Clinical Face Phenotype Space pipeline.
v1.2

Copyright (c) 06/5/2014 Christoffer Nellaker
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THE SOFTWARE.


Please cite the original publication:

http://dx.doi.org/10.7554/eLife.02020


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#  How to use code v1.2
#
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Installation of source code.
------------
Download the code from https://github.com/ChristofferNellaker/Clinical_Face_Phenotype_Space_Pipeline
Place in desired folder.
Install dependencies (list below)
Configure pipeline.ini with relative paths to models and dependencies.
Configure image_folders.ini to point to folders with images to be analysed.
Configure path_to_meta_data_parser.py 

Alternatively, there is an Ubuntu Virtual Box VM with a functioning compiled
pipeline available throught the vagrand cloud  chrisn/CFPS_VM

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Dependencies
------------ 
. Designed to run on Linux based operating systems.
. Python 2.7x
	https://www.python.org/
. Python modules 
	. Ruffus
		http://www.ruffus.org.uk/
	. optparse
		https://docs.python.org/2/library/optparse.html
. Automatic Naming of Characters in TV Video code set
	http://www.robots.ox.ac.uk/~vgg/research/nface/index.html
. OpenCV 
	http://opencv.org/
	Developed on v2.4
. Sqlite3
	https://sqlite.org/
. Sqlite3 driver for MATLAB
	http://www.cs.sunysb.edu/~kyamagu/software/matlab-sqlite3-driver/
. Serialize for MATLAB
	http://www.mathworks.com/matlabcentral/fileexchange/29457-serialize-deserialize/content/serialize.m
. MATLAB 2011b or later with a license and access to the Matlab compiler
. LIBSVM for MATLAB
	http://www.csie.ntu.edu.tw/~cjlin/libsvm/

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Running the Clinical Face Phenotype Space pipeline.
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Check the pipeline printout
cmd> python ./Clinical_Face_Phenotype_Space.py -vvvvn 

Run the pipeline
cmd> python ./Clinical_Face_Phenotype_Space.py -vvvv

Results will be output into:
./output_Diag_P0P1_acc.tab
./output_CIF_acc.tab

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Some notes on design principles applied
--------------------------------------------------
. The MATLAB scripts are compiled as the first step of the pipeline which allows them to be run in parallel.
. The variables for each script are passed in simple text files managed by the python ruffus pipeline. 
. Matlab output is stored in the sqlite3 database. The functions serialize and deserialise are used to encode these.