Merge pull request #866 from UWB-Biocomputing/VanessaDevelopment

varndorfer · web-flow · commit 642810131d0e · 2025-07-16T10:40:02.000-07:00
Output weight matrix
diff --git a/Simulator/Connections/Connections.cpp b/Simulator/Connections/Connections.cpp
@@ -81,9 +81,8 @@ void Connections::createEdgeIndexMap()
 
 ///  Update the connections status in every epoch.
 ///
-///  @param  vertices  The vertex list to search from.
 ///  @return true if successful, false otherwise.
-bool Connections::updateConnections(AllVertices &vertices)
+bool Connections::updateConnections()
 {
    return false;
 }
diff --git a/Simulator/Connections/Connections.h b/Simulator/Connections/Connections.h
@@ -67,9 +67,8 @@ class Connections {
 
    ///  Update the connections status in every epoch.
    ///
-   ///  @param  vertices  The vertex list to search from.
    ///  @return true if successful, false otherwise.
-   virtual bool updateConnections(AllVertices &vertices);
+   virtual bool updateConnections();
 
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive);
diff --git a/Simulator/Connections/NG911/Connections911.cpp b/Simulator/Connections/NG911/Connections911.cpp
@@ -63,7 +63,7 @@ void Connections911::printParameters() const
 
 #if !defined(USE_GPU)
 ///  Update the connections status in every epoch.
-bool Connections911::updateConnections(AllVertices &vertices)
+bool Connections911::updateConnections()
 {
    // Only run on the first epoch
    if (Simulator::getInstance().getCurrentStep() != 1) {
@@ -73,6 +73,7 @@ bool Connections911::updateConnections(AllVertices &vertices)
    // Record old type map
    int numVertices = Simulator::getInstance().getTotalVertices();
    Layout &layout = Simulator::getInstance().getModel().getLayout();
+   AllVertices &vertices = layout.getVertices();
    oldTypeMap_ = layout.vertexTypeMap_;
 
    // Erase PSAPs
diff --git a/Simulator/Connections/NG911/Connections911.h b/Simulator/Connections/NG911/Connections911.h
@@ -72,9 +72,8 @@ class Connections911 : public Connections {
    ///  Update the connections status in every epoch.
    ///  Uses the parent definition for USE_GPU
    ///
-   ///  @param  vertices The Vertex list to search from.
    ///  @return true if successful, false otherwise.
-   virtual bool updateConnections(AllVertices &vertices) override;
+   virtual bool updateConnections() override;
 
    /// Finds the outgoing edge from the given vertex to the Responder closest to
    /// the emergency call location
diff --git a/Simulator/Connections/Neuro/ConnGrowth.cpp b/Simulator/Connections/Neuro/ConnGrowth.cpp
@@ -126,10 +126,12 @@ void ConnGrowth::printParameters() const
 
 ///  Update the connections status in every epoch.
 ///
-///  @param  vertices  The vertex list to search from.
 ///  @return true if successful, false otherwise.
-bool ConnGrowth::updateConnections(AllVertices &vertices)
+bool ConnGrowth::updateConnections()
 {
+   Layout &layout = Simulator::getInstance().getModel().getLayout();
+   AllVertices &vertices = layout.getVertices();
+
    // Update Connections data
    updateConns(vertices);
 
diff --git a/Simulator/Connections/Neuro/ConnGrowth.h b/Simulator/Connections/Neuro/ConnGrowth.h
@@ -103,9 +103,8 @@ class ConnGrowth : public Connections {
 
    ///  Update the connections status in every epoch.
    ///
-   ///  @param  vertices  The vertex list to search from.
    ///  @return true if successful, false otherwise.
-   virtual bool updateConnections(AllVertices &vertices) override;
+   virtual bool updateConnections() override;
 
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive);
diff --git a/Simulator/Connections/Neuro/ConnGrowth_d.cpp b/Simulator/Connections/Neuro/ConnGrowth_d.cpp
@@ -77,6 +77,12 @@ void ConnGrowth::updateEdgesWeights(int numVertices, AllVertices &vertices, AllE
 
    // copy device synapse count to host memory
    edges.copyDeviceEdgeCountsToHost(allEdgesDevice);
-   // copy device synapse summation coordinate to host memory
-   dynamic_cast<AllSpikingSynapses &>(edges).copyDeviceEdgeSumIdxToHost(allEdgesDevice);
+
+   // copy device synapse summation coordinate and weights to host memory
+   AllSpikingSynapses &synapses = dynamic_cast<AllSpikingSynapses &>(edges);
+   synapses.copyDeviceEdgeSumIdxToHost(allEdgesDevice);
+   synapses.copyDeviceEdgeWeightsToHost(allEdgesDevice);
+
+   // output weight matrix every epoch
+   synapses.outputWeights(simulator.getCurrentStep());
 }
diff --git a/Simulator/Connections/Neuro/ConnStatic.cpp b/Simulator/Connections/Neuro/ConnStatic.cpp
@@ -89,3 +89,14 @@ void ConnStatic::loadParameters()
 void ConnStatic::printParameters() const
 {
 }
+
+///  Output the weights matrix after every epoch.
+///
+///  @return true if successful, false otherwise.
+bool ConnStatic::updateConnections()
+{
+   AllNeuroEdges &synapses = dynamic_cast<AllNeuroEdges &>(*edges_);
+   synapses.outputWeights(Simulator::getInstance().getCurrentStep());
+
+   return true;
+}
diff --git a/Simulator/Connections/Neuro/ConnStatic.h b/Simulator/Connections/Neuro/ConnStatic.h
@@ -80,6 +80,11 @@ class ConnStatic : public Connections {
       return destVertexIndexCurrentEpoch_;
    }
 
+   ///  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);
 
diff --git a/Simulator/Core/CPUModel.cpp b/Simulator/Core/CPUModel.cpp
@@ -35,7 +35,7 @@ void CPUModel::advance()
 void CPUModel::updateConnections()
 {
    // Update Connections data
-   if (connections_->updateConnections(layout_->getVertices())) {
+   if (connections_->updateConnections()) {
       connections_->updateEdgesWeights();
       // create edge inverse map
       connections_->createEdgeIndexMap();
diff --git a/Simulator/Core/GPUModel.cpp b/Simulator/Core/GPUModel.cpp
@@ -236,7 +236,7 @@ void GPUModel::updateConnections()
    vertices.copyFromDevice();
 
    // Update Connections data
-   if (connections_->updateConnections(vertices)) {
+   if (connections_->updateConnections()) {
       connections_->updateEdgesWeights(Simulator::getInstance().getTotalVertices(), vertices, edges,
                                        allVerticesDevice_, allEdgesDevice_, getLayout());
       // create edge index map
diff --git a/Simulator/Edges/Neuro/AllNeuroEdges.h b/Simulator/Edges/Neuro/AllNeuroEdges.h
@@ -84,6 +84,9 @@ class AllNeuroEdges : public AllEdges {
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive);
 
+   /// Output weights and srcIndex to xml
+   virtual void outputWeights(int epochNum) = 0;
+
 protected:
    ///  Setup the internal structure of the class (allocate memories and initialize them).
    ///
diff --git a/Simulator/Edges/Neuro/AllSpikingSynapses.cpp b/Simulator/Edges/Neuro/AllSpikingSynapses.cpp
@@ -333,3 +333,61 @@ void AllSpikingSynapses::printSynapsesProps() const
       }
    }
 }
+
+string vectorToXML(const vector<BGFLOAT> &matrix, int rows, int cols, const string &name)
+{
+   ostringstream os;
+   os << "<" << name << " rows=\"" << rows << "\" columns=\"" << cols << "\">\n";
+
+   int index = 0;
+   for_each(matrix.begin(), matrix.end(), [&](BGFLOAT value) mutable {
+      os << "   <value" << index << ">" << value << "</value" << index << ">\n";
+      index++;
+   });
+
+   os << "</" << name << ">\n";
+   return os.str();
+}
+
+string vectorToXML(const vector<int> &matrix, int rows, int cols, const string &name)
+{
+   ostringstream os;
+   os << "<" << name << " rows=\"" << rows << "\" columns=\"" << cols << "\">\n";
+
+   int index = 0;
+   for_each(matrix.begin(), matrix.end(), [&](int value) mutable {
+      os << "   <value" << index << ">" << value << "</value" << index << ">\n";
+
+      index++;
+   });
+
+   os << "</" << name << ">\n";
+   return os.str();
+}
+
+void AllSpikingSynapses::outputWeights(int epochNum)
+{
+   const std::string filename = "./Output/Results/weights-epoch-" + std::to_string(epochNum)
+                                + ".xml";   // Hardcoded filename
+   int vertexCount = Simulator::getInstance().getTotalVertices();
+
+   ofstream outFile(filename);
+   if (!outFile) {
+      cerr << "Error: Unable to open file " << filename << endl;
+      cerr << "Error details: " << strerror(errno) << endl;
+      return;
+   }
+
+   int maxEdges = Simulator::getInstance().getMaxEdgesPerVertex();
+
+   string wContent = vectorToXML(W_, vertexCount, maxEdges, "WeightMatrix");
+   string srcContent = vectorToXML(sourceVertexIndex_, vertexCount, maxEdges, "SourceVertexIndex");
+
+   outFile << "<Graph>\n";
+   outFile << wContent;
+   outFile << srcContent;
+   outFile << "</Graph>";
+   outFile.close();
+
+   cout << "Weights matrix output to: " << filename << endl;
+}
diff --git a/Simulator/Edges/Neuro/AllSpikingSynapses.h b/Simulator/Edges/Neuro/AllSpikingSynapses.h
@@ -87,6 +87,9 @@ class AllSpikingSynapses : public AllNeuroEdges {
    ///  Cereal serialization method
    template <class Archive> void serialize(Archive &archive);
 
+   /// Output weights and srcIndex to xml
+   virtual void outputWeights(int epochNum);
+
 protected:
    ///  Setup the internal structure of the class (allocate memories and initialize them).
    ///
@@ -191,6 +194,12 @@ class AllSpikingSynapses : public AllNeuroEdges {
    ///  @param  allEdgesDevice  GPU address of the allEdges struct on device memory.
    void copyDeviceEdgeSumIdxToHost(void *allEdgesDevice);
 
+   ///  Get weights matrix in AllEdges struct on device memory.
+   ///
+   ///  @param  allEdgesDevice  GPU address of the AllSpikingSynapsesDeviceProperties struct
+   ///                             on device memory.
+   virtual void copyDeviceEdgeWeightsToHost(void *allEdgesDevice);
+
 protected:
    ///  Allocate GPU memories to store all synapses' states,
    ///  and copy them from host to GPU memory.
diff --git a/Simulator/Edges/Neuro/AllSpikingSynapses_d.cpp b/Simulator/Edges/Neuro/AllSpikingSynapses_d.cpp
@@ -274,6 +274,28 @@ void AllSpikingSynapses::copyDeviceEdgeCountsToHost(void *allEdgesDevice)
    //allEdges.countVertices_ = 0;
 }
 
+///  Get weights matrix in AllEdges struct on device memory.
+///
+///  @param  allEdgesDevice  GPU address of the AllSpikingSynapsesDeviceProperties struct
+///                             on device memory.
+void AllSpikingSynapses::copyDeviceEdgeWeightsToHost(void *allEdgesDevice)
+{
+   AllSpikingSynapsesDeviceProperties allEdgesDeviceProps;
+
+   int numVertices = Simulator::getInstance().getTotalVertices();
+   BGSIZE maxTotalSynapses = Simulator::getInstance().getMaxEdgesPerVertex() * numVertices;
+
+   HANDLE_ERROR(cudaMemcpy(&allEdgesDeviceProps, allEdgesDevice,
+                           sizeof(AllSpikingSynapsesDeviceProperties), cudaMemcpyDeviceToHost));
+
+   // std::cout << "size: " << vertexCount * vertexCount * sizeof(BGFLOAT) << std::endl;
+   // std::cout << "W_.data(): " << W_.data() << std::endl;
+   // std::cout << "allEdgesDeviceProps.W_: " << allEdgesDeviceProps.W_ << std::endl;
+
+   HANDLE_ERROR(cudaMemcpy(W_.data(), allEdgesDeviceProps.W_, maxTotalSynapses * sizeof(BGFLOAT),
+                           cudaMemcpyDeviceToHost));
+}
+
 ///  Get summationCoord and in_use in AllEdges struct on device memory.
 ///
 ///  @param  allEdgesDevice  GPU address of the AllSpikingSynapsesDeviceProperties struct
diff --git a/Tools/XMLToGraphML/README.md b/Tools/XMLToGraphML/README.md
@@ -0,0 +1,17 @@
+# XML to GraphML Converter
+
+## Overview
+This script was created to parse the weight matrix output from neuro simulations and generate a graphml file for input into subsequent simulations.
+
+## `getGraphEdges`
+* Must be run with Python3.9
+* Takes a weight matrix xml file and existing graphml file as input
+* Adds the edge weights to the graphml file
+
+## Contributors
+- Vanessa Arndorfer
+
+
+
+
+
diff --git a/Tools/XMLToGraphML/getGraphEdges.py b/Tools/XMLToGraphML/getGraphEdges.py

Original file line number	Diff line number	Diff line change
`@@ -81,9 +81,8 @@ void Connections::createEdgeIndexMap()`
`81`	`81`
`82`	`82`	`/// Update the connections status in every epoch.`
`83`	`83`	`///`
`84`		`-/// @param vertices The vertex list to search from.`
`85`	`84`	`/// @return true if successful, false otherwise.`
`86`		`-bool Connections::updateConnections(AllVertices &vertices)`
	`85`	`+bool Connections::updateConnections()`
`87`	`86`	`{`
`88`	`87`	`return false;`
`89`	`88`	`}`
Original file line number	Diff line number	Diff line change
`@@ -35,7 +35,7 @@ void CPUModel::advance()`
`35`	`35`	`void CPUModel::updateConnections()`
`36`	`36`	`{`
`37`	`37`	`// Update Connections data`
`38`		`- if (connections_->updateConnections(layout_->getVertices())) {`
	`38`	`+ if (connections_->updateConnections()) {`
`39`	`39`	`connections_->updateEdgesWeights();`
`40`	`40`	`// create edge inverse map`
`41`	`41`	`connections_->createEdgeIndexMap();`