neurosnap / 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.

mudicom's Issues

no _gdcmswig.so

used apt-get install python-gdcm and see gdcm.py, gdcmswig.py and lsb_release.py but no _gdcmswig.so

issue in image.py in calling self.numpy()

Hi,
This is my code..

import mudicom
mu = mudicom.load("test.dcm")
img=mu.image
img.save_as_pil("test.jpg")
Error message:
Traceback (most recent call last):
File "", line 1, in
File "/home/user1/venv/local/lib/python2.7/site-packages/mudicom/image.py", line 122, in save_as_pil
pixel_array = self.numpy()
TypeError: 'numpy.ndarray' object is not callable

If I change the self.numpy() to self.numpy then all works fine.

Does it need to be fixed or if I am doing anything wrong? Thanks..