Merge pull request #679 from UWB-Biocomputing/issue-657-add-initDatasetforUpdatedTypeCONSTANTForHdf5Recorder

Implement the initDataSet, actually is 'saveSimData' for updated type CONSTANT

Author: Hsu0227

Simulator/Layouts/Layout.cpp

@@ -117,12 +117,12 @@ void Layout::setup()
    dist_ = sqrt(dist2_);
 
    // Register variable: vertex locations if need
-   // Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
-   // string baseName = "Location";
-   // string xLocation = "x_" + baseName;
-   // string yLocation = "y_" + baseName;
-   // recorder.registerVariable(xLocation, xloc_, Recorder::UpdatedType::CONSTANT);
-   // recorder.registerVariable(yLocation, yloc_, Recorder::UpdatedType::CONSTANT);
+   //Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
+   //string baseName = "Location";
+   //string xLocation = "x_" + baseName;
+   //string yLocation = "y_" + baseName;
+   //recorder.registerVariable(xLocation, xloc_, Recorder::UpdatedType::CONSTANT);
+   //recorder.registerVariable(yLocation, yloc_, Recorder::UpdatedType::CONSTANT);
 
    // test purpose
    // cout << "xloc_: " << &xloc_ << endl;

Simulator/Recorders/Hdf5Recorder.cpp

@@ -66,7 +66,7 @@ void Hdf5Recorder::init()
    try {
       // Create a new file using the default property lists
       resultOut_ = new H5File(resultFileName_, H5F_ACC_TRUNC);
-      initDataSet();
+
    } catch (FileIException &error) {
       cerr << "HDF5 File I/O Exception: " << endl;
       error.printErrorStack();
@@ -103,9 +103,23 @@ void Hdf5Recorder::term()
    }
 }
 
-//  Create data spaces and data sets of the hdf5 for recording histories.
-void Hdf5Recorder::initDataSet()
+// create the dataset for constant variable and store the data to dataset
+void Hdf5Recorder::saveSimData(const AllVertices &neurons)
 {
+   // Initialize datasets for constant variables
+   for (auto &variableInfo : variableTable_) {
+      if (variableInfo.variableType_ == UpdatedType::CONSTANT) {
+         // Define dimensions for the constant dataset
+         hsize_t constantDims[1]
+            = {static_cast<hsize_t>(variableInfo.variableLocation_.getNumElements())};
+         DataSpace constantSpace(1, constantDims);
+
+         // Create dataset
+         variableInfo.hdf5DataSet_ = resultOut_->createDataSet(
+            variableInfo.variableName_, variableInfo.hdf5Datatype_, constantSpace);
+         variableInfo.captureData();
+      }
+   }
 }
 
 /// Receives a recorded variable entity from the variable owner class

Simulator/Recorders/Hdf5Recorder.h

@@ -66,9 +66,7 @@ class Hdf5Recorder : public Recorder {
 
    // TODO: No parameters needed (AllVertices &vertices)
    /// Writes simulation results to an output destination.
-   virtual void saveSimData(const AllVertices &neurons) override
-   {
-   }
+   virtual void saveSimData(const AllVertices &neurons) override;
 
    /// Prints out all parameters to logging file.
    /// Registered to OperationManager as Operation::printParameters
@@ -93,6 +91,10 @@ class Hdf5Recorder : public Recorder {
    {
    }
 
+   virtual void initDataSet()
+   {
+   }
+
    struct singleVariableInfo {
       /// the name of each variable
       string variableName_;
@@ -127,31 +129,51 @@ class Hdf5Recorder : public Recorder {
          if (dataType_ == typeid(uint64_t).name()) {
             hdf5Datatype_ = PredType::NATIVE_UINT64;
          } else if (dataType_ == typeid(bool).name()) {
-            hdf5Datatype_ = PredType::NATIVE_UINT8;
+            hdf5Datatype_ = PredType::NATIVE_INT;
          } else if (dataType_ == typeid(int).name()) {
             hdf5Datatype_ = PredType::NATIVE_INT;
          } else if (dataType_ == typeid(float).name()) {
             hdf5Datatype_ = PredType::NATIVE_FLOAT;
          } else if (dataType_ == typeid(double).name()) {
             hdf5Datatype_ = PredType::NATIVE_DOUBLE;
          } else {
-            //string errorMsg = "Not supported type for type: " + dataType_;
             throw runtime_error("Unsupported data type");
          }
       }
 
-      // Creates a dynamic dataset in the HDF5 file
-      void createDynamicDataset(H5File *resultOut_)
+      // Method to capture and write data to the HDF5 dataset
+      void captureData()
       {
-         // Create dataspace with initial size and unlimited max size
-         hsize_t dims[1] = {static_cast<hsize_t>(variableLocation_.getNumElements())};
-         hsize_t maxDims[1] = {H5S_UNLIMITED};
-         DataSpace dataspace(1, dims, maxDims);
-
-         // Create dataset
-         hdf5DataSet_ = resultOut_->createDataSet(variableName_, hdf5Datatype_, dataspace);
-
-         std::cout << "Created dataset: " << variableName_ << std::endl;
+         // Ensure the dataset exists and data can be written
+         if (variableLocation_.getNumElements() > 0) {
+            // Prepare the data buffer based on the HDF5 data type
+            if (hdf5Datatype_ == PredType::NATIVE_FLOAT) {
+               vector<float> dataBuffer(variableLocation_.getNumElements());
+               for (int i = 0; i < variableLocation_.getNumElements(); ++i) {
+                  dataBuffer[i] = get<float>(variableLocation_.getElement(i));
+               }
+               // Write the data to the dataset
+               hdf5DataSet_.write(dataBuffer.data(), hdf5Datatype_);
+
+            } else if (hdf5Datatype_ == PredType::NATIVE_INT) {
+               vector<int> dataBuffer(variableLocation_.getNumElements());
+               for (int i = 0; i < variableLocation_.getNumElements(); ++i) {
+                  dataBuffer[i] = get<int>(variableLocation_.getElement(i));
+               }
+               hdf5DataSet_.write(dataBuffer.data(), hdf5Datatype_);
+
+            } else if (hdf5Datatype_ == PredType::NATIVE_UINT64) {
+               vector<uint64_t> dataBuffer(variableLocation_.getNumElements());
+               for (int i = 0; i < variableLocation_.getNumElements(); ++i) {
+                  dataBuffer[i] = get<uint64_t>(variableLocation_.getElement(i));
+               }
+               hdf5DataSet_.write(dataBuffer.data(), hdf5Datatype_);
+
+            } else {
+               // Throw an error if the data type is unsupported
+               throw runtime_error("Unsupported data type");
+            }
+         }
       }
    };
 
@@ -170,8 +192,6 @@ class Hdf5Recorder : public Recorder {
    }
 
 private:
-   virtual void initDataSet();
-
    /// Populates Starter neuron matrix based with boolean values based on starterMap state
    ///@param[in] matrix  starter neuron matrix
    ///@param starterMap  Bool vector to reference neuron matrix location from.
@@ -182,7 +202,7 @@ class Hdf5Recorder : public Recorder {
 
    // Member variables for HDF5 datasets
    H5File *resultOut_;
-   DataSet dataSetXloc_;
+   /*DataSet dataSetXloc_;
    DataSet dataSetYloc_;
    DataSet dataSetNeuronTypes_;
    DataSet dataSetNeuronThresh_;
@@ -204,7 +224,7 @@ class Hdf5Recorder : public Recorder {
    const H5std_string nameSimulationEndTime = "simulationEndTime";
    const H5std_string nameSpikesProbedNeurons = "spikesProbedNeurons";
    const H5std_string nameAttrPNUnit = "attrPNUint";
-   const H5std_string nameProbedNeurons = "probedNeurons";
+   const H5std_string nameProbedNeurons = "probedNeurons";*/
 
    // Keep track of where we are in incrementally writing spikes
    vector<hsize_t> offsetSpikesProbedNeurons_;

Testing/UnitTesting/Hdf5RecorderTests.cpp

@@ -3,11 +3,42 @@
 #include "RecordableBase.h"
 #include "RecordableVector.h"
 #include "Recorder.h"
+#include "VectorMatrix.h"
 #include "gtest/gtest.h"
 
 #if defined(HDF5)
    #include "H5Cpp.h"
 
+// Test case for initializing the Hdf5Recorder
+TEST(Hdf5RecorderTest, CreateInstanceSuccess)
+{
+   Recorder *recorder = Hdf5Recorder::Create();
+   ASSERT_TRUE(recorder != nullptr);
+}
+
+// Test case for init() and term()
+TEST(Hdf5RecorderTest, Hdf5InitAndTermTest)
+{
+   // Create an instance of Hdf5Recorder with a specific output file name
+   std::string outputFile = "../Testing/UnitTesting/TestOutput/Hdf5test_output_term.h5";
+   Hdf5Recorder recorder(outputFile);
+   recorder.init();
+
+   // Ensure the file has been created successfully by the constructor
+   FILE *f = fopen(outputFile.c_str(), "r");
+   ASSERT_TRUE(f != NULL);
+   fclose(f);
+
+   // Call the term() method to close the HDF5 file
+   recorder.term();
+
+   // Check if the file can be reopened, indicating it was closed properly
+   f = fopen(outputFile.c_str(), "r");
+   bool fileExist = f != NULL;
+   fclose(f);
+   ASSERT_TRUE(fileExist);
+}
+
 // Unit test for verifying the registerVariable method
 TEST(Hdf5RecorderTest, RegisterVariableTest)
 {
@@ -34,33 +65,51 @@ TEST(Hdf5RecorderTest, RegisterVariableTest)
    ASSERT_EQ(PredType::NATIVE_UINT64, varInfo.hdf5Datatype_);
 }
 
-// Test case for initializing the Hdf5Recorder
-TEST(Hdf5RecorderTest, CreateInstanceSuccess)
+// Define the test case for saving simulation data
+TEST(Hdf5RecorderTest, SaveSimDataTest)
 {
-   Recorder *recorder = Hdf5Recorder::Create();
-   ASSERT_TRUE(recorder != nullptr);
-}
+   // Define a temporary file path for testing
+   std::string outputFile = "../Testing/UnitTesting/TestOutput/Hdf5test_output_save.h5";
 
-// Test case for init() and term()
-TEST(Hdf5RecorderTest, Hdf5InitAndTermTest)
-{
-   // Create an instance of Hdf5Recorder with a specific output file name
-   std::string outputFile = "../Testing/UnitTesting/TestOutput/Hdf5test_output_term.h5";
+   // Create an instance of Hdf5Recorder
    Hdf5Recorder recorder(outputFile);
    recorder.init();
 
-   // Ensure the file has been created successfully by the constructor
-   FILE *f = fopen(outputFile.c_str(), "r");
-   ASSERT_TRUE(f != NULL);
-   fclose(f);
+   // Create and configure EventBuffer for testing
+   EventBuffer eventBuffer(5);   // Initialize with a size that matches the mock data
+   eventBuffer.insertEvent(1);
+   eventBuffer.insertEvent(2);
+   eventBuffer.insertEvent(3);
+   eventBuffer.insertEvent(4);
+   eventBuffer.insertEvent(5);
 
-   // Call the term() method to close the HDF5 file
-   recorder.term();
+   // Register the variable with Hdf5Recorder
+   recorder.registerVariable("test_var1", eventBuffer, Recorder::UpdatedType::CONSTANT);
 
-   // Check if the file can be reopened, indicating it was closed properly
-   f = fopen(outputFile.c_str(), "r");
-   bool fileExist = f != NULL;
-   fclose(f);
-   ASSERT_TRUE(fileExist);
+   // 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);
+
+   // Open the HDF5 file and read back the data
+   H5File file(outputFile, H5F_ACC_RDONLY);
+   DataSet dataset = file.openDataSet("test_var1");
+   DataSpace dataspace = dataset.getSpace();
+
+   hsize_t num_elements;
+   dataspace.getSimpleExtentDims(&num_elements, nullptr);
+
+   vector<uint64_t> dataBuffer(num_elements);
+   // Read the data into the buffer
+   dataset.read(dataBuffer.data(), PredType::NATIVE_UINT64);
+
+   // Verify the data matches the expected values
+   vector<uint64_t> expectedData = {1, 2, 3, 4, 5};
+   ASSERT_EQ(expectedData.size(), dataBuffer.size());
+   for (size_t i = 0; i < expectedData.size(); ++i) {
+      EXPECT_EQ(expectedData[i], dataBuffer[i]);
+   }
 }
+
 #endif   // HDF5