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

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niksirbi wants to merge 52 commits intomainfrom ns-nwb-io

+631-2

Commits on Dec 18, 2024

Create nwb_export.py

edeno
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niksirbi
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NWB requires one file per individual

edeno
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Add script

edeno
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Remove import error handling

edeno
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Add nwb optional dependencies

edeno
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niksirbi
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Fix linting based on pre-commit hooks

edeno
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niksirbi
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Add example docstring

edeno
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Rename to fit module naming pattern

edeno
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Add import from nwb

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

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

pre-commit-ci[bot]
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niksirbi
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Apply suggestions from code review

edeno
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niksirbi
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Update make pynwb and ndx-pose core dependencies

edeno
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niksirbi
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Cleanup of docstrings and variable names from code review

edeno
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niksirbi
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Rename function for clarity

edeno
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Update with example converting back to movement

edeno
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Add file validation and handling for single path

edeno
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Add preliminary tests

edeno
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Convert to numpy array

edeno
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Handle lack of confidence

edeno
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Display xarray

edeno
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niksirbi
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Refactor tests

edeno
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niksirbi
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Create nwb_export.py

edeno
authored and
niksirbi
committed
NWB requires one file per individual

edeno
authored and
niksirbi
committed
Remove import error handling

edeno
authored and
niksirbi
committed
Add nwb optional dependencies

edeno
authored and
niksirbi
committed
Fix linting based on pre-commit hooks

edeno
authored and
niksirbi
committed
Rename to fit module naming pattern

edeno
authored and
niksirbi
committed
Add import from nwb

edeno
authored and
niksirbi
committed
Update make pynwb and ndx-pose core dependencies

edeno
authored and
niksirbi
committed
Add file validation and handling for single path

edeno
authored and
niksirbi
committed
Convert to numpy array

edeno
authored and
niksirbi
committed
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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