Airway Generation

This tutorial is automatically generated from TestAirwayGenerationTutorial.hpp at revision 0a2ab4e09adf. Note that the code is given in full at the bottom of the page.

An example showing how generate a complete conducting airway model given segmentations of CT airways and lobes

In this tutorial we demonstrate using Chaste’s airway generation algorithm to create a complete model of the conducting airways (mean generation ~16) from computed tomography segmentations. Note that the execution time for this tutorial on a standard desktop PC is several minutes.

Note that the airway generation code is dependent of having VTK installed. However, we cannot put a guard around the whole file since that gives compiler errors if VTK is not installed. Instead we guard the internals of each test, and any includes that will be missing if VTK is not present.

#ifdef CHASTE_VTK

We include some VTK classes to allow STL files to be read

#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the strstream deprecated warning for now (gcc4.3)
#include "vtkSmartPointer.h"
#include "vtkPolyData.h"
#include "vtkSTLReader.h"

#endif // CHASTE_VTK

The usual headers are included

#include <cxxtest/TestSuite.h>

MultiLobeAirwayGenerator is the class that does most of the work in generating a complete airway tree

#include "MultiLobeAirwayGenerator.hpp"

All test suites should include either PetscSetupAndFinalize or FakePetscSetup. This code does not currently use any parallel functionality so it might include either.

#include "PetscSetupAndFinalize.hpp"

Define the test

class TestAirwayGenerationTutorial : public CxxTest::TestSuite
{
public: // Tests should be public!

    void TestGenerateAirways()
    {
#if defined(CHASTE_VTK) && ( (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 6) || VTK_MAJOR_VERSION >= 6)

        EXIT_IF_PARALLEL;

First, we load up a mesh containing the centre lines and radii of the central airways extracted from a CT image. The mesh needs to be of the type SPACE_DIM=3 and ELEMENT_DIM=1; that is it defines a mesh that exists in 3D space and is made up of 1D line elements. Each node in the mesh is expected to have two attributes associated with it. The first attribute specifies the radius of the airways that node. Thus the mesh defines a series of cylinders that represent the airways. The second attribute specifies whether the node is a terminal node or not.

        TetrahedralMesh<1,3> airways_mesh;
        VtkMeshReader<1,3> airways_mesh_reader("lung/test/data/TestSubject002MajorAirways.vtu");
        airways_mesh.ConstructFromMeshReader(airways_mesh_reader);

Note that the central airways mesh used here is defined in VTK unstructured grid format, for this format we have to manually copy over the node attribute information. This step would be unnecessary if using a mesh in !Triangles/Tetgen format.

        std::vector<double> node_radii;
        airways_mesh_reader.GetPointData("radius", node_radii);
        std::vector<double> terminal_marker;
        airways_mesh_reader.GetPointData("start_id", terminal_marker);
        for (TetrahedralMesh<1,3>::NodeIterator iter = airways_mesh.GetNodeIteratorBegin();
             iter != airways_mesh.GetNodeIteratorEnd();
             ++iter)
        {
            iter->AddNodeAttribute(node_radii[iter->GetIndex()]);
            iter->AddNodeAttribute(fmod(terminal_marker[iter->GetIndex()],2));
        }

We now define a MultiLobeAirwayGenerator to allow us to generate the distal airways to form a complete conducting airway tree. MultiLobeAirwayGenerator provides an easy to use interface to AirwayGenerator and facilitates the generation of airways into a complete lung, rather than the user having to do each lobe separately.

        MultiLobeAirwayGenerator generator(airways_mesh);

We need to set a number of parameters to ensure the resulting airway tree is consistent with known human morphometric data. The values given here can be considered standard for human lungs. The most important of these is the NumberOfPointsPerLung, which (approximately) specifies the number of terminals in the tree. The next is the BranchingFraction, which controls how long the generated airways will be. The diameter ratio is used to control the rate at which airway diameters decrease between airway orders.

        generator.SetNumberOfPointsPerLung(15000);
        generator.SetBranchingFraction(0.4);
        generator.SetDiameterRatio(1.15);

These parameters are less important for producing a consistent airway tree, but are useful for debugging etc.

        generator.SetMinimumBranchLength(0.00001);
        generator.SetPointLimit(1);
        generator.SetAngleLimit(180.0);

We now add lobar surface definitions for the five human lung lobes. Less ’lobes’ can be added if full lobar segmentation data is not available. Lobes must be tagged as ’left' or ‘right’ to enable the correct number of acini to be created. Lobes are represented by triangle surface definitions defined in STL files.

        vtkSmartPointer<vtkSTLReader> lll_reader = vtkSmartPointer<vtkSTLReader>::New();
        lll_reader->SetFileName("lung/test/data/lll.stl");
        lll_reader->Update();
        generator.AddLobe(lll_reader->GetOutput(), LEFT);

        vtkSmartPointer<vtkSTLReader> lul_reader = vtkSmartPointer<vtkSTLReader>::New();
        lul_reader->SetFileName("lung/test/data/lul.stl");
        lul_reader->Update();
        generator.AddLobe(lul_reader->GetOutput(), LEFT);

        vtkSmartPointer<vtkSTLReader> rll_reader = vtkSmartPointer<vtkSTLReader>::New();
        rll_reader->SetFileName("lung/test/data/rll.stl");
        rll_reader->Update();
        generator.AddLobe(rll_reader->GetOutput(), RIGHT);

        vtkSmartPointer<vtkSTLReader> rml_reader = vtkSmartPointer<vtkSTLReader>::New();
        rml_reader->SetFileName("lung/test/data/rml.stl");
        rml_reader->Update();
        generator.AddLobe(rml_reader->GetOutput(), RIGHT);

        vtkSmartPointer<vtkSTLReader> rul_reader = vtkSmartPointer<vtkSTLReader>::New();
        rul_reader->SetFileName("lung/test/data/rul.stl");
        rul_reader->Update();
        generator.AddLobe(rul_reader->GetOutput(), RIGHT);

We now perform two preprocessing steps prior to generation. AssignGrowthApices determine which lobe each of the terminal ends of the central airways segmentation are in.

        generator.AssignGrowthApices();

Distribute points creates the target acinar points within the lung volume. The number created is as specified previously using SetNumberOfPointsPerLung.

        generator.DistributePoints();

We now generate the distal airways. The output is automatically written as a mesh in both tetgen format and VTK unstructured grid format to $CHASTE_TEST_OUTPUT/TestAirwayGenerationTutorial/

The resulting geometry can most easily be viewed in Paraview by loading the unstructured grid file. Application of a ‘Extract Surface’ filter followed by a ‘Tube’ filter allows the centreline and radius information to be view as a series of tubes.

        generator.Generate("TestAirwayGenerationTutorial", "example_complete_conducting_airway");

#endif // VTK >= 5.6
    }
};

Full code

#ifdef CHASTE_VTK

#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the strstream deprecated warning for now (gcc4.3)
#include "vtkSmartPointer.h"
#include "vtkPolyData.h"
#include "vtkSTLReader.h"

#endif // CHASTE_VTK

#include <cxxtest/TestSuite.h>

#include "MultiLobeAirwayGenerator.hpp"

#include "PetscSetupAndFinalize.hpp"

class TestAirwayGenerationTutorial : public CxxTest::TestSuite
{
public: // Tests should be public!

    void TestGenerateAirways()
    {
#if defined(CHASTE_VTK) && ( (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 6) || VTK_MAJOR_VERSION >= 6)

        EXIT_IF_PARALLEL;

        TetrahedralMesh<1,3> airways_mesh;
        VtkMeshReader<1,3> airways_mesh_reader("lung/test/data/TestSubject002MajorAirways.vtu");
        airways_mesh.ConstructFromMeshReader(airways_mesh_reader);

        std::vector<double> node_radii;
        airways_mesh_reader.GetPointData("radius", node_radii);
        std::vector<double> terminal_marker;
        airways_mesh_reader.GetPointData("start_id", terminal_marker);
        for (TetrahedralMesh<1,3>::NodeIterator iter = airways_mesh.GetNodeIteratorBegin();
             iter != airways_mesh.GetNodeIteratorEnd();
             ++iter)
        {
            iter->AddNodeAttribute(node_radii[iter->GetIndex()]);
            iter->AddNodeAttribute(fmod(terminal_marker[iter->GetIndex()],2));
        }

        MultiLobeAirwayGenerator generator(airways_mesh);

        generator.SetNumberOfPointsPerLung(15000);
        generator.SetBranchingFraction(0.4);
        generator.SetDiameterRatio(1.15);

        generator.SetMinimumBranchLength(0.00001);
        generator.SetPointLimit(1);
        generator.SetAngleLimit(180.0);

        vtkSmartPointer<vtkSTLReader> lll_reader = vtkSmartPointer<vtkSTLReader>::New();
        lll_reader->SetFileName("lung/test/data/lll.stl");
        lll_reader->Update();
        generator.AddLobe(lll_reader->GetOutput(), LEFT);

        vtkSmartPointer<vtkSTLReader> lul_reader = vtkSmartPointer<vtkSTLReader>::New();
        lul_reader->SetFileName("lung/test/data/lul.stl");
        lul_reader->Update();
        generator.AddLobe(lul_reader->GetOutput(), LEFT);

        vtkSmartPointer<vtkSTLReader> rll_reader = vtkSmartPointer<vtkSTLReader>::New();
        rll_reader->SetFileName("lung/test/data/rll.stl");
        rll_reader->Update();
        generator.AddLobe(rll_reader->GetOutput(), RIGHT);

        vtkSmartPointer<vtkSTLReader> rml_reader = vtkSmartPointer<vtkSTLReader>::New();
        rml_reader->SetFileName("lung/test/data/rml.stl");
        rml_reader->Update();
        generator.AddLobe(rml_reader->GetOutput(), RIGHT);

        vtkSmartPointer<vtkSTLReader> rul_reader = vtkSmartPointer<vtkSTLReader>::New();
        rul_reader->SetFileName("lung/test/data/rul.stl");
        rul_reader->Update();
        generator.AddLobe(rul_reader->GetOutput(), RIGHT);

        generator.AssignGrowthApices();

        generator.DistributePoints();

        generator.Generate("TestAirwayGenerationTutorial", "example_complete_conducting_airway");

#endif // VTK >= 5.6
    }
};

ABC Parameterization of the Hodgkin-Huxley Model

Another Bidomain Simulation

Airway Generation

An example showing how generate a complete conducting airway model given segmentations of CT airways and lobes#

Full code#

An example showing how generate a complete conducting airway model given segmentations of CT airways and lobes

Full code