Protein Subcellular Location Image Database for Python
======================================================

Pre-Requisites
==============
-pyslic, numpy, scipy, mahotas, milk, matplotlib, libFreeImage, omero

To install the prerequesites in Ubuntu, try
#!/bin/bash
sudo apt-get update
sudo apt-get install setup-tools python-matplotlib
sudo easy_install pip
sudo pip install pyslic

This should install all the prerequisites except OMERO. This package assumes you
have installed OMERO server in the system running PySLID.

For instructions on installing OMERO visit
http://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-installation.html

For an updated helper script for installing the prerequisites visit
https://gist.github.com/3940962

Installation
============
Run
> sudo python setup.py install
 
Usage
=====
Packages
1) Features
2) Search
3) Utilities

Description
a) calculate( session, iid, set="slf34", pixels=0, timeseries=0 )
Calculates and returns features vector given a valid image identification (iid). It currently calculates SLF34.
@param session
@param image id (iid)
@param set slf set id or some other set
@param pixels
@return features' vector 

b) get( session, iid, set="slf34", field=True, rid=[], calculate=False )
Returns a features vector given an image id (iid)
@param session
@param image id (iid)
@param set name
@return features vector

c) link( session, iid, features, fids, field=True, rid=[], overwrite=False )
Creates a table from the features vector and links
the table to image with the given image id (iid). If the feature array is
of size 2xN, then it assumes the first column corresponds to the feature ids 
and the second column to the feature values. If the feature vector is of size 
1xN, then it assumes the vector contains the feature values and it assigns 
feature ids using the rule feature1, feature2,… featureN.
@param session
@param image id (iid)
@param features a 2xN or 1xN feature array
@param fids features ids
@param field true if field features, false otherwise
@param region id (rid) must be non-empty if field is False
@param overwrites
@param table returns the OMERO Table object

2) Search
Not implemented yet.

3) Utilities
a) connect( server, port )
b) csv2features
c) exportImage2Tif
d) exportPlanes2Tif
e) getDataset
f) getFile
g) getImage
h) getListOfDatasets
i) getListOfFiles
j) getListOfImages
k) getListOfPlanes
l) getListOfProjects
m) getListOfTables
n) getPlane
o) getProject
p) getTable
q) hasDataset
r) hasFile
s) hasImage
t) hasPlane
u) hasProject
v) hasTable( session, iid, set, field=True )
w) login( client, username, password )