This is a Chaste bolt-on project that contains all the code required to recreate
the results in

"Development and Analysis of Patient-Based Complete Conducting Airways Models"
Bordas et al. PLoS ONE 2015

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Installation

1.) The project must be checked out into a copy of the Chaste trunk source code
    in <chaste_directory>/projects/AirwayGeneration2015
    
2.) Unpack AirwayGeneration2015Segmentations.tar.gz somewhere. 
    This file contains the raw segmentation data used as the basis for the 
    study.

3.) Edit the environment variables in bin/airways_paper_setup.sh to match your 
    installation.

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Running

Tests in this project are not designed to be run directly through scons. Instead
you should first build the tests

cd <chaste_directory>
scons co=1 b=GccOptNative_ndebug projects/AirwayGeneration2015 

Then use provided scripts in the 'bin' directory to run the code using the 
segmentation data as input. airways_paper_setup.sh should be sourced prior to 
running them. For example, to generate the complete conducting airway tree models, 
run

source projects/AirwayGeneration2015/bin/airways_paper_setup.sh
projects/AirwayGeneration2015/bin/generate_airways.sh

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Data Analysis

Output data generated by the projects will be automatically copied to the 
directory where you unpacked AirwayGeneration2015Segmentations.tar.gz

A number of R scripts exist in the 'R' directory that can be used to recreate
plots and tables from Bordas 2015 using the data output from simulations

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There is a Chaste wiki page associated with this project that gives links to
more information on Chaste installation, 

https://chaste.cs.ox.ac.uk/cgi-bin/trac.cgi/wiki/PaperTutorials/AirwayGeneration2015