alfiyazi/mudicom

A python package that validates, reads, and extracts images from a DICOM file

mudicom

A light-weight python package that validates, reads, and extracts images from a DICOM file.

Requirements

Base:

• Python <= 2.7 (Should work with Python 3 but I haven't tested it)
• GDCM with python wrapper (http://mudicom.dcmdb.org/install.html)

Validator:

• dicom3tools (http://www.dclunie.com/dicom3tools.html)

Image:

• numpy (http://www.numpy.org/)
• PIL (https://github.com/python-pillow/Pillow); or
• Matplotlib (http://matplotlib.org/)

Quick How To

import mudicom
mu = mudicom.load("mudicom/tests/dicoms/ex1.dcm")

# returns array of data elements as dicts
mu.read()

# returns dict of errors and warnings for DICOM
mu.validate()

# basic anonymization
mu.anonymize()
# save anonymization
mu.save_as("dicom.dcm")

# creates image object
img = mu.image # before v0.1.0 this was mu.image()
# returns numpy array
img.numpy # before v0.1.0 this was mu.numpy()

# using Pillow, saves DICOM image
img.save_as_pil("ex1.jpg")
# using matplotlib, saves DICOM image
img.save_as_plt("ex1_2.jpg")

Documentation

Full documentation is available at http://mudicom.dcmdb.org/

Roadmap

• Extract multiple images from one single DICOM file
• Detect corrupted DICOM files
• Ability to anonymize DICOM file
• Ability to set data elements

Credits

Written by Eric Bower

Special thanks to Mathieu Malaterre (primary developer for GDCM), of whom without this package would not be possible.