Application Settings

Application Settings¶

This section descibes how to configure the application settings in the hdsemg-pipe application. The application settings allow you to specify the working directory of the application as described in the Opening Data section, as well as the path to the external hdsemg-select application and the openhdemg executable. The settings dialog can be accessed from the top menu bar under Settings -> Preferences.

Settings Dialog

Channel Selection App¶

The Channel Selection App section allows you to manage the installation of hdsemg-select, an external application used for channel selection. By default, the application will install the latest version of hdsemg-select from PyPI.

Work Folder¶

The Work Folder section allows you to specify the working directory of the application. This is the directory where all the data will be stored and processed. As soon as you open a file, the application will create a subdirectory in the working directory with the name of the file or folder. Detailed information can be found in the Opening Data section.

Line Noise Removal¶

The Line Noise Removal section allows you to configure how powerline interference (50/60 Hz) and harmonics are removed from your EMG signals. This is a new processing step introduced between Grid Association and Region of Interest definition.

Power Line Frequency Region¶

Select your geographic region to automatically configure the correct powerline frequencies:

🇺🇸 USA/North America (60 Hz): Removes 60, 120, 180, 240 Hz
🇪🇺 Europe/Asia (50 Hz): Removes 50, 100, 150, 200 Hz

Line Noise Removal Method¶

Choose from multiple filtering methods depending on your needs and available software:

Available Methods:

⚡ MNE-Python: Notch Filter (FIR) - Fast
Classic FIR notch filter
Very fast processing
Good quality
No additional software required
⭐ MNE-Python: Spectrum Fit (Adaptive) - Recommended
Adaptive spectrum fitting approach
Excellent quality with minimal distortion
Similar to CleanLine algorithm
No additional software required
This is the default and recommended method
🏆 MATLAB: CleanLine (EEGLAB Plugin) - Gold Standard
Original CleanLine algorithm from EEGLAB
Multi-taper with statistical validation
Best quality for time-varying line noise
Requires: MATLAB + EEGLAB + CleanLine plugin
Slowest but highest quality
🔬 MATLAB: IIR Notch Filter
Native MATLAB implementation
Very narrow-band filtering
Requires: MATLAB + MATLAB Engine for Python
🐙 Octave: IIR Notch Filter (Free)
MATLAB-compatible, open source
Free alternative to MATLAB
Requires: GNU Octave + oct2py

Installation Status¶

The settings dialog displays the installation status of optional dependencies: - ✓ MNE-Python: Always available (required dependency) - ✓/✗ MATLAB Engine: Shows if MATLAB is detected - ✓/✗ Octave + oct2py: Shows if Octave is detected

Methods that are not available (due to missing dependencies) will be disabled in the dropdown menu.

MATLAB Engine Installation Assistant¶

The application provides an installation assistant that generates the correct installation commands for your system:

Go to Settings → Preferences → Line Noise Removal
Scroll to the MATLAB Engine for Python section
Click Show Installation Instructions button
Follow the displayed instructions:
Option 1 (Recommended): Copy the command and run it in MATLAB
Option 2: Copy the command and run it in Terminal/CMD
Click "Copy Command" to copy the installation command to clipboard
Restart the application after installation

Benefits: - Automatically detects your MATLAB installation path - Provides copy-paste ready commands with correct paths - Works with all Python environments (including Windows Store Python) - No complex troubleshooting needed

Manual Installation Instructions¶

For MATLAB Engine (if automatic installation fails):

Option 1 - In MATLAB:

cd(fullfile(matlabroot,'extern','engines','python'))
system('python setup.py install')

Option 2 - In Terminal/CMD:

cd <matlabroot>/extern/engines/python
python setup.py install

For MATLAB CleanLine Plugin (Gold Standard):

# 1. Install MATLAB (license required)
# 2. Install EEGLAB from https://sccn.ucsd.edu/eeglab/download.php
# 3. In EEGLAB: File → Manage EEGLAB extensions → CleanLine
# 4. Add EEGLAB to MATLAB path (in startup.m or manually)
# 5. Install MATLAB Engine (see above or use automatic installation)

For Octave (Free):

# 1. Install Octave from https://octave.org/download
# 2. Install Python package:
pip install oct2py

After installing any optional dependencies, restart the application to detect them.

Methods Info Button¶

Click the "📖 Methods Info (Detailed Comparison)" button to open a comprehensive dialog comparing all methods with: - Detailed technical descriptions - Advantages and disadvantages - Speed and quality comparisons - Installation guides - Technical implementation details

For more information about the Line Noise Removal step, see Line Noise Removal.

Openhdemg Installation¶

hdsemg-pipe can install the openhdemg open source project automatically from PyPI. If the application is running from the sources, you can install openhdemg by going to Settings > Preferences > openhdemg > Install openhdemg. More information about the project can be found here: Official Openhdemg Documentation.

Logging Level¶

The Logging Level section allows you to specify the logging level of the application. This is useful for debugging and troubleshooting purposes. The available logging levels are: - DEBUG: Detailed information, useful for debugging. - INFO: General information about application operations. - WARNING: Indications of potential issues. - ERROR: Error messages indicating problems that need attention. - CRITICAL: Severe errors that may prevent the application from functioning.

The current logging level is displayed in the settings dialog, and you can change it by selecting a different level from the dropdown menu and pressing the "Apply" button.

As soon as the settings dialog is closed by pressing the "OK" button, the application will save the settings to a JSON file in the application data directory. The file is named config/config.json and contains all the configuration options, including the working directory, external hdsemg-select path, openhdemg executable path, and logging level.