Add I/O support for the ndx-pose NWB extension: take 2#360

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lochhh merged 112 commits intomainfrom

ns-nwb-io

May 29, 2025

Commits on May 29, 2025

Create nwb_export.py

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NWB requires one file per individual

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Add script

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Remove import error handling

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Add nwb optional dependencies

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Fix linting based on pre-commit hooks

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Add example docstring

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Rename to fit module naming pattern

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Add import from nwb

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[pre-commit.ci] auto fixes from pre-commit.com hooks

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[pre-commit.ci] auto fixes from pre-commit.com hooks

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Apply suggestions from code review

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Update make pynwb and ndx-pose core dependencies

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Cleanup of docstrings and variable names from code review

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Rename function for clarity

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Update with example converting back to movement

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Add file validation and handling for single path

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Add preliminary tests

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Convert to numpy array

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Handle lack of confidence

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Display xarray

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Refactor tests

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Create nwb_export.py

edeno
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NWB requires one file per individual

edeno
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lochhh
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Remove import error handling

edeno
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lochhh
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Add nwb optional dependencies

edeno
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lochhh
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Fix linting based on pre-commit hooks

edeno
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lochhh
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Rename to fit module naming pattern

edeno
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lochhh
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Add import from nwb

edeno
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lochhh
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Update make pynwb and ndx-pose core dependencies

edeno
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lochhh
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Add file validation and handling for single path

edeno
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Convert to numpy array

edeno
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fix logging module import

niksirbi
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constrained pynwb>=0.2.1

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fixed existing unit tests

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add key_name argument to convert_nwb_to_movement

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tests should only create temp file

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use Generator instead of legacy np.random.random

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reorder dims and use from_numpy for creating movement ds

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define default nwb kwargs as constants

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renamed and reformatted `add_movement_dataset_to_nwb` to `ds_to_nwb`

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Expanded module-level docstring

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use individual instead of subject

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refactored functions for loading ds from nwb

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make mypy happy with numpy typing

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rename nwb example

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renamed private func for creating pose estimation and skeletons objects

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incorporate NWB loading into load_poses module

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incorporate NWB saving function into save_poses module

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simplified private nwb functions

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provide examples in docstrings instead of sphinx gallery example

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fix docstring syntax error

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use pose estimation series rate if possible

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use dot notation to access pose estimation attributes

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remove underscore from _nwb.py file name

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move imports at the top of docstring example

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[pre-commit.ci] auto fixes from pre-commit.com hooks

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Fix deprecated logger calls
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Fix line too long
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Add load_nwb test case
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Move file fixtures to tests/fixtures/files.py
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Add NWB file validator
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Extend from_nwb_file tests
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Add to_nwb_file tests
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Rename NWBFile fixture
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Remove repeated default nwb kwargs
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Simplify `_ds_to_pose_and_skeleton_objects` test
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Add pynwb to intersphinx mapping
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Draft to_nwb_file refactor
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Allow single key dict for single-ind datasets
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Create Subject in NWBFile
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Refactor resolve_kwargs
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Reduce resolve_kwargs complexity
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Include nwb module in API docs
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Resolve pose_estimation_series_kwargs for single keypoint
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Refactor _ds_to_pose_and_skeleton_objects pt1
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Allow deprioritising input ids
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Add test for _ds_to_pose_and_skeletons
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Update docstrings
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Refactor NWBFileSaveConfig tests
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Allow 0-d individuals
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Link Subject in Skeleton
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Update docstrings + rename resolve methods
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Resolve pose_estimation_kwargs
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Resolve skeleton_kwargs
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Remove unused functions
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Refactor _write_behavior_processing_module
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Convert frames to seconds when saving
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Use numpy.random.Generator
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Refactor to_nwb_file tests
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Remove unused constant
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Add to_nwb_file example in docstrings
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Add load NWB in IO guide
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Add save NWB in IO guide
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Use rng fixture in NWBFile fixtures
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Apply docstring suggestions from code review

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[pre-commit.ci] auto fixes from pre-commit.com hooks

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Fix reference to NWBFileSaveConfig in docstrings
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Mention NWBFile config option in I/O guide
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Clarify from_file fps arg
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Replace `identifier` with `experimenter` in to_nwb_file config example
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Only set `source_file` attribute when loading from NWB file path
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Log warning for missing session_start_time in NWBFileSaveConfig
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Rename `is_multi_individual` to `from_multi_individual`
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Remove "open" when describing NWBFile objects
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Use full NWBFile module refs in docstrings
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Return a single NWBFile when saving single-individual datasets
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Remove `identifier` from nwbfile_kwargs defaults
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Gather NWB fixtures
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Allow specifying key for processing module
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Allow customising processing module via kwargs
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Update nwb test config and comments for clarity
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Add I/O support for the ndx-pose NWB extension: take 2#360lochhh merged 112 commits intomainneuroinformatics-unit/movement:mainfrom ns-nwb-ioneuroinformatics-unit/movement:ns-nwb-ioCopy head branch name to clipboard

Commits

Commits on May 29, 2025

Add I/O support for the ndx-pose NWB extension: take 2#360
lochhh merged 112 commits intomainfrom
ns-nwb-io