fix formatting

src/NWBFile.cpp

@@ -8,16 +8,15 @@
 
 #include "NWBFile.hpp"
 
-#include "io/BaseIO.hpp"
+#include "Utils.hpp"
+#include "device/Device.hpp"
 #include "file/ElectrodeGroup.hpp"
 #include "file/ElectrodeTable.hpp"
-#include "device/Device.hpp"
-#include "Utils.hpp"
+#include "io/BaseIO.hpp"
 
 using namespace AQNWBIO;
 namespace fs = std::filesystem;
 
-
 // NWBFile
 
 NWBFile::NWBFile(const std::string& idText, std::shared_ptr<BaseIO> io)
@@ -76,7 +75,7 @@ Status NWBFile::createFileStructure()
 
 Status NWBFile::startRecording()
 {
-  // Later channels/continuous array will be input from the acquisition system 
+  // Later channels/continuous array will be input from the acquisition system
   // with unknown size but self generating for now
   std::vector<int> continuousArray;
   for (int i = 1; i <= 1; ++i) {
@@ -100,21 +99,27 @@ Status NWBFile::startRecording()
     Device device = Device(devicePath, io, "description", "unknown");
     device.initialize();
 
-    ElectrodeGroup elecGroup = ElectrodeGroup(elecPath, io, "description", "unknown", device);
+    ElectrodeGroup elecGroup =
+        ElectrodeGroup(elecPath, io, "description", "unknown", device);
     elecGroup.initialize();
   }
 
   // Create electrode table
   std::string electrodePath = "general/extracellular_ephys/electrodes/";
   ElectrodeTable elecTable = ElectrodeTable(electrodePath, io, channels);
 
-
-  elecTable.electrodeDataset->dataset =
-      createRecordingData(BaseDataType::I32, SizeArray{1}, SizeArray{1}, electrodePath + "id");
-  elecTable.groupNamesDataset->dataset = createRecordingData(
-      BaseDataType::STR(250), SizeArray{0}, SizeArray{1}, electrodePath + "group_name");
-  elecTable.locationsDataset->dataset = createRecordingData(
-      BaseDataType::STR(250), SizeArray{0}, SizeArray{1}, electrodePath + "location");
+  elecTable.electrodeDataset->dataset = createRecordingData(
+      BaseDataType::I32, SizeArray {1}, SizeArray {1}, electrodePath + "id");
+  elecTable.groupNamesDataset->dataset =
+      createRecordingData(BaseDataType::STR(250),
+                          SizeArray {0},
+                          SizeArray {1},
+                          electrodePath + "group_name");
+  elecTable.locationsDataset->dataset =
+      createRecordingData(BaseDataType::STR(250),
+                          SizeArray {0},
+                          SizeArray {1},
+                          electrodePath + "location");
 
   elecTable.initialize();
 
@@ -150,11 +155,12 @@ void NWBFile::cacheSpecifications(const std::string& specPath,
     }
 }
 
-
-
 // recording data factory method /
 std::unique_ptr<BaseRecordingData> NWBFile::createRecordingData(
-    BaseDataType type, const SizeArray& size, const SizeArray& chunking, const std::string& path)
+    BaseDataType type,
+    const SizeArray& size,
+    const SizeArray& chunking,
+    const std::string& path)
 {
   return std::unique_ptr<BaseRecordingData>(
       io->createDataSet(type, size, chunking, path));

src/NWBFile.hpp

@@ -7,7 +7,8 @@
 using namespace AQNWBIO;
 
 /**
- * @brief The NWBFile class provides an interface for setting up and managing the NWB file.
+ * @brief The NWBFile class provides an interface for setting up and managing
+ * the NWB file.
  */
 class NWBFile
 {
@@ -35,7 +36,8 @@ class NWBFile
   ~NWBFile();
 
   /**
-   * @brief Initializes the NWB file by opening and setting up the file structure.
+   * @brief Initializes the NWB file by opening and setting up the file
+   * structure.
    */
   void initialize();
 
@@ -79,25 +81,32 @@ class NWBFile
    * @param size The size of the dataset.
    * @param chunking The chunking size of the dataset.
    * @param path The location in the file of the new dataset.
-   * @return std::unique_ptr<BaseRecordingData> The unique pointer to the created recording data.
+   * @return std::unique_ptr<BaseRecordingData> The unique pointer to the
+   * created recording data.
    */
   std::unique_ptr<BaseRecordingData> createRecordingData(
-    BaseDataType type, const SizeArray& size, const SizeArray& chunking, const std::string& path);
+      BaseDataType type,
+      const SizeArray& size,
+      const SizeArray& chunking,
+      const std::string& path);
 
   /**
    * @brief Saves the specification files for the schema.
    * @param specPath The location in the file to store the spec information.
    * @param versionNumber The version number of the specification files.
    */
-  void cacheSpecifications(const std::string& specPath, const std::string& versionNumber);
+  void cacheSpecifications(const std::string& specPath,
+                           const std::string& versionNumber);
 
   /**
    * @brief Creates a new dataset to hold text data (messages).
    * @param path The location in the file for the dataset.
    * @param name The name of the dataset.
    * @param text The text data to be stored in the dataset.
    */
-  void createTextDataSet(const std::string& path, const std::string& name, const std::string& text);
+  void createTextDataSet(const std::string& path,
+                         const std::string& name,
+                         const std::string& text);
 
   const std::string identifierText;
   std::shared_ptr<BaseIO> io;
@@ -106,7 +115,6 @@ class NWBFile
   SizeType bufferSize;
 };
 
-
 /**
  * @brief The NWBRecordingEngine class manages the recording process
  */
@@ -144,7 +152,8 @@ class NWBRecordingEngine
                  int recordingNumber);
 
   /**
-   * @brief Closes all the files and performs necessary cleanup when recording stops.
+   * @brief Closes all the files and performs necessary cleanup when recording
+   * stops.
    */
   void closeFiles();
 

src/Types.hpp

@@ -5,20 +5,25 @@
 /**
  * @brief Provides definitions for various types used in the project.
  */
-class Types {
+class Types
+{
 public:
-    /**
-     * @brief Represents the status of an operation.
-     */
-    enum Status {Success = 0, Failure = -1};
+  /**
+   * @brief Represents the status of an operation.
+   */
+  enum Status
+  {
+    Success = 0,
+    Failure = -1
+  };
 
-    /**
-     * @brief Alias for the size type used in the project.
-     */
-    using SizeType = size_t;
+  /**
+   * @brief Alias for the size type used in the project.
+   */
+  using SizeType = size_t;
 
-    /**
-     * @brief Alias for an array of size types used in the project.
-     */
-    using SizeArray = std::vector<size_t>;
+  /**
+   * @brief Alias for an array of size types used in the project.
+   */
+  using SizeArray = std::vector<size_t>;
 };

src/Utils.hpp

@@ -1,7 +1,7 @@
 #include <chrono>
 #include <ctime>
-#include <sstream>
 #include <iomanip>
+#include <sstream>
 
 #include <boost/uuid/uuid.hpp>
 #include <boost/uuid/uuid_generators.hpp>

src/device/Device.cpp

@@ -2,8 +2,13 @@
 
 // Device
 /** Constructor */
-Device::Device(const std::string& path, std::shared_ptr<BaseIO> io, const std::string& description, const std::string& manufacturer)
-  : Container(path, io), description(description), manufacturer(manufacturer)
+Device::Device(const std::string& path,
+               std::shared_ptr<BaseIO> io,
+               const std::string& description,
+               const std::string& manufacturer)
+    : Container(path, io)
+    , description(description)
+    , manufacturer(manufacturer)
 {
 }
 

src/device/Device.hpp

@@ -1,33 +1,39 @@
 #pragma once
 
 #include <string>
+
 #include "hdmf/base/Container.hpp"
 #include "io/BaseIO.hpp"
 
 using namespace AQNWBIO;
 
 /**
- * @brief Metadata about a data acquisition device, e.g., recording system, electrode, microscope.
+ * @brief Metadata about a data acquisition device, e.g., recording system,
+ * electrode, microscope.
  */
 class Device : public Container
 {
 public:
   /**
-   * @brief Constructer.
+   * @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);
+  Device(const std::string& path,
+         std::shared_ptr<BaseIO> io,
+         const std::string& description,
+         const std::string& manufacturer);
 
   /**
    * @brief Destructor
    */
   ~Device();
 
   /**
-   * @brief Initializes the device by creating NWB related attributes and writing the manufactor and description metadata.
+   * @brief Initializes the device by creating NWB related attributes and
+   * writing the manufactor and description metadata.
    */
   void initialize();
 
@@ -42,7 +48,7 @@ class Device : public Container
    * @return The description of the device.
    */
   std::string getDescription() const;
-  
+
 private:
   /**
    * @brief The description of the device.

src/file/ElectrodeGroup.cpp

@@ -3,8 +3,15 @@
 // ElectrodeGroup
 
 /** Constructor */
-ElectrodeGroup::ElectrodeGroup(const std::string& path, std::shared_ptr<BaseIO> io, const std::string& description, const std::string& location, const Device& device)
-  : Container(path, io), description(description), location(location), device(device)
+ElectrodeGroup::ElectrodeGroup(const std::string& path,
+                               std::shared_ptr<BaseIO> io,
+                               const std::string& description,
+                               const std::string& location,
+                               const Device& device)
+    : Container(path, io)
+    , description(description)
+    , location(location)
+    , device(device)
 {
 }
 
@@ -16,7 +23,6 @@ void ElectrodeGroup::initialize()
   io->createCommonNWBAttributes(path, "core", "ElectrodeGroup", description);
   io->createAttribute(location, path, "location");
   io->createLink("/" + path + "/device", "/" + device.getPath());
-
 }
 
 // Getter for description

src/file/ElectrodeGroup.hpp

@@ -1,27 +1,34 @@
 #pragma once
 
 #include <string>
+
+#include "device/Device.hpp"
 #include "hdmf/base/Container.hpp"
 #include "io/BaseIO.hpp"
-#include "device/Device.hpp"
 
 using namespace AQNWBIO;
 
 /**
- * @brief The ElectrodeGroup class represents a physical grouping of electrodes, e.g. a shank of an array.
+ * @brief The ElectrodeGroup class represents a physical grouping of electrodes,
+ * e.g. a shank of an array.
  */
 class ElectrodeGroup : public Container
 {
 public:
   /**
-   * @brief Constructer.
+   * @brief Constructor.
    * @param path The location in the file of the electrode group.
    * @param io A shared pointer to the IO object.
    * @param description The description of the electrode group.
-   * @param location The location of electrode group within the subject e.g. brain region.
+   * @param location The location of electrode group within the subject e.g.
+   * brain region.
    * @param device The device associated with the electrode group.
    */
-  ElectrodeGroup(const std::string& path, std::shared_ptr<BaseIO> io, const std::string& description, const std::string& location, const Device& device);
+  ElectrodeGroup(const std::string& path,
+                 std::shared_ptr<BaseIO> io,
+                 const std::string& description,
+                 const std::string& location,
+                 const Device& device);
 
   /**
    * @brief Destructor.
@@ -30,8 +37,9 @@ class ElectrodeGroup : public Container
 
   /**
    * @brief Initializes the ElectrodeGroup object.
-   * 
-   * Initializes the ElectrodeGroup by creating NWB related attributes and linking to the Device object.
+   *
+   * Initializes the ElectrodeGroup by creating NWB related attributes and
+   * linking to the Device object.
    */
   void initialize();
 
@@ -56,16 +64,17 @@ class ElectrodeGroup : public Container
 private:
   /**
    * @brief The description of the electrode group.
-   */ 
+   */
   std::string description;
 
   /**
-   * @brief The location of electrode group within the subject e.g. brain region.
-   */ 
+   * @brief The location of electrode group within the subject e.g. brain
+   * region.
+   */
   std::string location;
 
   /**
    * @brief The device associated with the electrode group.
-   */ 
+   */
   Device device;
 };