Merge branch 'add_read' into add_container_read

NeurodataWithoutBorders · Oct 22, 2024 · 415926c · 415926c
2 parents 423f3d7 + 69df3e0
commit 415926c
Show file tree

Hide file tree

Showing 5 changed files with 10 additions and 22 deletions.
diff --git a/src/io/ReadIO.hpp b/src/io/ReadIO.hpp
@@ -170,23 +170,21 @@ class DataBlock
 /// Helper struct to check if a StorageObjectType is allowed. Used in static
 /// assert.
 template<StorageObjectType T>
-struct is_allowed_storage_object_type : std::false_type
+struct isAllowedStorageObjectType : std::false_type
 {
 };
 
 /// Helper struct to check if a StorageObjectType is allowed. Used in static
 /// assert.
 template<>
-struct is_allowed_storage_object_type<StorageObjectType::Dataset>
-    : std::true_type
+struct isAllowedStorageObjectType<StorageObjectType::Dataset> : std::true_type
 {
 };
 
 /// Helper struct to check if a StorageObjectType is allowed. Used in static
 /// assert.
 template<>
-struct is_allowed_storage_object_type<StorageObjectType::Attribute>
-    : std::true_type
+struct isAllowedStorageObjectType<StorageObjectType::Attribute> : std::true_type
 {
 };
 
@@ -213,7 +211,7 @@ class ReadDataWrapper
    * slicing.
    */
   template<StorageObjectType U>
-  struct is_dataset
+  struct isDataset
       : std::integral_constant<bool, (U == StorageObjectType::Dataset)>
   {
   };
@@ -224,7 +222,7 @@ class ReadDataWrapper
    *  StorageObjectType::Attribute but not for other types, e.g., Group or
    * Undefined.
    */
-  static_assert(is_allowed_storage_object_type<OTYPE>::value,
+  static_assert(isAllowedStorageObjectType<OTYPE>::value,
                 "StorageObjectType not allowed for ReadDataWrapper");
 
   // Actual definition of the class
@@ -340,7 +338,7 @@ class ReadDataWrapper
    * @return An DataBlockGeneric structure containing the data and shape.
    */
   template<StorageObjectType U = OTYPE,
-           typename std::enable_if<is_dataset<U>::value, int>::type = 0>
+           typename std::enable_if<isDataset<U>::value, int>::type = 0>
   inline DataBlockGeneric valuesGeneric(
       const std::vector<SizeType>& start,
       const std::vector<SizeType>& count = {},
@@ -397,7 +395,7 @@ class ReadDataWrapper
    */
   template<typename T = VTYPE,
            StorageObjectType U = OTYPE,
-           typename std::enable_if<is_dataset<U>::value, int>::type = 0>
+           typename std::enable_if<isDataset<U>::value, int>::type = 0>
   inline DataBlock<VTYPE> values(const std::vector<SizeType>& start,
                                  const std::vector<SizeType>& count = {},
                                  const std::vector<SizeType>& stride = {},

diff --git a/src/io/hdf5/HDF5IO.hpp b/src/io/hdf5/HDF5IO.hpp
@@ -339,7 +339,6 @@ class HDF5IO : public BaseIO
 
 private:
   /**
-<<<<<<< HEAD:src/io/hdf5/HDF5IO.hpp
    * @brief Reads data from an HDF5 dataset or attribute into a vector of the
    * appropriate type.
    *

diff --git a/src/nwb/NWBFile.cpp b/src/nwb/NWBFile.cpp
@@ -147,16 +147,7 @@ Status NWBFile::createElectricalSeries(
         AQNWB::mergePaths(acquisitionPath, recordingName);
 
     // Check if device exists for groupName, create device and electrode group
-    // if not
-    if (!m_io->objectExists(devicePath)) {
-      Device device = Device(devicePath, m_io);
-      device.initialize("description", "unknown");
-
-      ElectrodeGroup elecGroup = ElectrodeGroup(electrodePath, m_io);
-      elecGroup.initialize("description", "unknown", device);
-    }
-
-    // Setup electrical series datasets
+    // if it does not
     if (!m_io->objectExists(devicePath)) {
       Device device = Device(devicePath, m_io);
       device.initialize("description", "unknown");

diff --git a/src/nwb/ecephys/ElectricalSeries.cpp b/src/nwb/ecephys/ElectricalSeries.cpp
@@ -65,6 +65,7 @@ void ElectricalSeries::initialize(const IO::BaseDataType& dataType,
   m_io->createAttribute(IO::BaseDataType::I32,
                         &axis_value,
                         AQNWB::mergePaths(getPath(), "channel_conversion"),
+                        this->getPath() + "/channel_conversion",
                         "axis",
                         1);
 

diff --git a/src/nwb/hdmf/base/Data.hpp b/src/nwb/hdmf/base/Data.hpp
@@ -47,7 +47,6 @@ class Data : public RegisteredType
    */
   inline bool isInitialized() { return m_dataset != nullptr; }
 
-  std::unique_ptr<IO::BaseRecordingData>
-      m_dataset;  // TODO We may not want this here if we need Data for read
+  std::unique_ptr<IO::BaseRecordingData> m_dataset;
 };
 }  // namespace AQNWB::NWB