wiki:PaperTutorials/AirwayGeneration2015

Development and analysis of patient-based complete conducting airway models

Welcome to the Chaste wiki.

This section contains pages generated automatically from the source code accompanying Bordas et al. "Development and analysis of patient-based complete conducting airway models", currently in review at PLoS ONE.

Before running these examples you will need to install Chaste's dependencies and the source code for the current Chaste trunk version. The easiest way to do this is using an Ubuntu machine (or an Ubuntu virtual machine) as discussed on InstallGuides/UbuntuPackage. Note that Chaste is only fully supported on Linux/Unix systems, so users of Windows or Mac OS X may need to follow the virtual machine route. For manual installation of each dependency, on any version of Linux, see DeveloperInstallGuide.

Before looking at this project, you may wish to look at some of the basic user tutorials, particularly those marked as Lung tutorials.

Getting the code and data

If you are reading this as a Wiki page and do not have the bolt-on project you can download it anonymously as an attachment to this page. The segmentation data (AirwayGeneration2015Segmentations.tgz) associated with the project be downloaded from the Chaste data repository.

Documentation

  • The project must be checked out into a copy of the Chaste trunk source code

in <chaste_directory>/projects/AirwayGeneration2015

  • Unpack AirwayGeneration2015Segmentations.tar.gz somewhere.

This file contains the raw segmentation data used as the basis for the study.

  • Edit the environment variables in bin/airways_paper_setup.sh to match your

installation.

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

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 et al. 2015 using the data output from simulations

For further information on using Chaste to solve these and related problems, see our extensive guide material.


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Last modified 9 years ago Last modified on Jul 20, 2015, 8:01:50 PM

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