Develop (#267)

* example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule * ci: update python to 3.8, update wxPython, update setup-python action * ci: pin ubuntu versions to 22.04, updated wxPython urls * ci: bumped psychopy to 2023.1.0 * build(deps): set upper supported numpy version to 1.23.x * chore: applied no_implicit_optional * update dependencies - for build (#220) * major update: merging develop to master (#217) * example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> * update dependencies - seaborn * docs/perf: reduced the imports: `cueing` example * bug: update deprecated `plot_psd()` method - feature of new `mne` version. - instead of doing plot_psd() from the `mne.io.Raw` object, must do this: - `raw.compute_psd().plot()` - i.e., has to pass through a `spectrum` object * updated deprec. `mne` function * perf: removed importage of unused packages from example - One of them, i.e., `collections.Iterable` is even deprecated. - Must use `collections.abc.Iterable` instead now. - Resulting in faster build/user run * bugfix: `plot_conditions` - due to `sns` deprecation * bugfix: resolved `psd_welch()` deprecation (`mne`) --------- Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]> * Updated psychopy (#215) * update psychopy for psychxr compatibility * updated n170 example to run again. * Updated doc examples for N170, P300 and SSVEP after Experiment Class Refactor (#218) * major update: merging develop to master (#217) * example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> * Updated doc examples * Update 00x__n170_run_experiment.py fix: typo in func param --------- Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Ore O <[email protected]> * fix error breaking n170 test (#223) * fixed requirements.txt so 'pip install -e .' would work on windows. (#229) * Get CI test builds working again! (#170) * Revert "Revert PR #167: "ci: fix broken CI" (#169)" This reverts commit 2d74871. * Update Makefile * fix: Update vep.py import * Update Makefile * Update vep.py * fix: typo in makefile * fix: update BaseExperiment class reference * Update Makefile * Update vep.py * Update 01r__n170_viz.py * makefile: install libnotify4 --------- Co-authored-by: Ore O <[email protected]> * fix macos build (#245) * Add devcontainer configuration for CPU environment * Fixed the python version needed * Fix plot conditions (#257) * fixed plot_conditions functoni issues * small change to viz n170 plotting example * small change to viz p300 plotting example * fixed to plotting issue * modify plot command * update example files * fix condition label bug * fix: set layout engine to fix colorbar error --------- Co-authored-by: Ore O <[email protected]> * Started the name switch (#251) * started renaming from eegnb to eegexpy * more eegnb renaming work * more eegnb switches * more relabelling * ssvep renamings * cueing eg * update for more misc files * more of the same * update * Update and rename available_notebooks.md to available_experiments.md * Add newlogo (#260) * Add files via upload * Update README.rst * added to enable eegexpy commands (#265) * started alias of main package for imports (#266) * Add multiple installation options (#263) * added newly separated analysis and streaming utils files * modified setup and requirements to allow for optional install types * updated imports in experiment examples * fixed some typos * Update requirements.txt moved click library to stim pres requirements section * Update requirements.txt Co-authored-by: Taha Morshedzadeh <[email protected]> * Update Makefile * Update docs.yml * Update Makefile this does a full build with all dependencies for EEG-ExPy --------- Co-authored-by: Ore O <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]> * Add support for /develop in docs site (#259) * feat: update action to build doc page in a folder * test: see if it works without if clause * test: change source for docs * Initial support for VR headsets (#241) * fixed requirements.txt so 'pip install -e .' would work on windows. * added support for n170 to run on rift * altered logic to add back in jitter * simplified logic * made fullscreen again * further simplified logic * decreased font size of instructions for vr * fixed instructions display, further simplified logic, removed logs * made code easier to read * reverted board back to muse * Enable headlocking to fix jittering - cancel out any rotation and translation coming from the headset. * fixed use_vr parameter to be set to False by default for existing experiments. * fix macos build * reverted unnecessary changes and made p300 experiment display correctly * added vr support for p300 and ssvep * fix psychxr version * adding vr doc * updated vr doco --------- Co-authored-by: John Griffiths <[email protected]> * ssaep volumefadingfixes (#81) * fixed duration on instructions screen * put sound object instantiation inside trials loop. fixes sound fading issue --------- Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Ore Ogundipe <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]>
NeuroTechX · Jun 21, 2024 · e03c52d · e03c52d
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -24,7 +24,7 @@ jobs:
         make install-deps-wxpython
     - name: Build project
       run: |
-        make build
+        make install-docs-build-dependencies
 
     - name: Build docs
       run: |
@@ -35,4 +35,9 @@ jobs:
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: doc/_build/html
-
+    - name: Deploy Dev Docs
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: doc/_build/html
+        destination_dir: develop
diff --git a/Makefile b/Makefile
@@ -1,6 +1,9 @@
 build:
 	# Use pep517 to install pygatt==4.0.5(deprecated setuptools/egg installer) on macos
-	pip install --use-pep517 .
+	pip install --use-pep517 .[full]
+
+install-docs-build-dependencies:
+	pip install -e .[docsbuild]
 
 test:
 	pytest

diff --git a/README.rst b/README.rst
@@ -12,9 +12,10 @@ EEG-ExPy
 .. |badge_binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/NeuroTechX/eeg-expy/master
 
-.. image:: https://github.com/NeuroTechX/EEG-ExPy/blob/master/doc/img/EEG-ExPy_Logo.png
+.. image:: ./doc/img/EEG-ExPy_Logo.png
    :align: center
 
+
 EEG-ExPy is a collection of classic EEG experiments, implemented in Python. The experimental protocols and analyses are quite generic, but are primarily taylored for low-budget / consumer EEG hardware such as the InteraXon MUSE and OpenBCI Cyton. The goal is to make cognitive neuroscience and neurotechnology more accessible, affordable, and scalable. 
 
 - **For an intro talk on the ***EEG-ExPy*** (formerly ***eeg-notebooks***) project see:** `JG's Brainhack Ontario presentation <https://www.crowdcast.io/e/brainhack-ontario/7>`_.  
@@ -87,7 +88,7 @@ The best place for general discussion on eeg-expy functionality is the `issues p
 
 
 
-.. image:: https://github.com/NeuroTechX/EEG-ExPy/blob/master/doc/img/eeg-notebooks_democratizing_the_cogneuro_experiment.png
+.. image:: ./doc/img/eeg-notebooks_democratizing_the_cogneuro_experiment.png
    :align: center
    :scale: 50
 
diff --git a/doc/getting_started/running_experiments.md b/doc/getting_started/running_experiments.md
@@ -139,3 +139,52 @@ eeg_device = EEG(device=board_name)
 # Run stimulus presentation
 n170.present(duration=record_duration, eeg=eeg_device, save_fn=save_fn)
 ```
+
+
+## Using virtual reality
+
+### Heads up display
+
+A heads-up display can be used for presenting experiments in a similar way to a monitor, without much modification.
+
+#### Features to be added in future releases:
+
+* Controller input
+* Controller haptic feedback
+
+### Prerequisites:
+* Oculus Rift compatible VR headset, e.g. Oculus Rift or Meta Quest series.
+* Native Windows installation with meta link compatible video card.
+* EEG device, e.g. OpenBCI Cyton or Muse
+
+If an experiment has the use_vr argument in its present method, it can have its stimulus presented to a subject's VR headset.
+The N170 experiment for example, can have its stimulus displayed on the VR headset with a simple modification to the 'use_vr' argument, when presenting an experiment:
+
+```python
+# Run stimulus presentation with VR enabled.
+n170.present(duration=record_duration, eeg=eeg_device, save_fn=save_fn, use_vr=True)
+```
+
+### 
+
+### Steps for running experiment in VR
+
+1. Launch the Oculus app on the Windows computer and the IDE or CLI to be used for running the experiment.
+2. Turn on the VR headset and put it on your head to make sure it is on and active, then take it off.
+3. Go to the 'Devices' view in the Oculus app, it will show the headset as connected and active, along with any inactive or connected controllers.
+4. Go to the 'Settings' view, under the 'Beta' title, enable 'Pass through over Oculus Link', double tapping the headset later with a fingertip will activate passthrough.
+5. Put the VR headset onto the head, activate passthrough to help with wearing the eeg device.
+6. Place the EEG device on top of the head.
+7. Ensure the electrodes are touching the scalp ok and not being blocked by the headset strap.
+8. From inside the VR headset's 'quick settings' dashboard, select 'Quest Link' and connect to the Oculus server running on windows, via air link or link cable.
+9. Once the Oculus menu has finished loading on the VR headset, open the built-in Oculus desktop app by using the touch controllers or gamepad.
+10. Try opening an eeg device raw data viwer and verify that the electrodes are receiving a good signal without too much noise, eg 'OpenBCI GUI'.
+11. Run the EEG-ExPy experiment from the command line or IDE, it should load and take control from the Oculus desktop app.
+12. Follow the experiment instructions, and press a key if necessary to begin the experiment and collect valid data.
+
+### Other experiments can have VR added too.
+
+1. Load/prepare stimulus in the same function as previously (def load_stimulus(self))
+2. Present stimulus in the same function as previously(def present_stimulus(self, current_trial: int))
+3. VR can be enabled for the experiment as part of the initializer to the base Experiment class, by default it is not enabled(use_vr=False) and will function the same as previously before VR functionality was added.
+
diff --git a/eegexpy/__init__.py b/eegexpy/__init__.py
@@ -0,0 +1,7 @@
+
+from eegnb.experiments import VisualN170,VisualP300,VisualSSVEP,AuditoryOddball
+
+from eegnb.analysis.utils import *
+
+
+