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

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

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a360d27
Create nwb_export.py
edeno Apr 18, 2024
44edddf
NWB requires one file per individual
edeno Apr 18, 2024
927c655
Add script
edeno Apr 19, 2024
7ccc5b6
Remove import error handling
edeno Apr 19, 2024
91eb4e5
Add nwb optional dependencies
edeno Apr 19, 2024
58b80c1
Fix linting based on pre-commit hooks
edeno Apr 19, 2024
32692c7
Add example docstring
edeno Apr 19, 2024
82e62ce
Rename to fit module naming pattern
edeno Apr 19, 2024
11c1317
Add import from nwb
edeno Apr 19, 2024
1b3253d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 22, 2024
e473eea
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 8, 2024
393ebbb
Apply suggestions from code review
edeno Jun 8, 2024
e7d2c68
Update make pynwb and ndx-pose core dependencies
edeno Jun 8, 2024
43c1a73
Cleanup of docstrings and variable names from code review
edeno Jun 8, 2024
0af1660
Rename function for clarity
edeno Jun 8, 2024
5a14ad1
Update with example converting back to movement
edeno Jun 8, 2024
54fe8f3
Add file validation and handling for single path
edeno Jun 8, 2024
510c8a9
Add preliminary tests
edeno Jun 8, 2024
48c1d94
Convert to numpy array
edeno Jun 9, 2024
9b81b49
Handle lack of confidence
edeno Jun 9, 2024
8a8f578
Display xarray
edeno Jun 9, 2024
9ebfeb9
Refactor tests
edeno Jun 9, 2024
58bdae2
Create nwb_export.py
edeno Apr 18, 2024
57841fa
NWB requires one file per individual
edeno Apr 18, 2024
d2fd039
Remove import error handling
edeno Apr 19, 2024
2c3fb89
Add nwb optional dependencies
edeno Apr 19, 2024
fd261e4
Fix linting based on pre-commit hooks
edeno Apr 19, 2024
001ea4b
Rename to fit module naming pattern
edeno Apr 19, 2024
08e9e33
Add import from nwb
edeno Apr 19, 2024
ee5cacb
Update make pynwb and ndx-pose core dependencies
edeno Jun 8, 2024
b625f8a
Add file validation and handling for single path
edeno Jun 8, 2024
f43a0ad
Convert to numpy array
edeno Jun 9, 2024
216b01d
fix logging module import
niksirbi Nov 29, 2024
f841f30
constrained pynwb>=0.2.1
niksirbi Nov 29, 2024
f065f3f
fixed existing unit tests
niksirbi Nov 29, 2024
ddeeea6
add key_name argument to convert_nwb_to_movement
niksirbi Nov 29, 2024
060e051
tests should only create temp file
niksirbi Dec 11, 2024
621e79c
use Generator instead of legacy np.random.random
niksirbi Dec 11, 2024
63eafb3
reorder dims and use from_numpy for creating movement ds
niksirbi Dec 12, 2024
e137cb3
define default nwb kwargs as constants
niksirbi Dec 12, 2024
b06ccbd
renamed and reformatted `add_movement_dataset_to_nwb` to `ds_to_nwb`
niksirbi Dec 12, 2024
51bb1af
Expanded module-level docstring
niksirbi Dec 12, 2024
179963d
use individual instead of subject
niksirbi Dec 12, 2024
cfeaca8
refactored functions for loading ds from nwb
niksirbi Dec 12, 2024
3b24d6d
make mypy happy with numpy typing
niksirbi Dec 18, 2024
c8d1b82
rename nwb example
niksirbi Dec 18, 2024
0e4849a
renamed private func for creating pose estimation and skeletons objects
niksirbi Dec 18, 2024
1e5bfef
incorporate NWB loading into load_poses module
niksirbi Dec 18, 2024
fa0c1db
incorporate NWB saving function into save_poses module
niksirbi Dec 18, 2024
84d7ead
simplified private nwb functions
niksirbi Dec 18, 2024
7adba94
provide examples in docstrings instead of sphinx gallery example
niksirbi Dec 18, 2024
b9305e4
fix docstring syntax error
niksirbi Dec 18, 2024
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Add import from nwb
@edeno @niksirbi
edeno authored and niksirbi committed Dec 18, 2024
commit 08e9e333fa64638221b8ce235aeb170ac0b1251c
149 changes: 0 additions & 149 deletions movement/io/export_nwb.py
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