c734753 | remrama | 01 April 2024, 04:04:08 UTC | First draft of evaluation module (#130) | 01 April 2024, 04:04:08 UTC |
776a257 | Raphael Vallat | 13 February 2024, 22:07:37 UTC | Remove deprecation warning for seaborn (#163) + bump seaborn>=0.12.0 | 13 February 2024, 22:07:37 UTC |
0035594 | Raphael Vallat | 13 February 2024, 22:05:35 UTC | Add back support for old hypnogram format in plot_hypnogram (#162) | 13 February 2024, 22:05:35 UTC |
5801251 | Raphael Vallat | 13 February 2024, 21:32:43 UTC | Update black (#161) | 13 February 2024, 21:32:43 UTC |
33dbd9d | Nabil Alibou | 13 February 2024, 21:28:47 UTC | Replace Error raised by less than 5 minutes of data by a Warning (#160) | 13 February 2024, 21:28:47 UTC |
ae9ccc7 | S.J. Guillot | 17 January 2024, 19:06:56 UTC | Update mne.pick_channels() to mne.pick() (#154) * Updated MNE pick function Updated mne.pick_channels() to mne.pick() * Fix * Fix * Update staging.py Fixed ```ordered=True``` issue with mne.pick() | 17 January 2024, 19:06:56 UTC |
6b37c63 | Raphael Vallat | 13 January 2024, 14:00:13 UTC | Release 0.6.4 (#153) * Update version * Update changelog and API * Disable FutureWarning * Remove warnings import * black * Upgrade requirements * Add back Hypnogram and simulate_hypnogram * Update changelog * Update doc * Add former * Update docs * Remove outdated * remove outdated in init * update doc * Add push_pypi.md * Update pytest version * Remove Python 3.7 tests * Update setup.py * Update doc * Disable test random array | 13 January 2024, 14:00:13 UTC |
58dfdd8 | Raphael Vallat | 13 January 2024, 13:00:05 UTC | Update pyproject.toml | 13 January 2024, 13:00:05 UTC |
7cbdb61 | Raphael Vallat | 13 January 2024, 12:56:10 UTC | black | 13 January 2024, 12:56:10 UTC |
58369f9 | Raphael Vallat | 13 January 2024, 12:51:36 UTC | Add warning definition of REM latency | 13 January 2024, 12:51:36 UTC |
9608fa4 | paulroujansky | 30 September 2023, 06:02:33 UTC | passing relative_prominence in rem_detect() (#151) Co-authored-by: Paul ROUJANSKY <paul.roujansky@bioserenity.com> | 30 September 2023, 06:02:33 UTC |
9d9fb74 | Raphael Vallat | 31 December 2022, 17:36:12 UTC | Update string representation of yasa.Hypnogram (#129) * Update string representation of yasa.Hypnogram * Add scorer to __repr__ * Update docstring * Add back ` | 31 December 2022, 17:36:12 UTC |
37058f2 | Raphael Vallat | 31 December 2022, 00:02:49 UTC | Default dtype of pandas.Series is now a categorical (#126) * Default dtype of pandas.Series is now a categorical * Fix CI in Pandas 1.3.5 (py37) * Rename `simulate_hypnogram` | 31 December 2022, 00:02:49 UTC |
9be559d | remrama | 30 December 2022, 16:54:01 UTC | Hypnogram plot_hypnogram method (#124) * first draft * a bit cleaner * datetime x-axis when hyp.start is present * unittests * formatting * update docstring examples * topoplot replace optional hypno with Hyp * formatting * changelog * unittest corrections * revert plot_spectrogram back to taking a hypno array * simpler plot_hypnogram docstrings example * typo * add Hypnogram.copy() method * copy hyp in plot_hypnogram * rm art/uns hypno highlighting code, which was not being implemented anyways :/ * fmt | 30 December 2022, 16:54:01 UTC |
b148205 | Raphael Vallat | 28 December 2022, 21:49:16 UTC | Add FutureWarning in hypnogram functions (#123) * Add futurewarning and improve docstrings * Minor doc fixes * remove duplicate see also * Review comments | 28 December 2022, 21:49:16 UTC |
3dfe2d6 | remrama | 28 December 2022, 17:41:34 UTC | Update simulate_hypno to return Hypnogram instance (#121) * first draft * Hypnogram.simulate_similar method * add example with Unscored * minor * corrections * unittests * change default trans_probas stage order * changelog * simulate_similar allows lower n_stages * critical: proper handling of freq in simulations * black fmt * minor edits from PR review * remove the walrus * remove n_stages and freq keywords | 28 December 2022, 17:41:34 UTC |
f55eb55 | Raphael Vallat | 24 December 2022, 14:24:01 UTC | First implementation of the Hypnogram class (#116) * Initial class creation for Hypnogram * Add properties + mapping * Add sleep_statistics and upsample * Add mapping for all n_stages + SFI * Fix in sleep_statistics when all WAKE * Minor edits * Added `scorer` and two new methods * Add docstring * Start adding unittest for Hypnogram class * Add more docstring * Add main docstring + unit test upsample_to_data * Uncommented upsample function * Add to API * Add unit tests for 3-5 stages hypnogram * Added consolidate_stages method * First minor comments from PR review * Initial class creation for Hypnogram * Add properties + mapping * Add sleep_statistics and upsample * Add mapping for all n_stages + SFI * Fix in sleep_statistics when all WAKE * Minor edits * Added `scorer` and two new methods * Add docstring * Start adding unittest for Hypnogram class * Add more docstring * Add main docstring + unit test upsample_to_data * Uncommented upsample function * Add to API * Add unit tests for 3-5 stages hypnogram * Added consolidate_stages method * First minor comments from PR review * Add docstring for method `upsample` * Added as_annotations method * Minor docstring edits * Epoch starts at 0 in `as_annotations` * Updated changelog * Fix typo | 24 December 2022, 14:24:01 UTC |
94be05b | Raphael Vallat | 24 December 2022, 14:23:07 UTC | First implementation of the Hypnogram class (#116) * Initial class creation for Hypnogram * Add properties + mapping * Add sleep_statistics and upsample * Add mapping for all n_stages + SFI * Fix in sleep_statistics when all WAKE * Minor edits * Added `scorer` and two new methods * Add docstring * Start adding unittest for Hypnogram class * Add more docstring * Add main docstring + unit test upsample_to_data * Uncommented upsample function * Add to API * Add unit tests for 3-5 stages hypnogram * Added consolidate_stages method * First minor comments from PR review * Initial class creation for Hypnogram * Add properties + mapping * Add sleep_statistics and upsample * Add mapping for all n_stages + SFI * Fix in sleep_statistics when all WAKE * Minor edits * Added `scorer` and two new methods * Add docstring * Start adding unittest for Hypnogram class * Add more docstring * Add main docstring + unit test upsample_to_data * Uncommented upsample function * Add to API * Add unit tests for 3-5 stages hypnogram * Added consolidate_stages method * First minor comments from PR review * Add docstring for method `upsample` * Added as_annotations method * Minor docstring edits * Epoch starts at 0 in `as_annotations` * Updated changelog * Fix typo | 24 December 2022, 14:23:07 UTC |
ca4a834 | Raphael Vallat | 23 December 2022, 15:55:19 UTC | Hotfix for MNE plot_topomap deprecation (#119) * Hotfix for MNE plot_topomap deprecation * Fix for show_names * Should work now * Stupid typo | 23 December 2022, 15:55:19 UTC |
8f807e0 | Raphael Vallat | 14 December 2022, 01:32:04 UTC | Release 0.6.3 | 14 December 2022, 01:32:04 UTC |
c72c9fa | remrama | 14 December 2022, 01:15:01 UTC | Hypno simulation (#110) * draft hypnogram simulator * update docstring * assertion checks * start n_stages * add consolidate_stages func and option in simulator * reorder trans_prob to w n1 n2 n3 r * require pandas classes for clearer stage orders * take random seed argument * unittests * pass flake8 * increase test coverage (and pass it) * pytest file formatting * pytest black formatting * black formatting * Use of rng to set random seed * Clearer TIB description in docstring * remap with Series.map instead of numpy indexing * update simulate_hypno tests * update hypno_consolidate_stages tests * updated changelog | 14 December 2022, 01:15:01 UTC |
9458bc5 | remrama | 11 December 2022, 19:29:50 UTC | swapped out range() --> zip() (#115) | 11 December 2022, 19:29:50 UTC |
806b08f | remrama | 11 December 2022, 00:18:04 UTC | Stairs plot (#108) * step -> stairs * avoid empty mask warnings from hlines * fill_color parameter * replace keyword fig-->ax * rm typo * plot continuous epochs with one line * use new stairs hypnoplot in plot_spectrogram * consolidate and clean a bit * unittests * updated changelog * lint cleanup * more lint cleanup * kill me * typo * Updated notebook * pass ax explicitly in docstring example * dont fill Art/Uns * cover hypnogram kwargs in plot_spectrogram tests * earlier arg validation Co-authored-by: Raphael Vallat <raphaelvallat9@gmail.com> | 11 December 2022, 00:18:04 UTC |
b98a4c0 | Raphael Vallat | 04 December 2022, 18:18:34 UTC | Update hypnogram in quickstart | 04 December 2022, 18:18:34 UTC |
399d984 | Darigov Research | 09 November 2022, 05:04:49 UTC | fix: Corrects small typo in readme (#100) | 09 November 2022, 05:04:49 UTC |
7a84060 | remrama | 03 October 2022, 14:15:55 UTC | Added lightgbm to setup.py (#98) | 03 October 2022, 14:15:55 UTC |
fc51d93 | Raphael Vallat | 27 August 2022, 01:21:03 UTC | Release v0.6.2 (#92) * Update version * Build doc | 27 August 2022, 01:21:03 UTC |
5d1ff92 | Raphael Vallat | 03 August 2022, 01:00:54 UTC | Add EEG-HRV coupling notebook (#89) * Added EEG-HRV coupling notebook * Minor updates | 03 August 2022, 01:00:54 UTC |
b3f153f | Matias Andina | 19 July 2022, 22:24:52 UTC | adding vmax vmin functionality with minimal tests #73 (#75) * adding vmax vmin functionality with minimal tests #73 * Black formatting * Update changelog + unit tests Co-authored-by: Raphael Vallat <raphaelvallat9@gmail.com> | 19 July 2022, 22:24:52 UTC |
65f033f | Raphael Vallat | 19 July 2022, 22:23:28 UTC | Functions to compare agreement of events detections (#71) * Initial commit of the compare_detection function * Add unit test for compare_detection + docstring * Add compare_channels and compare_detection methods * Add "Channel" as index name * Add unit tests for compare_detection and compare_channels * Updated changelog * Added methods in spindles notebook * Black formatting * Fix unit test | 19 July 2022, 22:23:28 UTC |
b1890be | Raphael Vallat | 08 July 2022, 22:50:31 UTC | Better handling of flat data in numba function and spindles detect (#86) | 08 July 2022, 22:50:31 UTC |
a281d55 | Raphael Vallat | 20 June 2022, 17:34:42 UTC | Black formatting (#83) * Use black code formatting + GH Actions * Reformat setup and conf | 20 June 2022, 17:34:42 UTC |
4d87b5c | Raphael Vallat | 20 June 2022, 17:28:00 UTC | Add conda install instructions (#76) | 20 June 2022, 17:28:00 UTC |
5e65ed5 | Raphael Vallat | 03 June 2022, 20:59:18 UTC | Updated changelog | 03 June 2022, 20:59:18 UTC |
a192252 | Raphael Vallat | 03 June 2022, 20:55:51 UTC | Use MNE for conversion Volts to uV (#70) * Bump MNE to 0.23 raw.get_data(units="uV") * use units="uV" in raw.get_data() instead of multiplication by 1e6 * Use a dict for units to handle multiple types in raw * Fix residual "multiply by 1e6" | 03 June 2022, 20:55:51 UTC |
34e40b6 | Raphael Vallat | 03 June 2022, 19:09:38 UTC | Add two new functions: a) find periods in hypnogram and b) heart rate by stage (#68) * Added hypno_find_periods * Updated api + docstrings * Add ECG dataset * Add sleepecg to requirements * Add is_sleepecg_installed * Add hrv stage function * Add unit tests * Update changelog and API * Fix typo in changelog * Fix windows unit tests? * Force dtype to int32 * Force int64? * do not check dtype * Add support for str dtype in hypno_find_periods * Implemented @remrama changes * Handle sf = array(...) | 03 June 2022, 19:09:38 UTC |
71c0a82 | Raphael Vallat | 15 March 2022, 16:59:45 UTC | Switch to 0.6.1 | 15 March 2022, 16:59:45 UTC |
d1cb4aa | Raphael Vallat | 15 March 2022, 16:49:31 UTC | CRITICAL: FIX FOR SPINDLES DETECTION! (#55) * CRITICAL: FIX FOR SPINDLES DETECTION! * Updated no.convolve in notebook * Removed notebook * Updated changelog | 15 March 2022, 16:49:31 UTC |
2383628 | Raphael Vallat | 20 February 2022, 22:22:33 UTC | Update notebooks | 20 February 2022, 22:22:33 UTC |
4cb74b0 | Raphael Vallat | 20 February 2022, 18:10:24 UTC | Reference to quickstart in doc | 20 February 2022, 18:10:24 UTC |
fa6ca6e | Raphael Vallat | 20 February 2022, 18:07:12 UTC | Use pd.concat instead of frame.append | 20 February 2022, 18:07:12 UTC |
021e306 | Raphael Vallat | 20 February 2022, 18:03:33 UTC | Remove python version badge from readme | 20 February 2022, 18:03:33 UTC |
11bb22a | Raphael Vallat | 20 February 2022, 17:51:44 UTC | Remove Travis CI and add cov to GH Actions | 20 February 2022, 17:51:44 UTC |
828fdd7 | Raphael Vallat | 20 February 2022, 17:45:00 UTC | Remove Python 3.6 from CI test | 20 February 2022, 17:45:00 UTC |
357dd2b | Raphael Vallat | 20 February 2022, 17:39:22 UTC | Updated docs | 20 February 2022, 17:39:22 UTC |
2b3c03b | Raphael Vallat | 20 February 2022, 17:33:18 UTC | Minor fix in quickstart | 20 February 2022, 17:33:18 UTC |
ac883f0 | Raphael Vallat | 20 February 2022, 17:29:40 UTC | Updated version number 0.6.0 | 20 February 2022, 17:29:40 UTC |
a467ffa | Raphael Vallat | 20 February 2022, 17:29:31 UTC | Updated changelog | 20 February 2022, 17:29:31 UTC |
daaffc9 | Raphael Vallat | 29 December 2021, 01:17:47 UTC | Merge branch 'master' into develop | 29 December 2021, 01:17:47 UTC |
6b2762f | Raphael Vallat | 29 December 2021, 01:16:56 UTC | Merge pull request #51 from snwnde/enh [ENH] Speed up `_index_to_events` | 29 December 2021, 01:16:56 UTC |
3338a31 | Senwen Deng | 24 December 2021, 09:29:26 UTC | speed up `_index_to_events` #50 | 24 December 2021, 09:29:26 UTC |
187841e | Raphael Vallat | 02 November 2021, 04:28:38 UTC | Finished first full draft of quickstart | 02 November 2021, 04:28:38 UTC |
88baf30 | Raphael Vallat | 30 October 2021, 00:59:05 UTC | ndPAC is now calculated including unreliable events + no propcoupled column | 30 October 2021, 00:59:05 UTC |
4b9764f | Raphael Vallat | 30 October 2021, 00:43:55 UTC | Added more unit test for sw_detection | 30 October 2021, 00:43:55 UTC |
6dadbbc | Raphael Vallat | 29 October 2021, 23:52:46 UTC | Use np.float64 instead of np.float | 29 October 2021, 23:52:46 UTC |
b3df180 | Raphael Vallat | 29 October 2021, 23:50:26 UTC | Add verbose parameter to hypno_upsample_to_data | 29 October 2021, 23:50:26 UTC |
d203a62 | Raphael Vallat | 29 October 2021, 23:33:29 UTC | flake8 + attempt to fix tests | 29 October 2021, 23:33:29 UTC |
7158805 | Raphael Vallat | 29 October 2021, 22:58:03 UTC | Added coupling_params to sw_detect + updated notebook | 29 October 2021, 22:58:03 UTC |
6aa4ecf | Raphael Vallat | 29 October 2021, 22:32:28 UTC | Added plot_hypnogram to API | 29 October 2021, 22:32:28 UTC |
bb822ef | Raphael Vallat | 29 October 2021, 22:28:53 UTC | Updated SW threshold in step-by-step notebook | 29 October 2021, 22:28:53 UTC |
1a41072 | Raphael Vallat | 29 October 2021, 22:21:38 UTC | Added references to eLife | 29 October 2021, 22:21:38 UTC |
4ac0111 | Raphael Vallat | 29 October 2021, 22:00:21 UTC | Clean conf.py file | 29 October 2021, 22:00:21 UTC |
10296fc | Raphael Vallat | 29 October 2021, 21:58:07 UTC | Added IRASA PR to changelog | 29 October 2021, 21:58:07 UTC |
0a4bec3 | Raphael Vallat | 29 October 2021, 21:55:19 UTC | Merge branch 'master' into develop | 29 October 2021, 21:55:19 UTC |
bd9f9ab | Raphael Vallat | 29 October 2021, 21:53:00 UTC | More conservative amplitude thresholds in sw_detect | 29 October 2021, 21:53:00 UTC |
ceb71d8 | Raphael Vallat | 29 October 2021, 18:20:05 UTC | SO-sigma coupling major changes * Use ± 1 sec around negative peak * Report thresholded ndPAC (unreliable set to zero) * Report ndPAC of supzero events + proportion of coupled events when using summary | 29 October 2021, 18:20:05 UTC |
68d96fb | Raphael Vallat | 29 October 2021, 16:59:43 UTC | Started working on quickstart | 29 October 2021, 16:59:43 UTC |
1f83229 | Raphael Vallat | 26 October 2021, 15:03:03 UTC | Merge pull request #42 from moritz-gerster/IRASA_fix Inform user about resampled fitting range | 26 October 2021, 15:03:03 UTC |
dee6432 | Moritz | 25 October 2021, 06:44:55 UTC | Change highpass/lowpass default behavior | 25 October 2021, 06:44:55 UTC |
e3290fc | Moritz | 23 October 2021, 08:11:28 UTC | Check if highpass and lowpass is known | 23 October 2021, 08:11:28 UTC |
4a54716 | Moritz | 23 October 2021, 08:07:56 UTC | Import and include set_log_level | 23 October 2021, 08:07:56 UTC |
fd18db2 | Moritz | 23 October 2021, 08:03:35 UTC | Add verbose in doc string | 23 October 2021, 08:03:35 UTC |
7684c8d | Moritz | 19 October 2021, 07:00:57 UTC | Modify warning messages | 19 October 2021, 07:00:57 UTC |
f049fc3 | Moritz | 18 October 2021, 15:39:54 UTC | Add reference | 18 October 2021, 15:39:54 UTC |
bc67c47 | Moritz | 18 October 2021, 15:20:06 UTC | Inform user about evaluated frequency ranges | 18 October 2021, 15:20:06 UTC |
70def16 | Moritz | 18 October 2021, 15:17:49 UTC | Retract last commit | 18 October 2021, 15:17:49 UTC |
de5ffc8 | Moritz | 18 October 2021, 13:06:12 UTC | Exchange natural logarithm with logarithm base 10 | 18 October 2021, 13:06:12 UTC |
f6f3285 | Raphael Vallat | 05 September 2021, 01:52:55 UTC | "From Stage" as index name in yasa.transition_matrix | 05 September 2021, 01:52:55 UTC |
4b99fff | Raphael Vallat | 05 September 2021, 01:52:34 UTC | yasa.topoplot is now case-insensitive for channel names | 05 September 2021, 01:52:34 UTC |
a7e2f75 | Raphael Vallat | 25 August 2021, 21:42:03 UTC | Updated API and changelog | 25 August 2021, 21:42:03 UTC |
ce78806 | Raphael Vallat | 23 August 2021, 18:42:43 UTC | Added plot_hypnogram function | 23 August 2021, 18:42:43 UTC |
af346bf | Raphael Vallat | 23 August 2021, 17:38:35 UTC | Removed modulation index from sw_detect | 23 August 2021, 17:38:35 UTC |
79b5871 | Raphael Vallat | 22 August 2021, 00:29:07 UTC | Add as_dataframe parameter in get_sync_events | 22 August 2021, 00:29:07 UTC |
30df6ed | Raphael Vallat | 21 August 2021, 23:26:26 UTC | Added mask=None in detection methods (slow-waves, spindles and REM) | 21 August 2021, 23:26:26 UTC |
fa5e6c0 | Raphael Vallat | 21 August 2021, 22:08:37 UTC | Add find_cooccurring_spindles and modulation index to yasa.sw_detect | 21 August 2021, 22:08:37 UTC |
4d23501 | Raphael Vallat | 18 August 2021, 03:37:20 UTC | Switch to 0.5.1 and added trained classifier to manifest | 18 August 2021, 03:37:20 UTC |
f5d6afa | Raphael Vallat | 11 August 2021, 22:44:34 UTC | Upload doc 0.5.0 | 11 August 2021, 22:44:34 UTC |
7e816e3 | Raphael Vallat | 11 August 2021, 22:00:28 UTC | Re-run all notebooks | 11 August 2021, 22:00:28 UTC |
168e035 | Raphael Vallat | 11 August 2021, 22:00:06 UTC | Major: add classifier for YASA 0.5.0 | 11 August 2021, 22:00:06 UTC |
c6ba8b4 | Raphael Vallat | 09 August 2021, 18:59:01 UTC | Minor improvements in general doc + updated dependency + flake8 100 lines | 09 August 2021, 18:59:01 UTC |
24edc66 | Raphael Vallat | 09 August 2021, 18:44:29 UTC | Change version in setup and init to 0.5.0 | 09 August 2021, 18:44:29 UTC |
c88ddee | Raphael Vallat | 09 August 2021, 18:42:09 UTC | Updated the size of the rolling windows in SleepStaging | 09 August 2021, 18:42:09 UTC |
c0deb5b | Raphael Vallat | 09 July 2021, 16:52:54 UTC | Updated notebook artefact rejection | 09 July 2021, 16:52:54 UTC |
aafcd97 | Raphael Vallat | 09 July 2021, 00:05:14 UTC | Updated requirements pyRiemann 0.2.7 (no restriction on sklearn) | 09 July 2021, 00:05:14 UTC |
fdf16a3 | Raphael Vallat | 02 July 2021, 18:21:53 UTC | Fix rolling window length in doc SleepStaging | 02 July 2021, 18:21:53 UTC |
2b8c262 | Raphael Vallat | 02 July 2021, 18:19:06 UTC | Add example phase and amplitude signal to notebook | 02 July 2021, 18:19:06 UTC |
592f8ff | Raphael Vallat | 22 June 2021, 23:51:47 UTC | BUGFIX: Slow-waves duration must be < max(dur_pos) + max(dur_neg) | 22 June 2021, 23:51:47 UTC |
4d0c540 | Raphael Vallat | 22 June 2021, 22:52:35 UTC | Add debug notebooks to gitignore | 22 June 2021, 22:52:35 UTC |
845622e | Raphael Vallat | 22 June 2021, 22:40:05 UTC | Remove flat electrode in compute_feature_stage + avoid in-place modification + add argument to disable slow 1/f | 22 June 2021, 22:40:05 UTC |
e954401 | Raphael Vallat | 18 June 2021, 17:12:27 UTC | Added coincidence matrix | 18 June 2021, 17:12:27 UTC |