ensemble-eeg 0.1.6

Package used to analyze preprocess edf files for the ENSEMBLE2 study

• ENSEMBLE EEG
  • Getting started
    • Prerequisites
    • Installation
  • Usage
    • Start python
    • Anonymizing EDF-files
    • Fixing EDF headers
    • Combine left and right aEEG channels into one single file
    • Rename EDF-files according to BIDS and ENSEMBLE standards
    • Example scripts for specific situations
      • 1) File is already .edf, but you do not know whether header is EDF+, the file is not anonymized, and not renamed
      • 2) Your file is .brm and you want to convert it to .edf
      • 3) Your files are .edf, but left and right channels are seperate
      • 4) You want to anonymize multiple .edf files in the same directory
      • 5) You want to convert multiple .brm files in the same directory
  • Acknowledgements

ENSEMBLE EEG

Ensemble EEG is a library of EEG analyis tools for the ENSEMBLE study. As of today it is focuses on 5 seperate things:

• Anonymizing EDF files in accordance with the ENSEMBLE study and the requirements of EDF+
• Fixing EDF headers to adhere to the EDF+ standard
• Converting BRM to EDF+ files
• Combining seperate aEEG channels into one EDF+ file
• Renaming EEG files according to ENSEMBLE and BIDS standards

Getting started

Prerequisites

The following is required for the use of this software

• Python 3.10 & pip
  • For instructions, please refer to the following link

Installation

python -m pip install ensemble_eeg

Usage

Start python

1. From command line
   1. Open cmd / terminal / powershell or your preferred command line interpreter
   2. Type python or python3
2. Using your preferred python interpreter
   1. Jupyter notebook
   2. PyCharm
   3. Spyder

Anonymizing EDF-files

from ensemble_eeg import ensemble_edf
ensemble_edf.anonymize_edf_header("path/2/your/edf/file") # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 

Fixing EDF headers

from ensemble_eeg import ensemble_edf
ensemble_edf.fix_edf_header("path/2/your/edf/file") # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 

Combine left and right aEEG channels into one single file

from ensemble_eeg import ensemble_edf
ensemble_edf.combine_aeeg_channels('path/2/your/left/channel', 'path/2/your/right/channel', 'new_filename') # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 

Rename EDF-files according to BIDS and ENSEMBLE standards

from ensemble_eeg import ensemble_edf
ensemble_edf.rename_for_ensemble('path/2/your/edf/file') # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 

Example scripts for specific situations

1) File is already .edf, but you do not know whether header is EDF+, the file is not anonymized, and not renamed

from ensemble_eeg import ensemble_edf
file = 'path/2/your/edf/file' # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 
ensemble_edf.fix_edf_header(file)       # for header check
ensemble_edf.anonymize_edf_header(file) # for anonymization

anonymized_file = 'path/2/your/anonymized/edf/file' # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 
ensemble_edf.rename_for_ensemble(file)  # for renaming

2) Your file is .brm and you want to convert it to .edf

from ensemble_eeg import brm_to_edf
from ensemble_eeg import ensemble_edf
brm_file = 'path/2/your/brm/file' # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/brm/file") 
brm_to_edf.convert_brm_to_edf(brm_file)     # for conversion, output edf is already anonymized
edf_file = 'path/2/your/edf/file'           # check which file was made in previous step
ensemble_edf.rename_for_ensemble(edf_file)  # for renaming

3) Your files are .edf, but left and right channels are seperate

from ensemble_eeg import ensemble_edf
left_file = 'path/2/your/left/edf/file' # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 
right_file = 'path/2/your/right/edf/file' # for windows, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 
ensemble_edf.combine_aeeg_channels(left_file, right_file) # output is automatically anonymized
ensemble_edf.rename_for_ensemble(file)                    # for renaming

4) You want to anonymize multiple .edf files in the same directory

from ensemble_eeg import ensemble_edf
import glob
import os
edf_directory = 'path/2/your/left/edf/directory' # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 
edf_files = glob.glob(os.path.join(edf_directory, "*.edf"))
for file in edf_files:
      ensemble_edf.fix_edf_header(file) 
      ensemble_edf.anonymize_edf_header(file) 
      
      anonymized_filename = Path(file).stem + "_ANONYMIZED" + Path(file).suffix
      ensemble_edf.rename_for_ensemble(anonymized_filename)                    

5) You want to convert multiple .brm files in the same directory

from ensemble_eeg import brm_to_edf
import glob
import os
brm_directory = 'path/2/your/left/edf/directory' # for windows users, type an r before the " to ensure the use of raw strings (r"path/2/your/edf/file") 
brm_files = glob.glob(os.path.join(brm_directory, "*.brm"))
for file in brm_files:
      brm_to_edf.convert_brm_to_edf(file) 

For more scripts, please refer to the demos folder

Acknowledgements

• edfrd
• Install-Python-Instructions

Software development has been funded by La Fondation Paralysie Cérébrale under grant ENSEMBLE.