MIT-LCP / MIT-LCP/wfdb-python

Handling WFDB header date and time problems

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Descripción

We should aim to prevent the creation of WFDB headers which aren't to specification (via the WFDB write functions). We should also provide clear messaging for errors related to already created WFDB headers (via he WFDB read functions).

Two sets of projects have had WFDB header issues related to base_date recently:

  1. 2020 and 2021 Challenges. These projects used -'s instead of /'s in the base_date and the date was given before the base_time: https://github.com/MIT-LCP/wfdb-python/issues/351 . As mentioned in this issue, the WFDB tools were not used to create these files, so these errorneous headers shouldn't come as a surprise.
    Error message: HeaderSyntaxError: invalid syntax in record line
  2. Cerebral projects. These projects had a year for the base_date and no time. This problem was initially noted in: https://github.com/MIT-LCP/wfdb-python/issues/307. More recently, another user sent an email about this issue.
    Error message: ValueError: time data '2006' does not match format '%d/%m/%Y' (ecg files in https://physionet.org/content/cerebral-perfusion-diabetes/1.0.0/)
    Error message: ValueError: unconverted data remains: 10 (ECG files in https://physionet.org/content/cded/1.0.0/)

It isn't clear how the WFDB files for 2. were created. There is some indication that MIT-LCP helped generate these files.

At the very least we should:

  • Use validation checks to prevent the creation of WFDB files with these issues in our WFDB toolboxes.
  • Catch these issues in all of our WFDB toolboxes and provide clear, consistent error messages.

Since we need to address multiple issues across 3 different toolboxes this issue may get messy. I will update this post to denote how updates to the Matlab and C toolboxes will be tracked once that is determined.

Finally, it would also be good if our wfdbcheck algorithm would catch these issues. This could prevent cases like those seen in the 2020, and 2021 challenges from getting through (i.e. even if a header is created outside of our toolboxes, we'd like to flag it if it isn't to specification).

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  1. Lee el issue completo y luego la guía de contribución del proyecto.
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  4. Abre un pull request que haga referencia al número del issue.

Línea de trabajo

Empieza rastreando las funciones de escritura y lectura de WFDB que manejan base_date y base_time; después, inspecciona cómo wfdbcheck procesa las cabeceras malformadas. Compara los formatos y errores no válidos enumerados; se considera terminado cuando la validación impide las cabeceras que no cumplen la especificación y las rutas de lectura/comprobación proporcionan mensajes claros y coherentes.

Escrito por el modelo de indexación a partir del texto del issue.

Evaluación

Stack tecnológico
python
Área
data
Tipo de issue
Error
Dificultad
5/5
Tiempo estimado
Más de una semana
Estado de actividad
Estancado
Claridad
Bastante claro
Aptitud para principiantes
30/100

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