Generation of Newborn Airways' Anatomy

This repository contains a Chaste User Project used to generate the anatomical surrogate of newborn airways.

Before starting

Edit your ~/.bashrc by adding the following lines at the end of the file:

	# ...at the end of ~/.bashrc
	export CHASTE_TEST_OUTPUT=$HOME/Chaste-Tests-Output
	export CHASTE_BUILD_DIR=$HOME/Builds/Chaste
	export CHASTE_REPO_DIR=$HOME/Repos/Chaste

Replace Chaste-Tests-Output with the preferred location for Tests' output.

It's possible to do that by using this command

	# Run this to append the former line.
	echo "export CHASTE_TEST_OUTPUT=$HOME/Chaste-Tests-Output" >> ~/.bashrc
	echo "export CHASTE_BUILD_DIR=$HOME/Builds/Chaste" >> ~/.bashrc
	echo "export CHASTE_REPO_DIR=$HOME/Repos/Chaste" >> ~/.bashrc

Source the file just modified and create the required folders:

	source ~/.bashrc
	mkdir -p $CHASTE_TEST_OUTPUT ~/Repos $CHASTE_BUILD_DIR

Clone Chaste repository.

	cd ~/Repos
	git clone https://github.com/Chaste/Chaste

Please refer to Chaste guide to complete this passage.

Navigate to $CHASTE_REPO_DIR/projects and clone this project in that location.

	cd $CHASTE_REPO_DIR/projects
	git clone https://github.com/andriluca/NewbornAirwayGeneration

Now Chaste repository is set. You can proceed and install Chaste and this project from source!

Compile the User Project

Run cmake from Chaste build folder.

	cd $CHASTE_BUILD_DIR
	cmake $CHASTE_REPO_DIR

Compile with make.

	# Number of available threads on your machine.
	N=4
	
	# Navigate to Chaste build directory and compile both `lung` and `TestNewbornAirwayGeneration` target.
	cd $CHASTE_BUILD_DIR
	make -j$N lung
	make -j$N TestNewbornAirwayGeneration
	
	# Run this test.
	ctest -V -R TestNewbornAirwayGeneration

Checkout if the test is 100% passed. If so congratulations, you have successfully installed this User Project.

Input

It's required to provide two pieces of input:

1. Major airways
2. Lobe segmentations

Major airways

It is possible to start from two source files:

1. airway.node: List of nodes. Each node represent a point in the major airways centreline with 3 coordinates (x, y, z) and two attributes: radius and start_id. radius (self explainatory) is evaluated in that point. start_id is a flag being 1 for generative points (i.e. points from which branching is allowed), 0 otherwise.
2. airway.edge: List of edges. Each edge is connecting two endpoints.

You can learn more about such files by referring to Chaste tests TestMultiLobeAirwayGenerator.hpp and TestAirwayGenerationTutorial.hpp.

It's also possible to start from one single vtu files:

• major_airways.vtu: vtk unstructured grid file

Lobe segmentations

They represent physical limits to airway "growth" process and should be five:

1. LLL.stl: Left, Lower Lung
2. LUL.stl: Left, Upper Lung
3. RLL.stl: Right Lower Lung
4. RML.stl: Right Mid Lung
5. RUL.stl: Right Upper Lung

Output

Generated output is located in $CHASTE_TEST_OUTPUT/TestNewbornAirwayGeneration/. Navigate to that folder and open the files complete_conducting_airway.node and complete_conducting_airway.edge. Other output files are available in the same folder. Use them at your will.

References

1. Chaste website
2. My MSc. thesis