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Quickstart

The :class:`~dicom_parser.image.Image` Class

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

>>> from dicom_parser import Image
>>> image = Image('/path/to/dicom/file.dcm')

Images have a :attr:`~dicom_parser.image.Image.header` attribute, which stores the parsed :class:`~dicom_parser.header.Header` instance.

>>> image.header
             Keyword                      VR                VM  Value
Tag
(0008, 0005)  SpecificCharacterSet         Code String       1   ISO_IR 100
(0008, 0008)  ImageType                    Code String       5   ('ORIGINAL', 'PRIMARY', ...
(0008, 0012)  InstanceCreationDate         Date              1   2018-05-01
...

dicom_parser provides :obj:`dict`-like access to the parsed values of the header's data-elements. The raw values as read by pydicom remain accessible through the :attr:`~dicom_parser.header.Header.raw` attribute. For a full comparison of the expected return types, see :ref:`value-representation`.

Note

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!"

The :class:`~dicom_parser.series.Series` Class

Another useful class this package offers is the :class:`~dicom_parser.series.Series` class, which enables reading an entire series' directory.

>>> from dicom_parser import Series
>>> series = Series('/some/dicom/series/')

Header Information

We can easily query the underlying images' headers using the :meth:`~dicom_parser.series.Series.get` method:

# Single value
>>> series.get('EchoTime')
3.04

# Multiple values
>>> series.get('InstanceNumber')
[1, 2, 3]

# No value
>>> series.get('MissingKey')
None

# Default value
>>> series.get('MissingKey', 'default_value')
'default_value'

Similarly to the :class:`~dicom_parser.image.Image` class, we can also use the indexing operator:

# Single value
>>> series['RepetitionTime']
7.6

# Multiple values
>>> series['SOPInstanceUID']
["1.123.1241.123124124.12.1",
 "1.123.1241.123124124.12.2",
 "1.123.1241.123124124.12.3"]

# No value
>>> series['MissingKey']
KeyError: "The keyword: 'MissingKey' does not exist in the header!"

Image Instances

Another useful feature of the indexing operator is for querying an :class:`~dicom_parser.image.Image` instance based on its index in the series:

>>> series[6]
dicom_parser.image.Image
>>> series[6].header['InstanceNumber]
7   # InstanceNumber is 1-indexed

Pixel Arrays

The data property returns a stacked volume of the images' pixel arrays:

>>> type(series.data)
numpy.ndarray
>>> series.data.shape
(224, 224, 208)