Merge pull request #539 from UWB-Biocomputing/issue-180-width-height-move

[ISSUE 180] Moved width_ and height_ parameter from Simulator to FixedLayout

Author: jardiamj

Simulator/Core/Model.cpp

@@ -14,7 +14,6 @@
  */
 
 #include "Model.h"
-#include "ConnGrowth.h"
 #include "Connections.h"
 #include "Factory.h"
 #include "ParameterManager.h"
@@ -106,55 +105,17 @@ void Model::setupSim()
    connections_->createEdgeIndexMap();
 }
 
+// Note: This method was previously used for debugging, but it is now dead code left behind.
 /// Log this simulation step.
-void Model::logSimStep() const
-{
-   ConnGrowth *pConnGrowth = dynamic_cast<ConnGrowth *>(connections_.get());
-   if (pConnGrowth == nullptr)
-      return;
-
-   cout << "format:\ntype,radius,firing rate" << endl;
-
-   for (int y = 0; y < Simulator::getInstance().getHeight(); y++) {
-      stringstream ss;
-      ss << fixed;
-      ss.precision(1);
-
-      for (int x = 0; x < Simulator::getInstance().getWidth(); x++) {
-         switch (layout_->vertexTypeMap_[x + y * Simulator::getInstance().getWidth()]) {
-            case EXC:
-               if (layout_->starterMap_[x + y * Simulator::getInstance().getWidth()])
-                  ss << "s";
-               else
-                  ss << "e";
-               break;
-            case INH:
-               ss << "i";
-               break;
-            case VTYPE_UNDEF:
-               assert(false);
-               break;
-         }
-
-         ss << " " << pConnGrowth->radii_[x + y * Simulator::getInstance().getWidth()];
-
-         if (x + 1 < Simulator::getInstance().getWidth()) {
-            ss.width(2);
-            ss << "|";
-            ss.width(2);
-         }
-      }
-
-      ss << endl;
-
-      for (int i = ss.str().length() - 1; i >= 0; i--) {
-         ss << "_";
-      }
-
-      ss << endl;
-      cout << ss.str();
-   }
-}
+// void Model::logSimStep() const
+// {
+//    FixedLayout *fixedLayout = dynamic_cast<FixedLayout *>(layout_.get());
+//    if (fixedLayout == nullptr) {
+//       return;
+//    }
+
+//    fixedLayout->printLayout();
+// }
 
 /// Update the simulation history of every epoch.
 void Model::updateHistory()

Simulator/Core/Model.h

@@ -80,8 +80,9 @@ class Model {
    virtual void updateConnections() = 0;
 
 protected:
+   // Note: This method was previously used for debugging, but it is now dead code left behind.
    /// Prints debug information about the current state of the network.
-   void logSimStep() const;
+   // void logSimStep() const;
 
    /// Copy GPU Edge data to CPU.
    virtual void copyGPUtoCPU() = 0;

Simulator/Core/Simulator.cpp

@@ -76,10 +76,6 @@ void Simulator::finish()
 /// Load member variables from configuration file
 void Simulator::loadParameters()
 {
-   ParameterManager::getInstance().getIntByXpath("//PoolSize/x/text()", width_);
-   ParameterManager::getInstance().getIntByXpath("//PoolSize/y/text()", height_);
-   // numVertices_ = width_ * height_;
-
    ParameterManager::getInstance().getBGFloatByXpath("//SimParams/epochDuration/text()",
                                                      epochDuration_);
    ParameterManager::getInstance().getIntByXpath("//SimParams/numEpochs/text()", numEpochs_);
@@ -110,7 +106,6 @@ void Simulator::printParameters() const
    LOG4CPLUS_DEBUG(fileLogger_,
                    "\nSIMULATION PARAMETERS"
                       << endl
-                      << "\tpool size x:" << width_ << " y:" << height_ << endl
                       << "\tTime between growth updates (in seconds): " << epochDuration_ << endl
                       << "\tNumber of epochs to run: " << numEpochs_ << endl
                       << "\tMax firing rate: " << maxFiringRate_ << endl
@@ -284,16 +279,6 @@ void Simulator::setStimulusFileName(const string &fileName)
  *  Accessors
  ***********************************************/
 ///@{
-int Simulator::getWidth() const
-{
-   return width_;
-}
-
-int Simulator::getHeight() const
-{
-   return height_;
-}
-
 int Simulator::getTotalVertices() const
 {
    return model_->getLayout().getNumVertices();

Simulator/Core/Simulator.h

@@ -61,10 +61,6 @@ class Simulator {
    *  Accessors
    ***********************************************/
    ///@{
-   int getWidth() const;   /// Width of neuron map (assumes square)
-
-   int getHeight() const;   /// Height of neuron map
-
    int getTotalVertices() const;   /// Count of neurons in the simulation
 
    int getCurrentStep() const;   /// Current simulation step
@@ -130,10 +126,6 @@ class Simulator {
    Simulator();   /// Constructor is private to keep a singleton instance of this
                   /// class.
 
-   int width_;   /// Width of neuron map (assumes square)
-
-   int height_;   /// Height of neuron map
-
    int totalNeurons_;   /// Count of neurons in the simulation
 
    int currentEpoch_;   /// Current epoch step

Simulator/Layouts/Neuro/FixedLayout.cpp

@@ -7,6 +7,7 @@
  */
 
 #include "FixedLayout.h"
+#include "ConnGrowth.h"
 #include "ParameterManager.h"
 #include "ParseParamError.h"
 #include "Util.h"
@@ -129,11 +130,10 @@ void FixedLayout::loadParameters()
                           + inhibitoryNListFilePath);
    }
 
-   // Get the total number of vertices
-   int width, height;
-   ParameterManager::getInstance().getIntByXpath("//PoolSize/x/text()", width);
-   ParameterManager::getInstance().getIntByXpath("//PoolSize/y/text()", height);
-   numVertices_ = width * height;
+   // Get width, height and total number of vertices
+   ParameterManager::getInstance().getIntByXpath("//PoolSize/x/text()", width_);
+   ParameterManager::getInstance().getIntByXpath("//PoolSize/y/text()", height_);
+   numVertices_ = width_ * height_;
 }
 
 ///  Returns the type of synapse at the given coordinates
@@ -164,14 +164,64 @@ void FixedLayout::initVerticesLocs()
    if (gridLayout_) {
       // grid layout
       for (int i = 0; i < numVertices; i++) {
-         xloc_[i] = i % Simulator::getInstance().getHeight();
-         yloc_[i] = i / Simulator::getInstance().getHeight();
+         xloc_[i] = i % height_;
+         yloc_[i] = i / height_;
       }
    } else {
       // random layout
       for (int i = 0; i < numVertices; i++) {
-         xloc_[i] = initRNG.inRange(0, Simulator::getInstance().getWidth());
-         yloc_[i] = initRNG.inRange(0, Simulator::getInstance().getHeight());
+         xloc_[i] = initRNG.inRange(0, width_);
+         yloc_[i] = initRNG.inRange(0, height_);
       }
    }
 }
+
+// Note: This code was previously used for debugging, but it is now dead code left behind
+// and it is never executed.
+void FixedLayout::printLayout()
+{
+   ConnGrowth &pConnGrowth
+      = dynamic_cast<ConnGrowth &>(Simulator::getInstance().getModel().getConnections());
+
+   cout << "format:\ntype,radius,firing rate" << endl;
+
+   for (int y = 0; y < height_; y++) {
+      stringstream ss;
+      ss << fixed;
+      ss.precision(1);
+
+      for (int x = 0; x < width_; x++) {
+         switch (vertexTypeMap_[x + y * width_]) {
+            case EXC:
+               if (starterMap_[x + y * width_])
+                  ss << "s";
+               else
+                  ss << "e";
+               break;
+            case INH:
+               ss << "i";
+               break;
+            case VTYPE_UNDEF:
+               assert(false);
+               break;
+         }
+
+         ss << " " << pConnGrowth.radii_[x + y * width_];
+
+         if (x + 1 < width_) {
+            ss.width(2);
+            ss << "|";
+            ss.width(2);
+         }
+      }
+
+      ss << endl;
+
+      for (int i = ss.str().length() - 1; i >= 0; i--) {
+         ss << "_";
+      }
+
+      ss << endl;
+      cout << ss.str();
+   }
+}

Simulator/Layouts/Neuro/FixedLayout.h

@@ -59,9 +59,16 @@ class FixedLayout : public Layout {
    /// @return type of the synapse.
    virtual edgeType edgType(const int srcVertex, const int destVertex) override;
 
+   /// Prints the layout, used for debugging.
+   void printLayout();
+
 private:
    /// initialize the location maps (xloc and yloc).
    void initVerticesLocs();
 
    bool gridLayout_;   ///< True if grid layout.
+
+   int width_;   /// Width of the layout (assumes square)
+
+   int height_;   /// Height of the layout
 };

Testing/UnitTesting/SimulatorTests.cpp

@@ -29,8 +29,6 @@ TEST(Simulator, ParametersInitializedSuccessfully)
    ParameterManager::getInstance().loadParameterFile("../configfiles/test-medium-500.xml");
    Simulator::getInstance().loadParameters();
 
-   EXPECT_EQ(30, Simulator::getInstance().getWidth());
-   EXPECT_EQ(30, Simulator::getInstance().getHeight());
    EXPECT_EQ(BGFLOAT(100), Simulator::getInstance().getEpochDuration());
    EXPECT_EQ(500, Simulator::getInstance().getNumEpochs());
    EXPECT_EQ(200, Simulator::getInstance().getMaxFiringRate());