Getting Started with pydicom¶
Brief overview of pydicom and how to install.
pydicom is a pure python package for working with DICOM files such as medical images, reports, and radiotherapy objects.
pydicom makes it easy to read these complex files into natural pythonic structures for easy manipulation. Modified datasets can be written again to DICOM format files.
Here is a simple example of using pydicom in an interactive session, to read a radiotherapy plan file, change the patient setup from head-first-supine to head-first-prone, and save to a new file:
>>> import dicom >>> plan = dicom.read_file("rtplan.dcm") >>> plan.PatientName 'Last^First^mid^pre' >>> plan.dir("setup") # get a list of tags with "setup" somewhere in the name ['PatientSetupSequence'] >>> plan.PatientSetupSequence (0018, 5100) Patient Position CS: 'HFS' (300a, 0182) Patient Setup Number IS: '1' (300a, 01b2) Setup Technique Description ST: '' >>> plan.PatientSetupSequence.PatientPosition = "HFP" >>> plan.save_as("rtplan2.dcm")
pydicom is not a DICOM server , and is not primarily about viewing images. It is designed to let you manipulate data elements in DICOM files with python code.
pydicom is easy to install and use, and because it is a pure python package, it should run anywhere python runs.
One limitation of pydicom: compressed pixel data (e.g. JPEG) cannot be altered in an intelligent way as it can be for uncompressed pixels. Files can always be read and saved, but compressed pixel data cannot easily be modified.
As a pure python package, pydicom is easy to install and has no requirements other than python itself (the NumPy library is recommended, but is only required if manipulating pixel data).
- python 2.4 through 2.6 (or python 2.3 can be used for pydicom < 0.9.4)
- [ NumPy (http://numpy.scipy.org/) ] – optional, only needed if manipulating pixel data
Installing on Windows¶
On Windows, pydicom can be installed using the executable installer from the Downloads tab.
Alternatively, pydicom can be installed with easy_install, pip, or from source, as described in the sections below.
Installing using easy_install or pip (all platforms)¶
if you have setuptools installed,
just use easy_install at the command line (you may need
sudo on linux):
Depending on your python version, there may be some warning messages, but the install should still be ok.
pip is a newer install tool that works quite similarly to easy_install and can also be used.
Installing from source (all platforms)¶
- download the source code from the Downloads tab or checkout the mercurial repository source
- at a command line, change to the directory with the setup.py file
- with admin privileges, run
python setup.py install
- with some linux variants, for example, use
sudo python setup.py install
- with other linux variants you may have to
subefore running the command.
- for python < 2.6, you may get a syntax error message when the python files are “built” – this is due to some python 2.6 specific code in one unit test file. The installation seems to still be ok.
Installing on Mac¶
The instructions above for easy_install or installing from source will work on Mac OS. There is also a MacPorts portfile (py25-pydicom) available at http://trac.macports.org/browser/trunk/dports/python/py25-pydicom. This is maintained by other users and may not immediately be up to the latest release.
Once installed, the package can be imported at a python command line or used
in your own python program with
import dicom (note the package name is
pydicom when used in code.
See the examples directory
for both kinds of uses. Also see the User Guide
for more details of how to use the package.
Please join the pydicom discussion group to ask questions, give feedback, post example code for others – in other words for any discussion about the pydicom code. New versions, major bug fixes, etc. will also be announced through the group.
To start learning how to use pydicom, see the Pydicom User Guide.
|||For DICOM network capabilities, see the pynetdicom project.|
|||If using python(x,y), other packages you might be interested in include IPython (an indispensable interactive shell with auto-completion, history etc), Numpy (optionally used by pydicom for pixel data), and ITK/VTK or PIL (image processing and visualization).|