Volume Slicing and Editing
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Readme.md

Volumina - Volume Slicing and Editing Library

Circle CI

Installing

First, test volumina

$ python setup.py nosetests

and then install:

$ python setup.py install

Developing with Volumina

In the following we assume an Ubuntu system.

After you entered a virtual environment you can automatically execute all the steps documented below by calling

$ ./install-development-reqs-virtualenv-ubuntu.sh

from the "requirements" directory in the volumina repository. Note, that we use distribute instead of setuptools. So, create your virtualenvs using mkvirtualenv --distribute.

  1. Virtual Python Environment

Make a new virtualenv for volumina

$ virtualenv --distribute voluminave/

and activate it

$ source voluminave/bin/activate
  1. Linking to PyQt and Sip

Installing PyQt/Sip via pip is currently (May 2012) broken. Therefore install the development versions of Qt4, Sip, and PyQt4 globally and link them into the virtual environment:

 $ cd voluminave/lib/python2.7/site-packages/ 
 $ ln -s /usr/lib/python2.7/dist-packages/PyQt4/
 $ ln -s /usr/lib/python2.7/dist-packages/sip.so
 $ ln -s /usr/lib/python2.7/dist-packages/sipdistutils.py
 $ ln -s /usr/lib/python2.7/dist-packages/sipconfig.py
 $ ln -s /usr/lib/python2.7/dist-packages/sipconfig_nd.py
  1. Building the development requirements

Make sure that g++ is installed on your system besides the usual gcc C++/C development toolchain. qimage2ndarray depends on numpy without requiring the dependency (as of June 2012). Therefore we need to install our requirements in a two stage procedure:

$ pip install -r requirements/development-stage1.txt
$ pip install -r requirements/development-stage2.txt