From 98d3b95607d6059fd9c0f1ce50e8d1475bd2b9ea Mon Sep 17 00:00:00 2001 From: Oliver Ruebel Date: Fri, 2 Aug 2024 00:20:47 -0700 Subject: [PATCH 1/3] Fix #50 Update docs to fix Doxygen build warnings --- README.md | 6 +++--- src/BaseIO.hpp | 1 - src/nwb/NWBFile.hpp | 6 ++++-- src/nwb/NWBRecording.hpp | 4 +++- src/nwb/base/TimeSeries.hpp | 13 +++++++++++++ src/nwb/ecephys/ElectricalSeries.hpp | 17 +++++++++++++++-- src/nwb/file/ElectrodeTable.hpp | 1 - src/nwb/hdmf/table/DynamicTable.hpp | 1 - 8 files changed, 38 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 42de8837..43e80e7b 100644 --- a/README.md +++ b/README.md @@ -41,7 +41,7 @@ multi-configuration generator: cmake --install build --config Release ``` -# Developing +## Developing Build system targets that are only useful for developers of this project are hidden if the `aq-nwb_DEVELOPER_MODE` option is disabled. Enabling this @@ -78,7 +78,7 @@ cmake --build --preset=dev --target= # Code of Conduct -This project and everyone participating in it is govered by our [code of conduct guidelines](./.github/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. +This project and everyone participating in it is govered by our [code of conduct guidelines](https://github.com/NeurodataWithoutBorders/aqnwb/blob/main/.github/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. # LICENSE @@ -132,4 +132,4 @@ of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative -works, and perform publicly and display publicly, and to permit others to do so. \ No newline at end of file +works, and perform publicly and display publicly, and to permit others to do so. diff --git a/src/BaseIO.hpp b/src/BaseIO.hpp index 80a72390..14ed1c76 100644 --- a/src/BaseIO.hpp +++ b/src/BaseIO.hpp @@ -291,7 +291,6 @@ class BaseIO /** * @brief Convenience function for creating timestamp related attributes. * @param path The location of the object in the file. - * @param interval Value is '1' * @return The status of the operation. */ Status createTimestampsAttributes(const std::string& path); diff --git a/src/nwb/NWBFile.hpp b/src/nwb/NWBFile.hpp index 31577b4e..8c7bece1 100644 --- a/src/nwb/NWBFile.hpp +++ b/src/nwb/NWBFile.hpp @@ -56,6 +56,9 @@ class NWBFile /** * @brief Create ElectricalSeries objects to record data into. * Created objects are stored in recordingContainers. + * @param recordingArrays vector of ChannelVector indicating the electrodes to + * record from. A seperate ElectricalSeries will be + * 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. */ @@ -84,8 +87,7 @@ class NWBFile const std::string HDMFExperimentalVersion = "0.5.0"; /** - * @brief Gets the TimeSeries object from the recording containers - * @param containerName The name of the timeseries group. + * @brief Gets the TimeSeries object from the recordingContainers * @param timeseriesInd The index of the timeseries dataset within the group. */ TimeSeries* getTimeSeries(const SizeType& timeseriesInd); diff --git a/src/nwb/NWBRecording.hpp b/src/nwb/NWBRecording.hpp index 94238933..a81f3d22 100644 --- a/src/nwb/NWBRecording.hpp +++ b/src/nwb/NWBRecording.hpp @@ -38,7 +38,9 @@ class NWBRecording * @param baseName The base name of the file (will be appended with * experiment number). * @param experimentNumber The experiment number. - * @param recordingNumber The recording number. + * @param recordingArrays ChannelVector objets indicating the electrodes to use for + * ElectricalSeries recordings + * @param IOType Type of backend IO to use */ Status openFile(const std::string& rootFolder, const std::string& baseName, diff --git a/src/nwb/base/TimeSeries.hpp b/src/nwb/base/TimeSeries.hpp index 3bd08793..e4411adf 100644 --- a/src/nwb/base/TimeSeries.hpp +++ b/src/nwb/base/TimeSeries.hpp @@ -17,8 +17,21 @@ class TimeSeries : public Container * @brief Constructor. * @param path The location of the TimeSeries in the file. * @param io A shared pointer to the IO object. + * @param dataType The data type to use for storing the recorded voltage signal + * @param unit Unit for the electrical signal. Must be "volts" * @param description The description of the TimeSeries. * @param comments Human-readable comments about the TimeSeries + * @param dsetSize Intial size of the main dataset. This must be a vector with two + * elements. The first element specifies the lenght in time and + * the second element must be equal to the lenght of channelVector + * @param chunkSize Chunk size to use. The number of elements must be two to + * specify the size of a chunk in the time and electrode dimension + * @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, stored + * in the specified by unit + * @param offset Scalar to add to the data after scaling by ‘conversion’ to finalize + * its coercion to the specified ‘unit' */ TimeSeries(const std::string& path, std::shared_ptr io, diff --git a/src/nwb/ecephys/ElectricalSeries.hpp b/src/nwb/ecephys/ElectricalSeries.hpp index cfc52c39..2083612f 100644 --- a/src/nwb/ecephys/ElectricalSeries.hpp +++ b/src/nwb/ecephys/ElectricalSeries.hpp @@ -18,9 +18,22 @@ class ElectricalSeries : public TimeSeries * @brief Constructor. * @param path The location of the ElectricalSeries in the file. * @param io A shared pointer to the IO object. + * @param dataType The data type to use for storing the recorded voltage signal + * @param channelVector The electrodes to use for recording + * @param electrodesTablePath Path to the electrodes table + * @param unit Unit for the electrical signal. Must be "volts". * @param description The description of the TimeSeries. - * @param electrodesTablePath Location of the ElectrodesTable this time series - * was generated from + * @param dsetSize Intial size of the main dataset. This must be a vector with two + * elements. The first element specifies the lenght in time and + * the second element must be equal to the lenght of channelVector + * @param chunkSize Chunk size to use. The number of elements must be two to + * specify the size of a chunk in the time and electrode dimension + * @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, stored + * in the specified by unit + * @param offset Scalar to add to the data after scaling by ‘conversion’ to finalize + * its coercion to the specified ‘unit' */ ElectricalSeries(const std::string& path, std::shared_ptr io, diff --git a/src/nwb/file/ElectrodeTable.hpp b/src/nwb/file/ElectrodeTable.hpp index 04ce56f0..c6470078 100644 --- a/src/nwb/file/ElectrodeTable.hpp +++ b/src/nwb/file/ElectrodeTable.hpp @@ -19,7 +19,6 @@ class ElectrodeTable : public DynamicTable * @brief Constructor. * @param path The path of the table. * @param io The shared pointer to the BaseIO object. - * @param channels The vector of channel numbers. * @param description The description of the table (default: "metadata about * extracellular electrodes"). */ diff --git a/src/nwb/hdmf/table/DynamicTable.hpp b/src/nwb/hdmf/table/DynamicTable.hpp index 0e9f6cf7..6cd8c2a5 100644 --- a/src/nwb/hdmf/table/DynamicTable.hpp +++ b/src/nwb/hdmf/table/DynamicTable.hpp @@ -64,7 +64,6 @@ class DynamicTable : public Container /** * @brief Adds a column of element identifiers to the table. - * @param idDescription The description of the column. * @param elementIDs A unique pointer to the `ElementIdentifiers` dataset. * @param values The vector of id values. */ From 7960cc5d33f868ab79ffcc1835acbba02621ff45 Mon Sep 17 00:00:00 2001 From: Oliver Ruebel Date: Fri, 2 Aug 2024 01:25:05 -0700 Subject: [PATCH 2/3] Fix spelling errors --- src/nwb/NWBFile.hpp | 2 +- src/nwb/NWBRecording.hpp | 2 +- src/nwb/base/TimeSeries.hpp | 6 +++--- src/nwb/ecephys/ElectricalSeries.hpp | 6 +++--- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/nwb/NWBFile.hpp b/src/nwb/NWBFile.hpp index 8c7bece1..c76587f3 100644 --- a/src/nwb/NWBFile.hpp +++ b/src/nwb/NWBFile.hpp @@ -57,7 +57,7 @@ class NWBFile * @brief Create ElectricalSeries objects to record data into. * Created objects are stored in recordingContainers. * @param recordingArrays vector of ChannelVector indicating the electrodes to - * record from. A seperate ElectricalSeries will be + * record from. A separate ElectricalSeries will be * 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. diff --git a/src/nwb/NWBRecording.hpp b/src/nwb/NWBRecording.hpp index a81f3d22..3cd79466 100644 --- a/src/nwb/NWBRecording.hpp +++ b/src/nwb/NWBRecording.hpp @@ -38,7 +38,7 @@ class NWBRecording * @param baseName The base name of the file (will be appended with * experiment number). * @param experimentNumber The experiment number. - * @param recordingArrays ChannelVector objets indicating the electrodes to use for + * @param recordingArrays ChannelVector objects indicating the electrodes to use for * ElectricalSeries recordings * @param IOType Type of backend IO to use */ diff --git a/src/nwb/base/TimeSeries.hpp b/src/nwb/base/TimeSeries.hpp index e4411adf..7753967f 100644 --- a/src/nwb/base/TimeSeries.hpp +++ b/src/nwb/base/TimeSeries.hpp @@ -21,9 +21,9 @@ class TimeSeries : public Container * @param unit Unit for the electrical signal. Must be "volts" * @param description The description of the TimeSeries. * @param comments Human-readable comments about the TimeSeries - * @param dsetSize Intial size of the main dataset. This must be a vector with two - * elements. The first element specifies the lenght in time and - * the second element must be equal to the lenght of channelVector + * @param dsetSize Initial size of the main dataset. This must be a vector with two + * elements. The first element specifies the length in time and + * the second element must be equal to the length of channelVector * @param chunkSize Chunk size to use. The number of elements must be two to * specify the size of a chunk in the time and electrode dimension * @param conversion Scalar to multiply each element in data to convert it to diff --git a/src/nwb/ecephys/ElectricalSeries.hpp b/src/nwb/ecephys/ElectricalSeries.hpp index 2083612f..156d4619 100644 --- a/src/nwb/ecephys/ElectricalSeries.hpp +++ b/src/nwb/ecephys/ElectricalSeries.hpp @@ -23,9 +23,9 @@ class ElectricalSeries : public TimeSeries * @param electrodesTablePath Path to the electrodes table * @param unit Unit for the electrical signal. Must be "volts". * @param description The description of the TimeSeries. - * @param dsetSize Intial size of the main dataset. This must be a vector with two - * elements. The first element specifies the lenght in time and - * the second element must be equal to the lenght of channelVector + * @param dsetSize Initial size of the main dataset. This must be a vector with two + * elements. The first element specifies the length in time and + * the second element must be equal to the length of channelVector * @param chunkSize Chunk size to use. The number of elements must be two to * specify the size of a chunk in the time and electrode dimension * @param conversion Scalar to multiply each element in data to convert it to From 2f6b164b606505a5470e400889e50c68ad3b4e43 Mon Sep 17 00:00:00 2001 From: Oliver Ruebel Date: Fri, 2 Aug 2024 01:42:47 -0700 Subject: [PATCH 3/3] Fix linter errors --- src/nwb/NWBFile.hpp | 2 +- src/nwb/NWBRecording.hpp | 6 +++--- src/nwb/base/TimeSeries.hpp | 21 +++++++++------------ src/nwb/ecephys/ElectricalSeries.hpp | 28 +++++++++++++++------------- 4 files changed, 28 insertions(+), 29 deletions(-) diff --git a/src/nwb/NWBFile.hpp b/src/nwb/NWBFile.hpp index c76587f3..3cc2887c 100644 --- a/src/nwb/NWBFile.hpp +++ b/src/nwb/NWBFile.hpp @@ -56,7 +56,7 @@ class NWBFile /** * @brief Create ElectricalSeries objects to record data into. * Created objects are stored in recordingContainers. - * @param recordingArrays vector of ChannelVector indicating the electrodes to + * @param recordingArrays vector of ChannelVector indicating the electrodes to * record from. A separate ElectricalSeries will be * created for each ChannelVector * @param dataType The data type of the elements in the data block. diff --git a/src/nwb/NWBRecording.hpp b/src/nwb/NWBRecording.hpp index 3cd79466..eb93501a 100644 --- a/src/nwb/NWBRecording.hpp +++ b/src/nwb/NWBRecording.hpp @@ -36,10 +36,10 @@ class NWBRecording * @brief Opens the file for recording. * @param rootFolder The root folder where the file will be stored. * @param baseName The base name of the file (will be appended with - * experiment number). + * experiment number). * @param experimentNumber The experiment number. - * @param recordingArrays ChannelVector objects indicating the electrodes to use for - * ElectricalSeries recordings + * @param recordingArrays ChannelVector objects indicating the electrodes to + * use for ElectricalSeries recordings * @param IOType Type of backend IO to use */ Status openFile(const std::string& rootFolder, diff --git a/src/nwb/base/TimeSeries.hpp b/src/nwb/base/TimeSeries.hpp index 7753967f..08537856 100644 --- a/src/nwb/base/TimeSeries.hpp +++ b/src/nwb/base/TimeSeries.hpp @@ -17,21 +17,18 @@ class TimeSeries : public Container * @brief Constructor. * @param path The location of the TimeSeries in the file. * @param io A shared pointer to the IO object. - * @param dataType The data type to use for storing the recorded voltage signal + * @param dataType The data type to use for storing the recorded signal * @param unit Unit for the electrical signal. Must be "volts" * @param description The description of the TimeSeries. * @param comments Human-readable comments about the TimeSeries - * @param dsetSize Initial size of the main dataset. This must be a vector with two - * elements. The first element specifies the length in time and - * the second element must be equal to the length of channelVector - * @param chunkSize Chunk size to use. The number of elements must be two to - * specify the size of a chunk in the time and electrode dimension - * @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, stored - * in the specified by unit - * @param offset Scalar to add to the data after scaling by ‘conversion’ to finalize - * its coercion to the specified ‘unit' + * @param dsetSize Initial size of the main dataset + * @param chunkSize Chunk size to use + * @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, + * stored in the specified by unit + * @param offset Scalar to add to the data after scaling by ‘conversion’ to + * finalize its coercion to the specified ‘unit' */ TimeSeries(const std::string& path, std::shared_ptr io, diff --git a/src/nwb/ecephys/ElectricalSeries.hpp b/src/nwb/ecephys/ElectricalSeries.hpp index 156d4619..6286fe62 100644 --- a/src/nwb/ecephys/ElectricalSeries.hpp +++ b/src/nwb/ecephys/ElectricalSeries.hpp @@ -18,22 +18,24 @@ class ElectricalSeries : public TimeSeries * @brief Constructor. * @param path The location of the ElectricalSeries in the file. * @param io A shared pointer to the IO object. - * @param dataType The data type to use for storing the recorded voltage signal + * @param dataType The data type to use for storing the recorded voltage * @param channelVector The electrodes to use for recording * @param electrodesTablePath Path to the electrodes table - * @param unit Unit for the electrical signal. Must be "volts". + * @param unit Unit for the electrical signal. Must be "volts". * @param description The description of the TimeSeries. - * @param dsetSize Initial size of the main dataset. This must be a vector with two - * elements. The first element specifies the length in time and - * the second element must be equal to the length of channelVector - * @param chunkSize Chunk size to use. The number of elements must be two to - * specify the size of a chunk in the time and electrode dimension - * @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, stored - * in the specified by unit - * @param offset Scalar to add to the data after scaling by ‘conversion’ to finalize - * its coercion to the specified ‘unit' + * @param dsetSize Initial size of the main dataset. This must be a vector + * with two elements. The first element specifies the length + * in time and the second element must be equal to the + * length of channelVector + * @param chunkSize Chunk size to use. The number of elements must be two to + * specify the size of a chunk in the time and electrode + * dimension + * @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, + * stored in the specified by unit + * @param offset Scalar to add to the data after scaling by ‘conversion’ to + * finalize its coercion to the specified ‘unit' */ ElectricalSeries(const std::string& path, std::shared_ptr io,