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# Analysis walkthrough

After launching the ADA GUI application, you will arrive at the Home page.

The Home page serves as the starting point of your analysis workflow. It displays the current configuration of your analysis, including selected files, the active pipeline, and the output directory for results.

The main navigation buttons on the Home page are:

Input file(s) (Step 1: Input file(s)), Analysis (Step 2: Analysis), Output directory (Step 3: Output directory), and Results (Step 5: Results browser). Each button opens a corresponding configuration panel. These options are also accessible through the pull-down menus.

## Step 1: Input file(s)

Click the Input file(s) button to open the file-selection window:
To select multiple files, use the Shift key or Ctrl Key while clicking the desired items:
After confirming your selection, the Home page will display metadata about the chosen files, including subject code, start time, sampling frequency, and available channels:
For detailed information about data formats and file dialog options, see Settings and help.

## Step 2: Analysis

Analysis options can be accessed from several locations:

1. The Analysis button on the Home page

2. The Analysis pull-down menu

3. The View menu (by selecting the Analysis option)

4. The Analysis tab

All entry points open the same analysis configuration window.

ADA offers two approaches for configuring analysis:

- Presets – one-click configurations with predefined settings

- Pipeline – full control over every analysis stage

A detailed description of algorithms and estimators is available in Presets and pipeline.

### Presets

To use a predefined preset click the Analysis button on the Home page and open the preset dialog by selecting Presets:
The algorithm selection window will appear:
After choosing a preset, the analysis options panel is displayed. At the bottom of the Analysis window you will find three buttons:

- ACCEPT — saves the configuration and returns to the Home page

- PRESETS — opens the preset dialog

- CANCEL — discards changes and returns to the Home page

To apply the default settings, click ACCEPT:
After confirmation, you will return to the Home page where the selected preset is displayed:

### Pipeline

For full control over analysis, you can configure each of the three pipeline stages. The pipeline consists of:

1. Collapsing data into epochs

2. Sleep/wake scoring

3. Circadian rhythm estimation

None of these stages is mandatory; however, their order is fixed. The output of the epoching stage always serves as input for subsequent stages. If epoching is skipped, scoring and rhythm estimation operate directly on the raw data.

In this tutorial, each stage is explained in detail. For algorithm descriptions, see Presets and pipeline.

To enable or disable element of the pipeline use checkbox to the left to its name.

When a stage checkbox is checked, its detail panel expands automatically (as if Show details were clicked). When unchecked, the panel collapses. The Show details and Hide details buttons remain available for manual control.

Each pipeline stage provides common saving options:

1. Save generic .csv — exports data from the current stage as a CSV file

2. Save .ada file — a compressed, application-specific format for efficient storage and fast loading (useful for intermediate results)

3. Plot results — when a single file is selected, plots open in a pop-up window with options to adjust and save them; for multiple files, plots are saved as PNG images

For Sleep/wake scoring and Circadian rhythm stages, you can also enable saving a summary report — a single CSV file containing metrics for all processed files. In case of the epocher, instead of summary you may produce a daily profile plot.
Collapsing into epochs

In addition to default saving options, you may enable daily profile export.

Within this stage you can:

- Change the algorithm type using the expandable list

- Adjust epoch length via the input field or plus/minus buttons or by writing a desired number

- Configure advanced options (described in Presets and pipeline)

Sleep/wake scoring

Within this stage you can:

- Select the scoring algorithm from the expandable list

- Configure advanced options (described in Presets and pipeline)

Circadian rhythms

Within this stage you can:

- Choose the rhythm estimator from the expandable list

- Configure advanced options (described in Presets and pipeline)

After configuring your desired options, click ACCEPT at the bottom of the window:
Once settings are accepted, you will return to the Home page where the active configuration is displayed:

## Step 3: Output directory

After configuring the analysis pipeline, select the output directory:

It is highly recommended to choose new, empty directory for the results. Click the button to choose where analysis results will be saved:

## Step 4: Running analysis

Once input files, the analysis pipeline, and the output directory are configured, click START PROCESSING on the Home page:

During processing, the button changes to CANCEL and a progress bar displays the current stage:
The status text below the progress bar indicates the active operation (for example, Epoching data (2/3)). You can cancel processing at any time by clicking CANCEL.

If analysis completes successfully, a pop-up window will display a confirmation:

## Step 5: Results browser

After successful analysis, you will be directed to the Results tab.

The results view includes:

- The output directory path (click to open in Finder or Explorer)

- A Results only (.png, .csv) checkbox When enabled (default), only result files (plots and tables) are listed. Disable it to display all files in the output directory.

- A Last analysis only checkbox When enabled (default), only files from the most recent analysis are shown.

- A list of generated result files

Scrolling further reveals inline previews:

- Image thumbnails for PNG files (for example, scored plots or cosinor fits)

- Table previews for CSV files (such as epoch data or summary reports)

Click a filename to open it in the system’s default application.

Click the directory path at the top to open the output folder.

For appearance settings and help, see Settings and help.