mudicom 0.1.2

Read, validate, anonymize, and extract images from a DICOM file using GDCM

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.

Change Log

v0.1.1, 05-07-2015

• Support for animations as 3-D pixel arrays

v0.1.0, 1-11-2015

• Re-organized package modules

• Added __version__ variable

• Added and updated unit tests

• mudicom.load() now accepts kwargs

• Dicom() has new method: validate()

• Dicom() has new attributes: errors, warnings, image

• mudicom.base.Dicom.image is now an attribute, breaks backwards compat

• mudicom.image.Image.numpy is now an attribute, breaks backwards compat

• Added mudicom.exceptions module with InvalidDicom exception

v0.0.9, 10-19-2014

• Added basic profile DICOM anonymization

• Added ability to save changes to DICOM file, “save as”

v0.0.8, 10-17-2014

• Fixed another python 3 issue with unit tests

• Added guide on basic usage

• Added str and repr properties to primary classes

• Ramped up documentation at http://mudicom.dcmdb.org/

v0.0.7, 10-16-2014

• Fixed python 3 issue with GDCM image encoding

v0.0.6, 09-08-2014

• Updated README for clarity

• Created bried roadmap

v0.0.5, 08-14-2014

• Updated MANIFEST.in to include .rst, I’m a dumbass

v0.0.4, 08-14-2014

• Removed LICENSE.rst from setup.py

v0.0.3, 08-14-2014

• PIP cannot read LICENSE.rst for some reason

v0.0.3, 08-14-2014

• Weird permission issues with the egg

v0.0.2, 08-14-2014

• Updated packaging description

v0.0.1, 04-04-2014

• Initial release.