Merge pull request #690 from UWB-Biocomputing/issue-659-add-registerVariableForVectorRecordableBaseForHdf5Recorder

Implement Hdf5Recorder::registerVariable() for vector of RecordableBase

Author: Hsu0227

Simulator/Core/Model.cpp

@@ -104,7 +104,6 @@ void Model::setupSim()
    // Init radii and rates history matrices with default values
    if (recorder_ != nullptr) {
       recorder_->init();
-      recorder_->initDefaultValues();
    }
 
    // Creates all the vertices and generates data for them.

Simulator/Recorders/Hdf5Recorder.cpp

@@ -225,10 +225,22 @@ void Hdf5Recorder::compileHistories()
 void Hdf5Recorder::registerVariable(const string &varName, RecordableBase &recordVar,
                                     UpdatedType variableType)
 {
-   // Create a singleVariableInfo object for the variable
-   singleVariableInfo hdf5VarInfo(varName, recordVar, variableType);
+   // Create a hdf5VariableInfo object for the variable
+   hdf5VariableInfo hdf5VarInfo(varName, recordVar, variableType);
 
    // Add the variable information to the variableTable_
    variableTable_.push_back(hdf5VarInfo);
 }
+
+/// Register a vector of instance of a class derived from RecordableBase
+void Hdf5Recorder::registerVariable(const string &varName, vector<RecordableBase *> &recordVars,
+                                    UpdatedType variableType)
+{
+   for (int i = 0; i < recordVars.size(); i++) {
+      string variableID = varName + to_string(i);
+      RecordableBase &address = *recordVars[i];
+      // add a new variable into the table
+      variableTable_.push_back(hdf5VariableInfo(variableID, address, variableType));
+   }
+}
 #endif   // HDF5

Simulator/Recorders/Hdf5Recorder.h

@@ -40,21 +40,6 @@ class Hdf5Recorder : public Recorder {
    /// @param[in] stateOutputFileName File name to save histories
    virtual void init() override;
 
-   /// Init radii and rates history matrices with default values
-   virtual void initDefaultValues() override
-   {
-   }
-
-   /// Init radii and rates history matrices with current radii and rates
-   virtual void initValues() override
-   {
-   }
-
-   /// Get the current radii and rates vlaues
-   virtual void getValues() override
-   {
-   }
-
    /// Terminate process
    virtual void term() override;
 
@@ -85,15 +70,10 @@ class Hdf5Recorder : public Recorder {
 
    /// Register a vector of instance of a class derived from RecordableBase.
    virtual void registerVariable(const string &varName, vector<RecordableBase *> &recordVars,
-                                 UpdatedType variableType) override
-   {
-   }
+                                 UpdatedType variableType) override;
 
-   virtual void initDataSet()
-   {
-   }
 
-   struct singleVariableInfo {
+   struct hdf5VariableInfo {
       /// the name of each variable
       string variableName_;
 
@@ -114,7 +94,7 @@ class Hdf5Recorder : public Recorder {
       RecordableBase &variableLocation_;
 
       // Constructor accepting the variable name, the address of recorded variable, the updated type
-      singleVariableInfo(const string &name, RecordableBase &location, UpdatedType variableType) :
+      hdf5VariableInfo(const string &name, RecordableBase &location, UpdatedType variableType) :
          variableLocation_(location), variableName_(name), variableType_(variableType)
       {
          dataType_ = location.getDataType();
@@ -184,7 +164,7 @@ class Hdf5Recorder : public Recorder {
    }
 
    // Accessor method to retrieve variableTable_
-   const vector<singleVariableInfo> &getVariableTable() const
+   const vector<hdf5VariableInfo> &getVariableTable() const
    {
       return variableTable_;
    }
@@ -201,15 +181,8 @@ class Hdf5Recorder : public Recorder {
    // Member variables for HDF5 datasets
    H5File *resultOut_;
 
-   // Keep track of where we are in incrementally writing spikes
-   vector<hsize_t> offsetSpikesProbedNeurons_;
-   // spikes history - history of accumulated spikes count of all neurons (10 ms bin)
-   vector<int> spikesHistory_;
-   // track spikes count of probed neurons
-   vector<vector<uint64_t>> spikesProbedNeurons_;
-
    /// List of registered variables for recording
-   vector<singleVariableInfo> variableTable_;
+   vector<hdf5VariableInfo> variableTable_;
    // Other member functions...
 };
 

Simulator/Recorders/NG911/Xml911Recorder.cpp

@@ -15,21 +15,6 @@
 #include "Connections911.h"
 // #include "Global.h"
 
-/// Init radii and rates history matrices with default values
-void Xml911Recorder::initDefaultValues()
-{
-}
-
-/// Init radii and rates history matrices with current radii and rates
-void Xml911Recorder::initValues()
-{
-}
-
-/// Get the current radii and rates vlaues
-void Xml911Recorder::getValues()
-{
-}
-
 /// Compile history information in every epoch
 ///
 /// @param[in] vertices   The entire list of vertices.

Simulator/Recorders/NG911/Xml911Recorder.h

@@ -28,15 +28,6 @@ class Xml911Recorder : public XmlRecorder {
       return new Xml911Recorder();
    }
 
-   /// Init radii and rates history matrices with default values
-   virtual void initDefaultValues() override;
-
-   /// Init radii and rates history matrices with current radii and rates
-   virtual void initValues() override;
-
-   /// Get the current radii and rates vlaues
-   virtual void getValues() override;
-
    /// Compile history information in every epoch
    ///
    /// @param[in] vertices   The entire list of vertices.