Test Node Based Cell Simulations Python Tutorial

This tutorial is automatically generated from TestNodeBasedCellSimulationsPythonTutorial at revision 98e266d4. Note that the code is given in full at the bottom of the page.

Introduction

In this tutorial we show how Chaste can be used to create, run and visualize node-based simulations. Full details of the mechanical model can be found in Pathamathan et al “A computational study of discrete mechanical tissue models”, Physical Biology. Vol. 6. No. 3. 2009.. DOI (10.1088/1478-3975/6/3/036001).

The Test

import unittest  # Python testing framework
import numpy as np  # Matrix tools
import chaste  # The PyChaste module
import chaste.mesh  # Contains meshes
import chaste.cell_based  # Contains cell populations
import chaste.visualization  # Visualization tools
chaste.init()  # Set up MPI

class TestRunningNodeBasedSimulationsTutorial(chaste.cell_based.AbstractCellBasedTestSuite):

Test 1 - A basic node-based simulation

In the first test, we run a simple node-based simulation, in which we create a monolayer of cells, using a nodes only mesh. Each cell is assigned a uniform cell-cycle model.

    def test_monolayer(self):

        # JUPYTER_SETUP

The first thing we do is generate a nodes only mesh. To do this we first create a MutableMesh to use as a generating mesh. To do this we can use the HoneycombMeshGenerator. This generates a honeycomb-shaped mesh, in which all nodes are equidistant. Here the first and second arguments define the size of the mesh - we have chosen a mesh that is 2 nodes (i.e. cells) wide, and 2 nodes high.

        chaste.core.OutputFileHandler("Python/TestNodeBasedCellSimulationsTutorial")
        generator = chaste.mesh.HoneycombMeshGenerator(2, 2)
        generating_mesh = generator.GetMesh()

Once we have a MutableMesh we can generate a NodesOnlyMesh from it using the following commands. Note you can also generate the NodesOnlyMesh from a collection of nodes.

        mesh = chaste.mesh.NodesOnlyMesh2()

To run node-based simulations you need to define a cut off length (second argument in ConstructNodesWithoutMesh), which defines the connectivity of the nodes by defining a radius of interaction.

        mesh.ConstructNodesWithoutMesh(generating_mesh, 1.5)

Having created a mesh, we now create a (wrapped) vector of CellPtrs. To do this, we use the CellsGenerator helper class, which is specialized for the type of cell model required (here UniformCellCycleModel) and the dimension. We create an empty vector of cells and pass this into the method along with the mesh. The second argument represents the size of that the vector cells should become - one cell for each node, the third argument specifies the proliferative type of the cell.

        transit_type = chaste.cell_based.TransitCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_2()
        cells = cell_generator.GenerateBasicRandom(mesh.GetNumNodes(), transit_type)

Now we have a mesh and a set of cells to go with it, we can create a CellPopulation. In general, this class associates a collection of cells with a mesh. For this test, because we have a NodesOnlyMesh, we use a particular type of cell population called a NodeBasedCellPopulation.

        cell_population = chaste.cell_based.NodeBasedCellPopulation2(mesh, cells)

We can set up a VtkScene to do a quick visualization of the population before running the analysis.

        scene = chaste.visualization.VtkScene2()
        scene.SetCellPopulation(cell_population)
        # JUPYTER_SHOW_FIRST
        scene.Start()  # JUPYTER_SHOW

We then pass in the cell population into an OffLatticeSimulation, and set the output directory, output multiple and end time

        simulator = chaste.cell_based.OffLatticeSimulation2_2(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedCellSimulationsTutorial")
        simulator.SetSamplingTimestepMultiple(100)
        simulator.SetEndTime(10.0)

We now pass a force law to the simulation.

        force = chaste.cell_based.GeneralisedLinearSpringForce2_2()
        simulator.AddForce(force)

Save snapshot images of the population during the simulation

        scene_modifier = chaste.cell_based.VtkSceneModifier2()
        scene_modifier.SetVtkScene(scene)
        scene_modifier.SetUpdateFrequency(100)
        simulator.AddSimulationModifier(scene_modifier)

To run the simulation, we call Solve(). We can again do a quick rendering of the population at the end of the simulation

        scene.Start()
        simulator.Solve()
        scene.End()

The next two lines are for test purposes only and are not part of this tutorial. If different simulation input parameters are being explored the lines should be removed.

        self.assertEqual(cell_population.GetNumRealCells(), 8)
        self.assertAlmostEqual(chaste.cell_based.SimulationTime.Instance().GetTime(), 10.0, 6)

        # JUPYTER_TEARDOWN

Test 2 - a basic node-based simulation in 3D

In the second test we run a simple node-based simulation in 3D. This is very similar to the 2D test with the dimension changed from 2 to 3 and instead of using a mesh generator we generate the nodes directly.

    def test_spheroid(self):

        # JUPYTER_SETUP

First, we generate a nodes only mesh. This time we specify the nodes manually by first creating a vector of nodes

        chaste.core.OutputFileHandler("Python/TestNodeBasedCellSimulationsSpheroidTutorial")
        nodes = []
        nodes.append(chaste.mesh.Node3(0, False, 0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(1, False, -0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(2, False, 0.0, 0.5, 0.0))
        nodes.append(chaste.mesh.Node3(3, False, 0.0, -0.5, 0.0))

Finally a NodesOnlyMesh is created and the vector of nodes is passed to the ConstructNodesWithoutMesh method.

        mesh = chaste.mesh.NodesOnlyMesh3()

To run node-based simulations you need to define a cut off length (second argument in ConstructNodesWithoutMesh), which defines the connectivity of the nodes by defining a radius of interaction.

        mesh.ConstructNodesWithoutMesh(nodes, 1.5)

Having created a mesh, we now create a std::vector of CellPtrs. As before, we do this with the CellsGenerator helper class (this time with dimension 3).

        transit_type = chaste.cell_based.TransitCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_3()
        cells = cell_generator.GenerateBasicRandom(mesh.GetNumNodes(), transit_type)

        cell_population = chaste.cell_based.NodeBasedCellPopulation3(mesh, cells)

We can set up a VtkScene to do a quick visualization of the population before running the analysis.

        scene = chaste.visualization.VtkScene3()
        scene.SetCellPopulation(cell_population)
        scene.Start() # JUPYTER_SHOW

We then pass in the cell population into an OffLatticeSimulation, and set the output directory, output multiple and end time

        simulator = chaste.cell_based.OffLatticeSimulation3_3(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedCellSimulationsSpheroidTutorial")
        simulator.SetSamplingTimestepMultiple(12)
        simulator.SetEndTime(10.0)

We now pass a force law to the simulation.

        force = chaste.cell_based.GeneralisedLinearSpringForce3_3()
        simulator.AddForce(force)

Save snapshot images of the population during the simulation

        scene_modifier = chaste.cell_based.VtkSceneModifier3()
        scene_modifier.SetVtkScene(scene)
        scene_modifier.SetUpdateFrequency(100)
        simulator.AddSimulationModifier(scene_modifier)

To run the simulation, we call Solve(). We can again do a quick rendering of the population at the end of the simulation

        scene.Start()
        simulator.Solve()
        scene.End()

The next two lines are for test purposes only and are not part of this tutorial. If different simulation input parameters are being explored the lines should be removed.

        self.assertEqual(cell_population.GetNumRealCells(), 8)
        self.assertAlmostEqual(chaste.cell_based.SimulationTime.Instance().GetTime(), 10.0, 6)

        # JUPYTER_TEARDOWN

Test 3 - a node-based simulation on a restricted geometry

    def test_spheroid_on_sphere(self):

        # JUPYTER_SETUP

In the third test we run a node-based simulation restricted to the surface of a sphere.

        chaste.core.OutputFileHandler("Python/TestNodeBasedCellSimulationsRestrictedSpheroidTutorial")
        nodes = []
        nodes.append(chaste.mesh.Node3(0, False, 0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(1, False, -0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(2, False, 0.0, 0.5, 0.0))
        nodes.append(chaste.mesh.Node3(3, False, 0.0, -0.5, 0.0))
        mesh = chaste.mesh.NodesOnlyMesh3()

To run node-based simulations you need to define a cut off length (second argument in ConstructNodesWithoutMesh), which defines the connectivity of the nodes by defining a radius of interaction.

        mesh.ConstructNodesWithoutMesh(nodes, 1.5)

        transit_type = chaste.cell_based.TransitCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_3()
        cells = cell_generator.GenerateBasicRandom(mesh.GetNumNodes(), transit_type)
        cell_population = chaste.cell_based.NodeBasedCellPopulation3(mesh, cells)

We can set up a VtkScene to do a quick visualization of the population before running the analysis.

        scene = chaste.visualization.VtkScene3()
        scene.SetCellPopulation(cell_population)
        scene.Start() # JUPYTER_SHOW

        simulator = chaste.cell_based.OffLatticeSimulation3_3(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedCellSimulationsRestrictedSpheroidTutorial")
        simulator.SetSamplingTimestepMultiple(12)
        simulator.SetEndTime(10.0)

We now pass a force law to the simulation.

        force = chaste.cell_based.GeneralisedLinearSpringForce3_3()
        simulator.AddForce(force)

This time we create a CellPopulationBoundaryCondition and pass this to the OffLatticeSimulation. Here we use a SphereGeometryBoundaryCondition which restricts cells to lie on a sphere (in 3D) or circle (in 2D). For a list of possible boundary conditions see subclasses of AbstractCellPopulationBoundaryCondition. Note that some of these boundary conditions are not compatible with node-based simulations see the specific class documentation for details, if you try to use an incompatible class then you will receive a warning. First we set the centre (0,0,1) and radius of the sphere (1).

        centre = np.array([0.0, 0.0, 1.0])
        radius = 5.0
        point2 = chaste.mesh.ChastePoint3(centre)
        boundary_condition = chaste.cell_based.SphereGeometryBoundaryCondition3(cell_population, point2.rGetLocation(), radius)
        simulator.AddCellPopulationBoundaryCondition(boundary_condition)

Save snapshot images of the population during the simulation scene_modifier = chaste.cell_based.VtkSceneModifier3()

        scene_modifier.SetVtkScene(scene)
        scene_modifier.SetUpdateFrequency(100)
        simulator.AddSimulationModifier(scene_modifier)

To run the simulation, we call Solve(). We can again do a quick rendering of the population at the end of the simulation

        scene.Start()
        simulator.Solve()
        scene.End()

The next two lines are for test purposes only and are not part of this tutorial. If different simulation input parameters are being explored the lines should be removed.

        self.assertEqual(cell_population.GetNumRealCells(), 8)
        self.assertAlmostEqual(chaste.cell_based.SimulationTime.Instance().GetTime(),
                               10.0, 6)

        # JUPYTER_TEARDOWN

if __name__ == '__main__':
    unittest.main(verbosity=2)

Full code

File name: TestNodeBasedCellSimulationsPythonTutorial.py

import unittest  # Python testing framework
import numpy as np  # Matrix tools
import chaste  # The PyChaste module
import chaste.mesh  # Contains meshes
import chaste.cell_based  # Contains cell populations
import chaste.visualization  # Visualization tools
chaste.init()  # Set up MPI

class TestRunningNodeBasedSimulationsTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
    def test_monolayer(self):

        # JUPYTER_SETUP

        chaste.core.OutputFileHandler("Python/TestNodeBasedCellSimulationsTutorial")
        generator = chaste.mesh.HoneycombMeshGenerator(2, 2)
        generating_mesh = generator.GetMesh()

        mesh = chaste.mesh.NodesOnlyMesh2()

        mesh.ConstructNodesWithoutMesh(generating_mesh, 1.5)

        transit_type = chaste.cell_based.TransitCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_2()
        cells = cell_generator.GenerateBasicRandom(mesh.GetNumNodes(), transit_type)

        cell_population = chaste.cell_based.NodeBasedCellPopulation2(mesh, cells)

        scene = chaste.visualization.VtkScene2()
        scene.SetCellPopulation(cell_population)
        # JUPYTER_SHOW_FIRST
        scene.Start()  # JUPYTER_SHOW

        simulator = chaste.cell_based.OffLatticeSimulation2_2(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedCellSimulationsTutorial")
        simulator.SetSamplingTimestepMultiple(100)
        simulator.SetEndTime(10.0)

        force = chaste.cell_based.GeneralisedLinearSpringForce2_2()
        simulator.AddForce(force)

        scene_modifier = chaste.cell_based.VtkSceneModifier2()
        scene_modifier.SetVtkScene(scene)
        scene_modifier.SetUpdateFrequency(100)
        simulator.AddSimulationModifier(scene_modifier)

        scene.Start()
        simulator.Solve()
        scene.End()

        self.assertEqual(cell_population.GetNumRealCells(), 8)
        self.assertAlmostEqual(chaste.cell_based.SimulationTime.Instance().GetTime(), 10.0, 6)

        # JUPYTER_TEARDOWN

    def test_spheroid(self):

        # JUPYTER_SETUP

        chaste.core.OutputFileHandler("Python/TestNodeBasedCellSimulationsSpheroidTutorial")
        nodes = []
        nodes.append(chaste.mesh.Node3(0, False, 0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(1, False, -0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(2, False, 0.0, 0.5, 0.0))
        nodes.append(chaste.mesh.Node3(3, False, 0.0, -0.5, 0.0))

        mesh = chaste.mesh.NodesOnlyMesh3()

        mesh.ConstructNodesWithoutMesh(nodes, 1.5)

        transit_type = chaste.cell_based.TransitCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_3()
        cells = cell_generator.GenerateBasicRandom(mesh.GetNumNodes(), transit_type)

        cell_population = chaste.cell_based.NodeBasedCellPopulation3(mesh, cells)

        scene = chaste.visualization.VtkScene3()
        scene.SetCellPopulation(cell_population)
        scene.Start() # JUPYTER_SHOW

        simulator = chaste.cell_based.OffLatticeSimulation3_3(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedCellSimulationsSpheroidTutorial")
        simulator.SetSamplingTimestepMultiple(12)
        simulator.SetEndTime(10.0)

        force = chaste.cell_based.GeneralisedLinearSpringForce3_3()
        simulator.AddForce(force)

        scene_modifier = chaste.cell_based.VtkSceneModifier3()
        scene_modifier.SetVtkScene(scene)
        scene_modifier.SetUpdateFrequency(100)
        simulator.AddSimulationModifier(scene_modifier)

        scene.Start()
        simulator.Solve()
        scene.End()

        self.assertEqual(cell_population.GetNumRealCells(), 8)
        self.assertAlmostEqual(chaste.cell_based.SimulationTime.Instance().GetTime(), 10.0, 6)

        # JUPYTER_TEARDOWN

    def test_spheroid_on_sphere(self):

        # JUPYTER_SETUP

        chaste.core.OutputFileHandler("Python/TestNodeBasedCellSimulationsRestrictedSpheroidTutorial")
        nodes = []
        nodes.append(chaste.mesh.Node3(0, False, 0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(1, False, -0.5, 0.0, 0.0))
        nodes.append(chaste.mesh.Node3(2, False, 0.0, 0.5, 0.0))
        nodes.append(chaste.mesh.Node3(3, False, 0.0, -0.5, 0.0))
        mesh = chaste.mesh.NodesOnlyMesh3()

        mesh.ConstructNodesWithoutMesh(nodes, 1.5)

        transit_type = chaste.cell_based.TransitCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_3()
        cells = cell_generator.GenerateBasicRandom(mesh.GetNumNodes(), transit_type)
        cell_population = chaste.cell_based.NodeBasedCellPopulation3(mesh, cells)

        scene = chaste.visualization.VtkScene3()
        scene.SetCellPopulation(cell_population)
        scene.Start() # JUPYTER_SHOW

        simulator = chaste.cell_based.OffLatticeSimulation3_3(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedCellSimulationsRestrictedSpheroidTutorial")
        simulator.SetSamplingTimestepMultiple(12)
        simulator.SetEndTime(10.0)

        force = chaste.cell_based.GeneralisedLinearSpringForce3_3()
        simulator.AddForce(force)

        centre = np.array([0.0, 0.0, 1.0])
        radius = 5.0
        point2 = chaste.mesh.ChastePoint3(centre)
        boundary_condition = chaste.cell_based.SphereGeometryBoundaryCondition3(cell_population, point2.rGetLocation(), radius)
        simulator.AddCellPopulationBoundaryCondition(boundary_condition)

        scene_modifier.SetVtkScene(scene)
        scene_modifier.SetUpdateFrequency(100)
        simulator.AddSimulationModifier(scene_modifier)

        scene.Start()
        simulator.Solve()
        scene.End()

        self.assertEqual(cell_population.GetNumRealCells(), 8)
        self.assertAlmostEqual(chaste.cell_based.SimulationTime.Instance().GetTime(),
                               10.0, 6)

        # JUPYTER_TEARDOWN

if __name__ == '__main__':
    unittest.main(verbosity=2)

Test Mesh Based Cell Simulations Python Tutorial

Test Potts Based Cell Simulations Python Tutorial

Test Node Based Cell Simulations Python Tutorial

Introduction#

The Test#

Test 1 - A basic node-based simulation#

Test 2 - a basic node-based simulation in 3D#

Test 3 - a node-based simulation on a restricted geometry#

Full code#

Introduction

The Test

Test 1 - A basic node-based simulation

Test 2 - a basic node-based simulation in 3D

Test 3 - a node-based simulation on a restricted geometry

Full code