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csv_to_wfdb writes to current dir; needs param to specify output folder #490

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jshaffer94247 opened this issue Jun 26, 2024 · 3 comments
Open

csv_to_wfdb writes to current dir; needs param to specify output folder #490

jshaffer94247 opened this issue Jun 26, 2024 · 3 comments

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@jshaffer94247
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csv_to_wfdb currently strips the path from the input .csv, then writes the output to .dat and .hea

Request is for
a) full path to be preserved for the output file (not backward compatible)
b) accept an optional parameter to specify the output folder (preserves backward compatibility)
@jshaffer94247 jshaffer94247 changed the title csv_to_wfdb writes to current dir csv_to_wfdb writes to current dir; needs param to specify output folder Jun 26, 2024
@tompollard
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@jshaffer94247 not ideal, it should definitely be possible to specify the output directory!

Does adding an output_dir argument sound okay, or do you have a cleaner suggestion?

def csv_to_wfdb(
    ...
    delimiter=",",
    verbose=False,
    output_dir=None,
):

@jshaffer94247
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I do not have a cleaner suggestion; that's what I'd do.

@tompollard tompollard mentioned this issue Jul 1, 2024
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tompollard added a commit that referenced this issue Jul 9, 2024
@tompollard
Add write_dir argument to csv_to_wfdb(). Ref #490.
17b9349
tompollard added a commit that referenced this issue Jul 9, 2024
@tompollard
Add write_dir argument to csv_to_wfdb(). Ref #490.
f874b1c
tompollard added a commit that referenced this issue Jul 11, 2024
@tompollard
Add write_dir argument to csv_to_wfdb. Fixes #67. (#492)
6a0de80 
As discussed in #490,
https://github.com/MIT-LCP/wfdb-python/blob/34b989e08435c1a82d31bdd2800c4c14147e3e93/wfdb/io/convert/csv.py#L10
currently "strips the path from the input .csv, then writes the output
to .dat and .hea".

It's inconvenient not to be able to specify the output directory. This
pull request adds a new `output_dir` argument to the `csv_to_wfdb`
function. By default `output_dir` is set to None, which will maintain
backwards compatibility. Setting `output_dir` to a directory will mean
that output files are saved to this directory.

I have set this to a WIP, because I haven't tested the new behaviour
(other than running `pytest`). @jshaffer94247, if you have an
opportunity to test the fix, I'd appreciate your feedback.
@tompollard
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write_dir will be available in the next release. If you'd like to use it now, you should be able to pip install from this repo with:

pip install git+https://github.com/MIT-LCP/wfdb-python.git@6a0de803b4d396fa22da583dfa0d19250d347217

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@tompollard @jshaffer94247