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Corpus 3 release fixes #86

Merged
merged 60 commits into from
Nov 13, 2024
Merged

Corpus 3 release fixes #86

merged 60 commits into from
Nov 13, 2024

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ibevers
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@ibevers ibevers commented Oct 11, 2024

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ibevers and others added 30 commits June 14, 2024 12:15
@ibevers
Add synthetic RedCap data generation function
ff83244
@ibevers
Fix CLI bug and add evaluation function for synthetic data
405a0ef
@ibevers
Create version of prepare for synthetic data
331a252
@alistairewj
fixes while running on corpus 3
4cf8333
@ibevers
Comment out column conversion since this was done manually
17ec192
@ibevers
Add non-pydra iterative feature extraction
c3edca8
@ibevers
Add update columns flag
2d7d9ca
@ibevers
Add language code to transcribe to fix bug
5d65f26
@ibevers
Add update_column_names arg to tests
fb61fdc
@alistairewj
rework so non-parallel extraction works and verifies content
d07d229
@alistairewj
add command to validate a BIDS folder has all the extracted features
d5db59b
@alistairewj @ibevers
add command to validate a BIDS folder has all the extracted features
ef57f2a
@ibevers
Add try/except and retry for transcription
c8d099d
@ibevers
Refactor transcription and move inside try
14b53a2
@ibevers
Merge branch 'alistair/corpus_3' into corpus-3-release-fixes
70baeb7
@ibevers
Remove redundant validate_bids_data function
9589071
@ibevers
Remove vestigial test update_redcap_df_column_names
f00353e
@ibevers
Add labels to coded mapping for updating synthetic csv
366a04e
@ibevers
Update wav_path to wav_paths
21247a2
@ibevers
Merge branch 'synthetic-data' into corpus-3-release-fixes
603ced3
@ibevers
Merge branch 'corpus-3-release-fixes' of https://github.com/sensein/b…
184687b 
…2aiprep into corpus-3-release-fixes
@ibevers
Fix Pydra workflow
f44cb1c
@ibevers
Add try/except for robustness when not connected to wifi
54673ea
@alistairewj
rename bids_like_data module to bids
9f9f774
@alistairewj
put click commands in commands.py to simplify cli.py
f918d5c
@alistairewj
rewrite prepare bids and output a derivatives parquet file
4c7c509
@alistairewj
add a few useful signal processing functions
f044462
@alistairewj
tidy
cd14309
@alistairewj
remove unused imports
2587458
@satra
ref: remove unneeded file
9f0f016
satra added 22 commits November 11, 2024 13:26
@satra
ref: update feature extraction to use the latest senselab feature ext…
cc1eb8e 
…ractors
@satra
ref: clean up cli imports and comment synthetic data generation
9d2d54c
@satra
enh: return audio paths by group and size
f7a61c9
@satra
ref: adjust extractor to use different parameters and rework parallel…
bcb68d2 
…ization
@satra
ref: update docstring
3be718c
@satra
enh: add cache support and refactor command line
383c259
@satra
enh: add list of speech tasks
b845bdc
@satra
fix: make sure audiodir is a Path
7da49ba
@satra
enh: add dask support and add isspeech for parselmouth
5356335
@satra
fix: plugin args is a dict
cbdd899
@satra
fix: features
8bcecec
@satra
fix: features already popped
f43d10a
@satra
ref: get paths now returns a list of dictionaries
2eedf4a
@satra
ref: single file extraction and bids path reorg
779de5b
@satra
enh: add overwrite flag
a533df1
@satra
fix: make bids directory a path in call
30e5d0e
@satra
fix: more paths
d7b48aa
@satra
fix: force multiprocessing spawn
15781dd
@satra
ref: move multiprocessing start context to cli
4f15452
@satra
fix: revert to using multiprocessing just before call
3be77b4
@satra
enh: add percentile flag for reducing resource consumption by very la…
2a5d69e 
…rge files
@satra
Merge pull request #91 from sensein/fix/corpus-3
f71ed9a 
[WIP] Fixes for b2aiprep for data release
@satra satra marked this pull request as ready for review November 13, 2024 19:08
@alistairewj alistairewj merged commit 1cc5897 into main Nov 13, 2024
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3 participants
@ibevers @alistairewj @satra