NWBFile.hpp

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#pragma once
 
#include <array>
#include <cstdint>
#include <memory>
#include <string>
#include <string_view>
#include <vector>
 
#include "Types.hpp"
#include "Utils.hpp"
#include "io/BaseIO.hpp"
#include "io/ReadIO.hpp"
#include "nwb/RecordingContainers.hpp"
#include "nwb/base/TimeSeries.hpp"
#include "nwb/file/ElectrodeTable.hpp"
#include "nwb/hdmf/base/Container.hpp"

namespace AQNWB::NWB
{

class NWBFile : public Container
{
public:
  // Register the ElectrodeTable as a subclass of Container
  REGISTER_SUBCLASS(NWBFile, "core")
 
  
  NWBFile(std::shared_ptr<IO::BaseIO> io);

  NWBFile(const std::string& path, std::shared_ptr<IO::BaseIO> io);

  NWBFile(const NWBFile&) = delete;

  NWBFile& operator=(const NWBFile&) = delete;

  ~NWBFile();

  Status initialize(const std::string& identifierText,
                    const std::string& description = "a recording session",
                    const std::string& dataCollection = "",
                    const std::string& sessionStartTime = "",
                    const std::string& timestampsReferenceTime = "");

  bool isInitialized() const;

  Status finalize();

  Status createElectricalSeries(
      std::vector<Types::ChannelVector> recordingArrays,
      std::vector<std::string> recordingNames,
      const IO::BaseDataType& dataType = IO::BaseDataType::I16,
      RecordingContainers* recordingContainers = nullptr,
      std::vector<SizeType>& containerIndexes = emptyContainerIndexes);

  Status createSpikeEventSeries(
      std::vector<Types::ChannelVector> recordingArrays,
      std::vector<std::string> recordingNames,
      const IO::BaseDataType& dataType = IO::BaseDataType::I16,
      RecordingContainers* recordingContainers = nullptr,
      std::vector<SizeType>& containerIndexes = emptyContainerIndexes);

  Status createAnnotationSeries(
      std::vector<std::string> recordingNames,
      RecordingContainers* recordingContainers = nullptr,
      std::vector<SizeType>& containerIndexes = emptyContainerIndexes);
 
protected:
  Status createFileStructure(const std::string& identifierText,
                             const std::string& description,
                             const std::string& dataCollection,
                             const std::string& sessionStartTime,
                             const std::string& timestampsReferenceTime);
 
private:
  std::unique_ptr<IO::BaseRecordingData> createRecordingData(
      IO::BaseDataType type,
      const SizeArray& size,
      const SizeArray& chunking,
      const std::string& path);

  template<SizeType N>
  void cacheSpecifications(
      const std::string& specPath,
      const std::string& versionNumber,
      const std::array<std::pair<std::string_view, std::string_view>, N>&
          specVariables);
 
  inline const static std::string acquisitionPath = "/acquisition";
  static std::vector<SizeType> emptyContainerIndexes;
 
  DEFINE_FIELD(readNWBVersion,
               AttributeField,
               std::string,
               "nwb_version",
               File version string)
 
  DEFINE_FIELD(readFileCreateDate,
               DatasetField,
               std::any,
               "file_create_date",
               A record of the date the file was created and of subsequent
                   modifications)
 
  DEFINE_FIELD(readIdentifier,
               DatasetField,
               std::string,
               "identifier",
               A unique text identifier for the file)
 
  DEFINE_FIELD(readSessionDescription,
               DatasetField,
               std::string,
               "session_description",
               A description of the experimental session and data in the file)
 
  DEFINE_FIELD(readSessionStartTime,
               DatasetField,
               std::any,
               "session_start_time",
               Date and time of the experiment or session start)
 
  DEFINE_FIELD(readTimestampsReferenceTime,
               DatasetField,
               std::any,
               "timestamps_reference_time",
               Date and time corresponding to time zero of all timestamps)
 
private:
  std::unique_ptr<ElectrodeTable> m_electrodeTable;
};
 
}  // namespace AQNWB::NWB