dicompyler-core

A library of core radiation therapy modules for DICOM / DICOM RT used by dicompyler <http://www.dicompyler.com>__. This package includes:

dicomparser: parse DICOM objects in an easy-to-use manner
dvh: Pythonic access to dose volume histogram (DVH) data
dvhcalc: Independent DVH calculation using DICOM RT Dose & RT Structure Set
dose: Pythonic access to RT Dose data including dose summation

Other information

Free software: BSD license <https://github.com/dicompyler/dicompyler-core/blob/master/LICENSE>__
Documentation: Read the docs <https://dicompyler-core.readthedocs.io>__
Tested on Python 3.7+

Dependencies

numpy <http://www.numpy.org>__ 1.2 or higher
pydicom <https://pydicom.github.io>__ 0.9.9 or higher (pydicom 1.0 compatible)
matplotlib <http://matplotlib.org>__ 1.3.0 or higher (for DVH calculation)
Optional:
- Pillow <https://pillow.readthedocs.io>__ (for image display)
- Shapely <https://github.com/Toblerity/Shapely>__ (for structure volume calculation)
- scikit-image <http://scikit-image.org/>__ (for DVH interpolation)
- scipy <https://scipy.org/>__ (for dose grid summation using interpolation)

Basic Usage

.. code-block:: python

from dicompylercore import dicomparser, dvh, dvhcalc
dp = dicomparser.DicomParser("rtss.dcm")

# i.e. Get a dict of structure information
structures = dp.GetStructures()

>>> structures[5]
{'color': array([255, 128, 0]), 'type': 'ORGAN', 'id': 5, 'empty': False, 'name': 'Heart'}

# Access DVH data
rtdose = dicomparser.DicomParser("rtdose.dcm")
heartdvh = dvh.DVH.from_dicom_dvh(rtdose.ds, 5)

>>> heartdvh.describe()
Structure: Heart
DVH Type:  cumulative, abs dose: Gy, abs volume: cm3
Volume:    437.46 cm3
Max Dose:  3.10 Gy
Min Dose:  0.02 Gy
Mean Dose: 0.64 Gy
D100:      0.00 Gy
D98:       0.03 Gy
D95:       0.03 Gy
D2cc:      2.93 Gy

# Calculate a DVH from DICOM RT data
calcdvh = dvhcalc.get_dvh("rtss.dcm", "rtdose.dcm", 5)

>>> calcdvh.max, calcdvh.min, calcdvh.D2cc
(3.0899999999999999, 0.029999999999999999, dvh.DVHValue(2.96, 'Gy'))

Advanced Usage and Examples can be found in Binder: |Binder|

Citing dicompyler-core

A DOI for dicompyler-core with various citation styles can be found at Zenodo: |Zenodo|

Credits

This package was created with Cookiecutter <https://github.com/audreyr/cookiecutter> and the audreyr/cookiecutter-pypackage <https://github.com/audreyr/cookiecutter-pypackage> project template.