aroethen / rbdtector

RBDtector detects phasic, tonic and any events linked to REM sleep behaviour disorder. It closely follows SINBAR and AASM scoring guidelines.

RBDtector

A python software tool to detect REM sleep behavioral disorder (RBD) in .edf files. Relies on .txt files of previously classified periods of sleep phases and arousals.

Table of contents:

1. How to install
   1. Windows
   2. Mac and Linux
2. License
3. Acknowledgements

How to install

Windows

1. Download the zipped version of RBDtector here: dist/RBDtector.zip
2. Extract the zip file into a folder of your choice
3. Click the extracted RBDtector.exe to run RBDtector

In some cases, Windows Defender SmartScreen will flag RBDtector as an 'Application of unknown source'. This warning can simply be clicked away. If you want to, you can also submit the file to Windows' malware analysis before trusting it.

Mac and Linux

Installing RBDtector under MacOS or Linux requires the usage of simple terminal commands. General commands that work in the terminals of both operating systems can be found here.

0. Prerequisites: Ensure you have a version of Git and Python 3 installed (including pip and tkinter - usually already included in Python 3)
   • Git
   • Python
   • pip
   • tkinter
1. Open a terminal
2. (optional: navigate to a folder into which you want to place RBDtector)
3. Enter the following commands line by line:
   1. Clone git repository git clone https://github.com/aroethen/RBDtector.git
   2. Install requirements python3 -m pip -r RBDtector/requirements.txt
   3. Change into folder with main.py cd RBDtector/RBDtector
   4. Run with python3 main.py

License

This project is licensed under the MIT License (s. LICENSE file).

Acknowledgements

This project gratefully uses the following third-party open source libraries:

Library	License
pyEDFlib	BSD 2-Clause "Simplified" License
numpy	[BSD 3-Clause "New" or "Revised" License] (https://github.com/numpy/numpy/blob/main/LICENSE.txt)
pandas	[BSD 3-Clause "New" or "Revised" License] (https://github.com/pandas-dev/pandas/blob/main/LICENSE)
scipy	[BSD 3-Clause "New" or "Revised" License] (https://github.com/scipy/scipy/blob/main/LICENSE.txt)
openpyxl	[MIT License] (https://foss.heptapod.net/openpyxl/openpyxl/-/blob/branch/3.0/LICENCE.rst)

rbdtector's Issues

README install requirements is missing pip argument

README has command for installing the requirements from requirements.txt but the command is missing the install argument. Right now the readme has python3 -m pip -r RBDtector/requirements.txt but should be python3 -m pip install -r RBDtector/requirements.txt

Compatibility with RemLogic

Hello,

I'm trying to run your program with edf and txt file extracted from RemLogic. We are working for a Swiss University Hospital.

I'm getting the following error:

### 25.04.2023 10:44:17 ###   edf: C:\Users\emp8124242\dev\RBDtector\Data\Test_AM_10_20_230216_(1).edf
### 25.04.2023 10:48:04 ###   Unexpected error in file C:/Users/emp8124242/dev/RBDtector/Data:
 'sleep_profile'
, ### 25.04.2023 10:48:04 ###   Traceback (most recent call last):
  File "C:\Users\emp8124242\dev\RBDtector\RBDtector\app_logic\PSG_controller.py", line 110, in single_psg_run
    PSGController.run_rbd_detection(input_path, output_path)
  File "C:\Users\emp8124242\dev\RBDtector\RBDtector\app_logic\PSG_controller.py", line 26, in run_rbd_detection
    raw_data, annotation_data = ir.read_input(directory_name=input_path,
  File "C:\Users\emp8124242\dev\RBDtector\RBDtector\input_handling\input_reader.py", line 48, in read_input
    annotation_data: AnnotationData = __read_txt_files(filenames, read_baseline, read_human_rating)
  File "C:\Users\emp8124242\dev\RBDtector\RBDtector\input_handling\input_reader.py", line 158, in __read_txt_files
    sleep_profile = __read_sleep_profile(filenames['sleep_profile'])
KeyError: 'sleep_profile'

The extract of RemLogic gives us a single txt file, with all the data required to run your analysis. I believe we just need to convert into a similar format as yours. I don't mind writing a script to parse the txt file, but I would like to know what is the format of the files Sleep profile, Flow Events, Classification Arousals, Start-Baseline, and Generic.
The best would be if you would push sample files with synthetic data.

Bests
Guillaume