HDF5IO.hpp

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#pragma once
 
#include <iostream>
#include <memory>
#include <string>
 
#include <H5Opublic.h>
 
#include "BaseIO.hpp"
#include "Types.hpp"
 
namespace H5
{
class DataSet;
class H5File;
class DataType;
class Exception;
}  // namespace H5
 
namespace AQNWB::HDF5
{
class HDF5RecordingData;  // declare here because gets used in HDF5IO class
 
class HDF5IO : public BaseIO
{
public:
  HDF5IO(const std::string& fileName, const bool disableSWMRMode = false);
 
  ~HDF5IO();
 
  Status open() override;
 
  Status open(bool newfile) override;
 
  Status close() override;
 
  Status flush() override;
 
  Status createAttribute(const BaseDataType& type,
                         const void* data,
                         const std::string& path,
                         const std::string& name,
                         const SizeType& size = 1) override;
 
  Status createAttribute(const std::string& data,
                         const std::string& path,
                         const std::string& name) override;
 
  Status createAttribute(const std::vector<std::string>& data,
                         const std::string& path,
                         const std::string& name) override;
 
  Status createAttribute(const std::vector<const char*>& data,
                         const std::string& path,
                         const std::string& name,
                         const SizeType& maxSize) override;
 
  Status createReferenceAttribute(const std::string& referencePath,
                                  const std::string& path,
                                  const std::string& name) override;
 
  Status createGroup(const std::string& path) override;
 
  Status createLink(const std::string& path,
                    const std::string& reference) override;
 
  Status createStringDataSet(const std::string& path,
                             const std::string& value) override;
 
  Status createStringDataSet(const std::string& path,
                             const std::vector<std::string>& values) override;
 
  Status createReferenceDataSet(
      const std::string& path,
      const std::vector<std::string>& references) override;
 
  Status startRecording() override;
 
  Status stopRecording() override;
 
  bool canModifyObjects() override;
 
  std::unique_ptr<BaseRecordingData> createArrayDataSet(
      const BaseDataType& type,
      const SizeArray& size,
      const SizeArray& chunking,
      const std::string& path) override;
 
  std::unique_ptr<BaseRecordingData> getDataSet(
      const std::string& path) override;
 
  bool objectExists(const std::string& path) override;
 
  H5O_type_t getObjectType(const std::string& path);
 
  static H5::DataType getNativeType(BaseDataType type);
 
  static H5::DataType getH5Type(BaseDataType type);
 
protected:
  Status createGroupIfDoesNotExist(const std::string& path) override;
 
private:
  std::unique_ptr<H5::H5File> m_file;
  bool m_disableSWMRMode;
};
 
class HDF5RecordingData : public BaseRecordingData
{
public:
  HDF5RecordingData(std::unique_ptr<H5::DataSet> data);
 
  HDF5RecordingData(const HDF5RecordingData&) = delete;
 
  HDF5RecordingData& operator=(const HDF5RecordingData&) = delete;
 
  ~HDF5RecordingData();
 
  Status writeDataBlock(const std::vector<SizeType>& dataShape,
                        const std::vector<SizeType>& positionOffset,
                        const BaseDataType& type,
                        const void* data);
 
  inline const H5::DataSet* getDataSet() const { return m_dataset.get(); }
 
private:
  Status checkStatus(int status);
 
  std::unique_ptr<H5::DataSet> m_dataset;
};
}  // namespace AQNWB::HDF5