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Python implementation of TypiC: Typical Image Selection

Project description

typic is a python implementation of the Typical Image Chooser as described in

TypIC is also available as a service in the Protein Subcellular Location Image Database (PSLID); though the latter version is not the one described in this repository.

Master branch status

https://travis-ci.org/icaoberg/typic.svg?branch=master

Development branch status

https://travis-ci.org/icaoberg/typic.svg?branch=dev

Pre-Requisites

  • numpy
  • scipy

To install the prerequisites in Ubuntu 12.04

sudo apt-get install update
sudo apt-get install python-numpy python-scipy

Installation

There are several ways to install typic. The most common way is to download the source code, unzip/untar the source code package and run the command

sudo python setup.py install

I have plans of submitting this package to the Python Package Index. If I do so, then should be able to install it by running the command

sudo pip install typic

COMMENT: halcon depends on numpy and scipy. Installing these packages in Windows and MacOSX is not a trivial task. For more information refer to the documentation.

If you wish to install typic in a virtual enviroment, then you can do

virtualenv typic
cd typic
source ./bin/activate
pip install numpy
pip install scipy
mkdir src
cd src
git clone git@github.com:icaoberg/typic.git
cd typic
python setup.py install
cd ../../
deactivate

COMMENT: The previous snippet assumes that you have virtualenv installed in your working system.

Documentation

Documentation was written using Sphinx. To generate documentation use the following commands.

To generate html

cd docs
make html

To generate PDF document

cd docs
make latexpdf

To generate epub document

cd docs
make epub

Bugs and Questions

To submit bugs about the source code visit

https://github.com/icaoberg/typic

To submit bugs about the documentation visit

https://github.com/icaoberg/typic-docs

For any other inquiries visit those links as well.

Project details


Release history Release notifications

This version
History Node

0.0.1

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