Merge pull request #817 from UWB-Biocomputing/SainiGMDevelopment

[ISSUE-648] GraphManager Final Update

Author: jasleenksaini

Simulator/Connections/NG911/Connections911.cpp

@@ -22,7 +22,7 @@ void Connections911::setup()
    AllVertices &vertices = layout.getVertices();
 
    // Get list of edges sorted by target in ascending order from GraphManager
-   GraphManager &gm = GraphManager::getInstance();
+   GraphManager<NG911VertexProperties> &gm = GraphManager<NG911VertexProperties>::getInstance();
    auto sorted_edge_list = gm.edgesSortByTarget();
 
    // add sorted edges

Simulator/Core/Core.cpp

@@ -147,11 +147,22 @@ int Core::runSimulation(string executableName, string cmdLineArguments)
 
    // Ask all objects to register their Graph properties
    OperationManager::getInstance().executeOperation(Operations::registerGraphProperties);
-   // Read graph from GraphML file. Uses ParameterManager to get the file name.
-   // TODO: This method returns false if it fails to read the graph, we ignore it at the
-   //    moment since it currently fails for the Neural Network model because they don't
-   //    yet use GraphML.
-   GraphManager::getInstance().readGraph();
+
+   // Retrieve class attribute from the 'LayoutParams' in the config file
+   // This value indicate the simulation type (Neural or NG911) for graph manager configuration
+   // Log fatal error if no simulation type is found and terminate
+   string configData;
+   ParameterManager::getInstance().getStringByXpath("//LayoutParams/@class", configData);
+
+   if (configData.find("Neur")) {
+      GraphManager<NeuralVertexProperties>::getInstance().readGraph();
+   }
+   if (configData.find("91")) {
+      GraphManager<NG911VertexProperties>::getInstance().readGraph();
+   } else {
+      LOG4CPLUS_FATAL(consoleLogger, "ERROR: Unknown simulation type'");
+      return -1;
+   }
 
    // Invoke instantiated simulator objects to load parameters from the configuration file
    LOG4CPLUS_TRACE(consoleLogger, "Loading parameters from configuration file");

Simulator/Layouts/Layout.cpp

@@ -66,17 +66,18 @@ int Layout::getNumVertices() const
 /// Load member variables from configuration file. Registered to OperationManager as Operations::op::loadParameters
 void Layout::loadParameters()
 {
-   numVertices_ = GraphManager::getInstance().numVertices();
+   numVertices_ = GraphManager<NeuralVertexProperties>::getInstance().numVertices();
 }
 
 void Layout::registerGraphProperties()
 {
-   GraphManager &gm = GraphManager::getInstance();
-   gm.registerProperty("y", &VertexProperty::y);
-   gm.registerProperty("x", &VertexProperty::x);
-   gm.registerProperty("type", &VertexProperty::type);
+   GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
+   gm.registerProperty("y", &VertexProperties::y);
+   gm.registerProperty("x", &VertexProperties::x);
+   gm.registerProperty("type", &VertexProperties::type);
 }
 
+
 /// Setup the internal structure of the class.
 /// Allocate memories to store all layout state, no sequential dependency in this method
 void Layout::setup()
@@ -92,8 +93,8 @@ void Layout::setup()
    vertexTypeMap_.assign(numVertices_, vertexType::VTYPE_UNDEF);
 
    // Loop over all vertices and set their x and y locations
-   GraphManager::VertexIterator vi, vi_end;
-   GraphManager &gm = GraphManager::getInstance();
+   GraphManager<NeuralVertexProperties>::VertexIterator vi, vi_end;
+   GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
    for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
       assert(*vi < numVertices_);
       xloc_[*vi] = gm[*vi].x;
@@ -134,8 +135,8 @@ void Layout::setup()
 /// Prints out all parameters to logging file. Registered to OperationManager as Operation::printParameters
 void Layout::printParameters() const
 {
-   GraphManager::VertexIterator vi, vi_end;
-   GraphManager &gm = GraphManager::getInstance();
+   GraphManager<NeuralVertexProperties>::VertexIterator vi, vi_end;
+   GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
    stringstream output;
    output << "\nLAYOUT PARAMETERS" << endl;
    output << "\tEndogenously active neuron positions: ";

Simulator/Layouts/NG911/Layout911.cpp

@@ -21,22 +21,22 @@ void Layout911::registerGraphProperties()
    // We are passing a pointer to a data member of the VertexProperty
    // so Boost Graph Library can use it for loading the graphML file.
    // Look at: https://www.studytonight.com/cpp/pointer-to-members.php
-   GraphManager &gm = GraphManager::getInstance();
-   gm.registerProperty("objectID", &VertexProperty::objectID);
-   gm.registerProperty("name", &VertexProperty::name);
-   gm.registerProperty("type", &VertexProperty::type);
-   gm.registerProperty("y", &VertexProperty::y);
-   gm.registerProperty("x", &VertexProperty::x);
-   gm.registerProperty("servers", &VertexProperty::servers);
-   gm.registerProperty("trunks", &VertexProperty::trunks);
-   gm.registerProperty("segments", &VertexProperty::segments);
+   GraphManager<NG911VertexProperties> &gm = GraphManager<NG911VertexProperties>::getInstance();
+   gm.registerProperty("objectID", &NG911VertexProperties::objectID);
+   gm.registerProperty("name", &NG911VertexProperties::name);
+   gm.registerProperty("type", &NG911VertexProperties::type);
+   gm.registerProperty("y", &NG911VertexProperties::y);
+   gm.registerProperty("x", &NG911VertexProperties::x);
+   gm.registerProperty("servers", &NG911VertexProperties::servers);
+   gm.registerProperty("trunks", &NG911VertexProperties::trunks);
+   gm.registerProperty("segments", &NG911VertexProperties::segments);
 }
 
 // Loads Layout911 member variables.
 void Layout911::loadParameters()
 {
    // Get the number of verticese from the GraphManager
-   numVertices_ = GraphManager::getInstance().numVertices();
+   numVertices_ = GraphManager<NG911VertexProperties>::getInstance().numVertices();
 }
 
 // Setup the internal structure of the class.
@@ -47,8 +47,8 @@ void Layout911::setup()
    Layout::setup();
 
    // Loop over all vertices and set their x and y locations
-   GraphManager::VertexIterator vi, vi_end;
-   GraphManager &gm = GraphManager::getInstance();
+   GraphManager<NG911VertexProperties>::VertexIterator vi, vi_end;
+   GraphManager<NG911VertexProperties> &gm = GraphManager<NG911VertexProperties>::getInstance();
    for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
       assert(*vi < numVertices_);
       xloc_[*vi] = gm[*vi].x;
@@ -93,8 +93,8 @@ void Layout911::generateVertexTypeMap()
    map<string, int> vTypeCount;
 
    // Add all vertices
-   GraphManager::VertexIterator vi, vi_end;
-   GraphManager &gm = GraphManager::getInstance();
+   GraphManager<NG911VertexProperties>::VertexIterator vi, vi_end;
+   GraphManager<NG911VertexProperties> &gm = GraphManager<NG911VertexProperties>::getInstance();
    LOG4CPLUS_DEBUG(fileLogger_, "\nvertices in graph: " << gm.numVertices());
    for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
       assert(*vi < numVertices_);

Simulator/Layouts/Neuro/LayoutNeuro.cpp

@@ -28,8 +28,8 @@ void LayoutNeuro::registerGraphProperties()
    // We are passing a pointer to a data member of the VertexProperty
    // so Boost Graph Library can use it for loading the graphML file.
    // Look at: https://www.studytonight.com/cpp/pointer-to-members.php
-   GraphManager &gm = GraphManager::getInstance();
-   gm.registerProperty("active", &VertexProperty::active);
+   GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
+   gm.registerProperty("active", &NeuralVertexProperties::active);
 }
 
 ///  Prints out all parameters to logging file.
@@ -52,8 +52,8 @@ void LayoutNeuro::generateVertexTypeMap()
    int numExcititoryNeurons;
 
    // Set Neuron Type from GraphML File
-   GraphManager::VertexIterator vi, vi_end;
-   GraphManager &gm = GraphManager::getInstance();
+   GraphManager<NeuralVertexProperties>::VertexIterator vi, vi_end;
+   GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
 
    for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
       assert(*vi < numVertices_);
@@ -85,8 +85,8 @@ void LayoutNeuro::initStarterMap()
    Layout::initStarterMap();
 
    // Set Neuron Activity from GraphML File
-   GraphManager::VertexIterator vi, vi_end;
-   GraphManager &gm = GraphManager::getInstance();
+   GraphManager<NeuralVertexProperties>::VertexIterator vi, vi_end;
+   GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
 
    for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
       assert(*vi < numVertices_);

Simulator/Utils/CircularBuffer.h

@@ -1,5 +1,5 @@
 /**
- * @file GraphManager.h
+ * @file CircularBuffer.h
  * @author Jardi A. M. Jordan ([email protected])
  * @date 01-22-2023
  * Supervised by Dr. Michael Stiber, UW Bothell CSSE Division

Simulator/Utils/Global.h

@@ -264,30 +264,34 @@ extern const string MATRIX_INIT;
 // classes (Layout, Connections, etc) need to do this before we can load the
 // graph.
 
-/// Struct for vertex attributes
-struct VertexProperty {
-   // Common Properties:
+/// @brief Parent structure to store common properties for all graph vertices
+struct VertexProperties {
    string type;
    double x;
    double y;
+};
 
-   // 911 Properties
+/// @brief Derived structure for NG911-specific properties
+/// Inherits from VertexProperty and includes attributes specific to 911 networks
+struct NG911VertexProperties : public VertexProperties {
    string objectID;
    string name;
    int servers = 0;
    int trunks = 0;
    string segments;
+};
 
-   // Neural Properties
+/// @brief Derived structure for Neural Network-specific properties
+struct NeuralVertexProperties : public VertexProperties {
    bool active;
 };
 
 /// @brief  The structure to hold the edge properties
-struct EdgeProperty {
+struct EdgeProperties {
    // TODO: Edge Properties
 };
 
 /// @brief The structure to hold the Graph properties
-struct GraphProperty {
+struct GraphProperties {
    // TODO: Graph Properties
 };