Update ElectrodesTable type (#214)

* Update ElectrodesTable type

* Rename ElectrodeTable to ElectrodesTable

* Fix linter

* Update docs/pages/devdocs/registered_types.dox

---------

Co-authored-by: Steph Prince <[email protected]>

Author: oruebel

CMakeLists.txt

@@ -33,7 +33,7 @@ add_library(
     src/nwb/ecephys/ElectricalSeries.cpp
     src/nwb/ecephys/SpikeEventSeries.cpp
     src/nwb/file/ElectrodeGroup.cpp
-    src/nwb/file/ElectrodeTable.cpp
+    src/nwb/file/ElectrodesTable.cpp
     src/nwb/misc/AnnotationSeries.cpp
     src/nwb/hdmf/base/Container.cpp
     src/nwb/hdmf/base/Data.cpp

docs/pages/devdocs/read_design.dox

@@ -327,12 +327,12 @@
  * via the \ref AQNWB::NWB::VectorData::readData "VectorData::readData" method for reading.
  *
  * In some cases, the data type for `VectorData` may be predetermined in the schema. For example, the `location` column
- * of the \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable" requires string data. To simplify reading in such cases where
+ * of the \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable" requires string data. To simplify reading in such cases where
  * the data type is fixed, AqNWB defines \ref AQNWB::NWB::VectorDataTyped "VectorDataTyped<DTYPE>", which inherits from
  * \ref AQNWB::NWB::VectorData "VectorData". This class allows the data type to be specified at compile time via the class
  * template, enabling \ref AQNWB::NWB::VectorDataTyped "VectorDataTyped<DTYPE>::readData" to expose the data with the type
  * already set at compile time. When used in combination with the \ref DEFINE_REGISTERED_FIELD macro, this approach allows
- * \ref AQNWB::NWB::ElectrodeTable::readLocationColumn "ElectrodeTable::readLocationColumn" to return the data to the user
+ * \ref AQNWB::NWB::ElectrodesTable::readLocationColumn "ElectrodesTable::readLocationColumn" to return the data to the user
  * with the type already set. The same approach is also applied in the case of \ref AQNWB::NWB::Data "Data" and its derived
  * class \ref AQNWB::NWB::DataTyped "DataTyped".
  *

docs/pages/devdocs/registered_types.dox

@@ -91,7 +91,7 @@
  *
  * 6. Similarly, we use the \ref DEFINE_REGISTERED_FIELD macro to define getter methods for other 
  *    \ref AQNWB::NWB::RegisteredType "RegisteredType" objects that we own, such as a
- *     \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable" that owns 
+ *     \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable" that owns 
  *    predefined \ref AQNWB::NWB::VectorData "VectorData" columns:
  *    @code
  *    DEFINE_REGISTERED_FIELD(readGroupNameColumn, VectorData<std::string>, "group_name", "the name of the ElectrodeGroup")
@@ -273,7 +273,7 @@
  * the same as the `neurodata_type`. However, in some cases this may not be possible. 
  * In this case, we need to use \ref REGISTER_SUBCLASS_WITH_TYPENAME macro instead of 
  * \ref REGISTER_SUBCLASS. E.g. using
- * ``REGISTER_SUBCLASS_WITH_TYPENAME(ElectrodeTable, "core", "DynamicTable")``, 
+ * ``REGISTER_SUBCLASS_WITH_TYPENAME(ElectrodesTable, "core", "DynamicTable")``, 
  * the class will be registered in the registry,  under the ``core::ElectrodesTable`` key, 
  * but with "DynamicTable" as the typename value and the `ElectrodesTable.getTypeName` 
  * automatic override returning the indicated typename instead of the classname.
@@ -284,12 +284,12 @@
  *    An example is \ref AQNWB::NWB::VectorData "VectorData" which uses a template parameter to define the 
  *    data type of data that is manages. 
  * 2. A class for a modified type that does not have its  own `neurodata_type` 
- *    in the NWB schema. An example is `ElectrodesTable` in NWB <v2.7, which
+ *    in the NWB schema. An example is `ElectrodesTable` in NWB <v2.9, which
  *    did not have an assigned `neurodata_type`, but was implemented as a regular
- *    `DynamicTable`. To allow us to define a class `ElectrodeTable` to help with writing the table
- *    we can then use ``REGISTER_SUBCLASS_WITH_TYPENAME(ElectrodeTable, "core", "DynamicTable")``
- *    in the \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable" class. This ensures that the `neurodata_type` attribute is set
- *   correctly to `DynamicTable` on write instead of `ElectrodeTable`. 
+ *    `DynamicTable`. To allow us to define a class `ElectrodesTable` to help with writing the table
+ *    we can then use ``REGISTER_SUBCLASS_WITH_TYPENAME(ElectrodesTable, "core", "DynamicTable")``
+ *    in the \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable" class. This ensures that the `neurodata_type` attribute is set
+ *   correctly to `DynamicTable` on write instead of `ElectrodesTable`. 
  *
  * \subsection implement_templated_registered_type Templated RegisteredType Classes
  *
@@ -387,21 +387,21 @@
  *
  * The main limitaton of the  \ref REGISTER_SUBCLASS_WITH_TYPENAME approach is that on read, AqNWB 
  * will use the default class associated with the `neurodata_type`. E.g., in the case of 
- * the \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable" class, by default the regular 
+ * the \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable" class, by default the regular 
  * \ref AQNWB::NWB::DynamicTable "DynamicTable" class will be used since that is what 
  * the schema is indicating to use. Similarly, for \ref AQNWB::NWB::VectorData "VectorData" 
  * the default `VectorData<std::any>` will be used on read. To support reading using the
  * more specific types, we can use the \ref DEFINE_REGISTERED_FIELD macro to define
  * read methods that will return the approbriate type, e.g.:
  *
  * \code
- * DEFINE_REGISTERED_FIELD(readElectrodeTable,
- *                         ElectrodeTable,
- *                         ElectrodeTable::electrodeTablePath,
+ * DEFINE_REGISTERED_FIELD(readElectrodesTable,
+ *                         ElectrodesTable,
+ *                         ElectrodesTable::electrodeTablePath,
  *                         "table with the extracellular electrodes")
  * \endcode
  *
- * in \ref AQNWB::NWB::NWBFile "NWBFile" to read the \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable",
+ * in \ref AQNWB::NWB::NWBFile "NWBFile" to read the \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable",
  * or 
  *
  * \code
@@ -412,7 +412,7 @@
  *     "the name of the ElectrodeGroup this electrode is a part of")
  * \endcode
  *
- * in the \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable" to read the `group_name` column
+ * in the \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable" to read the `group_name` column
  * as `VectorData<std::string>` with the data type already specified as `std::string` at compile time.
  *
  * \section using_schematype_to_aqnwb Using the schematype_to_aqnwb.py Utility

docs/pages/userdocs/read.dox

@@ -32,8 +32,8 @@
  * When the path and type of objects is fixed in the schema (or we know them based on other conventions),
  * then we can read the types directly from the file. E.g., here we first read the 
  * \ref AQNWB::NWB::NWBFile "NWBFile" directly, which we know exists at the root "/" 
- * of the file. We then read the \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable"
- * via the predefined \ref AQNWB::NWB::NWBFile::readElectrodeTable "NWBFile::readElectrodeTable"
+ * of the file. We then read the \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable"
+ * via the predefined \ref AQNWB::NWB::NWBFile::readElectrodesTable "NWBFile::readElectrodesTable"
  * method. The advantage of this approach is that we do not need to manually specify paths
  * or object types. Similarly, when we read the `locations` columns, we do not need to
  * specify the name or the data type to use. 

docs/pages/userdocs/workflow.dox

@@ -15,7 +15,7 @@
  * 3. Create the \ref AQNWB::NWB::NWBFile "NWBFile" object used for managing and creating NWB
  *    file contents.
  * 4. Create the recording metadata stored in ``/general`` in NWB, e.g., the  
- *    \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable" object used for 
+ *    \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable" object used for 
  *    saving electrodes information. 
  * 5. Create the \ref AQNWB::NWB::Container "Container" objects (e.g.,
  *    \ref AQNWB::NWB::ElectricalSeries "ElectricalSeries") used for recording and add them
@@ -59,7 +59,7 @@
  *
  * \subsection create_recmeta 4. Create the recording metadata 
  * \subsubsection create_recmeta_ecephys Create the extracellular recording metadata
- * Next, construct the \ref AQNWB::NWB::ElectrodeTable "ElectrodeTable" object, 
+ * Next, construct the \ref AQNWB::NWB::ElectrodesTable "ElectrodesTable" object, 
  * using the `recordingArrays` as an input. Note that in many cases, you will be recording from 
  * all electrodes detected by the device and this `recordingArrays` structure will be the same as
  * is used to create the \ref AQNWB::NWB::ElectricalSeries "ElectricalSeries". However in some cases

src/nwb/NWBFile.cpp

@@ -178,8 +178,8 @@ Status NWBFile::createFileStructure(const std::string& identifierText,
 Status NWBFile::createElectrodesTable(
     std::vector<Types::ChannelVector> recordingArrays)
 {
-  std::unique_ptr<NWB::ElectrodeTable> electrodeTable =
-      std::make_unique<NWB::ElectrodeTable>(m_io);
+  std::unique_ptr<NWB::ElectrodesTable> electrodeTable =
+      std::make_unique<NWB::ElectrodesTable>(m_io);
   electrodeTable->initialize();
   for (const auto& channelVector : recordingArrays) {
     electrodeTable->addElectrodes(channelVector);
@@ -229,7 +229,7 @@ Status NWBFile::createElectricalSeries(
 
   // Setup electrode table if it was not yet created
   bool electrodeTableCreated =
-      m_io->objectExists(ElectrodeTable::electrodeTablePath);
+      m_io->objectExists(ElectrodesTable::electrodeTablePath);
   if (!electrodeTableCreated) {
     std::cerr << "NWBFile::createElectricalSeries requires an electrodes table "
                  "to be present"
@@ -282,7 +282,7 @@ Status NWBFile::createSpikeEventSeries(
 
   // Setup electrode table if it was not yet created
   bool electrodeTableCreated =
-      m_io->objectExists(ElectrodeTable::electrodeTablePath);
+      m_io->objectExists(ElectrodesTable::electrodeTablePath);
   if (!electrodeTableCreated) {
     std::cerr << "NWBFile::createElectricalSeries requires an electrodes table "
                  "to be present"

src/nwb/NWBFile.hpp

@@ -13,7 +13,7 @@
 #include "io/ReadIO.hpp"
 #include "nwb/RecordingContainers.hpp"
 #include "nwb/base/TimeSeries.hpp"
-#include "nwb/file/ElectrodeTable.hpp"
+#include "nwb/file/ElectrodesTable.hpp"
 #include "nwb/hdmf/base/Container.hpp"
 #include "spec/core.hpp"
 
@@ -31,7 +31,7 @@ namespace AQNWB::NWB
 class NWBFile : public Container
 {
 public:
-  // Register the ElectrodeTable as a subclass of Container
+  // Register the ElectrodesTable as a subclass of Container
   REGISTER_SUBCLASS(NWBFile, AQNWB::SPEC::CORE::namespaceName)
 
   /**
@@ -165,9 +165,9 @@ class NWBFile : public Container
                                 RecordingContainers* recordingContainers,
                                 std::vector<SizeType>& containerIndexes);
 
-  DEFINE_REGISTERED_FIELD(readElectrodeTable,
-                          ElectrodeTable,
-                          ElectrodeTable::electrodeTablePath,
+  DEFINE_REGISTERED_FIELD(readElectrodesTable,
+                          ElectrodesTable,
+                          ElectrodesTable::electrodeTablePath,
                           "table with the extracellular electrodes")
 
   DEFINE_ATTRIBUTE_FIELD(readNWBVersion,
@@ -244,9 +244,9 @@ class NWBFile : public Container
   inline const static std::string m_specificationsPath = "/specifications";
 
   /**
-   * @brief The ElectrodeTable for the file
+   * @brief The ElectrodesTable for the file
    */
-  std::unique_ptr<ElectrodeTable> m_electrodeTable;
+  std::unique_ptr<ElectrodesTable> m_electrodeTable;
 };
 
 }  // namespace AQNWB::NWB

src/nwb/ecephys/ElectricalSeries.cpp

@@ -1,7 +1,7 @@
 #include "nwb/ecephys/ElectricalSeries.hpp"
 
 #include "Utils.hpp"
-#include "nwb/file/ElectrodeTable.hpp"
+#include "nwb/file/ElectrodesTable.hpp"
 
 using namespace AQNWB::NWB;
 
@@ -39,7 +39,7 @@ Status ElectricalSeries::initialize(const IO::ArrayDataSetConfig& dataConfig,
 
   // get the number of electrodes from the electrode table
   std::string idPath =
-      AQNWB::mergePaths(ElectrodeTable::electrodeTablePath, "id");
+      AQNWB::mergePaths(ElectrodesTable::electrodeTablePath, "id");
   std::vector<SizeType> elecTableDsetSize = m_io->getStorageObjectShape(idPath);
   SizeType numElectrodes = elecTableDsetSize[0];
 
@@ -94,7 +94,7 @@ Status ElectricalSeries::initialize(const IO::ArrayDataSetConfig& dataConfig,
   m_io->createAttribute("the electrodes that generated this electrical series",
                         electrodesPath,
                         "description");
-  m_io->createReferenceAttribute(ElectrodeTable::electrodeTablePath,
+  m_io->createReferenceAttribute(ElectrodesTable::electrodeTablePath,
                                  AQNWB::mergePaths(getPath(), "electrodes"),
                                  "table");
 

src/nwb/ecephys/ElectricalSeries.hpp

@@ -7,7 +7,7 @@
 #include "io/BaseIO.hpp"
 #include "io/ReadIO.hpp"
 #include "nwb/base/TimeSeries.hpp"
-#include "nwb/file/ElectrodeTable.hpp"
+#include "nwb/file/ElectrodesTable.hpp"
 #include "spec/core.hpp"
 
 namespace AQNWB::NWB
@@ -112,7 +112,7 @@ class ElectricalSeries : public TimeSeries
 
   DEFINE_REFERENCED_REGISTERED_FIELD(
       readElectrodesTable,
-      ElectrodeTable,
+      ElectrodesTable,
       "electrodes/table",
       The electrodes table retrieved from the object referenced in the 
       `electrodes / table` attribute.)

src/nwb/file/ElectrodeTable.cpp renamed to src/nwb/file/ElectrodesTable.cpp

@@ -1,16 +1,16 @@
-#include "nwb/file/ElectrodeTable.hpp"
+#include "nwb/file/ElectrodesTable.hpp"
 
 #include "Channel.hpp"
 #include "Utils.hpp"
 
 using namespace AQNWB::NWB;
 
-// ElectrodeTable
+// ElectrodesTable
 // Initialize the static registered_ member to trigger registration
-REGISTER_SUBCLASS_IMPL(ElectrodeTable)
+REGISTER_SUBCLASS_IMPL(ElectrodesTable)
 
 /** Constructor */
-ElectrodeTable::ElectrodeTable(std::shared_ptr<IO::BaseIO> io)
+ElectrodesTable::ElectrodesTable(std::shared_ptr<IO::BaseIO> io)
     : DynamicTable(electrodeTablePath,  // use the electrodeTablePath
                    io)
     , m_electrodeDataset(std::make_unique<ElementIdentifiers>(
@@ -22,8 +22,8 @@ ElectrodeTable::ElectrodeTable(std::shared_ptr<IO::BaseIO> io)
 {
 }
 
-ElectrodeTable::ElectrodeTable(const std::string& path,
-                               std::shared_ptr<IO::BaseIO> io)
+ElectrodesTable::ElectrodesTable(const std::string& path,
+                                 std::shared_ptr<IO::BaseIO> io)
     : DynamicTable(electrodeTablePath, io)
     , m_electrodeDataset(std::make_unique<ElementIdentifiers>(
           AQNWB::mergePaths(electrodeTablePath, "id"), io))
@@ -32,14 +32,14 @@ ElectrodeTable::ElectrodeTable(const std::string& path,
     , m_locationsDataset(std::make_unique<VectorData>(
           AQNWB::mergePaths(electrodeTablePath, "location"), io))
 {
-  assert(path == this->electrodeTablePath && "ElectrodeTable object is required to appear at /general/extracellular_ephys/electrodes");
+  assert(path == this->electrodeTablePath && "ElectrodesTable object is required to appear at /general/extracellular_ephys/electrodes");
 }
 
 /** Destructor */
-ElectrodeTable::~ElectrodeTable() {}
+ElectrodesTable::~ElectrodesTable() {}
 
 /** Initialization function*/
-Status ElectrodeTable::initialize(const std::string& description)
+Status ElectrodesTable::initialize(const std::string& description)
 {
   // create group
   DynamicTable::initialize(description);
@@ -64,7 +64,7 @@ Status ElectrodeTable::initialize(const std::string& description)
   return electrodeStatus && groupNameStatus && locationStatus;
 }
 
-void ElectrodeTable::addElectrodes(std::vector<Channel> channelsInput)
+void ElectrodesTable::addElectrodes(std::vector<Channel> channelsInput)
 {
   // create datasets
   for (const auto& ch : channelsInput) {
@@ -76,7 +76,7 @@ void ElectrodeTable::addElectrodes(std::vector<Channel> channelsInput)
   }
 }
 
-Status ElectrodeTable::finalize()
+Status ElectrodesTable::finalize()
 {
   Status rowIdStatus = setRowIDs(m_electrodeDataset, m_electrodeNumbers);
   Status locationColStatus = addColumn(m_locationsDataset, m_locationNames);