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PIXL DICOM de-identifier

The pixl_dcmd package provides helper functions for de-identifying DICOM data. It is currently only used by the orthanc-anon plugin.

For external users, the pixl_dcmd package provides the following functionality:

  • anonymise_dicom(): Applies the anonymisation operations for the appropriate tag scheme using Kitware Dicom Anonymizer and deletes any tags not mentioned in the tag scheme. The dataset is updated in place.
    • Will throw a PixlSkipInstanceError for any series based on the project config file. Specifically, an error will be thrown if:
      • the series description matches any series in series_filters (usually to remove localiser series)
      • the modality of the DICOM is not in modalities
  • anonymise_and_validate_dicom(): Compares DICOM validation issues before and after calling anonymise_dicom and returns a dictionary of the new issues
import os
import pathlib
import pydicom

from core.project_config.pixl_config_model import load_config_and_validate
from pixl_dcmd import anonymise_and_validate_dicom

config_dir = pathlib.Path().cwd().parents[2] / "projects" / "configs"
config_path = config_dir / "test-external-user.yaml"
os.environ["PROJECT_CONFIGS_DIR"] = config_dir.as_posix()  # needed to validate config
config = load_config_and_validate(config_path)

dataset_path = pydicom.data.get_testdata_file(
    "MR-SIEMENS-DICOM-WithOverlays.dcm", download=True,
)
dataset = pydicom.dcmread(dataset_path)

# the dataset is updated inplace
validation_issues = anonymise_and_validate_dicom(dataset, config=config)
assert validation_issues == {}
assert dataset != pydicom.dcmread(dataset_path)

Installation

Install the Python dependencies from the pixl_dcmd directory:

python -m pip install -e ../pixl_core/ -e ".[test,dev]"

Test

pytest

Tag scheme anonymisation

The tag schemes for anonymisation are taken from the YAML files defined in the project configuration. This should include at least a base, and optionally a manufacturer_overrides.

If a manufacturer_overrides is defined, it will be used to override the base tags, if the manufacturer of the DICOM file matches the manufacturer in the manufacturer_overrides. Any tags in the manufacturer_overrides that are not in the base will be added to the scheme as well.