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Improve the SR anonymisation #1524

Merged
merged 23 commits into from
Nov 20, 2023
Merged

Improve the SR anonymisation #1524

merged 23 commits into from
Nov 20, 2023

Commits on Apr 19, 2023

  1. CTP_SRAnonTool.sh - accept -y default.yaml

    howff committed Apr 19, 2023
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  2. CTP_SRAnonTool.sh - if output file does not exist then copy input file 

    instead of giving an error
    howff committed Apr 19, 2023
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  3. Added modify_SR.py to randomly add real names into a DICOM SR

    howff committed Apr 19, 2023
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Commits on Apr 20, 2023

  1. Added news

    howff committed Apr 20, 2023
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  2. StructuredReport - added a list of all tags which contain names (vr i… 

    …s PN)

plus a few which may contain an address (to be used in new anonymiser, see CogStack-SemEHR)
    howff committed Apr 20, 2023
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  3. DicomText - output a list of all names (tags where vr is PN) in the [… 

    …[Other Names]] header
    howff committed Apr 20, 2023
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  4. StructuredReport - handle a contentsequence value of dict { 'Alphabet… 

    …ic': 'text' }
    howff committed Apr 20, 2023
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  5. StructuredReport - oops, call self._SR_parse_key()

    howff committed Apr 20, 2023
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  6. StructuredReport - test a PersonName tag

    howff committed Apr 20, 2023
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  7. Dicom - add 'atomic' parameter to tag_val() so it can extract text fr… 

    …om a single-element list
    howff committed Apr 20, 2023
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  8. CTP_DicomToText.py - decode SOPInstanceUID better when constructing f… 

    …ilename for JSON input

because JSON from dcm2json is more verbose than the MongoDB JSON
    howff committed Apr 20, 2023
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  9. StructuredReport - output a set of [[Other Names]] headers for all th… 

    …e "PersonName" tags in the JSON

to match the code in the DicomText module. As used by the CogStack-SemEHR anonymiser.py code.
    howff committed Apr 20, 2023
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Commits on Oct 24, 2023

  1. StructuredReport - comment out print

    howff committed Oct 24, 2023
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  2. Merge branch 'master' into feature/srmod

    howff committed Oct 24, 2023
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Commits on Oct 25, 2023

  1. StructuredReport - find more Names, and add test

    howff committed Oct 25, 2023
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Oct 25, 2023
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  3. CTP_SRAnonTool.sh - don't override PYTHONPATH

    howff committed Oct 25, 2023
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  4. CTP_SRAnonTool.sh - pass on custom semehr_dir option to semehr_anon

    howff committed Oct 25, 2023
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  5. DicomText.py - redact dates to 1111 not 9999 so that they validate ok

    howff committed Oct 25, 2023
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Commits on Oct 26, 2023

  1. CTP_XMLToDicom.py - also takes args --replace-html and --replace-newl… 

    …ines

just like CTP_DicomToText.py otherwise redaction offsets wouldn't match
    howff committed Oct 26, 2023
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  2. DicomText.py - refactor common code into function

    howff committed Oct 26, 2023
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Commits on Oct 31, 2023

  1. DicomText.py - fix parsing headers

    howff committed Oct 31, 2023
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Commits on Nov 20, 2023

  1. Ensure output file is writeable

    abrooks committed Nov 20, 2023
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