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DICOM files parser meant to facilitate data access.

Project description

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dicom_parser

dicom_parser is a utility python package meant to facilitate access to DICOM header information by extending the functionality of pydicom.

Essentially, dicom_parser uses DICOM's data-element value-representation (VR), as well as prior knowledge on vendor-specific private tags or encoding schemes, in order to transform them to more "pythonic" data structures when possible.

For more information, please see the documentation.


Installation

To install the latest version of dicom_parser, simply run:

    pip install dicom_parser

Quickstart

The most basic usage case is reading a single DICOM image (.dcm file) as an Image instance.

    from dicom_parser import Image

    # Create a DICOM Image object
    image = Image('/path/to/dicom/file.dcm')

Coversion to Python's native types

dicom_parser provides dict-like access to the parsed values of the header's data-elements. The raw values as read by pydicom remain accessible through the raw attribute.

Examples

Decimal String (DS) to float using the Header class's get method:

    raw_value = image.header.raw['ImagingFrequency'].value
    raw_value
    >> "123.25993"
    type(raw_value)
    >> str

    parsed_value = image.header.get('ImagingFrequency')
    parsed_value
    >> 123.25993
    type(parsed_value)
    >> float

Age String (AS) to float:

    raw_value = image.header.raw['PatientAge'].value
    raw_value
    >> "027Y"
    type(raw_value)
    >> str

    parsed_value = image.header.get('PatientAge')
    parsed_value
    >> 27.0
    type(parsed_value)
    >> float

Date String (DA) to datetime.date using the Header class's indexing operator/subscript notation:

    raw_value = image.header.raw['PatientBirthDate'].value
    raw_value
    >> "19901214"
    type(raw_value)
    >> str

    parsed_value = image.header['PatientBirthDate']
    parsed_value
    >> datetime.date(1990, 12, 14)
    type(parsed_value)
    >> datetime.date

Et cetera.

The dict-like functionality also includes safe getting:

    image.header.get('MissingKey')
    >> None
    image.header.get('MissingKey', 'DefaultValue')
    >> 'DefaultValue'

As well as raising a KeyError for missing keys with the indexing operator:

    image.header['MissingKey']
    >> ...
    >> KeyError: "The keyword: 'MissingKey' does not exist in the header!"

Read DICOM series directory as a Series

Another useful class this package offers is the Series class:

    from dicom_parser import Series

    series = Series('/path/to/dicom/series/')

    # Read stacked pixel arrays as a 3D volume
    type(series.data)
    >>> numpy.ndarray
    series.data.shape
    >> (224, 224, 208)

    # Access the underlying Image instances
    series.images[6].header.get('InstanceNumber')
    >> 7    # instance numbers are 1-indexed

Reading Siemens 4D data encoded as mosaics is also supported:

    fmri_series = Series('/path/to/dicom/fmri/')
    fmri_series.data.shape
    >> (96, 96, 64, 200)

For more information, please see the documentation.

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