Add swmr mode

README.md

@@ -22,7 +22,7 @@ Below is a high-level overview of the project structure and capabilities we are
 # Requirements
 * A C++17-compliant compiler
 * CMake `>= 3.15`
-* HDF5
+* HDF5 `>= 1.10`
 * Boost
 * Additional requirements for building the documentation (optional)
     * Doxygen

src/BaseIO.cpp

@@ -49,6 +49,11 @@ 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/BaseIO.hpp

@@ -238,6 +238,27 @@ class BaseIO
   virtual Status createReferenceDataSet(
       const std::string& path, const std::vector<std::string>& references) = 0;
 
+  /**
+   * @brief Starts the recording process.
+   * @return The status of the operation.
+   */
+  virtual Status startRecording() = 0;
+
+  /**
+   * @brief Stops the recording process.
+   * @return The status of the operation.
+   */
+  virtual Status stopRecording() = 0;
+
+  /**
+   * @brief Returns true if the file is in a mode where objects can
+   * be added or deleted. Note, this does not apply to the modification
+   * of raw data on already existing objects. Derived classes should
+   * 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();
+
   /**
    * @brief Creates an extendable dataset with a given base data type, size,
    * chunking, and path.

src/hdf5/HDF5IO.cpp

@@ -7,6 +7,7 @@
 #include "HDF5IO.hpp"
 
 #include <H5Cpp.h>
+#include <H5Fpublic.h>
 
 #include "Utils.hpp"
 
@@ -17,8 +18,9 @@ using namespace AQNWB::HDF5;
 
 HDF5IO::HDF5IO() {}
 
-HDF5IO::HDF5IO(const std::string& fileName)
+HDF5IO::HDF5IO(const std::string& fileName, const bool disableSWMRMode)
     : filename(fileName)
+    , disableSWMRMode(disableSWMRMode)
 {
 }
 
@@ -48,15 +50,16 @@ Status HDF5IO::open(bool newfile)
   if (opened)
     return Status::Failure;
 
-  FileAccPropList props = FileAccPropList::DEFAULT;
+  FileAccPropList fapl = FileAccPropList::DEFAULT;
+  H5Pset_libver_bounds(fapl.getId(), H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
 
   if (newfile)
     accFlags = H5F_ACC_TRUNC;
   else
     accFlags = H5F_ACC_RDWR;
 
   file = std::make_unique<H5::H5File>(
-      getFileName(), accFlags, FileCreatPropList::DEFAULT, props);
+      getFileName(), accFlags, FileCreatPropList::DEFAULT, fapl);
   opened = true;
 
   return Status::Success;
@@ -298,6 +301,9 @@ Status HDF5IO::createGroupIfDoesNotExist(const std::string& path)
 /** Creates a link to another location in the file */
 Status HDF5IO::createLink(const std::string& path, const std::string& reference)
 {
+  if (!opened)
+    return Status::Failure;
+
   herr_t error = H5Lcreate_soft(reference.c_str(),
                                 file->getLocId(),
                                 path.c_str(),
@@ -310,6 +316,9 @@ Status HDF5IO::createLink(const std::string& path, const std::string& reference)
 Status HDF5IO::createReferenceDataSet(
     const std::string& path, const std::vector<std::string>& references)
 {
+  if (!opened)
+    return Status::Failure;
+
   const hsize_t size = references.size();
 
   hobj_ref_t* rdata = new hobj_ref_t[size * sizeof(hobj_ref_t)];
@@ -377,6 +386,49 @@ Status HDF5IO::createStringDataSet(const std::string& path,
   return Status::Success;
 }
 
+Status HDF5IO::startRecording()
+{
+  if (!opened)
+    return Status::Failure;
+
+  if (!disableSWMRMode) {
+    herr_t status = H5Fstart_swmr_write(this->file->getId());
+    return checkStatus(status);
+  }
+  return Status::Success;
+}
+
+Status HDF5IO::stopRecording()
+{
+  // if SWMR mode is disabled, stopping the recording will leave the file open
+  if (!disableSWMRMode) {
+    close();
+  }
+  return Status::Success;
+}
+
+bool HDF5IO::canModifyObjects()
+{
+  if (!opened)
+    return false;
+
+  // Get the file access intent
+  unsigned int intent;
+  herr_t status = H5Fget_intent(this->file->getId(), &intent);
+  if (status < 0) {
+    return false;  // We could not access the file so modifying objects is not
+                   // going to work
+  }
+
+  // Check if SWMR mode is enabled
+  if (intent & (H5F_ACC_SWMR_READ | H5F_ACC_SWMR_WRITE)) {
+    return false;  // File is in SWMR mode
+  } else {
+    return true;  // File is not in SWMR mode
+  }
+  return true;
+}
+
 std::unique_ptr<AQNWB::BaseRecordingData> HDF5IO::getDataSet(
     const std::string& path)
 {

src/hdf5/HDF5IO.hpp

@@ -37,7 +37,7 @@ class HDF5IO : public BaseIO
    * @brief Constructor for the HDF5IO class that takes a file name as input.
    * @param fileName The name of the HDF5 file.
    */
-  HDF5IO(const std::string& fileName);
+  HDF5IO(const std::string& fileName, const bool disableSWMRMode = false);
 
   /**
    * @brief Destructor for the HDF5IO class.
@@ -176,6 +176,26 @@ class HDF5IO : public BaseIO
       const std::string& path,
       const std::vector<std::string>& references) override;
 
+  /**
+   * @brief Start SWMR write to start recording process
+   * @return The status of the start recording operation.
+   */
+  Status startRecording() override;
+
+  /**
+   * @brief Stops the recording process.
+   * @return The status of the stop recording operation.
+   */
+  Status stopRecording() override;
+
+  /**
+   * @brief Checks whether the file is in a mode where objects
+   * can be added or deleted. Note, this does not apply to the modification
+   * of raw data on already existing objects.
+   * @return Whether objects can be modified.
+   */
+  bool canModifyObjects() override;
+
   /**
    * @brief Creates an extendable dataset with a given base data type, size,
    * chunking, and path.
@@ -232,6 +252,7 @@ class HDF5IO : public BaseIO
 
 private:
   std::unique_ptr<H5::H5File> file;
+  bool disableSWMRMode;
 };
 
 /**

src/nwb/NWBFile.cpp

@@ -30,24 +30,28 @@ NWBFile::NWBFile(const std::string& idText, std::shared_ptr<BaseIO> io)
 
 NWBFile::~NWBFile() {}
 
-void NWBFile::initialize()
+Status NWBFile::initialize()
 {
   if (std::filesystem::exists(io->getFileName())) {
-    io->open(false);
+    return io->open(false);
   } else {
     io->open(true);
-    createFileStructure();
+    return createFileStructure();
   }
 }
 
-void NWBFile::finalize()
+Status NWBFile::finalize()
 {
   recordingContainers.reset();
-  io->close();
+  return io->close();
 }
 
 Status NWBFile::createFileStructure()
 {
+  if (!io->canModifyObjects()) {
+    return Status::Failure;
+  }
+
   io->createCommonNWBAttributes("/", "core", "NWBFile", "");
   io->createAttribute(NWBVersion, "/", "nwb_version");
 
@@ -82,6 +86,10 @@ Status NWBFile::createElectricalSeries(
     std::vector<Types::ChannelVector> recordingArrays,
     const BaseDataType& dataType)
 {
+  if (!io->canModifyObjects()) {
+    return Status::Failure;
+  }
+
   // store all recorded data in the acquisition group
   std::string rootPath = "/acquisition/";
 
@@ -128,7 +136,15 @@ Status NWBFile::createElectricalSeries(
   return Status::Success;
 }
 
-void NWBFile::stopRecording() {}
+Status NWBFile::startRecording()
+{
+  return io->startRecording();
+}
+
+void NWBFile::stopRecording()
+{
+  io->stopRecording();
+}
 
 void NWBFile::cacheSpecifications(const std::string& specPath,
                                   const std::string& versionNumber)

src/nwb/NWBFile.hpp

@@ -46,19 +46,22 @@ class NWBFile
    * @brief Initializes the NWB file by opening and setting up the file
    * structure.
    */
-  void initialize();
+  Status initialize();
 
   /**
    * @brief Finalizes the NWB file by closing it.
    */
-  void finalize();
+  Status finalize();
 
   /**
    * @brief Create ElectricalSeries objects to record data into.
    * Created objects are stored in recordingContainers.
+   * Note, this function will fail if the file is in a mode where
+   * new objects cannot be added, which can be checked via
+   * nwbfile.io->canModifyObjects()
    * @param recordingArrays vector of ChannelVector indicating the electrodes to
    *                        record from. A separate ElectricalSeries will be
-   *                        created for each ChannelVector
+   *                        created for each ChannelVector.
    * @param dataType The data type of the elements in the data block.
    * @return Status The status of the object creation operation.
    */
@@ -67,7 +70,12 @@ class NWBFile
       const BaseDataType& dataType = BaseDataType::I16);
 
   /**
-   * @brief Closes the relevant datasets.
+   * @brief Starts the recording.
+   */
+  Status startRecording();
+
+  /**
+   * @brief Stops the recording.
    */
   void stopRecording();
 
@@ -95,6 +103,9 @@ class NWBFile
 protected:
   /**
    * @brief Creates the default file structure.
+   * Note, this function will fail if the file is in a mode where
+   * new objects cannot be added, which can be checked via
+   * nwbfile.io->canModifyObjects()
    * @return Status The status of the file structure creation.
    */
   Status createFileStructure();

src/nwb/NWBRecording.cpp

@@ -30,13 +30,15 @@ Status NWBRecording::openFile(const std::string& rootFolder,
                                            createIO(IOType, filename));
   nwbfile->initialize();
 
+  // create the datasets
+  nwbfile->createElectricalSeries(recordingArrays);
+
   // start the new recording
-  return nwbfile->createElectricalSeries(recordingArrays);
+  return nwbfile->startRecording();
 }
 
 void NWBRecording::closeFile()
 {
-  nwbfile->stopRecording();
   nwbfile->finalize();
 }
 

tests/CMakeLists.txt

@@ -27,6 +27,16 @@ target_compile_features(aq-nwb_test PRIVATE cxx_std_17)
 
 catch_discover_tests(aq-nwb_test)
 
+# ---- Custom Executable ----
+
+add_executable(reader_executable
+    reader.cpp)
+target_link_libraries(
+    reader_executable PRIVATE
+    aq-nwb_lib
+)
+target_compile_features(reader_executable PRIVATE cxx_std_17)
+
 # ---- End-of-file commands ----
 
 add_folders(aq-nwbTests)