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* ENH: Remove 15-char limit for FIF * FIX: Public API
…s#8889) Must not be merged before mne-tools/mne-tools.github.io#23
* Fixing missing info for some templates Fixing missing info for the 2mo and the 18mo templates * Adding missing ANTS2-0Months3T.txt file. * STY: Flake Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* ENH: Allow channel-specific annotations * FIX: rename, drop, example, doc * DOC: Clarify
* BUG: Fix bug with empty dim * Update latest.inc
* macOS 11 compatiblity for PyVista STC plots Sets `QT_MAC_WANTS_LAYER=1` for STC plots via PyVista. Was required on my system with macOS 11.2.1, Qt 5.12.9, pyqt 5.12.3 (installed from `conda-forge`) Previous fix via mne-tools#8554 didn't cover STC plots. cc @cbrnr, @GuillaumeFavelier * Remove backend check * Update changelog * Better changelog
* Ensure times at which chpi are fitted are valid samples * SKip zero-length annotation
* remove css theme overrides * remove obsolete javascript after upstream theme fixes * update theme commit number * missed one * Update requirements_doc.txt * FIX: Workaround pip Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* Ica_plot_sources_exc * Fix Typo * fix spelling * touch example to trigger CI rendering * restrict ch_names to picks before plotting Co-authored-by: Daniel McCloy <dan@mccloy.info>
* Fix indexing dipoles read from a bdip file * Fix test * Update what's new Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>
* Add basic dock * Move time controller * Update toggle_interface * Move speed controller * Rename controller to widget * Rename * Add renderer selector * Move smoothing and clim widgets * Fix UpdateColorbarScale * Fix restore_user_scaling * Improve select_renderer * Migrate orientation widget * Fix time actor * Refactor * Make the time widget a slider * Fix test_layered_mesh * Fix test_brain_time_viewer * Fix _clean * Mitigate pain of test_brain_screenshot * Remove cruft * Fix test_brain_traces * Fix test_brain_linkviewer * Simplify diff * Patch notebook for now * Simplify diff * Remove cruft * Refactor * Use combo_box.currentTextChanged * Fix test_notebook * Refactor notebook * Fix widgets * Refactor * Refactor colormap widget * Refactor * Turn the renderer widget into a QComboBox * Refactor label parameters * Add spacer before help button * Update tests * Refactor * Move Restore from tool_bar to Colormap group * Update test * Refactor layout management * Change playback speed default * Add compact parameter * Disband the time group * Rework alignment * Tweak UI * Rename * Add time group * Update notebook branch * Improve playback * Rename * Fix * Fix * Add QFloatSlider * Refactor * make pydocstyle * Improve Qt isolation * Move labels at the top * Fix * Refactor * Update color limits group * Update color limits group * Fix * Fix toggle_interface * Fix * Fix * Fix * Refactor * Add _AbstractDock * Rename * Rename * Add license * Refactor * Rename * Fix * Refactor * Remove cruft * Fix * Fix [skip azp][skip github] * Move builtin * Refactor * Fix * Refactor * MAINT: Refactor * FIX: Missed one * FIX: Scrollin * FIX: Notebook * Fix * Do not use _qt_screenshot * FIX: Restore * Fix Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* Fix * ENH: Uniform lighting Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* MAINT: Skip matplotlib pre for now * FIX: Follow order of pip * FIX: Better naming * FIX: Missed one * FIX: Export * FIX: Move back * FIX: To script * FIX: RC1
* fix CSS to scroll dataframes * touch tutorial to trigger rendering
) * Adding time frequency pr. * Adding change entry. * Clean up docstring. * Fixing docstring. * Fix docstring. * Adding unit tests. * Adding docstring. * Fixing docstring. * Fixi flake. * Fix docstring. * Fix docstring. * Update mne/fixes.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Fix docstring. Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* Fixing wrong channel-adjacency-matrix for Neuromag122 * Fixing too long line * Removed neuromag122_neighb.mat * Update version of testing-dataset * Test for Computation of Neuromag122-Channel-Adjacency * Removed too long line * Update md5-hash for testing * Update mne/channels/tests/test_channels.py Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * Add . in docstring Co-authored-by: Eric Larson <larson.eric.d@gmail.com> Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* add option to penalized large rotations * Use Bias Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* ENH: Better float slider spacing and interaction * STY: Flake8 * Add _dock_named_layout * ENH: Use buttons * FIX: Flake [ci skip] * Fix callback * Fix * FIX: Fix for macOS Co-authored-by: Guillaume Favelier <guillaume.favelier@gmail.com>
* converted Dominik's tutorial to .py for sphinx * removed an unnecessary line * collapsed an unnecessary section into the next one * workaround for missing electrodes.tsv and coordsystem.json no files -> warnings -> docs won't build * reformatted headings * consistent use of SSVEP/vSSR * removed multitaper code * fixed list formatting * fixed a typo * added explanation about snr from Dominik * moved variable definition closer to the first use * remove minor namespace issues and typos * adapt author email * adapt mne-bids data loader to newest version * add section for grand average SNR topoplot * add data retrieval from osf source * Update tutorials/time-freq/ssvep.py Co-authored-by: kalenkovich <e.kalenkovich@gmail.com> * add config-type for dataset to utils/config.py * a more concise snr calculation * switched to using Dominik's snr plotting function * start stems from 1 - snr of noise By default, pyplot.stem draw stems starting from 0 which is not appropriate for SNR. * minor: formatting * use line plot for grand averages Using a stem plot is left as an option. * don't let the user plot too much in the background * switch to grey for background plotting * joined the code for trial- and channel- averaged snrs * removed SNR-plotting function Also changed "trial average" to "averaged over trials", etc. * updated general intro combine preprocessing steps into single cell * first rough rearrangement of psd/snr overview plots * better texts etc for section 2 (psd and snr spectra) * Update tutorials/time-freq/ssvep.py remove typo Co-authored-by: Zhenya <e.kalenkovich@gmail.com> * first reorderd version of the trial subsetting and topoplot section. needs further polishing * finishing trial subsetting and topoplot section. * change welch parameter to yield 0.1hz resolution * simple stats section with bar plot and t-tests * preallocation of an wrap-up section :) * a new series of plots on the effect of trial length on SNR we might or might not want to (partly) include and discuss this * ..fix sphinx issue * timewindow snr: - switch orientation of boxplots - small tweak of welch window overlap * snr + harmonics: - take fewer lines to plot the bars * fix: exchange false trial duration throughout (30s -> 20s) * vssr over time: 2s sliding window * house keeping, tweaking the texts etc.. * fix typos Co-authored-by: Zhenya <e.kalenkovich@gmail.com> * further cleaning: - add short debriefing - tighten open science lesson - typos * pep8 style * pep8 style * pep8 style * rename to plot_ssvep.py * remove mne-bids dependency * pep8 * aftermath of mne-bids removal * ci: fix sphinx warning * ci: fix sphinx warning? * Apply suggestions from code review Co-authored-by: Robert Luke <748691+rob-luke@users.noreply.github.com> Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * formatting by @larsoner * formatting by @larsoner * use matplotlib's OOP interface * Apply agramfort's formatting suggestions from review Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * docstring * switch to using plain FFT and exclude 1st second of each trial * minor adjustments of the texts adding references remove a section to speed up build * pep8 * move dataset info to datasets_index.rst * add dataset_version via version.txt * Apply suggestions from code review add internal doc links Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * add dataset to dataset.rst * Revert "add dataset to dataset.rst" This reverts commit 9a4104b * add ssvep dataset to datasets.rst * Apply agramfords suggestions from code review Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * apply agramfort's further suggestions * apply rob-luke's suggestions: - remove notch and low-pass filter - denote stimulation frequency and trial duration more exactly * apply rob-luke's suggestions: - switch to sequential greyscale for last plot * pep8 * sphinx * snr topoplot without private methods * better docstring for snr def * fix typo * conditional data download on circleci * fix conditional data download on circleci * sphinx formatting: - automatic TOC * trailing whitespace * TOC depth * Apply rob-luke's suggestions from code review Co-authored-by: Robert Luke <748691+rob-luke@users.noreply.github.com> * edit changelog * Apply suggestions by @larsoner Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * move changelog entry up Co-authored-by: kalenkovich <e.kalenkovich@gmail.com> Co-authored-by: Robert Luke <748691+rob-luke@users.noreply.github.com> Co-authored-by: Eric Larson <larson.eric.d@gmail.com> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* BUG: Fix interactive update of mapping * MAINT: Test * FIX: Fix tol * FIX: Always explicit * FIX: Faster updates * FIX: No need * FIX: Simpler
* Touch example * Touch example * Revert _qt_disable_paint[skip azp][skip github] * Revert "Revert _qt_disable_paint[skip azp][skip github]" This reverts commit 5ac2141. * Update & ProcessEvents? [skip azp][skip github] * Again but this time with other tests * Fix
* BUG: Fix positioning of flatmaps * FIX: Missed paren
* change csd to average reference * put back and take out depreciated note * shouldn't have taken down notes
* Reproduce [circle front][skip azp][skip github] * Touch example [skip azp][skip github] * TST: Mitigate * Revert example * Build doc [circle full] * Refactor * Refactor * Touch example
* Add XDF to "Reading EEG data" tutorial * Fix flake8 warning * [circle full] add comment * Use examples of formats, not exhaustive list Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Better motivation for not having an XDF loader Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> * Include .fdt in EEGLAB section * Provide EDF links earlier * Forgot > in hyperlink * Rewording Co-authored-by: Daniel McCloy <dan@mccloy.info> * ENH: Add separate example * FIX: Double link * Apply suggestions from code review Co-authored-by: Daniel McCloy <dan@mccloy.info> Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org> Co-authored-by: Daniel McCloy <dan@mccloy.info> Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* MAINT: Rename examples and tutorials * FIX: Links * move almost everything * ditch redundant tutorial & add reference to sklearn version * add note to filtering bkgd tutorial * order the new "forward" and "inverse" categories * update reports tutorial * overhaul in-place processing tutorial * fix crossref * move simulation tuts too * add custom redirects * fix target paths; allow overwriting existing redirects * remove unnecessary bits * patch theme * FIX: Build again [skip azp] [skip github] * MAINT: Move [skip github] [skip azp] Co-authored-by: Daniel McCloy <dan@mccloy.info>
* FIX brainvision I/O: Software Filters section * TEST brainvision VHDR with long sensor name and software filters * FIX: Line endings Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* MAINT: Check name URLs [circle linkcheck] [skip azp] [skip github] * FIX: URLs [circle linkcheck] [skip azp] [skip github] * FIX: One more [circle linkcheck] [skip azp] [skip github] * FIX: One more [circle linkcheck] [skip github] [skip azp]
…ip github] [skip azp] (mne-tools#9329) This is already mentioned in the text above the respective code block, but the question came up anyway on the forum. So let's be even more explicit. https://mne.discourse.group/t/annotating-continuous-data
* remove blitting code for vlines * fix scrolling bug
* Add cathode-location and fix doc * Implementing matrix-multiplication approach (by @jasmainak) * Fix returning ref_to from _check_before_reference * Refine how Info is copied to new channels to avoid mixups and pass tests * Adjust test comparing info of anode/cathode and bipolar-channel to also pass when bipolar-channels are appended * Concatenation of Reference-Instances outside the loop * Using @-operator for matrix-multiplication * Update test_set_bipolar_reference to show info-keys responsible for the errors * Improve performance by creating reference-instance from scratch * channel-information including location is taken from anode * Update test for info just taken from anode * Fix import of create_info, improve docs * Addition to latest.inc * Fix latest.inc * Refactor assert-statements in test_reference.py as suggested by @larsoner * Update latest.inc as suggested by @jasmainak Co-authored-by: Mainak Jas <jasmainak@users.noreply.github.com> Co-authored-by: Mainak Jas <jasmainak@users.noreply.github.com>
* MAINT: Better split of reqs * FIX: Manifest
* Change default camera focalpoint * Touch more examples * Review * Revert * Touch again
…nis montage (mne-tools#9141) * Add raw montage files sent by Artinis * Initial pseudo code * Tweaks * Draft _set_montage_fnirs * Tweaks * Example with optode montage as elc file * Clean up and add Brite 23 * Tweak skeleton code and push example * Add TODOs * Update also dig * Fix optodes in the brain * Add fetch_fsaverage * Set montage with str in tutorial * Add example of how to load unstructured data * Typo * More typos * Typos * Fix linking * Small doc tweaks * Add tests. More needed * More tests * Update doc and tests * Fix pydocstyle * Add more warning and limitations * added wrong file * Fix reverted source and detector * Typo * More warnings * Check fNIRS ch_names and add wavelength * No modification of wavelength * Test Brite, intensity, OD * Use _check_channels_ordered with new API * Simplify _set_montage_fnirs Co-authored-by: Robert Luke <748691+rob-luke@users.noreply.github.com> * Add tests for channel variations * TST: Test rough equivalent with fsaverage * Test 2 more built in montages (OctaMon & Brite 23) * Update tutorial * Describe changes * Update latest * Apply suggestions from code review Co-authored-by: Robert Luke <748691+rob-luke@users.noreply.github.com> * Fix ref * Update in-line comments * Fix refs * Move channel info and add read_custom_montage Co-authored-by: Johann Benerradi <johann.benerradi@gmail.com> Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
* Add functionality to export to set files. Import channel location data from csv files. * Fix formatting. * Fix formatting. Remove redundant code. Add docstrings. * Fix ch_names bug. Finish basic tests. Remove unnecessary public functions. * Fix docstrings & formatting. Fix channel location bug. Add channel location to tests. Add raw save_set test. * Add docstrings to tests. * Move export_set to pyeeglab. * Rename to eeglabio. * Change to MNE-independent eeglabio implementation. * Fix formatting. * Change to multi-format export. * Fix drop channel in-place. * Fix typo. * set to list * Fix docstrings. Check eeglabio installation. * Add eeglabio docs support. * Fix warning messages. * Link to eeglabio. * Fix test docstrings. * Fix docstrings. * Fix tests by adding eeglabio check. * Add what's new entry. * Switch export set test to pytest skip. * Modularize exports and docstrings. Clarify and verify export formats. * Fix what's new. * Add verbose decorator. * Fix docstrings and what's new. * Switch export supported formats to dict. Fix docstrings. * Add docs for _infer_check_export_fmt. * Pretty print supported formats. * Expand supported string code. Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com> * Remove redundant check in test_export_set. * Add eeglabio requirement. * Refactor export docdict, imports, function names. * Fix als coords fn name. Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>
* nitpicks in eeglab export * FIX: Tweak tol Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
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Sorry this isn't what I wanted to do. I was trying to just rebase your original PR. I think I made a mess. I am closing this. |
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Ok no worries. Let me know if I need to do something here, I'm not used to deal with PRs. |
rderollepot
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Nov 28, 2022
* start abstraction of Browser-Classes * outline of data-management-class * wip refactoring MNEBrowserFigure * refactored Browser-Initialization into MNEDataBrowser * fix some style-issues and remove remnants * start with integration of pyqtgraph-prototype * make pyqtgraph optional (just for development, can be removed again for final PR) * more refactoring of mpl-methods into BrowserBase * fixes for failing tests * add docstrings in _browser.py * move _update_projector-call into BrowserBase * add use/set/get for browser * rename 2D to Browser to avoid confusion * move inheritance of BrowserBaser from MNEFigure to MNEBrowseFigure * refactored _annotation_helper from test_raw.py * fix flake * move base-classes/funcs from _browser.py back to _figure.py to facilitate review * update from upstream * remove set/get/use-browser from __init__.py again to prevent make docstring from failing * add show_browser and other adjustments for pyqtgraph * refactoring _close into BrowserBase * add block for pyqtgraph * [revert for PR] adjust plot-function to accept kwargs from benchmark * fix annotation-key still working when plotting epochs * add docstring to show_browser * refactor midpoints into BrowserBase for epochs * add show to show_broser * add pyqtgraph to browse_backend-fixture * fix block not supported in Figure.show() * WIP adapt test_raw.test_plot_raw_traces * adapt test_plot_raw_traces to make it work for matplotlib and pyqtgraph * refactor _redraw * refactor _update_data * change bad-color from rgb to hex * pyqtgraph always blocks execution * reinsert block for pyqtgraph * make _redraw not abstract anymore (not needed for pyqtgraph) * add pyqtgraph-backend * fix butterfly-bug showing channels still in old y-position [ci skip] * rebase on main [ci skip] * Set usage of OpenGL to false by default * organize keyboard-shortcuts [ci skip] * clarify index-system for traces and set z-values for traces and annotations [ci skip] * add exception-hook from pytest-qt [ci skip] * actually raise exceptions from qt [ci skip] * fix bugs annotations (removing decription/select visible) [ci skip] * reorganize imports [ci skip] * fix bug _update_regions_colors [ci skip] * add '=' to keyboard-shortcuts and make scale-steps smaller [ci skip] * import pg-backend from separate repo[ci skip] * remove pg-backend from PR[ci skip] * update repo-link to mne-tools[ci skip] * Update mne/viz/_figure.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * remove _pg_figure from _backends[ci skip] * add browser-backend-functions to documentation[ci skip] * avoid codespell-failure [ci skip] * remove pyqtgraph from tests (tests will be run in mne-qt-browser for now) * update parameters for Raw.plot() * fix flake * fix pip install link * fix table in set_browser_backend * fix butterfly showing always all channels despite of selection * adjust test_scale_bar for pyqtgraph [ci skip] * refactor channel context figs [ci skip] * change to relative imports [ci skip] * refactor _new_child_figure [ci skip] * update some key-presses [ci skip] * adapt test_plot_raw_ssp_interaction to pyqtgraph [ci skip] * adapt test_plot_raw_child_figures to pyqtgraph [ci skip] * change default of event_lines to list [ci skip] * add drag to _fake_click [ci skip] * adapt test_annotations to pyqtgraph [ci skip] * adapt test_clock_xticks to pyqtgraph [ci skip] * remove install-question [ci skip] * adapt pyqtgraph-backend to test_plot_raw_selection [ci skip] * adapt pyqtgraph-backend to test_min_window_size [ci skip] * adapt pyqtgraph-backend to test_plot_raw_groupby [ci skip] * fix multiple tests [ci skip] * adapt annotation-test for pyqtgraph [ci skip] * fix more test-issues [ci skip] * add pyqtgraph to test_raw-suite [ci skip] * fix flake * update feature-grid * update from main branch * fix checkbox-click issue (inconsistent across OS) * fix test_plot_raw_ssp_interaction for linux * update from upstream2 * fix flake * simplify ssp_interaction * fix test_min_window_size for Windows-CI * fix flake * implement review-feedback #1 * fix _proj_click_all for inconsistent fake-click-behaviour * clarify docs for preload * fix flake * [Refactor]: browser_backend-fixture for consistency * DOC: Add doc comments for block * add speed test * rename preload to precompute * fix unused import * remove unnecessary parameters * remove speed-test * remove automatic installation of mne-qt-browser * revert removal of automatic installation until mne-qt-browser is uploaded to PyPi * FIX: Route through call * add mne-qt-browser to requirements.txt * update latest.inc * fix flake * fix latest.inc * update test-dependencies * specify docs regarding block-behaviour * fix typo in github_actions_dependencies.sh * fix docstring for plot_raw * fix docstring for plot_raw again * fix docstring for plot_raw * add mne-qt-browser to azure_dependencies.sh * add mne-qt-browser to environment.yml * specify latest.inc * specifiy use_opengl documentation * Update mne/viz/_figure.py Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * FIX: Fix test [skip azp] [skip circle] * FIX: Path [skip azp] [skip circle] * revert color-name-changes * MAINT: Test only on one run * FIX: Remove * MNT: Add to mne sys_info * DOC: Fix doc build * FIX: Better * DOC: Add link to mne-qt-browser issues in docs * Update mne/utils/docs.py Co-authored-by: Daniel McCloy <dan@mccloy.info> * Update mne/utils/docs.py Co-authored-by: Daniel McCloy <dan@mccloy.info> * Update mne/viz/raw.py Co-authored-by: Daniel McCloy <dan@mccloy.info> * FIX: fix flake * FIX: Test * FIX: Correct check * STY: Flake * FIX: One more mark Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> Co-authored-by: Eric Larson <larson.eric.d@gmail.com> Co-authored-by: Daniel McCloy <dan@mccloy.info>
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I wish to push in to mne-tools#7936, not sure if this GitHub magic will work.
First I have just rebased to main