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Move HDF5RecordingData to its own hpp/cpp files
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| Original file line number | Diff line number | Diff line change |
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| #include <codecvt> | ||
| #include <filesystem> | ||
| #include <iostream> | ||
| #include <memory> | ||
| #include <vector> | ||
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| #include "io/hdf5/HDF5RecordingData.hpp" | ||
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| #include <H5Cpp.h> | ||
| #include <H5Fpublic.h> | ||
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| #include "Utils.hpp" | ||
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| using namespace H5; | ||
| using namespace AQNWB::IO::HDF5; | ||
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| // HDF5RecordingData | ||
| HDF5RecordingData::HDF5RecordingData(std::unique_ptr<H5::DataSet> data) | ||
| { | ||
| DataSpace dSpace = data->getSpace(); | ||
| DSetCreatPropList prop = data->getCreatePlist(); | ||
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| int nDimensions = dSpace.getSimpleExtentNdims(); | ||
| std::vector<hsize_t> dims(nDimensions), chunk(nDimensions); | ||
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| nDimensions = dSpace.getSimpleExtentDims( | ||
| dims.data()); // TODO -redefine here or use original? | ||
| prop.getChunk(static_cast<int>(nDimensions), chunk.data()); | ||
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| this->size = std::vector<SizeType>(nDimensions); | ||
| for (int i = 0; i < nDimensions; ++i) { | ||
| this->size[i] = dims[i]; | ||
| } | ||
| this->nDimensions = nDimensions; | ||
| this->position = std::vector<SizeType>( | ||
| nDimensions, 0); // Initialize position with 0 for each dimension | ||
| this->dSet = std::make_unique<H5::DataSet>(*data); | ||
| } | ||
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| // HDF5RecordingData | ||
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| HDF5RecordingData::~HDF5RecordingData() | ||
| { | ||
| // Safety | ||
| dSet->flush(H5F_SCOPE_GLOBAL); | ||
| } | ||
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| Status HDF5RecordingData::writeDataBlock( | ||
| const std::vector<SizeType>& dataShape, | ||
| const std::vector<SizeType>& positionOffset, | ||
| const BaseDataType& type, | ||
| const void* data) | ||
| { | ||
| try { | ||
| // check dataShape and positionOffset inputs match the dimensions of the | ||
| // dataset | ||
| if (dataShape.size() != nDimensions || positionOffset.size() != nDimensions) | ||
| { | ||
| return Status::Failure; | ||
| } | ||
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| // Ensure that we have enough space to accommodate new data | ||
| std::vector<hsize_t> dSetDims(nDimensions), offset(nDimensions); | ||
| for (int i = 0; i < nDimensions; ++i) { | ||
| offset[i] = static_cast<hsize_t>(positionOffset[i]); | ||
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| if (dataShape[i] + offset[i] > size[i]) // TODO - do I need offset here | ||
| dSetDims[i] = dataShape[i] + offset[i]; | ||
| else | ||
| dSetDims[i] = size[i]; | ||
| } | ||
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| // Adjust dataset dimensions if necessary | ||
| dSet->extend(dSetDims.data()); | ||
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| // Set size to new size based on updated dimensionality | ||
| DataSpace fSpace = dSet->getSpace(); | ||
| fSpace.getSimpleExtentDims(dSetDims.data()); | ||
| for (int i = 0; i < nDimensions; ++i) { | ||
| size[i] = dSetDims[i]; | ||
| } | ||
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| // Create memory space with the shape of the data | ||
| // DataSpace mSpace(dimension, dSetDim.data()); | ||
| std::vector<hsize_t> dataDims(nDimensions); | ||
| for (int i = 0; i < nDimensions; ++i) { | ||
| if (dataShape[i] == 0) { | ||
| dataDims[i] = 1; | ||
| } else { | ||
| dataDims[i] = static_cast<hsize_t>(dataShape[i]); | ||
| } | ||
| } | ||
| DataSpace mSpace(static_cast<int>(nDimensions), dataDims.data()); | ||
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| // Select hyperslab in the file space | ||
| fSpace.selectHyperslab(H5S_SELECT_SET, dataDims.data(), offset.data()); | ||
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| // Write the data | ||
| DataType nativeType = HDF5IO::getNativeType(type); | ||
| dSet->write(data, nativeType, mSpace, fSpace); | ||
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| // Update position for simple extension | ||
| for (int i = 0; i < dataShape.size(); ++i) { | ||
| position[i] += dataShape[i]; | ||
| } | ||
| } catch (DataSetIException error) { | ||
| error.printErrorStack(); | ||
| } catch (DataSpaceIException error) { | ||
| error.printErrorStack(); | ||
| } catch (FileIException error) { | ||
| error.printErrorStack(); | ||
| } | ||
| return Status::Success; | ||
| } | ||
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| const H5::DataSet* HDF5RecordingData::getDataSet() | ||
| { | ||
| return dSet.get(); | ||
| }; |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,74 @@ | ||
| #pragma once | ||
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| #include "io/BaseIO.hpp" | ||
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| namespace H5 | ||
| { | ||
| class DataSet; | ||
| } // namespace H5 | ||
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| namespace AQNWB::IO::HDF5 | ||
| { | ||
| /** | ||
| * @brief Represents an HDF5 Dataset that can be extended indefinitely | ||
| * in blocks. | ||
| * | ||
| * This class provides functionality for reading and writing blocks of data | ||
| * to an HDF5 dataset. | ||
| */ | ||
| class HDF5RecordingData : public AQNWB::IO::BaseRecordingData | ||
| { | ||
| public: | ||
| /** | ||
| * @brief Constructs an HDF5RecordingData object. | ||
| * @param data A pointer to the HDF5 dataset. | ||
| */ | ||
| HDF5RecordingData(std::unique_ptr<H5::DataSet> data); | ||
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| /** | ||
| * @brief Deleted copy constructor to prevent construction-copying. | ||
| */ | ||
| HDF5RecordingData(const HDF5RecordingData&) = delete; | ||
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| /** | ||
| * @brief Deleted copy assignment operator to prevent copying. | ||
| */ | ||
| HDF5RecordingData& operator=(const HDF5RecordingData&) = delete; | ||
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| /** | ||
| * @brief Destroys the HDF5RecordingData object. | ||
| */ | ||
| ~HDF5RecordingData(); | ||
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| /** | ||
| * @brief Writes a block of data to the HDF5 dataset. | ||
| * @param dataShape The size of the data block. | ||
| * @param positionOffset The position of the data block to write to. | ||
| * @param type The data type of the elements in the data block. | ||
| * @param data A pointer to the data block. | ||
| * @return The status of the write operation. | ||
| */ | ||
| Status writeDataBlock(const std::vector<SizeType>& dataShape, | ||
| const std::vector<SizeType>& positionOffset, | ||
| const AQNWB::IO::BaseDataType& type, | ||
| const void* data); | ||
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| /** | ||
| * @brief Gets a const pointer to the HDF5 dataset. | ||
| * @return A const pointer to the HDF5 dataset. | ||
| */ | ||
| const H5::DataSet* getDataSet(); | ||
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| private: | ||
| /** | ||
| * @brief Pointer to an extendable HDF5 dataset | ||
| */ | ||
| std::unique_ptr<H5::DataSet> dSet; | ||
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| /** | ||
| * @brief Return status of HDF5 operations. | ||
| */ | ||
| Status checkStatus(int status); | ||
| }; | ||
| } // namespace AQNWB::IO::HDF5 |
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