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https://github.com/KitwareMedical/dicom-anonymizer

Tool to anonymize DICOM files according to the DICOM standard
https://github.com/KitwareMedical/dicom-anonymizer

Last synced: 3 months ago
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Tool to anonymize DICOM files according to the DICOM standard

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# DicomAnonymizer



Python package to anonymize DICOM files.

The anonymization answer to the standard . More information about dicom fields for anonymization can be found [here](http://dicom.nema.org/dicom/2013/output/chtml/part15/chapter_E.html#table_E.1-1).



The default behaviour of this package is to anonymize DICOM fields referenced in [dicomfields](dicomanonymizer/dicomfields.py).



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 random ones. 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**|

| ALL_TAGS | | Contains all previous defined tags



# How to install it?



Installation can be done via pip `pip install dicom-anonymizer` or conda `conda install -c conda-forge dicom-anonymizer`.



# How to test it?

- One time set up:

  - virtual environment for this package and activate it. For

  example set up using `virtualenv venv` and activate using

  `venv\Scripts\activate.bat` (on Windows)

  - Install editable version and development requirements using

  `pip install -e .[dev]`

- Run unit test using `pytest`



# How to build it?

These instructions rely on wheel build-package format. Install it if you have not done it already using:

`pip install wheel`



The sources files can be packaged by using:

`python ./setup.py bdist_wheel`



This command will generate a wheel package in `dist` folder which can be then installed as a python package using

`pip install ./dist/dicom_anonymizer-1.0.11-py2.py3-none-any.whl`



On Windows, if you see a warning message

`'./dist/dicom_anonymizer-1.0.11-py2.py3-none-any.whl' looks like a filename, but the file does not exist`,

this could be due to pip not being able to handle relative path (See issue https://github.com/pypa/pip/issues/10808). As a work-around, change directory to `dist` and then install it using

`pip install dicom_anonymizer-1.0.11-py2.py3-none-any.whl`



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 overridden).

The way on how the DICOM fields are anonymized can also be overridden.



- **[required]** InputPath = Full path to a single DICOM image or to a folder which contains dicom files

- **[required]** OutputPath = Full path to the anonymized DICOM image or to a folder. This folder has to exist.

- [optional] ActionName = Defined an action name that will be applied to the DICOM tag.

- [optional] Dictionary = Path to a JSON file which defines actions that will be applied on specific dicom tags (see below)



## Default behaviour



You can use the default anonymization behaviour describe above.



```python

dicom-anonymizer Input Output

```



## Private tags



Default behavior of the dicom anonymizer is to delete private tags.

But you can bypass it:

- Solution 1: Use regexp to define which private tag you want to keep/update (cf [custom rules](#custom-rules))

- Solution 2: Use dicom-anonymizer.exe option to keep all private tags : `--keepPrivateTags`



## Custom rules

You can manually add new rules in order to have different behaviors with certain tags.

This will allow you to override default rules:



**Executable**:

```python

dicom-anonymizer InputFilePath OutputFilePath -t '(0x0001, 0x0001)' ActionName -t '(0x0001, 0x0005)' ActionName2

```

This will apply the `ActionName` to the tag `'(0x0001, 0x0001)'` and `ActionName2` to `'(0x0001, 0x0005)'`



**Note**: ActionName has to be defined in [actions list](#actions-list)



Example 1: The default behavior of the patient's ID is to be replaced by an empty or null value. If you want to keep this value, then you'll have to run :

```python

python anonymizer.py InputFilePath OutputFilePath -t '(0x0010, 0x0020)' keep

```

This command will override the default behavior executed on this tag and the patient's ID will be kept.



Example 2: We just want to change the study date from 20080701 to 20080000, then we'll use the regexp

```python

python anonymizer.py InputFilePath OutputFilePath -t '(0x0008, 0x0020)' 'regexp' '0701$' '0000'

```



## Custom rules with dictionary file



Instead of having a big command line with several new actions, you can create your own dictionary by creating a json file `dictionary.json` :

```json

{

    "(0x0002, 0x0002)": "ActionName",

    "(0x0003, 0x0003)": "ActionName",

    "(0x0004, 0x0004)": "ActionName",

    "(0x0005, 0x0005)": "ActionName"

}

```

Same as before, the `ActionName` has to be defined in the [actions list](#actions-list).



```python

dicom-anonymizer InputFilePath OutputFilePath --dictionary dictionary.json

```



If you want to use the **regexp** action in a dictionary:

```json

{

    "(0x0002, 0x0002)": "ActionName",

    "(0x0008, 0x0020)": {

        "action": "regexp",

        "find": "0701$",

        "replace": "0000"

    }

}

```



## Custom/overrides actions



Here is a small example which keeps all metadata but updates the series description

by adding a suffix passed as a parameter.



```python

import argparse

from dicomanonymizer import ALL_TAGS, anonymize, keep



def main():

    parser = argparse.ArgumentParser(add_help=True)

    parser.add_argument('input', help='Path to the input dicom file or input directory which contains dicom files')

    parser.add_argument('output', help='Path to the output dicom file or output directory which will contains dicom files')

    parser.add_argument('--suffix', action='store', help='Suffix that will be added at the end of series description')

    args = parser.parse_args()



    input_dicom_path = args.input

    output_dicom_path = args.output



    extra_anonymization_rules = {}



    def setup_series_description(dataset, tag):

        element = dataset.get(tag)

        if element is not None:

            element.value = f'{element.value}-{args.suffix}'



    # ALL_TAGS variable is defined on file dicomfields.py

    # the 'keep' method is already defined into the dicom-anonymizer

    # It will overrides the default behaviour

    for i in ALL_TAGS:

        extra_anonymization_rules[i] = keep



    if args.suffix:

        extra_anonymization_rules[(0x0008, 0x103E)] = setup_series_description



    # Launch the anonymization

    anonymize(input_dicom_path, output_dicom_path, extra_anonymization_rules, delete_private_tags=False)



if __name__ == '__main__':

    main()

```



See the full application in the `examples` folder.



In your own file, you'll have to define:

- Your custom functions. Be careful, your functions always have in inputs a dataset and a tag

- A dictionary which map your functions to a tag



## Anonymize dicom tags for a dataset



You can also anonymize dicom fields in-place for pydicom's DataSet using `anonymize_dataset`. See this example:

```python

import pydicom



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()

```



See the full application in the `examples` folder.



For more information about the pydicom's Dataset, please refer [here](https://pydicom.github.io/pydicom/stable/reference/generated/pydicom.dataset.Dataset.html).



You can also add `extra_anonymization_rules` as above:

```python

    anonymize_dataset(data_ds, extra_anonymization_rules, delete_private_tags=True)

```



# 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** |

| deleteOrEmptyOrReplace | 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** |

|regexp| These action is not a common action. It allows to use regexp to modify values|



** VR: Value Representation



Work originally done by Edern Haumont