Start refactor containers for read

src/nwb/NWBFile.cpp

@@ -25,16 +25,16 @@ constexpr SizeType CHUNK_XSIZE = 2048;
 
 // NWBFile
 
-NWBFile::NWBFile(const std::string& idText, std::shared_ptr<BaseIO> io)
-    : identifierText(idText)
-    , io(io)
+NWBFile::NWBFile(std::shared_ptr<BaseIO> io)
+    : Container("/", io)
 {
 }
 
 NWBFile::~NWBFile() {}
 
-Status NWBFile::initialize()
+Status NWBFile::initialize(const std::string& idText)
 {
+  this->identifierText = idText;
   if (std::filesystem::exists(io->getFileName())) {
     return io->open(false);
   } else {
@@ -114,8 +114,8 @@ Status NWBFile::createElectricalSeries(
     std::string electrodePath = "/general/extracellular_ephys/" + groupName;
     std::string electricalSeriesPath = rootPath + groupName;
 
-    Device device = Device(devicePath, io, "description", "unknown");
-    device.initialize();
+    Device device = Device(devicePath, io);
+    device.initialize("description", "unknown");
 
     ElectrodeGroup elecGroup =
         ElectrodeGroup(electrodePath, io, "description", "unknown", device);
@@ -124,14 +124,14 @@ Status NWBFile::createElectricalSeries(
     // Setup electrical series datasets
     auto electricalSeries = std::make_unique<ElectricalSeries>(
         electricalSeriesPath,
-        io,
+        io);
+    electricalSeries->initialize(
         dataType,
         channelVector,
         "Stores continuously sampled voltage data from an "
         "extracellular ephys recording",
         SizeArray {0, channelVector.size()},
         SizeArray {CHUNK_XSIZE, 0});
-    electricalSeries->initialize();
     recordingContainers->addData(std::move(electricalSeries));
 
     // Add electrode information to electrode table (does not write to datasets

src/nwb/NWBFile.hpp

@@ -24,15 +24,15 @@ class RecordingContainers;  // declare here because gets used in NWBFile class
  * @brief The NWBFile class provides an interface for setting up and managing
  * the NWB file.
  */
-class NWBFile
+class NWBFile : public Container
 {
 public:
   /**
    * @brief Constructor for NWBFile class.
    * @param idText The identifier text for the NWBFile.
    * @param io The shared pointer to the IO object.
    */
-  NWBFile(const std::string& idText, std::shared_ptr<BaseIO> io);
+  NWBFile(std::shared_ptr<BaseIO> io);
 
   /**
    * @brief Deleted copy constructor to prevent construction-copying.
@@ -53,7 +53,7 @@ class NWBFile
    * @brief Initializes the NWB file by opening and setting up the file
    * structure.
    */
-  Status initialize();
+  Status initialize(const std::string& idText);
 
   /**
    * @brief Finalizes the NWB file by closing it.
@@ -140,8 +140,7 @@ class NWBFile
   std::unique_ptr<RecordingContainers> recordingContainers =
       std::make_unique<RecordingContainers>("RecordingContainers");
 
-  const std::string identifierText;
-  std::shared_ptr<BaseIO> io;
+  std::string identifierText;  // TODO Remove this for read
 };
 
 /**

src/nwb/NWBRecording.cpp

@@ -27,9 +27,8 @@ Status NWBRecording::openFile(const std::string& filename,
   }
 
   // initialize nwbfile object and create base structure
-  nwbfile = std::make_unique<NWB::NWBFile>(generateUuid(),
-                                           createIO(IOType, filename));
-  nwbfile->initialize();
+  nwbfile = std::make_unique<NWB::NWBFile>(createIO(IOType, filename));
+  nwbfile->initialize(generateUuid());
 
   // create the datasets
   nwbfile->createElectricalSeries(recordingArrays);

src/nwb/base/TimeSeries.cpp

@@ -6,36 +6,28 @@ using namespace AQNWB::NWB;
 
 /** Constructor */
 TimeSeries::TimeSeries(const std::string& path,
-                       std::shared_ptr<BaseIO> io,
-                       const BaseDataType& dataType,
-                       const std::string& unit,
-                       const std::string& description,
-                       const std::string& comments,
-                       const SizeArray& dsetSize,
-                       const SizeArray& chunkSize,
-                       const float& conversion,
-                       const float& resolution,
-                       const float& offset)
+                       std::shared_ptr<BaseIO> io)
     : Container(path, io)
-    , dataType(dataType)
-    , unit(unit)
-    , description(description)
-    , comments(comments)
-    , dsetSize(dsetSize)
-    , chunkSize(chunkSize)
-    , conversion(conversion)
-    , resolution(resolution)
-    , offset(offset)
 {
 }
 
 /** Destructor */
 TimeSeries::~TimeSeries() {}
 
-void TimeSeries::initialize()
+void TimeSeries::initialize(const BaseDataType& dataType,
+                            const std::string& unit,
+                            const std::string& description,
+                            const std::string& comments,
+                            const SizeArray& dsetSize,
+                            const SizeArray& chunkSize,
+                            const float& conversion,
+                            const float& resolution,
+                            const float& offset)
 {
   Container::initialize();
 
+  this->dataType = dataType;
+
   // setup attributes
   io->createCommonNWBAttributes(path, "core", neurodataType, description);
   io->createAttribute(comments, path, "comments");

src/nwb/base/TimeSeries.hpp

@@ -17,30 +17,9 @@ class TimeSeries : public Container
    * @brief Constructor.
    * @param path The location of the TimeSeries in the file.
    * @param io A shared pointer to the IO object.
-   * @param dataType The data type to use for storing the recorded signal
-   * @param unit Unit for the electrical signal. Must be "volts"
-   * @param description The description of the TimeSeries.
-   * @param comments Human-readable comments about the TimeSeries
-   * @param dsetSize Initial size of the main dataset
-   * @param chunkSize Chunk size to use
-   * @param conversion Scalar to multiply each element in data to convert it to
-   *                   the specified ‘unit’
-   * @param resolution Smallest meaningful difference between values in data,
-   *                   stored in the specified by unit
-   * @param offset Scalar to add to the data after scaling by ‘conversion’ to
-   *               finalize its coercion to the specified ‘unit'
    */
   TimeSeries(const std::string& path,
-             std::shared_ptr<BaseIO> io,
-             const BaseDataType& dataType,
-             const std::string& unit,
-             const std::string& description = "no description",
-             const std::string& comments = "no comments",
-             const SizeArray& dsetSize = SizeArray {0},
-             const SizeArray& chunkSize = SizeArray {1},
-             const float& conversion = 1.0f,
-             const float& resolution = -1.0f,
-             const float& offset = 0.0f);
+             std::shared_ptr<BaseIO> io);
 
   /**
    * @brief Destructor
@@ -65,8 +44,29 @@ class TimeSeries : public Container
   /**
    * @brief Initializes the TimeSeries by creating NWB related attributes and
    * writing the description and comment metadata.
+   *
+   * @param dataType The data type to use for storing the recorded signal
+   * @param unit Unit for the electrical signal. Must be "volts"
+   * @param description The description of the TimeSeries.
+   * @param comments Human-readable comments about the TimeSeries
+   * @param dsetSize Initial size of the main dataset
+   * @param chunkSize Chunk size to use
+   * @param conversion Scalar to multiply each element in data to convert it to
+   *                   the specified ‘unit’
+   * @param resolution Smallest meaningful difference between values in data,
+   *                   stored in the specified by unit
+   * @param offset Scalar to add to the data after scaling by ‘conversion’ to
+   *               finalize its coercion to the specified ‘unit'
    */
-  void initialize();
+  void initialize(const BaseDataType& dataType,
+                  const std::string& unit,
+                  const std::string& description = "no description",
+                  const std::string& comments = "no comments",
+                  const SizeArray& dsetSize = SizeArray {0},
+                  const SizeArray& chunkSize = SizeArray {1},
+                  const float& conversion = 1.0f,
+                  const float& resolution = -1.0f,
+                  const float& offset = 0.0f);
 
   /**
    * @brief Pointer to data values.
@@ -88,57 +88,6 @@ class TimeSeries : public Container
    */
   BaseDataType timestampsType = BaseDataType::F64;
 
-  /**
-   * @brief Base unit of measurement for working with the data. Actual stored
-   * values are not necessarily stored in these units. To access the data in
-   * these units, multiply ‘data’ by ‘conversion’ and add ‘offset’.
-   */
-  std::string unit;
-
-  /**
-   * @brief The description of the TimeSeries.
-   */
-  std::string description;
-
-  /**
-   * @brief Human-readable comments about the TimeSeries.
-   */
-  std::string comments;
-
-  /**
-   * @brief Size used in dataset creation. Can be expanded when writing if
-   * needed.
-   */
-  SizeArray dsetSize;
-
-  /**
-   * @brief Chunking size used in dataset creation.
-   */
-  SizeArray chunkSize;
-
-  /**
-   * @brief Scalar to multiply each element in data to convert it to the
-   * specified ‘unit’.
-   */
-  float conversion;
-
-  /**
-   * @brief Smallest meaningful difference between values in data, stored in the
-   * specified by unit.
-   */
-  float resolution;
-
-  /**
-   * @brief Scalar to add to the data after scaling by ‘conversion’ to finalize
-   * its coercion to the specified ‘unit’.
-   */
-  float offset;
-
-  /**
-   * @brief The starting time of the TimeSeries.
-   */
-  float startingTime = 0.0;
-
 private:
   /**
    * @brief The neurodataType of the TimeSeries.

src/nwb/device/Device.cpp

@@ -5,34 +5,19 @@ using namespace AQNWB::NWB;
 // Device
 /** Constructor */
 Device::Device(const std::string& path,
-               std::shared_ptr<BaseIO> io,
-               const std::string& description,
-               const std::string& manufacturer)
+               std::shared_ptr<BaseIO> io)
     : Container(path, io)
-    , description(description)
-    , manufacturer(manufacturer)
 {
 }
 
 /** Destructor */
 Device::~Device() {}
 
-void Device::initialize()
+void Device::initialize(const std::string& description,
+                        const std::string& manufacturer)
 {
   Container::initialize();
 
   io->createCommonNWBAttributes(path, "core", "Device", description);
   io->createAttribute(manufacturer, path, "manufacturer");
 }
-
-// Getter for manufacturer
-std::string Device::getManufacturer() const
-{
-  return manufacturer;
-}
-
-// Getter for description
-std::string Device::getDescription() const
-{
-  return description;
-}

src/nwb/device/Device.hpp

@@ -18,13 +18,9 @@ class Device : public Container
    * @brief Constructor.
    * @param path The location of the device in the file.
    * @param io A shared pointer to the IO object.
-   * @param description The description of the device.
-   * @param manufacturer The manufacturer of the device.
    */
   Device(const std::string& path,
-         std::shared_ptr<BaseIO> io,
-         const std::string& description,
-         const std::string& manufacturer);
+         std::shared_ptr<BaseIO> io);
 
   /**
    * @brief Destructor
@@ -34,8 +30,12 @@ class Device : public Container
   /**
    * @brief Initializes the device by creating NWB related attributes and
    * writing the manufactor and description metadata.
+   *
+   * @param description The description of the device.
+   * @param manufacturer The manufacturer of the device.
    */
-  void initialize();
+  void initialize(const std::string& description,
+                  const std::string& manufacturer);
 
   /**
    * @brief Gets the manufacturer of the device.
@@ -49,15 +49,5 @@ class Device : public Container
    */
   std::string getDescription() const;
 
-private:
-  /**
-   * @brief The description of the device.
-   */
-  std::string description;
-
-  /**
-   * @brief The manufacturer of the device.
-   */
-  std::string manufacturer;
 };
 }  // namespace AQNWB::NWB