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ivadomed / utilities

Repository containing utility scripts for handling various aspects in a DL model training pipeline
MIT License
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`compute_metrics_reloaded.py` - consider other output type than CSV #51

Open valosekj opened 3 months ago

valosekj commented 3 months ago

The compute_metrics_reloaded.py script currently outputs the segmentation performance metrics into CSV files:

https://github.com/ivadomed/utilities/blob/1e72f5d08fcbe1e4525f59cb97d7f4f596a0cf68/compute_metrics/compute_metrics_reloaded.py#L254-L262

The CSV files might be tricky to read in the terminal (due to CSV formatting).

A possible solution is to use a workaround such as function column_csv { column -t -s $';' ${1} }, followed by column_csv <file.csv>. But this does not work well if the CSV file has a lot of columns.

--> we can explore other ways how to save the metrics, such as pandas.DataFrame.to_markdown.

valosekj commented 3 months ago

Note that the script has been moved: https://github.com/ivadomed/MetricsReloaded/pull/5