`deid` CLI tool never saves dicom output

[WillForan]

I've maybe misunderstood the intended workflow of died's main. I expected to run

deid --debug --outfolder /tmp/phi-clean/ --format dicom --overwrite identifiers --action all --deid ./deid-py.cfg --input phi/

and see new dicoms in /tmp/phi-clean. But the folder is left empty.

When put is requested for action identifiers, replace_identifiers is called but the default save is never changed, left as the default False. While the script ending output message is "files at {output_folder}", that folder will never get new dicoms(?)

https://github.com/pydicom/deid/blob/master/deid/main/identifiers.py#L66

    cleaned_files = replace_identifiers(
            dicom_files=dicom_files,
            ids=ids,
            deid=args.deid,
            overwrite=args.overwrite,
            output_folder=output_folder,
        )

https://github.com/pydicom/deid/blob/master/deid/dicom/header.py#L91

def replace_identifiers(
    dicom_files,
    ids=None,
    deid=None,
    save=False,
    ...

[vsoch]

The --overwrite flag means that you will write over the input dicoms. Do you see changes there?

[WillForan]

ohhh! hmmm

If I start fresh and don't use --overwrite, I still don't see any files in my /tmp/phi-clean

But if I use a modified version (#276) with of identifiers.main where replace_identifiers(save=True) and run the same command twice without --overwrite I think I see an expected error:

ERROR phi.dcm already exists, overwrite set to False. Not writing.

---

# clear out any files
rm /tmp/phi-clean/*

# modified replace_identifiers(save=True)
deid --debug --outfolder /tmp/phi-clean/ --format dicom identifiers --action all --deid ./deid-py.cfg --input phi/ 
GET and PUT identifiers from 
1 dicom files at /tmp/phi-clean/

# rerun with out overwrite, get expected error
deid --debug --outfolder /tmp/phi-clean/ --format dicom identifiers --action all --deid ./deid-py.cfg --input phi/ 
GET and PUT identifiers from 
ERROR phi.dcm already exists, overwrite set to False. Not writing.
1 dicom files at /tmp/phi-clean/

[vsoch]

That looks right! See my comment in your PR.

[vsoch]

Closed with #276