Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[electrophysiology_browser] Updated module documentation #8692

Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@

This module allows you to review, filter and download EEG recordings and metadata. Downloads are organized according to the EEG-BIDS standard.

Individual sessions can be accessed by clicking on the *raw* (for raw datasets) or *all types* (for all data) links of one of the rows under the links column, which will redirect you to the *View Session* page.
Individual sessions can be accessed by clicking on the *raw* (for raw datasets) or *all types* (for all data) links belonging to one of the rows under the 'Links' column, which will redirect you to the *View Session* page.
4 changes: 2 additions & 2 deletions modules/electrophysiology_browser/help/sessions.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,6 @@ Files can be downloaded containing only the recording signal, the events, or oth
- All files (tgz): a compressed folder containing all the recording data as well as the metadata for the EEG scan session.
- EEG: the file containing the session recording data.
- Electrode info (tsv): contains electrode locations.
- Channels info (tsv): channel status and filter settings.
- Channels info (tsv): channel status and filter settings.
- Events (tsv): events (both stimuli and responses) recorded during the session.

- Annotations (tsv): annotations (both stimuli and responses) recorded during the session.
Original file line number Diff line number Diff line change
Expand Up @@ -79,10 +79,9 @@ Hovering channel names while in 'isolate' mode will make that signal the only vi
### Electrode Map
The current implementation of the Electrode Map supports 2 display modes: 2D and 3D.

| 2D View | 3D View |
|:-------------------------:|:-------------------------:|
|<img width="300" src="https://images.loris.ca/eeg-browser/electrodes-2d-hover.png"/><br/> The 2D view is a stereographic projection of the electrodes position. Electrodes are indexed and their name is
displayed on mouse hover. | <img width="300" src="https://images.loris.ca/eeg-browser/electrodes-3d.png" /><br/> The 3D view displays the exact position of the electrodes on the brain. |
| 2D View | 3D View |
|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:-------------------------:|
| <img width="300" src="https://images.loris.ca/eeg-browser/electrodes-2d-hover.png"/><br/> The 2D view is a stereographic projection of the electrodes position. Electrodes are indexed and their name is displayed on mouse hover. | <img width="300" src="https://images.loris.ca/eeg-browser/electrodes-3d.png" /><br/> The 3D view displays the exact position of the electrodes on the brain. |


### Future developements to come
Expand Down
9 changes: 7 additions & 2 deletions modules/electrophysiology_browser/test/TestPlan.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@
* Check that if a session does not have annotation files, the `Annotations` download button is not clickable
* Check that if the session has annotation files, the `Annotations` download button is clickable and downloads the proper files
12. Test Breadcrumb link back to Electrophysiology Browser. [Automated Testing]
13. Test that if changes have been made to the session's annotations, the downloaded annotation files are correctly updated to match [Manual Testing]

### C. Visualization

Expand All @@ -29,10 +28,16 @@ and make sure the `Signal Viewer panel` displays correctly on the screen. (Docum
14. Delete `modules/electrophysiology_browser/jsx/react-series-data-viewer/src/protocol-buffers/chunk_pb.js` and set `useEEGBrowserVisualizationComponents` to false to simulate an environment for which the extra installation steps
have not been run yet.
Make sure `make dev` runs without failing, and that except the Signal Viewer panel, all the other components in the page display well.
15. Temporarily desactivate an entry in `physiological_parameter_file`
15. Temporarily deactivate an entry in `physiological_parameter_file`
for a ParameterTypeID IN (SELECT ParameterTypeID from parameter_type WHERE Name = 'electrophysiology_chunked_dataset_path')
and a chosen PhysiologicalFileID to simulate an environment for which the visualization components are not loaded.
Load the corresponding session page and make sure that except the `Signal Viewer panel`, the rest of the page displays well, either with or without the extra installation steps.
16. Test all the buttons on the interface to ensure they perform the action that the [react-series-data-viewer README](../jsx/react-series-data-viewer/README.md#Signal Viewer) states it will perform.
17. Hover over a signal to ensure it responds to being hovered. It should change to a color and its value should be displayed below the signal plot.
18. Ensure that 'Stacked View' and 'Isolate Mode' behave as stateed in the [react-series-data-viewer README](../jsx/react-series-data-viewer/README.md).
19. Ensure that the electrodes on the 'Electrode Map' 2D view are visible and their index can be hovered to reveal their channel name.
20. Ensure that the electrodes on the 'Electrode Map' 3D view are visible and the mesh can be manipulated/rotated with the mouse.


_For extra credit: Verify LORIS Menu permissions_
User can view the top-level LORIS Menu _Electrophysiology_ and Menu item : _Electrophysiology Browser_ if and only if user has either permission:
Expand Down