resolve some problem like: eliminate unnecessary parameters, put more message and explanation

Hsu0227 · Hsu0227 · commit 4dbfb86e78b7 · 2024-08-02T15:48:21.000-07:00
diff --git a/Simulator/Core/Model.cpp b/Simulator/Core/Model.cpp
@@ -67,7 +67,7 @@ Model::Model()
 void Model::saveResults()
 {
    if (recorder_ != nullptr) {
-      recorder_->saveSimData(layout_->getVertices());
+      recorder_->saveSimData();
    }
 }
 
@@ -146,7 +146,7 @@ void Model::updateHistory()
       LOG4CPLUS_INFO(fileLogger_, "ERROR: Recorder class is null.");
    }
    if (recorder_ != nullptr) {
-      recorder_->compileHistories(layout_->getVertices());
+      recorder_->compileHistories();
    }
 }
 
diff --git a/Simulator/Recorders/Hdf5Recorder.cpp b/Simulator/Recorders/Hdf5Recorder.cpp
@@ -104,7 +104,7 @@ void Hdf5Recorder::term()
 }
 
 // create the dataset for constant variable and store the data to dataset
-void Hdf5Recorder::saveSimData(const AllVertices &neurons)
+void Hdf5Recorder::saveSimData()
 {
    // Initialize datasets for constant variables
    for (auto &variableInfo : variableTable_) {
@@ -124,9 +124,11 @@ void Hdf5Recorder::saveSimData(const AllVertices &neurons)
 }
 
 // Processes and updates HDF5 datasets for variables marked as DYNAMIC
-void Hdf5Recorder::compileHistories(AllVertices &vertices)
+void Hdf5Recorder::compileHistories()
 {
    // Define the maximum chunk size for datasets to optimize storage and access
+   // This defines the maximum number of elements per chunk
+   // If the dataset size exceeds this value, HDF5 will create multiple chunks to store the data
    const hsize_t max_chunk_size = 1024;
 
    // Iterate over each variableInfo object in the variable table
@@ -178,29 +180,30 @@ void Hdf5Recorder::compileHistories(AllVertices &vertices)
 
                // Prepare the data buffer and write the new data to the dataset
                if (variableInfo.hdf5Datatype_ == PredType::NATIVE_FLOAT) {
-                  std::vector<float> dataBuffer(variableInfo.variableLocation_.getNumElements());
+                  vector<float> dataBuffer(variableInfo.variableLocation_.getNumElements());
                   for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {
                      dataBuffer[i] = get<float>(variableInfo.variableLocation_.getElement(i));
                   }
                   variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,
                                                   memSpace, fileSpace);
                } else if (variableInfo.hdf5Datatype_ == PredType::NATIVE_INT) {
-                  std::vector<int> dataBuffer(variableInfo.variableLocation_.getNumElements());
+                  vector<int> dataBuffer(variableInfo.variableLocation_.getNumElements());
                   for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {
                      dataBuffer[i] = get<int>(variableInfo.variableLocation_.getElement(i));
                   }
                   variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,
                                                   memSpace, fileSpace);
                } else if (variableInfo.hdf5Datatype_ == PredType::NATIVE_UINT64) {
-                  std::vector<uint64_t> dataBuffer(variableInfo.variableLocation_.getNumElements());
+                  vector<uint64_t> dataBuffer(variableInfo.variableLocation_.getNumElements());
                   for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {
                      dataBuffer[i] = get<uint64_t>(variableInfo.variableLocation_.getElement(i));
                   }
                   variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,
                                                   memSpace, fileSpace);
                } else {
                   // Throw an exception if the data type is unsupported
-                  throw std::runtime_error("Unsupported data type");
+                  throw runtime_error("Unsupported data type for variable: "
+                                      + variableInfo.variableName_);
                }
             }
          }
diff --git a/Simulator/Recorders/Hdf5Recorder.h b/Simulator/Recorders/Hdf5Recorder.h
@@ -58,13 +58,13 @@ class Hdf5Recorder : public Recorder {
    /// Terminate process
    virtual void term() override;
 
-   // TODO: No parameters needed (AllVertices &vertices)
+   
    /// Compile/capture variable history information in every epoch
-   virtual void compileHistories(AllVertices &neurons) override;
+   virtual void compileHistories() override;
 
-   // TODO: No parameters needed (AllVertices &vertices)
+   
    /// Writes simulation results to an output destination.
-   virtual void saveSimData(const AllVertices &neurons) override;
+   virtual void saveSimData() override;
 
    /// Prints out all parameters to logging file.
    /// Registered to OperationManager as Operation::printParameters
diff --git a/Simulator/Recorders/NG911/Xml911Recorder.cpp b/Simulator/Recorders/NG911/Xml911Recorder.cpp
@@ -33,14 +33,14 @@ void Xml911Recorder::getValues()
 /// Compile history information in every epoch
 ///
 /// @param[in] vertices   The entire list of vertices.
-void Xml911Recorder::compileHistories(AllVertices &vertices)
+void Xml911Recorder::compileHistories()
 {
 }
 
 /// Writes simulation results to an output destination.
 ///
 /// @param  vertices the Vertex list to search from.
-void Xml911Recorder::saveSimData(const AllVertices &vertices)
+void Xml911Recorder::saveSimData()
 {
    auto &conns = Simulator::getInstance().getModel().getConnections();
    Connections911 &conns911 = dynamic_cast<Connections911 &>(conns);
diff --git a/Simulator/Recorders/NG911/Xml911Recorder.h b/Simulator/Recorders/NG911/Xml911Recorder.h
@@ -40,12 +40,12 @@ class Xml911Recorder : public XmlRecorder {
    /// Compile history information in every epoch
    ///
    /// @param[in] vertices   The entire list of vertices.
-   virtual void compileHistories(AllVertices &vertices) override;
+   virtual void compileHistories() override;
 
    /// Writes simulation results to an output destination.
    ///
    /// @param  vertices the Vertex list to search from.
-   virtual void saveSimData(const AllVertices &vertices) override;
+   virtual void saveSimData() override;
 
    ///  Prints out all parameters to logging file.
    ///  Registered to OperationManager as Operation::printParameters
diff --git a/Simulator/Recorders/Recorder.h b/Simulator/Recorders/Recorder.h
@@ -52,13 +52,13 @@ class Recorder {
    /// Terminate process
    virtual void term() = 0;
 
-   // TODO: No parameters needed (AllVertices &vertices)
+   
    /// Compile/capture variable history information in every epoch
-   virtual void compileHistories(AllVertices &vertices) = 0;
+   virtual void compileHistories() = 0;
 
-   // TODO: No parameters needed (AllVertices &vertices)
+   
    /// Writes simulation results to an output destination.
-   virtual void saveSimData(const AllVertices &vertices) = 0;
+   virtual void saveSimData() = 0;
 
    /// Prints loaded parameters to logging file.
    virtual void printParameters() = 0;
diff --git a/Simulator/Recorders/XmlRecorder.cpp b/Simulator/Recorders/XmlRecorder.cpp
@@ -73,7 +73,7 @@ void XmlRecorder::term()
 
 // TODO : @param[in] vertices will be removed eventually after HDF5Recorder implementing
 /// Compile history information in every epoch
-void XmlRecorder::compileHistories(AllVertices &vertices)
+void XmlRecorder::compileHistories()
 {
    //capture data information in each epoch
    for (int rowIndex = 0; rowIndex < variableTable_.size(); rowIndex++) {
@@ -86,7 +86,7 @@ void XmlRecorder::compileHistories(AllVertices &vertices)
 
 // TODO : @param[in] vertices will be removed eventually after HDF5Recorder implementing
 /// Writes simulation results to an output destination.
-void XmlRecorder::saveSimData(const AllVertices &vertices)
+void XmlRecorder::saveSimData()
 {
    // Write XML header information:
    string header = "<?xml version=\"1.0\" standalone=\"no\"?>\n";
diff --git a/Simulator/Recorders/XmlRecorder.h b/Simulator/Recorders/XmlRecorder.h
@@ -60,13 +60,13 @@ class XmlRecorder : public Recorder {
    /// Terminate process
    virtual void term() override;
 
-   // TODO: No parameters needed (AllVertices &vertices)
+   
    /// Compile/capture variable history information in every epoch
-   virtual void compileHistories(AllVertices &vertices) override;
+   virtual void compileHistories() override;
 
-   // TODO: No parameters needed (AllVertices &vertices)
+   
    /// Writes simulation results to an output destination.
-   virtual void saveSimData(const AllVertices &vertices) override;
+   virtual void saveSimData() override;
 
    ///  Prints out all parameters to logging file.
    ///  Registered to OperationManager as Operation::printParameters
diff --git a/Testing/UnitTesting/Hdf5RecorderTests.cpp b/Testing/UnitTesting/Hdf5RecorderTests.cpp
@@ -86,11 +86,8 @@ TEST(Hdf5RecorderTest, SaveSimDataTest)
    // Register the variable with Hdf5Recorder
    recorder.registerVariable("test_var1", eventBuffer, Recorder::UpdatedType::CONSTANT);
 
-   // Create a unique_ptr to an empty AllVertices object
-   unique_ptr<AllVertices> vertices = 0;
-
    // Call saveSimData() to write the data to the file
-   recorder.saveSimData(*vertices);
+   recorder.saveSimData();
 
    // Open the HDF5 file and read back the data
    H5File file(outputFile, H5F_ACC_RDONLY);
@@ -129,8 +126,6 @@ TEST(Hdf5RecorderTest, CompileHistoriesTest)
    // Register the variable with Hdf5Recorder as DYNAMIC
    recorder.registerVariable("test_var_int", eventBufferInt, Recorder::UpdatedType::DYNAMIC);
 
-   // Create a unique_ptr to an empty AllVertices object
-   unique_ptr<AllVertices> vertices = 0;
 
    // Call compileHistories() multiple times to simulate multiple epochs
    for (int epoch = 0; epoch < 3; ++epoch) {
@@ -142,7 +137,7 @@ TEST(Hdf5RecorderTest, CompileHistoriesTest)
       eventBufferInt.insertEvent(4 * (epoch + 1));
       eventBufferInt.insertEvent(5 * (epoch + 1));
 
-      recorder.compileHistories(*vertices);
+      recorder.compileHistories();
    }
 
    // Open the HDF5 file and read back the data
diff --git a/Testing/UnitTesting/XmlRecorderTests.cpp b/Testing/UnitTesting/XmlRecorderTests.cpp
@@ -146,7 +146,7 @@ TEST(XmlRecorderTest, CompileHistoriesTest)
    buffer0.insertEvent(2);
 
    // Call the compileHistories method
-   recorderTest_->compileHistories(*vertices.get());
+   recorderTest_->compileHistories();
    vector<std::variant<uint64_t, bool, int, BGFLOAT>> history = recorderTest_->getHistory(0);
 
    // Verify the events compiled hisotry
@@ -214,9 +214,9 @@ TEST(XmlRecorderTest, SaveSimDataTest)
    buffer.insertEvent(3);
 
    // Call the compileHistories method
-   recorderTest_->compileHistories(*vertices.get());
+   recorderTest_->compileHistories();
    // Call the saveSimData() function
-   recorderTest_->saveSimData(*vertices.get());
+   recorderTest_->saveSimData();
 
    // Open the test_output.xml file and read its content
    std::ifstream inputFile("../Testing/UnitTesting/TestOutput/test_output.xml");

Original file line number	Diff line number	Diff line change
`@@ -67,7 +67,7 @@ Model::Model()`
`67`	`67`	`void Model::saveResults()`
`68`	`68`	`{`
`69`	`69`	`if (recorder_ != nullptr) {`
`70`		`- recorder_->saveSimData(layout_->getVertices());`
	`70`	`+ recorder_->saveSimData();`
`71`	`71`	`}`
`72`	`72`	`}`
`73`	`73`
`@@ -146,7 +146,7 @@ void Model::updateHistory()`
`146`	`146`	`LOG4CPLUS_INFO(fileLogger_, "ERROR: Recorder class is null.");`
`147`	`147`	`}`
`148`	`148`	`if (recorder_ != nullptr) {`
`149`		`- recorder_->compileHistories(layout_->getVertices());`
	`149`	`+ recorder_->compileHistories();`
`150`	`150`	`}`
`151`	`151`	`}`
`152`	`152`
Original file line number	Diff line number	Diff line change
`@@ -104,7 +104,7 @@ void Hdf5Recorder::term()`
`104`	`104`	`}`
`105`	`105`
`106`	`106`	`// create the dataset for constant variable and store the data to dataset`
`107`		`-void Hdf5Recorder::saveSimData(const AllVertices &neurons)`
	`107`	`+void Hdf5Recorder::saveSimData()`
`108`	`108`	`{`
`109`	`109`	`// Initialize datasets for constant variables`
`110`	`110`	`for (auto &variableInfo : variableTable_) {`
`@@ -124,9 +124,11 @@ void Hdf5Recorder::saveSimData(const AllVertices &neurons)`
`124`	`124`	`}`
`125`	`125`
`126`	`126`	`// Processes and updates HDF5 datasets for variables marked as DYNAMIC`
`127`		`-void Hdf5Recorder::compileHistories(AllVertices &vertices)`
	`127`	`+void Hdf5Recorder::compileHistories()`
`128`	`128`	`{`
`129`	`129`	`// Define the maximum chunk size for datasets to optimize storage and access`
	`130`	`+ // This defines the maximum number of elements per chunk`
	`131`	`+ // If the dataset size exceeds this value, HDF5 will create multiple chunks to store the data`
`130`	`132`	`const hsize_t max_chunk_size = 1024;`
`131`	`133`
`132`	`134`	`// Iterate over each variableInfo object in the variable table`
`@@ -178,29 +180,30 @@ void Hdf5Recorder::compileHistories(AllVertices &vertices)`
`178`	`180`
`179`	`181`	`// Prepare the data buffer and write the new data to the dataset`
`180`	`182`	`if (variableInfo.hdf5Datatype_ == PredType::NATIVE_FLOAT) {`
`181`		`- std::vector<float> dataBuffer(variableInfo.variableLocation_.getNumElements());`
	`183`	`+ vector<float> dataBuffer(variableInfo.variableLocation_.getNumElements());`
`182`	`184`	`for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {`
`183`	`185`	`dataBuffer[i] = get<float>(variableInfo.variableLocation_.getElement(i));`
`184`	`186`	`}`
`185`	`187`	`variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,`
`186`	`188`	`memSpace, fileSpace);`
`187`	`189`	`} else if (variableInfo.hdf5Datatype_ == PredType::NATIVE_INT) {`
`188`		`- std::vector<int> dataBuffer(variableInfo.variableLocation_.getNumElements());`
	`190`	`+ vector<int> dataBuffer(variableInfo.variableLocation_.getNumElements());`
`189`	`191`	`for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {`
`190`	`192`	`dataBuffer[i] = get<int>(variableInfo.variableLocation_.getElement(i));`
`191`	`193`	`}`
`192`	`194`	`variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,`
`193`	`195`	`memSpace, fileSpace);`
`194`	`196`	`} else if (variableInfo.hdf5Datatype_ == PredType::NATIVE_UINT64) {`
`195`		`- std::vector<uint64_t> dataBuffer(variableInfo.variableLocation_.getNumElements());`
	`197`	`+ vector<uint64_t> dataBuffer(variableInfo.variableLocation_.getNumElements());`
`196`	`198`	`for (size_t i = 0; i < variableInfo.variableLocation_.getNumElements(); ++i) {`
`197`	`199`	`dataBuffer[i] = get<uint64_t>(variableInfo.variableLocation_.getElement(i));`
`198`	`200`	`}`
`199`	`201`	`variableInfo.hdf5DataSet_.write(dataBuffer.data(), variableInfo.hdf5Datatype_,`
`200`	`202`	`memSpace, fileSpace);`
`201`	`203`	`} else {`
`202`	`204`	`// Throw an exception if the data type is unsupported`
`203`		`- throw std::runtime_error("Unsupported data type");`
	`205`	`+ throw runtime_error("Unsupported data type for variable: "`
	`206`	`+ + variableInfo.variableName_);`
`204`	`207`	`}`
`205`	`208`	`}`
`206`	`209`	`}`
Original file line number	Diff line number	Diff line change
`@@ -33,14 +33,14 @@ void Xml911Recorder::getValues()`
`33`	`33`	`/// Compile history information in every epoch`
`34`	`34`	`///`
`35`	`35`	`/// @param[in] vertices The entire list of vertices.`
`36`		`-void Xml911Recorder::compileHistories(AllVertices &vertices)`
	`36`	`+void Xml911Recorder::compileHistories()`
`37`	`37`	`{`
`38`	`38`	`}`
`39`	`39`
`40`	`40`	`/// Writes simulation results to an output destination.`
`41`	`41`	`///`
`42`	`42`	`/// @param vertices the Vertex list to search from.`
`43`		`-void Xml911Recorder::saveSimData(const AllVertices &vertices)`
	`43`	`+void Xml911Recorder::saveSimData()`
`44`	`44`	`{`
`45`	`45`	`auto &conns = Simulator::getInstance().getModel().getConnections();`
`46`	`46`	`Connections911 &conns911 = dynamic_cast<Connections911 &>(conns);`