.. _EEGInspector: 

=======================
Inspect EEG channels
=======================

**EEG Inspector** is an interactive app for visually inspecting EEG data and creating artifact annotations for further analysis in Snooz.  
With the EEG Inspector, you can easily mark non-brain channels, bad channels, and noisy epochs to generate reliable annotations for preprocessing.

The tool works in several simple steps:

1. **Open your EEG file** and select a montage.
2. **Select non-brain channels** to mark them for exclusion.
3. **Mark fully artifact channels** via visual inspection.
4. **Inspect and mark noisy epochs** by segmenting your data.
5. **Review the Power Spectral Density (PSD)** of the cleaned signal.
6. **Save your annotations** for use in Snooz or other analysis tools.

Here is the overview of the steps taken to prepare annotations for a sample dataset:

.. image:: ./snooz_beta-2.1.0__EEGInspector_overview_Step1.png
   :width: 800
   :alt: EEG Inspector Step 1 - Open File

**Step 1** – Open the EEG Inspector app and select a montage, then select non-brain channels (e.g., ECG, EOG) for exclusion.

.. image:: ./snooz_beta-2.1.0__EEGInspector_overview_Step2.png
   :width: 800
   :alt: EEG Inspector Step 2 - Mark Bad Channels

**Step 2** – Visually inspect the EEG and mark fully artifact channels.

.. image:: ./snooz_beta-2.1.0__EEGInspector_overview_Step3.png
   :width: 800
   :alt: EEG Inspector Step 3 - Mark Noisy Epochs

**Step 3** – Segment the data into epochs and mark noisy ones.

.. image:: ./snooz_beta-2.1.0__EEGInspector_overview_Step4.png
   :width: 800
   :alt: EEG Inspector Step 4 - Check the PSD of cleaned signal.

**Step 4** – Check the PSD of cleaned signal and save the annotations properly.


Open your EEG file
-----------------------

To open the EEG Inspector in Snooz:

* Navigate to **"Preprocessing" → "Inspect EEG channels"**.

Then, use the **Browse** button to select your EEG file.

* After opening, select the appropriate montage.
* A table will list all available channels.

Select non-brain channels
-----------------------------

The app may automatically suggest some common non-brain channels.

* If the suggested selection is not correct, you can **uncheck** any channels or **check** the correct ones manually.
* Mark channels such as EOG, EMG, ECG, or other sensors that should be excluded.
* Click **Confirm Selection** when done, or click **Skip** if you don’t need to remove any channels.

Wait for the data to load.

.. warning::
    
    Do not interact with the Snooz interface while the file is loading.

.. warning::

   The EEG Inspector currently supports only **continuous EEG signals**.  
   If your signal is discontinuous, you will see an error.  
   Support for discontinuous signals will be added in a future release.

.. note::

   For visualization only, signals are downsampled to 250 Hz (if needed) and low-pass filtered at 100 Hz. This does **not** modify your original data.

Mark fully artifact channels
---------------------------------

Once the data loads, a scrolling EEG viewer will open.

* Click channels in the plot to mark them as **fully artifact** — they will appear in **red**.
* Use the **→** and **←** keys to scroll horizontally.
* Press **+** or **-** to adjust amplitude scaling.
* Hold **Shift** + **→** to scroll faster.
* For more shortcuts, press **Help** in the bottom-left corner.

.. note::

   For long sleep files, scrolling may have a small delay — please be patient.

When finished, click **Next**.

Inspect and mark noisy epochs
------------------------------------

Your data will be automatically divided into epochs:

* If your file is **over 1 hour**, you can choose **5 min** or **15 min** epochs.
* If under 1 hour, you can choose **10 s** or **30 s** epochs.

Select the desired epoch length, click **Apply**, and inspect the segments.

* Click on a noisy epoch to mark it — it will turn **red**.

Click **Next** when finished.

Review the PSD
-------------------

In the final step, the app shows the **Power Spectral Density (PSD)** of the cleaned data.

* Check the PSD to confirm that your signal is clean.

If satisfied, save your annotations.

Save annotations
----------------------

* Check **Same File** to write to the original file, or **Browse** to select a new file path.
* To overwrite old annotations with the same `group` and `name`, check **Overwrite**.

Press **Save File** — a dialog will confirm that the annotations were saved.

Annotations are saved as: 

* `group`: `art_inspector`
* `name`: `non_brain`, `art_channel` or `art_epoch`
* `start_sec`: start time in seconds
* `duration_sec`: duration in seconds
* `channels`: list of affected channels

Your EEG data is now ready for reliable further processing in Snooz.

Version History
-----------------

* v2.0.0 : Distributed with CEAMS package version 7.3.0 — Snooz beta 2.1.0
    - Initial release of the tool.