mcsltd/annotateptbxl

The program is used to convert annotations of the PTB-XL database into annotations in the ecg.ru format.

annotateptbxl

The program is used to convert annotations of the PTB-XL database into annotations in the ecg.ru format.

Resources

Professional tool for physicians and biomedical engineers
https://ecg.ru/

PTB-XL, a large publicly available electrocardiography dataset
https://physionet.org/content/ptb-xl/1.0.1/

Usage

Python (3.4 or later) must be installed on the user's computer to run the program. The program accepts file with PTB-XL annotaions in CSV format, JSON-file with PTB-XL annotation codes description and output directory path. The launch is done through the command line as shown below.

$ python annotateptbxl.py ann_file dict_file out_dir

• ann_file is a path to file in CSV format with PTB-XL annotations;
• dict_file is a path to file with annotatin codes description organized in dictionary in JSON format;
• out-dir is a directory path for result annotation files.

Output format

The format of the output files are described there. Annotations from the CSV are converted into text form and written in the comment field. The rest of the fields are filled in as follows

• type: STANDARD,
• annotator: PTB-XL annotators,
• database: PTB-XL ECG Dataset,
• conclusionThesaurus: PTB-XL,
• conclusions: empty array, [],
• record: record id.

Output file example

{
  "version": 1,
  "type": "STANDARD",
  "date": "2021-06-21T08:35:06.835255Z",
  "annotator": "PTB-XL annotators",
  "database": "PTB-XL ECG Dataset",
  "record": "00001_hr",
  "conclusionThesaurus": "PTB-XL ECG Dataset",
  "conclusions": [],
  "comment": "Аннотация PTB-XL:\nНеопределенная ЭОС\nНормальная ЭКГ\nНизкий вольтаж QRS\nСинусовый ритм\n\nPTB-XL annotation:\nUnknown axis\nNormal ECG\nLow QRS voltages in the frontal and horizontal leads\nSinus rhythm"
}