPLUS_DEBUG(edgeLogger_, "Source: " << srcV << " Dest: " << destV << " Dist: " << dist);
 
-      BGSIZE iEdg;
-      edges_->addEdge(iEdg, type, srcV, destV, Simulator::getInstance().getDeltaT());
+      BGSIZE iEdg = edges_->addEdge(type, srcV, destV, Simulator::getInstance().getDeltaT());
       added++;
    }
 
@@ -190,8 +189,8 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
       }
 
       // Insert Caller to PSAP edge
-      BGSIZE iEdg;
-      edges_->addEdge(iEdg, CP, srcVertex, closestPSAP, Simulator::getInstance().getDeltaT());
+      BGSIZE iEdg
+         = edges_->addEdge(CP, srcVertex, closestPSAP, Simulator::getInstance().getDeltaT());
 
       // Record added edge
       ChangedEdge addedEdge;
@@ -218,8 +217,8 @@ bool Connections911::erasePSAP(AllVertices &vertices, Layout &layout)
       }
 
       // Insert PSAP to Responder edge
-      BGSIZE iEdg;
-      edges_->addEdge(iEdg, PR, closestPSAP, destVertex, Simulator::getInstance().getDeltaT());
+      BGSIZE iEdg
+         = edges_->addEdge(PR, closestPSAP, destVertex, Simulator::getInstance().getDeltaT());
 
       // Record added edge
       ChangedEdge addedEdge;

Simulator/Connections/Neuro/ConnGrowth.cpp

@@ -240,6 +240,11 @@ void ConnGrowth::updateSynapsesWeights()
    for (int srcVertex = 0; srcVertex < numVertices; srcVertex++) {
       // and each destination neuron 'b'
       for (int destVertex = 0; destVertex < numVertices; destVertex++) {
+         if (destVertex == srcVertex) {
+            // we don't create a synapse between the same neuron
+            continue;
+         }
+
          // visit each synapse at (xa,ya)
          bool connected = false;
          edgeType type = layout.edgType(srcVertex, destVertex);
@@ -278,9 +283,8 @@ void ConnGrowth::updateSynapsesWeights()
          // if not connected and weight(a,b) > 0, add a new synapse from a to b
          if (!connected && (W_(srcVertex, destVertex) > 0)) {
             added++;
-            BGSIZE iEdg;
-            synapses.addEdge(iEdg, type, srcVertex, destVertex,
-                             Simulator::getInstance().getDeltaT());
+            BGSIZE iEdg = synapses.addEdge(type, srcVertex, destVertex,
+                                           Simulator::getInstance().getDeltaT());
             synapses.W_[iEdg] = W_(srcVertex, destVertex) * synapses.edgSign(type)
                                 * AllNeuroEdges::SYNAPSE_STRENGTH_ADJUSTMENT;
          }

Simulator/Connections/Neuro/ConnStatic.cpp

@@ -79,11 +79,9 @@ void ConnStatic::setup()
                          "Source: " << srcVertex << " Dest: " << destVertex
                                     << " Dist: " << distDestVertices[srcVertex][i].dist);
 
-         BGSIZE iEdg;
-         edges_->addEdge(iEdg, type, srcVertex, destVertex, simulator.getDeltaT());
+         BGSIZE iEdg = edges_->addEdge(type, srcVertex, destVertex, simulator.getDeltaT());
          added++;
 
-
          // set edge weight
          // TODO: we need another synaptic weight distibution mode (normal distribution)
          if (neuroEdges.edgSign(type) > 0) {

Simulator/Edges/AllEdges.cpp

@@ -250,14 +250,15 @@ void AllEdges::eraseEdge(const int iVert, const BGSIZE iEdg)
 
 ///  Adds an edge to the model, connecting two Vertices.
 ///
-///  @param  iEdg        Index of the edge to be added.
 ///  @param  type        The type of the edge to add.
 ///  @param  srcVertex  The Vertex that sends to this edge.
 ///  @param  destVertex The Vertex that receives from the edge.
 ///  @param  deltaT      Inner simulation step duration
-void AllEdges::addEdge(BGSIZE &iEdg, edgeType type, const int srcVertex, const int destVertex,
-                       const BGFLOAT deltaT)
+///  @return  iEdg      Index of the edge to be added.
+BGSIZE AllEdges::addEdge(edgeType type, const int srcVertex, const int destVertex,
+                         const BGFLOAT deltaT)
 {
+   BGSIZE iEdg;
    if (edgeCounts_[destVertex] >= maxEdgesPerVertex_) {
       LOG4CPLUS_FATAL(edgeLogger_, "Vertex : " << destVertex << " ran out of space for new edges.");
       throw runtime_error("Vertex " + to_string(destVertex)
@@ -278,4 +279,5 @@ void AllEdges::addEdge(BGSIZE &iEdg, edgeType type, const int srcVertex, const i
 
    // create an edge
    createEdge(iEdg, srcVertex, destVertex, deltaT, type);
+   return iEdg;
 }

Simulator/Edges/AllEdges.h

@@ -36,13 +36,13 @@ class AllEdges {
 
    ///  Adds a Edge to the model, connecting two Vertices.
    ///
-   ///  @param  iEdg        Index of the edge to be added.
    ///  @param  type        The type of the Edge to add.
    ///  @param  srcVertex   The Vertex that sends to this Edge.
    ///  @param  destVertex  The Vertex that receives from the Edge.
    ///  @param  deltaT      Inner simulation step duration
-   virtual void addEdge(BGSIZE &iEdg, edgeType type, const int srcVertex, const int destVertex,
-                        const BGFLOAT deltaT);
+   ///  @return  iEdg        Index of the edge to be added.
+   virtual BGSIZE addEdge(edgeType type, const int srcVertex, const int destVertex,
+                          const BGFLOAT deltaT);
 
    ///  Create a Edge and connect it to the model.
    ///

Simulator/Edges/NG911/All911Edges.cpp

@@ -14,33 +14,20 @@ All911Edges::All911Edges(const int numVertices, const int maxEdges)
 
 void All911Edges::setupEdges()
 {
-   int numVertices = Simulator::getInstance().getTotalVertices();
-   int maxEdges = Simulator::getInstance().getMaxEdgesPerVertex();
-   BGSIZE maxTotalEdges = maxEdges * numVertices;
-
-   isAvailable_ = make_unique<bool[]>(maxTotalEdges);
-   fill_n(isAvailable_.get(), maxTotalEdges, true);
-
-   isRedial_ = make_unique<bool[]>(maxTotalEdges);
-   fill_n(isRedial_.get(), maxTotalEdges, false);
-
-   call_.resize(maxTotalEdges);
-
-   maxEdgesPerVertex_ = maxEdges;
-   totalEdgeCount_ = 0;
-   countVertices_ = numVertices;
-
-   // To do: Figure out whether we need all of these
-   // Jardi: Removing this seems to break the creating of the EdgeIndexMap
-   if (maxTotalEdges != 0) {
-      // psr_.assign(maxTotalEdges, 0.0);
-      W_.assign(maxTotalEdges, 0);
-      type_.assign(maxTotalEdges, ETYPE_UNDEF);
-      edgeCounts_.assign(numVertices, 0);
-      destVertexIndex_.assign(maxTotalEdges, 0);
-      sourceVertexIndex_.assign(maxTotalEdges, 0);
-      inUse_ = make_unique<bool[]>(maxTotalEdges);
-      fill_n(inUse_.get(), maxTotalEdges, false);
+   // Setup the variables in the Super Class
+   AllEdges::setupEdges();
+
+   // Setup the variables in the sub Class
+   BGSIZE maxTotalEdges = maxEdgesPerVertex_ * countVertices_;
+
+   if (maxTotalEdges > 0) {
+      isAvailable_ = make_unique<bool[]>(maxTotalEdges);
+      fill_n(isAvailable_.get(), maxTotalEdges, true);
+
+      isRedial_ = make_unique<bool[]>(maxTotalEdges);
+      fill_n(isRedial_.get(), maxTotalEdges, false);
+
+      call_.resize(maxTotalEdges);
    }
 }
 
@@ -108,15 +95,6 @@ void All911Edges::advanceEdges(AllVertices &vertices, EdgeIndexMap &edgeIndexMap
          }
       }
    }
-   // All911Vertices *allVertices = dynamic_cast<All911Vertices *>(vertices);
-   // for (BGSIZE i = 0; i < totalEdgeCount_; i++) {
-   //    if (!inUse_[i]) {
-   //       continue;
-   //    }
-   //    // if the edge is in use...
-   //    BGSIZE iEdg = edgeIndexMap->incomingEdgeIndexMap_[i];
-   //    advance911Edge(iEdg, allVertices);
-   // }
 }
 
 ///  Advance one specific edge.

Simulator/Edges/Neuro/AllSynapsesDeviceFuncs_d.cpp

@@ -552,6 +552,11 @@ __global__ void updateSynapsesWeightsDevice(int numVertices, BGFLOAT deltaT, BGF
 
    // and each destination neuron 'b'
    for (int srcVertex = 0; srcVertex < numVertices; srcVertex++) {
+      if (destVertex == srcVertex) {
+         // we don't create a synapse between the same neuron
+         continue;
+      }
+
       // visit each synapse at (xa,ya)
       bool connected = false;
       edgeType type = edgType(neuronTypeMap_d, srcVertex, destVertex);

Simulator/Layouts/NG911/Layout911.cpp

@@ -110,19 +110,6 @@ void Layout911::generateVertexTypeMap(int numVertices)
    LOG4CPLUS_INFO(fileLogger_, "Finished initializing vertex type map");
 }
 
-void Layout911::initStarterMap(const int numVertices)
-{
-   Layout::initStarterMap(numVertices);
-}
-
-// Get the zone of the vertex
-// Only built for 10x10 grid
-// See: https://docs.google.com/spreadsheets/d/1DqP8sjkfJ_pkxtETzuEdoVZbWOGu633EMQAeShe5k68/edit?usp=sharing
-int Layout911::zone(int index)
-{
-   return (index % 10 >= 5) + 2 * (index < 50);
-}
-
 ///  Returns the type of synapse at the given coordinates
 ///
 ///  @param    srcVertex  integer that points to a Neuron in the type map as a source.

Simulator/Layouts/NG911/Layout911.h

@@ -51,17 +51,6 @@ class Layout911 : public Layout {
    ///  @param  numVertices number of the vertices to have in the type map.
    virtual void generateVertexTypeMap(int numVertices) override;
 
-   ///  Populates the starter map.
-   ///
-   ///  @param  numVertices number of vertices to have in the map.
-   virtual void initStarterMap(const int numVertices) override;
-
-   /// Get the zone of the vertex
-   /// Only built for 10x10 grid
-   /// See: https://docs.google.com/spreadsheets/d/1DqP8sjkfJ_pkxtETzuEdoVZbWOGu633EMQAeShe5k68/edit?usp=sharing
-   /// @param  index    the index of the vertex
-   int zone(int index);
-
    /// Returns the type of synapse at the given coordinates
    /// @param    srcVertex  integer that points to a Neuron in the type map as a source.
    /// @param    destVertex integer that points to a Neuron in the type map as a destination.

Simulator/Vertices/NG911/All911Vertices.cpp

@@ -17,15 +17,6 @@ void All911Vertices::setupVertices()
 {
    AllVertices::setupVertices();
 
-   callNum_.resize(size_);
-   dispNum_.resize(size_);
-   respNum_.resize(size_);
-
-   // Populate arrays with 0
-   callNum_.assign(size_, 0);
-   dispNum_.assign(size_, 0);
-   respNum_.assign(size_, 0);
-
    // Resize and fill vectors with 0
    numAgents_.assign(size_, 0);
    numTrunks_.assign(size_, 0);
@@ -83,69 +74,10 @@ void All911Vertices::createAllVertices(Layout &layout)
 
    // Read Input Events using the InputManager
    inputManager_.readInputs();
-
-
-   // TODO: The code below is from previous version. I am keeping because
-   // it is usefull for testing the output against the previous version.
-   vector<int> psapList;
-   vector<int> respList;
-   psapList.clear();
-   respList.clear();
-
-   int callersPerZone[] = {0, 0, 0, 0};
-   int respPerZone[] = {0, 0, 0, 0};
-
-   Layout911 &layout911 = dynamic_cast<Layout911 &>(layout);
-
-   for (int i = 0; i < Simulator::getInstance().getTotalVertices(); i++) {
-      // Create all callers
-      if (layout.vertexTypeMap_[i] == CALR) {
-         callNum_[i] = initRNG.inRange(callNumRange_[0], callNumRange_[1]);
-         callersPerZone[layout911.zone(i)] += callNum_[i];
-      }
-
-      // Find all PSAPs
-      if (layout.vertexTypeMap_[i] == PSAP) {
-         psapList.push_back(i);
-      }
-
-      // Find all resps
-      if (layout.vertexTypeMap_[i] == RESP) {
-         respList.push_back(i);
-         respPerZone[layout911.zone(i)] += 1;
-      }
-   }
-
-   // Create all psaps
-   // Dispatchers in a psap = [callers in the zone * k] + some randomness
-   for (int i = 0; i < psapList.size(); i++) {
-      int psapQ = layout911.zone(i);
-      int dispCount = (callersPerZone[psapQ] * dispNumScale_) + initRNG.inRange(-5, 5);
-      if (dispCount < 1) {
-         dispCount = 1;
-      }
-      dispNum_[psapList[i]] = dispCount;
-   }
-
-   // Create all responders
-   // Responders in a node = [callers in the zone * k]/[number of responder nodes] + some randomness
-   for (int i = 0; i < respList.size(); i++) {
-      int respQ = layout911.zone(respList[i]);
-      int respCount
-         = (callersPerZone[respQ] * respNumScale_) / respPerZone[respQ] + initRNG.inRange(-5, 5);
-      if (respCount < 1) {
-         respCount = 1;
-      }
-      respNum_[respList[i]] = respCount;
-   }
 }
 
 void All911Vertices::loadParameters()
 {
-   ParameterManager::getInstance().getIntByXpath("//CallNum/min/text()", callNumRange_[0]);
-   ParameterManager::getInstance().getIntByXpath("//CallNum/max/text()", callNumRange_[1]);
-   ParameterManager::getInstance().getBGFloatByXpath("//DispNumScale/text()", dispNumScale_);
-   ParameterManager::getInstance().getBGFloatByXpath("//RespNumScale/text()", respNumScale_);
    ParameterManager::getInstance().getBGFloatByXpath("//RedialP/text()", redialP_);
 }
 
@@ -297,37 +229,4 @@ void All911Vertices::advanceVertices(AllEdges &edges, const EdgeIndexMap &edgeIn
       }
    }
 }
-
-///  Update internal state of the indexed Neuron (called by every simulation step).
-///
-///  @param  index       Index of the Neuron to update.
-void All911Vertices::advanceVertex(const int index)
-{
-   // BGFLOAT &Vm = this->Vm_[index];
-   // BGFLOAT &Vthresh = this->Vthresh_[index];
-   // BGFLOAT &summationPoint = this->summationPoints_[index];
-   // BGFLOAT &I0 = this->I0_[index];
-   // BGFLOAT &Inoise = this->Inoise_[index];
-   // BGFLOAT &C1 = this->C1_[index];
-   // BGFLOAT &C2 = this->C2_[index];
-   // int &nStepsInRefr = this->numStepsInRefractoryPeriod_[index];
-
-   // if (nStepsInRefr > 0) {
-   //     // is neuron refractory?
-   //     --nStepsInRefr;
-   // } else if (Vm >= Vthresh) {
-   //     // should it fire?
-   //     fire(index);
-   // } else {
-   //     summationPoint += I0; // add IO
-   //     // add noise
-   //     BGFLOAT noise = (*rgNormrnd)();
-   //     //LOG4CPLUS_DEBUG(vertexLogger_, "ADVANCE NEURON[" << index << "] :: Noise = " << noise);
-   //     summationPoint += noise * Inoise; // add noise
-   //     Vm = C1 * Vm + C2 * summationPoint; // decay Vm and add inputs
-   // }
-   // // clear synaptic input for next time step
-   // summationPoint = 0;
-}
-
 #endif