Handling WFDB header date and time problems
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Description
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:
- 2020 and 2021 Challenges. These projects used -'s instead of /'s in the
base_dateand the date was given before thebase_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 - Cerebral projects. These projects had a year for the
base_dateand 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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Par où commencer
- Lisez l'issue en entier, puis le guide de contribution du projet.
- Signalez en commentaire que vous la prenez — cela évite que deux personnes fassent le même travail.
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- Ouvrez une pull request qui référence le numéro de l'issue.
Piste de recherche
Commencez par suivre les fonctions d’écriture et de lecture de WFDB qui gèrent base_date et base_time, puis examinez comment wfdbcheck traite les en-têtes malformés. Comparez les formats et les erreurs invalides répertoriés ; le travail est terminé lorsque la validation empêche les en-têtes non conformes à la spécification et que les chemins de lecture/vérification fournissent des messages clairs et cohérents.
Rédigé par le modèle d'indexation à partir du texte de l'issue.
Évaluation
- Stack technique
- python
- Domaine
- data
- Type d'issue
- Bug
- Difficulté
- 5/5
- Temps estimé
- Plus d'une semaine
- Activité
- À l'abandon
- Clarté
- Plutôt claire
- Accessibilité débutants
- 30/100