Skip to content

Commit

Permalink
Update README to reflect Py3 compatibility
Browse files Browse the repository at this point in the history
  • Loading branch information
jni committed Feb 8, 2015
1 parent f6ce749 commit bda9509
Showing 1 changed file with 20 additions and 19 deletions.
39 changes: 20 additions & 19 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
# gala: segmentation of nD images [![Picture](https://raw.github.com/janelia-flyem/janelia-flyem.github.com/master/images/gray_janelia_logo.png)](http://janelia.org/)

Gala is a python library for performing and evaluating image segmentation,
distributed under the open-source [Janelia Farm license](http://janelia-flyem.github.com/janelia_farm_license.html). It implements the algorithm
described in [Nunez-Iglesias *et al*.](http://arxiv.org/abs/1303.6163), PLOS
ONE, 2013.
Gala is a Python library for performing and evaluating image segmentation,
distributed under the open-source, BSD-like
[Janelia Farm license](http://janelia-flyem.github.com/janelia_farm_license.html).
It implements the algorithm described in
[Nunez-Iglesias *et al*.](http://arxiv.org/abs/1303.6163), PLOS ONE, 2013.

If you use this library in your research, please cite:

Expand All @@ -21,17 +22,18 @@ If you use or compare to the GALA algorithm in your research, please cite:
> *PLoS ONE 8(8): e71715.* doi:10.1371/journal.pone.0071715
Gala supports n-dimensional images (images, volumes, videos, videos of
volumes...) and multiple channels per image.
volumes...) and multiple channels per image. It is compatible with both
Python 3.4 and Python 2.7.

[![Build Status](https://travis-ci.org/janelia-flyem/gala.png?branch=master)](https://travis-ci.org/janelia-flyem/gala)
[![Coverage Status](https://img.shields.io/coveralls/janelia-flyem/gala.svg)](https://coveralls.io/r/janelia-flyem/gala)

## Requirements

* Python 2.7
* Python 3.4 or 2.7
* numpy 1.7+
* scipy 0.10+
* Image (a.k.a. Python Imaging Library or PIL) 1.1.7
* Image (a.k.a. Python Imaging Library or PIL) 1.1.7 or Pillow 2.5+
* networkx 1.6+
* HDF5 and h5py 1.5+
* cython 0.17+
Expand All @@ -46,17 +48,18 @@ volumes...) and multiple channels per image.

In its original incarnation, this project used Vigra for the random forest
classifier. Installation is less simple than scikit-learn, which has emerged
in the last year as a truly excellent implementation and is now recommended.
in recent years as a truly excellent implementation and is now recommended.
Tests in the test suite expect scikit-learn rather than Vigra.
You can also use any of the scikit-learn classifiers,
including their newly-excellent random forest.
including their world-class random forest implementation.

## Installation

### Installing gala

Gala is a Python library with limited Cython extensions and can be
installed in two ways:
installed in three ways:
* Use pip: `pip install gala`.
* Add the gala directory to your PYTHONPATH environment variable, or
* Use distutils to install it into your preferred python environment:

Expand Down Expand Up @@ -93,19 +96,17 @@ On Mac, you might have to install compilers (such as gcc, g++, and gfortran).

### Testing

The test coverage is rather tiny, but it is still a nice way to check you
haven't completely screwed up your installation. Note: the test scripts
*must* be run from the `tests` directory.
The test coverage is rather small, but it is still a nice way to check you
haven't completely screwed up your installation. After installing gala, go
to the code directory and type:

```bash
$ cd tests
$ python test_agglo.py
$ python test_features.py
$ python test_watershed.py
$ python test_optimized.py
$ python test_gala.py
$ py.test
```

You need to have pytest and pytest-cov installed, both of which are
available through PyPI.

## Usage

An example script, `example.py`, exists in the `tests/example-data`
Expand Down

0 comments on commit bda9509

Please sign in to comment.