eyelink sync #2

behinger · 2024-05-21T14:10:04Z

Prepare for 1.4.0 release (Prepare for 1.4.0 release mne-tools/mne-bids-pipeline#753)
MAINT: Cleanup dependencies and doc build (MAINT: Cleanup dependencies and doc build mne-tools/mne-bids-pipeline#755)
ENH: Add annotation of head velocity (ENH: Add annotation of head velocity mne-tools/mne-bids-pipeline#757)
BUG: Fix bug with cache invalidation (BUG: Fix bug with cache invalidation mne-tools/mne-bids-pipeline#756)
ENH: Add T1 and FLASH BEM to website (ENH: Add T1 and FLASH BEM to website mne-tools/mne-bids-pipeline#758)
BUG: Fix bug with empty room processing (BUG: Fix bug with empty room processing mne-tools/mne-bids-pipeline#761)
ENH: More compact logging (ENH: More compact logging mne-tools/mne-bids-pipeline#764)
ENH: Add eSSS (ENH: Add eSSS mne-tools/mne-bids-pipeline#762)
ENH: Cache grand-average steps (ENH: Cache grand-average steps mne-tools/mne-bids-pipeline#765)
MAINT: Test MD5 hashing too (MAINT: Test MD5 hashing too mne-tools/mne-bids-pipeline#768)
ENH: Better logging of distances (ENH: Better logging of distances mne-tools/mne-bids-pipeline#769)
MAINT: pre-commit.ci (MAINT: pre-commit.ci mne-tools/mne-bids-pipeline#774)
Added deriv_root argument to CLI (Added deriv_root argument to CLI mne-tools/mne-bids-pipeline#773)
MAINT: Use pooch for downloading web data (MAINT: Use pooch for downloading web data mne-tools/mne-bids-pipeline#775)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#776)
API: Change default to _cache (API: Change default to _cache mne-tools/mne-bids-pipeline#778)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#780)
ENH: Validate inputs with pydantic (ENH: Validate inputs with pydantic mne-tools/mne-bids-pipeline#779)
TST: Rerun CIs (TST: Rerun CIs mne-tools/mne-bids-pipeline#781)
BUG: Fix bug where individual invs were not rendered (BUG: Fix bug where individual invs were not rendered mne-tools/mne-bids-pipeline#782)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#784)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#786)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#787)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#788)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#789)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#790)
MAINT: Fix bug with item (MAINT: Fix bug with item mne-tools/mne-bids-pipeline#791)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#792)
Ensure link in "You're not viewing the latest stable version" banner is readable in light and dark theme (Ensure link in "You're not viewing the latest stable version" banner is readable in light and dark theme mne-tools/mne-bids-pipeline#793)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#795)
Reduce logging output when creating and saving reports (Reduce logging output when creating and saving reports mne-tools/mne-bids-pipeline#799)
Use inst.pick() instead of inst.pick_types() (Use inst.pick() instead of inst.pick_types() mne-tools/mne-bids-pipeline#800)
Use cleaned epochs for sensor-space decoding (Use cleaned epochs for sensor-space decoding, time-frequency analysis, and covariance calculation mne-tools/mne-bids-pipeline#796)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#803)
Add "picard-extended_infomax" ICA algorithm (Add "picard-extended_infomax" ICA algorithm mne-tools/mne-bids-pipeline#801)
Do not reject epochs based on PTP threshold before ICA cleaning (Do not reject epochs based on PTP threshold before ICA cleaning mne-tools/mne-bids-pipeline#806)
Add "autoreject_local" as new option for preprocessing/ptp_reject (Add "autoreject_local" as new option for preprocessing/ptp_reject mne-tools/mne-bids-pipeline#807)
ENH: Table sorting and ds004229 updates (ENH: Table sorting and ds004229 updates mne-tools/mne-bids-pipeline#809)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#811)
Add support for autoreject (local) before running ICA (Add support for autoreject (local) before running ICA mne-tools/mne-bids-pipeline#810)
BUG: Fix bug with verbosity
Do not interpolate bad segments using autoreject before ICA (Do not interpolate bad segments using autoreject before ICA mne-tools/mne-bids-pipeline#816)
Omit bad channels when gathering data used for decoding (Omit bad channels when gathering data used for decoding mne-tools/mne-bids-pipeline#817)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#818)
Allow decoding using epochs at different stages of pre-processing (Allow decoding using epochs at different stages of pre-processing mne-tools/mne-bids-pipeline#819)
Prepare for 1.5.0 release (Prepare for 1.5.0 release mne-tools/mne-bids-pipeline#821)
FIX: PyQt6 (FIX: PyQt6 mne-tools/mne-bids-pipeline#822)
The "Behavior changes" heading was incorrectly commented out in the changelog (The "Behavior changes" heading was incorrectly commented out in the changelog mne-tools/mne-bids-pipeline#823)
MAINT: Fix CIs (MAINT: Fix CIs mne-tools/mne-bids-pipeline#824)
Switch build backend to hatchling (Switch build backend to hatchling mne-tools/mne-bids-pipeline#825)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#826)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#827)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#828)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#829)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#830)
FIX: Paths and pyarrow (FIX: Paths and pyarrow mne-tools/mne-bids-pipeline#834)
MAINT: Test result caching (MAINT: Test result caching mne-tools/mne-bids-pipeline#836)
MAINT: Enable more ruff rules (MAINT: Enable more ruff rules mne-tools/mne-bids-pipeline#838)
ENH: Add artifact regression (ENH: Add artifact regression mne-tools/mne-bids-pipeline#837)
BUG: Fix several bugs (BUG: Fix several bugs mne-tools/mne-bids-pipeline#839)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#843)
ENH: Write out raw data and SSP events (ENH: Write out raw data and SSP events mne-tools/mne-bids-pipeline#840)
BUG: Fix bug with Maxwell step when find_noise_channels_meg=False (BUG: Fix bug with Maxwell step when find_noise_channels_meg=False mne-tools/mne-bids-pipeline#847)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#851)
BUG: Fix bug with multichannel classification (BUG: Fix bug with multichannel classification mne-tools/mne-bids-pipeline#853)
ENH: Better event count rep and noise_cov_method (ENH: Better event count rep and noise_cov_method mne-tools/mne-bids-pipeline#854)
BUG: Fix bug with split epochs and ICA (BUG: Fix bug with split epochs and ICA mne-tools/mne-bids-pipeline#855)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#856)
DOC: Automatic flowchart (DOC: Automatic flowchart mne-tools/mne-bids-pipeline#860)
DOC: Automatically document settings (DOC: Automatically document settings mne-tools/mne-bids-pipeline#863)
add image_kwargs to report (add image_kwargs to report mne-tools/mne-bids-pipeline#859)
MAINT: Remove datalad (MAINT: Remove datalad mne-tools/mne-bids-pipeline#867)
ENH: Split ICA into multiple steps (ENH: Split ICA into multiple steps mne-tools/mne-bids-pipeline#865)
ENH: Document relevant steps (ENH: Document relevant steps mne-tools/mne-bids-pipeline#866)
ENH: Doc config in sheet (ENH: Doc config in sheet mne-tools/mne-bids-pipeline#869)
Fix a typo in the readme (Fix a typo in the readme mne-tools/mne-bids-pipeline#871)
Enable stricter linting (Enable stricter linting mne-tools/mne-bids-pipeline#872)
Improve logging during cache invalidation (Improve logging during cache invalidation mne-tools/mne-bids-pipeline#877)
Update contributing instructions and remove outdated building instructions (Update contributing instructions and remove outdated building instructions mne-tools/mne-bids-pipeline#875)
Fix handling of analyze_channels for EEG data, where some steps (like ERP calculation) would previously fail (Fix handling of analyze_channels for EEG data, where some steps (like ERP calculation) would previously fail mne-tools/mne-bids-pipeline#883)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#885)
Remove ancient config parameter shortest_event (Remove ancient config parameter shortest_event mne-tools/mne-bids-pipeline#888)
Add missing release dates to changelog (Add missing release dates to changelog mne-tools/mne-bids-pipeline#887)
Explicitly depend on annotated-types (Explicitly depend on annotated-types mne-tools/mne-bids-pipeline#886)
MAINT: Check that all options are used (MAINT: Check that all options are used mne-tools/mne-bids-pipeline#889)
BUG: Fix bug with CSP computation and Maxwell filter (BUG: Fix bug with CSP computation and Maxwell filter mne-tools/mne-bids-pipeline#890)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#891)
MAINT: Print longer traceback on report error (MAINT: Print longer traceback on report error mne-tools/mne-bids-pipeline#892)
Set up Dependabot to automatically keep GitHub Actions up-to-date (Set up Dependabot to automatically keep GitHub Actions up-to-date mne-tools/mne-bids-pipeline#893)
[dependabot]: Bump actions/setup-python from 4 to 5 ([dependabot]: Bump actions/setup-python from 4 to 5 mne-tools/mne-bids-pipeline#894)
[dependabot]: Bump actions/download-artifact from 3 to 4 ([dependabot]: Bump actions/download-artifact from 3 to 4 mne-tools/mne-bids-pipeline#895)
[dependabot]: Bump actions/upload-artifact from 3 to 4 ([dependabot]: Bump actions/upload-artifact from 3 to 4 mne-tools/mne-bids-pipeline#896)
[dependabot]: Bump codecov/codecov-action from 3 to 4 ([dependabot]: Bump codecov/codecov-action from 3 to 4 mne-tools/mne-bids-pipeline#898)
[dependabot]: Bump actions/checkout from 3 to 4 ([dependabot]: Bump actions/checkout from 3 to 4 mne-tools/mne-bids-pipeline#897)
add n sbs to report (Add number of subjects to grand-average report mne-tools/mne-bids-pipeline#902)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#903)
Drop support for Python 3.9, drop Optional and Union from type hints (Drop support for Python 3.9, drop Optional and Union from type hints mne-tools/mne-bids-pipeline#908)
Render type annotations in the documentation again (Render type annotations in the documentation again mne-tools/mne-bids-pipeline#909)
MAINT: Ensure input changes cause output changes (MAINT: Ensure input changes cause output changes mne-tools/mne-bids-pipeline#904)
Add number of subjects to grand-average report (cont'd) (Add number of subjects to grand-average report (cont'd) mne-tools/mne-bids-pipeline#910)
Do not show Annotated types in configuration options documentation (Do not show Annotated types in configuration options documentation mne-tools/mne-bids-pipeline#911)
Try to fix documentation deployment (Do not show Annotated types in configuration options documentation (cont'd) mne-tools/mne-bids-pipeline#913)
Restructure configuration options documentation sections (Restructure configuration options documentation sections mne-tools/mne-bids-pipeline#914)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#917)
enhance documentation of caching, continuation of Restructure configuration options documentation sections mne-tools/mne-bids-pipeline#914 (enhance documentation of caching, continuation of #914 mne-tools/mne-bids-pipeline#918)
Improve documentation and config validation of loose and depth parameters; drop support for loose=None (Improve documentation and config validation of loose and depth parameters; drop support for loose=None mne-tools/mne-bids-pipeline#915)
change default for info to use for inverse STC saturated – rank problem? mne-tools/mne-bids-pipeline#905 (change default for info to use for inverse #905 mne-tools/mne-bids-pipeline#919)
ENH: Streamline ICA reporting (ENH: Streamline ICA reporting mne-tools/mne-bids-pipeline#899)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#923)
Support variable time windows for epochs metadata creation (Support variable time windows for epochs metadata creation mne-tools/mne-bids-pipeline#874)
Raise a more helpful error message when requested subjects are missing from the dataset (Raise a more helpful error message when requested subjects are missing from the dataset mne-tools/mne-bids-pipeline#928)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#929)
Fix report section on original raw data (didn't contain bad channels and subject or experimenter name) (Fix report section on original raw data (didn't contain bad channels and subject or experimenter name) mne-tools/mne-bids-pipeline#931)
In the report TOC, don't put the run numbers in quotation marks (In the report TOC, don't put the run numbers in quotation marks mne-tools/mne-bids-pipeline#933)
Rename ica_ctps_ecg_threshold to ica_ecg_threshold (Rename ica_ctps_ecg_threshold to ica_ecg_threshold mne-tools/mne-bids-pipeline#935)
Improve logging output when rejecting epochs; and log number of reconstructed ICA and SSP epochs (Improve logging output when rejecting epochs; and log number of reconstructed ICA and SSP epochs mne-tools/mne-bids-pipeline#936)
Save ECG and EOG evokeds created during ICA artifact detection to disk (Save ECG and EOG evokeds created during ICA artifact detection to disk mne-tools/mne-bids-pipeline#938)
Improve logging during ICA artifact discovery and rejection (Improve logging during ICA artifact discovery and rejection mne-tools/mne-bids-pipeline#937)
DOC: Fix typo (DOC: Fix typo mne-tools/mne-bids-pipeline#940)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#942)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#945)
MAINT: Cleaner hook into mkdocstrings-python (MAINT: Cleaner hook into mkdocstrings-python mne-tools/mne-bids-pipeline#943)
[pre-commit.ci] pre-commit autoupdate ([pre-commit.ci] pre-commit autoupdate mne-tools/mne-bids-pipeline#947)
remove ref-names from .git_archival.txt (remove ref-names from .git_archival.txt mne-tools/mne-bids-pipeline#948)
initial new step for sync

Before merging …

Changelog has been updated (docs/source/changes.md)

…nization

…line into eyelink_sync

…and EEG

behinger and others added 9 commits May 21, 2024 14:09

initial new step for sync

fb3116d

added extras

ed6538f

adapted parameters of the combine_annotations function to fix synchro…

fc75863

…nization

added edf conversion

ab66145

Merge branch 'eyelink_sync' of https://github.com/s-ccs/mne-bids-pipe…

aaf5b32

…line into eyelink_sync

Replace nan values in the ET data with zeros before synchronizing ET …

1e96e2d

…and EEG

Use EEG sync event regex if ET sync event regex is not given

f54ca71

Only use EEG channels for the ICA, needs to be more general

0c2ece1

Added some comments and fixed mistakes

f7e2303

behinger changed the base branch from main_hochberger to ic_label February 7, 2025 13:23

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behinger commented May 21, 2024

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behinger commented May 21, 2024

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