Add read tests for TimeSeries , VectorData, Data, ElementIdentifers, Device`

src/io/BaseIO.cpp

@@ -43,45 +43,12 @@ BaseIO::~BaseIO() {}
 
 Status BaseIO::createCommonNWBAttributes(const std::string& path,
                                          const std::string& objectNamespace,
-                                         const std::string& neurodataType,
-                                         const std::string& description)
+                                         const std::string& neurodataType)
 {
   createAttribute(objectNamespace, path, "namespace");
   createAttribute(generateUuid(), path, "object_id");
   if (neurodataType != "")
     createAttribute(neurodataType, path, "neurodata_type");
-  if (description != "")
-    createAttribute(description, path, "description");
-  return Status::Success;
-}
-
-Status BaseIO::createDataAttributes(const std::string& path,
-                                    const float& conversion,
-                                    const float& resolution,
-                                    const std::string& unit)
-{
-  createAttribute(BaseDataType::F32,
-                  &conversion,
-                  AQNWB::mergePaths(path, "data"),
-                  "conversion");
-  createAttribute(BaseDataType::F32,
-                  &resolution,
-                  AQNWB::mergePaths(path, "data"),
-                  "resolution");
-  createAttribute(unit, path + "/data", "unit");
-
-  return Status::Success;
-}
-
-Status BaseIO::createTimestampsAttributes(const std::string& path)
-{
-  int interval = 1;
-  createAttribute(BaseDataType::I32,
-                  static_cast<const void*>(&interval),
-                  path + "/timestamps",
-                  "interval");
-  createAttribute("seconds", path + "/timestamps", "unit");
-
   return Status::Success;
 }
 

src/io/BaseIO.hpp

@@ -446,34 +446,11 @@ class BaseIO
    * @param path The location of the object in the file.
    * @param objectNamespace The namespace of the object.
    * @param neurodataType The neurodata type of the object.
-   * @param description The description of the object (default is empty).
    * @return The status of the operation.
    */
   Status createCommonNWBAttributes(const std::string& path,
                                    const std::string& objectNamespace,
-                                   const std::string& neurodataType = "",
-                                   const std::string& description = "");
-
-  /**
-   * @brief Convenience function for creating data related attributes.
-   * @param path The location of the object in the file.
-   * @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.
-   * @param unit Base unit of measurement for working with the data.
-   * @return The status of the operation.
-   */
-  Status createDataAttributes(const std::string& path,
-                              const float& conversion,
-                              const float& resolution,
-                              const std::string& unit);
-
-  /**
-   * @brief Convenience function for creating timestamp related attributes.
-   * @param path The location of the object in the file.
-   * @return The status of the operation.
-   */
-  Status createTimestampsAttributes(const std::string& path);
+                                   const std::string& neurodataType = "");
 
   /**
    * @brief Returns true if the file is open.

src/io/ReadIO.hpp

@@ -62,6 +62,9 @@ class DataBlockGeneric
    */
   std::type_index typeIndex = typeid(void);
 
+  /** \brief The base data type for the data block */
+  IO::BaseDataType baseDataType;
+
   /**
    * \brief Default constructor
    */

src/io/hdf5/HDF5IO.cpp

@@ -332,6 +332,9 @@ AQNWB::IO::DataBlockGeneric HDF5IO::readAttribute(
     numElements *= v;
   }
 
+  // Set the base data type for the attribute
+  result.baseDataType = getBaseDataType(dataType);
+
   // Read the attribute into a vector of the appropriate type
   if (dataType.getClass() == H5T_STRING) {
     if (dataType.isVariableStr()) {
@@ -517,6 +520,7 @@ AQNWB::IO::DataBlockGeneric HDF5IO::readDataset(
 
   // Read the dataset into a vector of the appropriate type
   H5::DataType dataType = dataset.getDataType();
+  result.baseDataType = getBaseDataType(dataType);
   if (dataType.getClass() == H5T_STRING) {
     // Use readStringDataHelper to read string data
     result.data =
@@ -1127,6 +1131,49 @@ H5::DataType HDF5IO::getNativeType(IO::BaseDataType type)
   }
 }
 
+AQNWB::IO::BaseDataType HDF5IO::getBaseDataType(const H5::DataType& nativeType)
+{
+  if (nativeType == H5::PredType::NATIVE_INT8) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_I8);
+  } else if (nativeType == H5::PredType::NATIVE_INT16) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_I16);
+  } else if (nativeType == H5::PredType::NATIVE_INT32) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_I32);
+  } else if (nativeType == H5::PredType::NATIVE_INT64) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_I64);
+  } else if (nativeType == H5::PredType::NATIVE_UINT8) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_U8);
+  } else if (nativeType == H5::PredType::NATIVE_UINT16) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_U16);
+  } else if (nativeType == H5::PredType::NATIVE_UINT32) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_U32);
+  } else if (nativeType == H5::PredType::NATIVE_UINT64) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_U64);
+  } else if (nativeType == H5::PredType::NATIVE_FLOAT) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_F32);
+  } else if (nativeType == H5::PredType::NATIVE_DOUBLE) {
+    return IO::BaseDataType(IO::BaseDataType::Type::T_F64);
+  } else if (nativeType.getClass() == H5T_STRING) {
+    if (nativeType.isVariableStr()) {
+      return IO::BaseDataType(IO::BaseDataType::Type::V_STR);
+    } else {
+      // Fixed length string: get the size
+      size_t size = nativeType.getSize();
+      return IO::BaseDataType(IO::BaseDataType::Type::T_STR, size);
+    }
+  } else if (nativeType.getClass() == H5T_ARRAY) {
+    // Array type: get the base type and size
+    hid_t nativeTypeId = nativeType.getId();
+    H5::ArrayType arrayType(nativeTypeId);
+    H5::DataType baseType = arrayType.getSuper();
+    hsize_t size = arrayType.getArrayNDims();
+    return IO::BaseDataType(getBaseDataType(baseType).type, size);
+  } else {
+    // Default case: return a 32-bit integer type
+    return IO::BaseDataType(IO::BaseDataType::Type::T_I32);
+  }
+}
+
 H5::DataType HDF5IO::getH5Type(IO::BaseDataType type)
 {
   H5::DataType baseType;
@@ -1177,3 +1224,46 @@ H5::DataType HDF5IO::getH5Type(IO::BaseDataType type)
   } else
     return baseType;
 }
+
+/*
+IO::BaseDataType HDF5IO::getBaseType(const H5::DataType &nativeType)
+{
+    if (nativeType == H5::PredType::NATIVE_INT8) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_I8);
+    } else if (nativeType == H5::PredType::NATIVE_INT16) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_I16);
+    } else if (nativeType == H5::PredType::NATIVE_INT32) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_I32);
+    } else if (nativeType == H5::PredType::NATIVE_INT64) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_I64);
+    } else if (nativeType == H5::PredType::NATIVE_UINT8) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_U8);
+    } else if (nativeType == H5::PredType::NATIVE_UINT16) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_U16);
+    } else if (nativeType == H5::PredType::NATIVE_UINT32) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_U32);
+    } else if (nativeType == H5::PredType::NATIVE_UINT64) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_U64);
+    } else if (nativeType == H5::PredType::NATIVE_FLOAT) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_F32);
+    } else if (nativeType == H5::PredType::NATIVE_DOUBLE) {
+        return IO::BaseDataType(IO::BaseDataType::Type::T_F64);
+    } else if (nativeType.getClass() == H5T_STRING) {
+        if (nativeType.isVariableStr()) {
+            return IO::BaseDataType(IO::BaseDataType::Type::V_STR);
+        } else {
+            // Fixed length string: get the size
+            size_t size = nativeType.getSize();
+            return IO::BaseDataType(IO::BaseDataType::Type::T_STR, size);
+        }
+    } else if (nativeType.getClass() == H5T_ARRAY) {
+        // Array type: get the base type and size
+        H5::ArrayType arrayType(nativeType);
+        H5::DataType baseType = arrayType.getSuper();
+        hsize_t size = arrayType.getArrayNDims();
+        return IO::BaseDataType(getBaseType(baseType).type, size);
+    } else {
+        // Default case: return a 32-bit integer type
+        return IO::BaseDataType(IO::BaseDataType::Type::T_I32);
+    }
+}*/

src/io/hdf5/HDF5IO.hpp

@@ -328,6 +328,16 @@ class HDF5IO : public BaseIO
    */
   static H5::DataType getNativeType(IO::BaseDataType type);
 
+  /**
+   * @brief Returns the BaseDataType for a given HDF5 native data type
+   *
+   * This function implements the opposite mapping of getNativeType.
+   *
+   * @param nativeType The native data type.
+   * @return The corresponding BaseDataType
+   */
+  static IO::BaseDataType getBaseDataType(const H5::DataType& nativeType);
+
   /**
    * @brief Returns the HDF5 data type for a given base data type.
    *

src/nwb/NWBFile.cpp

@@ -70,7 +70,7 @@ Status NWBFile::createFileStructure(const std::string& identifierText,
     return Status::Failure;
   }
   m_io->createCommonNWBAttributes(
-      m_path, this->getNamespace(), this->getTypeName(), "");
+      m_path, this->getNamespace(), this->getTypeName());
   m_io->createAttribute(AQNWB::SPEC::CORE::version, "/", "nwb_version");
   m_io->createGroup("/acquisition");
   m_io->createGroup("/analysis");

src/nwb/RegisteredType.hpp

@@ -7,7 +7,9 @@
 #include <unordered_set>
 
 #include "Types.hpp"
+#include "Utils.hpp"
 #include "io/BaseIO.hpp"
+#include "io/ReadIO.hpp"
 
 namespace AQNWB
 {