Merge branch 'add_read' into add_container_read

docs/pages/userdocs/workflow.dox

@@ -60,9 +60,9 @@
  * object so that it can mana ge access and data writing during the recording process.
  * When adding containers, ownership of the \ref AQNWB::NWB::Container "Container"  is transferred to the
  * \ref AQNWB::NWB::RecordingContainers "RecordingContainers" object, so that we can access it again via
- * its index. New containers will always be appended to the end of the
- * \ref AQNWB::NWB::RecordingContainers::containers "containers" object and their index can be tracked
- * using the size of the input `recordingArrays`.
+ * its index. New containers will always be appended to the end of the private member
+ * ``RecordingContainers::m_containers`` object and their index can be tracked
+ * using the \ref AQNWB::NWB::RecordingContainers::size "RecordingContainers.size" of the input `recordingArrays`.
  *
  * \snippet tests/examples/testWorkflowExamples.cpp example_workflow_datasets_snippet
  *

src/Channel.cpp

@@ -14,32 +14,17 @@ Channel::Channel(const std::string name,
                  const float bitVolts,
                  const std::array<float, 3> position,
                  const std::string comments)
-    : name(name)
-    , groupName(groupName)
-    , groupIndex(groupIndex)
-    , localIndex(localIndex)
-    , globalIndex(globalIndex)
-    , position(position)
-    , conversion(conversion)
-    , samplingRate(samplingRate)
-    , bitVolts(bitVolts)
-    , comments(comments)
+    : m_name(name)
+    , m_groupName(groupName)
+    , m_groupIndex(groupIndex)
+    , m_localIndex(localIndex)
+    , m_globalIndex(globalIndex)
+    , m_position(position)
+    , m_conversion(conversion)
+    , m_samplingRate(samplingRate)
+    , m_bitVolts(bitVolts)
+    , m_comments(comments)
 {
 }
 
 Channel::~Channel() {}
-
-float Channel::getConversion() const
-{
-  return bitVolts / conversion;
-}
-
-float Channel::getSamplingRate() const
-{
-  return samplingRate;
-}
-
-float Channel::getBitVolts() const
-{
-  return bitVolts;
-}

src/Channel.hpp

@@ -36,73 +36,159 @@ class Channel
    */
   ~Channel();
 
+  /**
+   * @brief Copy constructor
+   */
+  Channel(const Channel& other) = default;
+
+  /**
+   * @brief Move constructor
+   */
+  Channel(Channel&& other) = default;
+
+  /**
+   * @brief Assignment operator
+   */
+  Channel& operator=(const Channel& other) = default;
+
+  /**
+   * @brief Move assignment operator
+   */
+  Channel& operator=(Channel&& other) = default;
+
   /**
    * @brief Getter for conversion factor
    * @return The conversion value.
    */
-  float getConversion() const;
+  inline float getConversion() const { return m_bitVolts / m_conversion; }
 
   /**
-   * @brief Getter for samplingRate
-   * @return The samplingRate value.
+   * @brief Getter for sampling rate of the channel.
+   * @return The sampling rate value.
    */
-  float getSamplingRate() const;
+  inline float getSamplingRate() const { return m_samplingRate; }
 
   /**
-   * @brief Getter for bitVolts
+   * @brief Getter for bitVolts floating point value of microvolts per bit
    * @return The bitVolts value.
    */
-  float getBitVolts() const;
+  inline float getBitVolts() const { return m_bitVolts; }
 
   /**
-   * @brief Name of the channel.
+   * @brief Get the name of the array group the channel belongs to.
+   * @return The groupName value.
    */
-  std::string name;
+  inline std::string getGroupName() const { return m_groupName; }
 
   /**
-   * @brief Name of the array group the channel belongs to.
+   * @brief Get the name of the channel
+   * @return The name value.
    */
-  std::string groupName;
+  inline std::string getName() const { return m_name; }
 
   /**
-   * @brief Index of array group the channel belongs to.
+   * @brief Get the array group index the channel belongs to
+   * @return The groupIndex value.
    */
-  SizeType groupIndex;
+  inline SizeType getGroupIndex() const { return m_groupIndex; }
 
   /**
-   * @brief Index of channel within the recording array.
+   * @brief Get the index of the channel within the recording array.
+   * @return The localIndex value.
    */
-  SizeType localIndex;
+  inline SizeType getLocalIndex() const { return m_localIndex; }
 
   /**
-   * @brief Index of channel across the recording system.
+   * @brief Get the index of the channel across the recording system.
+   * @return The globalIndex value.
    */
-  SizeType globalIndex;
+  inline SizeType getGlobalIndex() const { return m_globalIndex; }
 
   /**
-   * @brief Coordinates of channel (x, y, z) within the recording array.
+   * @brief Get the coordinates of channel (x, y, z) within the recording array.
+   * @return The position value.
    */
-  std::array<float, 3> position;
+  inline const std::array<float, 3>& getPosition() const { return m_position; }
 
   /**
-   * @brief Comments about the channel.
+   * @brief Get comments about the channel
+   * @return The comments value.
+   */
+  inline std::string getComments() const { return m_comments; }
+
+  /**
+   * @brief Set comments about the channel.
+   * @param comments The comments to set.
+   */
+  inline void setComments(const std::string& comments)
+  {
+    m_comments = comments;
+  }
+
+  /**
+   * @brief Set coordinates of channel (x, y, z) within the recording array.
+   * @param position The position to set.
+   */
+  inline void setPosition(const std::array<float, 3>& position)
+  {
+    m_position = position;
+  }
+
+  /**
+   * @brief Set name of the channel.
+   * @param name The name to set.
    */
-  std::string comments;
+  inline void setName(const std::string& name) { m_name = name; }
 
 private:
+  /**
+   * @brief Comments about the channel.
+   */
+  std::string m_comments;
+
+  /**
+   * @brief Coordinates of channel (x, y, z) within the recording array.
+   */
+  std::array<float, 3> m_position;
+
+  /**
+   * @brief Index of channel across the recording system.
+   */
+  SizeType m_globalIndex;
+
+  /**
+   * @brief Index of channel within the recording array.
+   */
+  SizeType m_localIndex;
+
+  /**
+   * @brief Index of array group the channel belongs to.
+   */
+  SizeType m_groupIndex;
+
+  /**
+   * @brief Name of the channel.
+   */
+  std::string m_name;
+
+  /**
+   * @brief Name of the array group the channel belongs to.
+   */
+  std::string m_groupName;
+
   /**
    * @brief Conversion factor.
    */
-  float conversion;
+  float m_conversion;
 
   /**
    * @brief Sampling rate of the channel.
    */
-  float samplingRate;
+  float m_samplingRate;
 
   /**
    * @brief floating point value of microvolts per bit
    */
-  float bitVolts;
+  float m_bitVolts;
 };
-}  // namespace AQNWB
+}  // namespace AQNWB

src/io/BaseIO.cpp

@@ -32,29 +32,15 @@ const BaseDataType BaseDataType::DSTR = BaseDataType(T_STR, DEFAULT_STR_SIZE);
 
 // BaseIO
 
-BaseIO::BaseIO()
-    : readyToOpen(true)
-    , opened(false)
+BaseIO::BaseIO(const std::string& filename)
+    : m_filename(filename)
+    , m_readyToOpen(true)
+    , m_opened(false)
 {
 }
 
 BaseIO::~BaseIO() {}
 
-bool BaseIO::isOpen() const
-{
-  return opened;
-}
-
-bool BaseIO::isReadyToOpen() const
-{
-  return readyToOpen;
-}
-
-bool BaseIO::canModifyObjects()
-{
-  return true;
-}
-
 Status BaseIO::createCommonNWBAttributes(const std::string& path,
                                          const std::string& objectNamespace,
                                          const std::string& neurodataType,

src/io/BaseIO.hpp

@@ -100,7 +100,7 @@ class BaseIO
   /**
    * @brief Constructor for the BaseIO class.
    */
-  BaseIO();
+  BaseIO(const std::string& filename);
 
   /**
    * @brief Copy constructor is deleted to prevent construction-copying.
@@ -121,7 +121,7 @@ class BaseIO
    * @brief Returns the full path to the file.
    * @return The full path to the file.
    */
-  virtual std::string getFileName() = 0;
+  virtual std::string getFileName() const { return m_filename; }
 
   /**
    * @brief  Get the storage type (Group, Dataset, Attribute) of the object at
@@ -318,7 +318,7 @@ class BaseIO
    * override this function to check if objects can be modified.
    * @return True if the file is in a modification mode, false otherwise.
    */
-  virtual bool canModifyObjects();
+  virtual bool canModifyObjects() { return true; }
 
   /**
    * @brief Creates an extendable dataset with a given base data type, size,
@@ -389,20 +389,20 @@ class BaseIO
    * @brief Returns true if the file is open.
    * @return True if the file is open, false otherwise.
    */
-  bool isOpen() const;
+  inline bool isOpen() const { return m_opened; }
 
   /**
    * @brief Returns true if the file is able to be opened.
    * @return True if the file is able to be opened, false otherwise.
    */
-  bool isReadyToOpen() const;
+  inline bool isReadyToOpen() const { return m_readyToOpen; }
 
+protected:
   /**
    * @brief The name of the file.
    */
-  const std::string filename;
+  const std::string m_filename;
 
-protected:
   /**
    * @brief Creates a new group if it does not already exist.
    * @param path The location of the group in the file.
@@ -413,12 +413,12 @@ class BaseIO
   /**
    * @brief Whether the file is ready to be opened.
    */
-  bool readyToOpen;
+  bool m_readyToOpen;
 
   /**
    * @brief Whether the file is currently open.
    */
-  bool opened;
+  bool m_opened;
 };
 
 /**