De-identifying DICOM files

import multiprocessing
import time
from pathlib import Path
from typing import List
import glob
import os
from encord import EncordUserClient
from encord.objects.common import (
    DeidentifyRedactTextMode,
    SaveDeidentifiedDicomConditionNotSubstr,
    SaveDeidentifiedDicomConditionIn
)

# Replace s3://EXAMPLE-BUCKET/raw/ with the path to the file storage you're using 
def filelist_helper(dir,prefix='s3://EXAMPLE-BUCKET/raw/'):
    fl = [prefix+os.path.basename(f) for f in glob.glob(dir+"*.dcm")]
    return fl

# Add criteria to evaluate each file. See the 'Setting evaluation criteria' section below for more info. 
criteria = [
    SaveDeidentifiedDicomConditionNotSubstr("PRIMARY","ImageType"),              
    SaveDeidentifiedDicomConditionIn(["ct","pt","nm","mr","mg","pt"],"Modality") 
]

def deidentify(
    integration_title: str,
    dicom_urls: List[str],
) -> List[str]:

# Authenticate with Encord using the path to your private key
user_client = EncordUserClient.create_with_ssh_private_key(ssh_private_key_path="<private_key_path>")

    integration_hash = None

    # Find integration_hash for requested integration_title
    for integration in user_client.get_cloud_integrations():
        if integration.title == integration_title:
            integration_hash = integration.id

    if not integration_hash:
        raise Exception(f"Integration with integration_title={integration_title} not found")

    deidentified_dicom_urls = []

    # 'dicom_urls' should be a a single list containing the URLs of all instances of a series to be de-identified. Splitting a series into multiple lists might lead to inaccurate results and is therefore not recommended
    deidentified_dicom_url = user_client.deidentify_dicom_files(
        dicom_urls=dicom_urls,
        integration_hash=integration_hash,
        redact_dicom_tags = True,
        redact_pixels_mode = DeidentifyRedactTextMode.REDACT_ALL_TEXT,
        save_conditions = criteria,
        upload_dir = "s3://EXAMPLE-BUCKETt/output"
    )
    print(f"Deidentified url: {deidentified_dicom_url}")
    deidentified_dicom_urls += deidentified_dicom_url

    return deidentified_dicom_urls

# Replace MY-ENCORD-INTEGRATION with the title of your private cloud integration
_integration_title = "MY-ENCORD-INTEGRATION"

_deidentified_dicom_urls = deidentify(
    _integration_title,
    _dicom_urls,
)