Comments (7)
vsoch
commented on August 28, 2024
oup! looks like we need a shutil.rmtree. Give me a few minutes to look into this!
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vsoch
commented on August 28, 2024
Could you please show me the way you are invoking clean? If done with a general client, we can't just delete the entire folder at the end of a function call (we lose the files!) and so we would want to remove the directory given some circumstances. Let me know your calls and I'll figure out the best approach!
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fimafurman
commented on August 28, 2024
Vanessa,
In my case, all I do is:
client = DicomCleaner(deid=recipe_path)
detect = client.detect(path)
and throw away the object, so, perhaps, since the folder is created in
_init_, should it be deleted in _exit_?
def __exit__(self, exc_type, exc_value, traceback):
for file in self.files:
os.unlink(file)
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vsoch
commented on August 28, 2024
hey @fimafurman ! I'm bad so I didn't test this, but would you care to do the honors? Here is the PR and the branch #69. The exit_ was a good idea, but we can't be sure that the user doesn't want the folder to exist after exiting python. So instead I create the folder on init, and then remote it and only re-create it given that a save is called. In your case, it shouldn't be called so you shouldn't see the extra temporary folders created. Let me know if it works, and I can merge and upload to pypi.
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fimafurman
commented on August 28, 2024
I will test my workflow shortly. Thank you and your comment makes about the
destructor.
…On Tue, Sep 18, 2018 at 5:40 PM Vanessa Sochat ***@***.***> wrote:
hey @fimafurman <https://github.com/fimafurman> ! I'm bad so I didn't
test this, but would you care to do the honors? Here is the PR and the
branch #69 <#69>. The *exit*_ was a
good idea, but we can't be sure that the user doesn't want the folder to
exist after exiting python. So instead I create the folder on init, and
then remote it and only re-create it given that a save is called. In your
case, it shouldn't be called so you shouldn't see the extra temporary
folders created. Let me know if it works, and I can merge and upload to
pypi.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#68 (comment)>, or mute
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<https://github.com/notifications/unsubscribe-auth/Ak2KXCUta0T4bXBPaYFrgd_X3b9924dlks5ucWg_gaJpZM4WuwRc>
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fimafurman
commented on August 28, 2024
I tested my workflow and the folder is properly deleted right after creation. Not sure if there's a way to just come up with the safe name, or whether the file could be created only when needed.
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vsoch
commented on August 28, 2024
Yes! Let me try this, I have an idea.
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Related Issues (20)
- get skull pixel data HOT 12
- Specify more than one coordinates in the filter HOT 37
- Error on get_files import HOT 4
- ImportError: cannot import name 'clean_pixel_data' from 'deid.dicom.pixels' HOT 9
- Minimum Required Versions - Python >=3.7; Numpy >= 1.20 HOT 10
- Update documentation with correct package name ("deid-data" -> "deid") HOT 2
- Add pre-commit for linting HOT 1
- Photometric Interpretation of the dataset is YBG_FULL_422 [...] You may need to change the Photometric Interpretation to the correct value HOT 14
- BLANK Action only applicable to US and SS VRs HOT 3
- Tags within sequences (nested fields) are not affected by header actions HOT 2
- REPLACE action fails on numeric VR HOT 1
- Documentation Issue - Recipe Headers HOT 2
- Circular import for config HOT 3
- Possible incorrect coordinate definition HOT 5
- Anonymise DICOM pixel data using OCR HOT 8
- How to specify Private tags in the recipes HOT 6
- Deidentification Exception in Filters
- DEID dropping UIDs HOT 11
- (7fe0, 0010) Pixel Data doesn't appear in the dictionary when using get_identifiers HOT 4
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