DicomAnonymizer

Current Fork Notes

Hi, this fork is breaking original project functionality, providing updated one instead.

I have added batch-anonymization. It is working with nested folders of dicom-files or with a single folder. In short, you can give a source and destination root directories, source should contain (possibly nested) directories with dicom files (but no dicom files in the root folder itself). The tool will find all folders inside the root, anonymize dicom-files and save anonymized data under the destination root, preserving the original directories structure.

Here is the use example:

git clone git@github.com:ademyanchuk/dicom-anonymizer.git
pip install . after cd into the project directory
you can now run dicom-anonymizer path/to/source path/to/destination
run dicom-anonymizer --help for more options

TODO: Add a Changelog and describe changes made since forking the project

End of Current Fork Note

Python package to anonymize DICOM files. This project provide a CLI tool for de-identification of dicom-files' headers as required by DICOM-standard basic de-identification profile. More information about dicom fields for anonymization can be found here.

The default behaviour of this package is to anonymize DICOM fields referenced in dicomfields.

Dicom fields are separated into different groups. Each groups will be anonymized in a different way.

Group	Action	Action definition
D_TAGS	replace	Replace with a non-zero length value that may be a dummy value and consistent with the VR**
Z_TAGS	empty	Replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR**
X_TAGS	delete	Completely remove the tag
U_TAGS	replace_UID	Replace all UID's number with a random one in order to keep consistent. Same UID will have the same replaced value
Z_D_TAGS	empty_or_replace	Replace with a non-zero length value that may be a dummy value and consistent with the VR**
X_Z_TAGS	delete_or_empty	Replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR**
X_D_TAGS	delete_or_replace	Replace with a non-zero length value that may be a dummy value and consistent with the VR**
X_Z_D_TAGS	delete_or_empty_or_replace	Replace with a non-zero length value that may be a dummy value and consistent with the VR**
X_Z_U_STAR_TAGS	delete_or_empty_or_replace_UID	If it's a UID, then all numbers are randomly replaced. Else, replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR**

How to install it?

Here is install example:

git clone git@github.com:ademyanchuk/dicom-anonymizer.git
pip install . after cd into the project directory

TODO: Provide as Pypi package

Installing this package will also install an executable named dicom-anonymizer. In order to use it, please refer to the next section.

How to use it ?

This package allows to anonymize a selection of DICOM field (defined or overrided). The way on how the DICOM fields are anonymized can also be overrided.

[required] src - full path to a folder which contains dicom files or folder contained nested folders with dicom files
[required] dst - full path to the anonymized DICOM image or to a folder. This folder will be created if not exist. If folder with a nested structure was provided as a src, the structure will be recreated at dst
[optional] --type - either batch for nested collection of folder with dicom files or folder for single folder with dicom files, default is batch
[optional] --no-extra - only use a rules from DICOM-standard basic de-id profile
[optional] --extra-rules - Path to json file defining extra rules for additional tags. Defalult extra_rules.json (see below)

Default behaviour

You can use the default anonymization behaviour describe above. This will assume the provided src is a nested collection of folders containing dicom files, will anonymize and save into dst recreating original folder structure. Anonymization will be done by processing the fields defiened in the DICOM-standard basic de-id profile and tags in the extra_rules.json. As was mentioned, add --no-extra flag to not use additional rules.

dicom-anonymizer src dst

Run dicom-anonymizer --help for help.

Private tags

Default behavior of the dicom anonymizer is to delete private tags. TODO: Add an option to save private tags

Custom rules with dictionary file

For advanced use cases you can create your own dictionary by creating a json file extra_rules.json, here is a default example from project extra_rules.json:

{
    "delete": [
        [
            "0x0008",
            "0x0012"
        ],
        [
            "0x0008",
            "0x0013"
        ],
        [
            "0x0018",
            "0x1012"
        ],
        [
            "0x0018",
            "0x1014"
        ]
    ]
}

See all valid action names in the actions list.

Then run:

dicom-anonymizer src dst --extra-rules dictionary.json

Anonymize dicom tags without dicom file

If for some reason, you need to anonymize dicom fields without initial dicom file (extracted from a database for example). Here is how you can do it:

from dicomanonymizer import anonymize_dataset

def main():

  # Create a list of tags object that should contains id, type and value
  fields = [
    { # Replaced by Anonymized
      'id': (0x0040, 0xA123),
      'type': 'LO',
      'value': 'Annie de la Fontaine',
    },
    { # Replaced with empty value
      'id': (0x0008, 0x0050),
      'type': 'TM',
      'value': 'bar',
    },
    { # Deleted
      'id': (0x0018, 0x4000),
      'type': 'VR',
      'value': 'foo',
    }
  ]

  # Create a readable dataset for pydicom
  data = pydicom.Dataset()

  # Add each field into the dataset
  for field in fields:
    data.add_new(field['id'], field['type'], field['value'])

  anonymize_dataset(data)

if __name__ == "__main__":
    main()

For more information about the pydicom's Dataset, please refer here. You can also add a dictionnary as previously :

    dictionary = {}

    def newMethod(dataset, tag):
        element = dataset.get(tag)
        if element is not None:
            element.value = element.value + '- generated with new method'

    dictionary[(0x0008, 0x103E)] = newMethod
    anonymize_dataset(data, dictionary)

Actions list

Action	Action definition
empty	Replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR**
delete	Completely remove the tag
keep	Do nothing on the tag
clean	Don't use it for now. This is not implemented!
replace_UID	Replace all UID's number with a random one in order to keep consistent. Same UID will have the same replaced value
empty_or_replace	Replace with a non-zero length value that may be a dummy value and consistent with the VR**
delete_or_empty	Replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR**
delete_or_replace	Replace with a non-zero length value that may be a dummy value and consistent with the VR**
delete_or_empty_or_replace	Replace with a non-zero length value that may be a dummy value and consistent with the VR**
delete_or_empty_or_replace_UID	If it's a UID, then all numbers are randomly replaced. Else, replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR**

** VR: Value Representation

Work originally done by Edern Haumont

ademyanchuk / dicom-anonymizer