ElectrodeTable.hpp

#pragma once

#include <string>

#include "hdmf/table/DynamicTable.hpp"
#include "hdmf/table/ElementIdentifiers.hpp"
#include "hdmf/table/VectorData.hpp"
#include "io/BaseIO.hpp"

namespace AQNWBIO
{
/**
 * @brief Represents a table containing electrode metadata.
 */
class ElectrodeTable : public DynamicTable
{
public:
  /**
   * @brief Constructor.
   * @param path The path of the table.
   * @param io The shared pointer to the BaseIO object.
   * @param channels The vector of channel numbers.
   * @param description The description of the table (default: "metadata about
   * extracellular electrodes").
   */
  ElectrodeTable(const std::string& path,
                 std::shared_ptr<BaseIO> io,
                 const std::vector<int>& channels,
                 const std::string& description =
                     "metadata about extracellular electrodes");

  /**
   * @brief Destructor.
   */
  ~ElectrodeTable();

  /**
   * @brief Initializes the ElectrodeTable.
   *
   * Initializes the ElectrodeTable by creating NWB related attributes and
   * adding required columns.
   */
  void initialize();

  /**
   * @brief Sets up the ElectrodeTable by adding electrodes and their metadata.
   *
   */
  void addElectrodes();

  /**
   * @brief Gets the column names of the ElectrodeTable.
   * @return The vector of column names.
   */
  const std::vector<std::string>& getColNames() override;

  /**
   * @brief Sets the column names of the ElectrodeTable.
   * @param newColNames The vector of new column names.
   */
  void setColNames(const std::vector<std::string>& newColNames);

  /**
   * @brief Gets the group path of the ElectrodeTable.
   * @return The group path.
   */
  std::string getGroupPath() const;

  /**
   * @brief Sets the group path of the ElectrodeTable.
   * @param groupPath The new group path.
   */
  void setGroupPath(const std::string& groupPath);

  std::unique_ptr<ElementIdentifiers> electrodeDataset =
      std::make_unique<ElementIdentifiers>(); /**< The electrode dataset. */
  std::unique_ptr<VectorData> groupNamesDataset =
      std::make_unique<VectorData>(); /**< The group names dataset. */
  std::unique_ptr<VectorData> locationsDataset =
      std::make_unique<VectorData>(); /**< The locations dataset. */

private:
  /**
   * @brief The channel information from the acquisition system.
   */
  std::vector<int> channels;

  /**
   * @brief The global indices for each electrode.
   */
  std::vector<int> electrodeNumbers;

  /**
   * @brief The names of the ElectrodeGroup object for each electrode.
   */
  std::vector<std::string> groupNames;

  /**
   * @brief The location names for each electrode.
   */
  std::vector<std::string> locationNames;

  /**
   * @brief The references to the ElectrodeGroup object for each electrode.
   */
  std::vector<std::string> groupReferences;

  /**
   * @brief The vector of column names for the table.
   */
  std::vector<std::string> colNames = {"group", "group_name", "location"};

  /**
   * @brief The references path to the ElectrodeGroup
   */
  std::string groupPath = "/general/extracellular_ephys/array1";
};
}  // namespace AQNWBIO