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Add data read#85

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oruebel merged 211 commits intomainNeurodataWithoutBorders/aqnwb:mainfrom add_readNeurodataWithoutBorders/aqnwb:add_readCopy head branch name to clipboardJan 13, 2025

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Commits

Commits on Aug 31, 2024

• Define base classes for reading

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• First draft of reading datasets and attributes

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• Split reading of attribute and dataset to separate functions

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• Remove debug print

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• Add functions to construct ReadDatasetWrapper and ReadAttributeWrapper from BaseIO

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• Fix formatting

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• Add test for using the ReadDatasetWrapper

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• Start refactor containers for read

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• Fix format

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Commits on Sep 1, 2024

• Read ElectricalSeries.data example working

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• Revert change to tests used for debugging

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• Fix codespell issue

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• Move read example to an example file

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• Fix bug in Container::create

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• Add example for data read

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• Fix spelling error

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• Add user docs for data read

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• Update read user docs

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Commits on Sep 2, 2024

• Add toc

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• Add read software design figure and more details on the design

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• Some adjustment to the edges in the fig

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• Some adjustment to the edges in the fig

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• Add intro for data read page

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Commits on Sep 3, 2024

• Make Container::create inline

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• Make DataBlock::fromGeneric inline

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• Implement function to allow us to get the storage object type for a given path

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• Rename getObjectType to getStroageObjectType

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• Fix reading of attributes and add TimeSeries.resolution read

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• Add example for reading an attribute

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• Add ReadDataWrapperBase as common base class for ReadDatasetWrapper and ReadAttributeWrapper

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• Fix docstring

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• Minor fixed to docs

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• Mention ReadDataWrapperBase in the read dox page

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• Merge branch 'main' into add_read

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• Fix unit tests after merge

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• Remove NWBFile.identifierText property

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Commits on Sep 4, 2024

• Allow setting of value type template parameter for ReadDataWrapperBase and subtypes

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• Save the std::type_index as part of the DataBlock to support runtime checking

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Commits on Sep 5, 2024

• Fix #88 move io classes to their own module

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• Refactor to add IO namespace to match folder structure

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• Move HDF5RecordingData to its own hpp/cpp files

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• Moved read I/O classes to new ReadIO.hpp

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• Refactor the read data wrappers to use a single ReadDataWrapper class for both Attributes and Datasets

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Commits on Sep 6, 2024

• Replace redundant ReadObjectType with StorageObjectType

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• Add traits for ReadObjectWrapper to prevent instantiation for Group and Undefined types

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• Fix formatting

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• Fix spelling error

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• Inline functions in ReadIO.hpp

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• Some minor fixes

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Commits on Sep 7, 2024

• Merge branch 'main' into add_read

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Commits on Sep 8, 2024

• First draft of Container registry

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• Update ElectrodGroup to provide standard Container constructor and move args to initalize

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• Fix formatting

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• Merge branch 'add_read' into add_container_read

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• Register subtypes

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• Move the registry to a new RegisteredType class to also cover non-Group types, e.g., Data, VectorData etc.

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• Fix formatting

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• Ensure all neurodata_types are registered correctly

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• Add unittest for RegisteredTrype

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• Add developer docs for RegisteredTypes

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• Fix name of the unit test file for RegisteredType

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• Add example code for RegisteredType

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• Use both namespace and type name to register and access subtypes

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• Update documentation to clarify the use of namespace::classname to manage container classes

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• Update read test to use the registry to construct the class

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• Minor dox fixes

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Commits on Sep 9, 2024

• Fix getTypeName and getNamespace and use them instead of hard-coded values

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• Update docs for getTypeName add getNamespace

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• Merge branch 'main' into add_read

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• Fix ElectricalSeries

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• Merge branch 'add_read' into add_container_read

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• Attempt to fix reading of string attribute

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• Fix read neurodata_type attribute read test

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• Add test for reading a TimeSeries Container back

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• Add RegisteredType::create method to read a type from file

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• Fix path ecephys read test

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• Change RegisteredType::create to return shared pointer to support casting

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• Update ecephys read example

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• Updated read tutorial and example

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• Add missing comment

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• Clarify read docs and rename workflow docs

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Commits on Sep 19, 2024

• Run test workflows on all PRs

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• Merge branch 'add_read' into add_container_read

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• Fix static assert for ReadDataWrapper

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• Sync add_read with main branch (#101)

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• Merge branch 'add_read' into add_container_read

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• Merge branch 'main' into add_read

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Commits on Sep 20, 2024

• Merge branch 'main' into add_read

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• Fix formatting and docs error after merge with main

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• Merge branch 'add_read' into add_container_read

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• Fix formatting after merge

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• Remove SpikeEventSeries.neurodata_type

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• Register SpikeEventSeries as a type

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Commits on Sep 21, 2024

• Updated RegisterTypes to allow overwrite of the typename to use and overwrite the typename for ElectrodeTable

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• Fix code formatting

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• Add missing description for DynamicTableRegion

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• Fix #109 Add missing axis attribute for channel_conversion and remove extra attributes

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• Remove undefined functions from Device

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• Rename member variable in ElectricalSeries

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• Rename member variable in SpikeEventSeries

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• Added mergePaths functions and made functions in Utils.hpp static inline

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• Updated ElectrodeTable to use mergePaths method

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• Updated DynamicTable to use mergePaths method

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• Update ElectrodeGroup to use mergePaths

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• Updated ElectricalSeries to use mergePaths

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• Updated TimerSeries to use mergePaths function

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• Updated NWBFile to use the mergePaths function

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Commits on Sep 22, 2024

• Updated ElectrodeTable static paths to not used trailing / for consistency

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• Fix Doxygen error by extracting also static members in the docs

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• Fix section level in install.dox

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• Update ReadDataWrapper to use m_ member naming convention

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• Updated DataBlock / DataBlockGeneric to avoid shadowing of constructor args

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• Fix reference error in read.dox

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• Add ReadDataWrapper isType, getPath, getIO methods and update docstrings

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• Create macro DEFINE_FIELD to simplify creating access methods for fields in RegisteredType subclasses

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• Replace previous field access methods in TimeSeries with DEFINE_FIELD macro calls

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• Replace TimeSeries.dataLazy and resolutionLazy with DEFINE_FIELD definitions

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• Update the Doxygen built to expand the DEFINE_FIELD macro to document the generated functions

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• Fix spellcheck

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• Fix section levels in read.dox

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• Add docs for using the DEFINE_FIELD macro

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• Added attributeExists method on IO and ReadDataWrapper::exists methods to check that an object actually exists

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• Add TimeSeries.descriptionLazy field to test that reading string attributes works

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• Added function getGroupObjects to the I/O to allow gettings all objects contained in a group

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• Add BaseIO::findTypes method to search for neurodata_types in a file

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Commits on Sep 23, 2024

• Add example for searching for typed objects

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• Update ElectrodeTable to use m_ member names

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• Added field definitions for TimeSeries

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Commits on Sep 24, 2024

• Add some design docs about reading registered types

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• Update read types design figure

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• Minor update to docs of RegisteredType

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• Update docs/pages/userdocs/read.dox

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• Update src/io/ReadIO.hpp

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• Update src/io/ReadIO.hpp

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• Rename ReadDataWrapper.is_dataset

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• Update src/io/hdf5/HDF5IO.hpp

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• Remove duplicate code in NWBFile

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• Remove outdated ToDo item

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Commits on Oct 2, 2024

• Apply suggestions on docs from code review

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Commits on Oct 22, 2024

• Merge branch 'main' into add_read

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• Fix build error after merge

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• Merge branch 'add_read' into add_container_read

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• Fix build error due to error during merge with base branch

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Commits on Oct 23, 2024

• Fix read.dox figure based on suggestion

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• Fix docs based on code review

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Commits on Dec 12, 2024

• update getAttribute method to detect object type

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• update read example

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• add file mode options and readonly mode to io

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• update example to use readonly

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Commits on Dec 18, 2024

• add getter functions to Container classes with attributes

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• fix formatting

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• update lint workflow

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Commits on Dec 19, 2024

• add NWBFile fields

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• update filenames

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• remove duplicate file mode checks

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• Merge pull request #91 from NeurodataWithoutBorders/add_container_read

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Commits on Dec 22, 2024

• Merge branch 'main' into add_read

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• Fix spelling and complete merge

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• Fix missing merge in file

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• Install Boost multi-array in windows action

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• Use std::vector instead of variable-length arrays to avoid Windows built errors

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• Add note to docs to clarify non-virtual DEFINE_FIELD

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Commits on Jan 8, 2025

• Merge branch 'main' into add_read

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• Add HDF5IO tests for add_read PR (#118)

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• Update read example

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Commits on Jan 9, 2025

• Add missing offset attriubte for TimeSeries.data

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• Add basic unit test for TimeSeries read

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• Add more REQUIRE checks

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• Add missing TimeSerires.conitnuity field for write. Move timeseries-specific write method from BaseIO to TimeSeries

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• Fix spellcheck errors

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• Add read test for timestamps.unit and timestamps.interval

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• Support using starting_time and rate with TimeSeries

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• Add missing timeseries control and control description. Fix chunking of timestamps

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• Move neurodata_type and namespace attributes to Container

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Commits on Jan 10, 2025

• address validation errors in add_read (#125)

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• Merge branch 'add_read' into add_read_field_read_tests

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• Merge branch 'add_read' into add_read_examples

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• Fix #126 Initiallization of VectorData

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• Renamed testBase to testTimeSeries

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• Add initial unit tests for VectorData

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