PHI-finder

Local testing (docker required)

conda create -n phi-finder python==3.11
conda activate phi-finder
pip install -e .[dev,test] --no-cache-dir
pytest .

Building

python -m pip install --upgrade build

python -m build

pip install dist/phi_finder-0.1.13-py3-none-any.whl

Basic usage (headers only)

import pydicom as dicom
from phi_finder.dicom_tools import anonymise_dicom

path = "/path/to/some/dicom.dcm"
dcm = dicom.dcmread(path)
anonymised_dcm = anonymise_dicom.anonymise_image(dcm)
anonymised_dcm.save_as('/path/to/some/dicom_anon.dcm')

More advanced usage

import pydicom as dicom
from presidio_image_redactor import (
    DicomImageRedactorEngine, ImageAnalyzerEngine, ContrastSegmentedImageEnhancer)
from phi_finder.dicom_tools import anonymise_dicom

path = "/path/to/some/dicom.dcm"
dcm = dicom.dcmread(path)
score_threshold=.15
analyser = anonymise_dicom._build_presidio_analyser(score_threshold, "en_core_web_lg")
image_redactor = DicomImageRedactorEngine(
    image_analyzer_engine=ImageAnalyzerEngine(
        analyzer_engine=analyser, 
        image_preprocessor=ContrastSegmentedImageEnhancer(),
        ))
anonymised_dcm = anonymise_dicom.anonymise_image(dcm,score_threshold=score_threshold,
                                                 analyser=analyser,
                                                 image_redactor=image_redactor,
                                                 )
anonymised_dcm.save_as('/path/to/some/dicom_anon.dcm')