Skip to content

TestNodeBasedCellSimulationsPythonLiteratePaper

Jump to bottom
jmsgrogan edited this page Nov 7, 2016 · 3 revisions

This tutorial is automatically generated from the file test/python/cell_based/tutorials/TestNodeBasedCellSimulationsPythonLiteratePaper.py. 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
import chaste.core
chaste.init()
import chaste.cell_based
import chaste.mesh
import chaste.visualization

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):

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.

        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.

        cells = chaste.cell_based.VecCellPtr()
        transit_type = chaste.cell_based.TransitCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_2()
        cell_generator.GenerateBasicRandom(cells, 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 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/TestNodeBasedCellPopulation")
        simulator.SetSamplingTimestepMultiple(12)
        simulator.SetEndTime(10.0)

We now pass a force law to the simulation.

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

To run the simulation, we call Solve().

        simulator.Solve();

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)

To visualize the results, open a new terminal, cd to the Chaste directory, then cd to anim. Then do: java Visualize2dCentreCells /tmp/$USER/testoutput/NodeBasedMonolayer/results_from_time_0. We need to select the 'Cells as circles' option to be able to visualize the cells, as opposed to just the centres. We may have to do: javac Visualize2dCentreCells.java beforehand to create the java executable. Alternatively to view in Paraview Load the file /tmp/$USER/testoutput/NodeBasedMonolayer/results_from_time_0/results.pvd, and add glyphs to represent cells. An option is to use 3D spherical glyphs and then make a planar cut.

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):

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

        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).

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

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/TestNodeBasedSpheroidCellPopulation")
        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)

To run the simulation, we call Solve().

        simulator.Solve();

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)

Note that you cannot view the results of a 3D simulation using the Java visualiser but to visualize the results, use Paraview. See the UserTutorials/VisualizingWithParaview tutorial for more information.

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

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_on_sphere(self):

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

        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)

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

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

        simulator = chaste.cell_based.OffLatticeSimulation3_3(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedOnSphereCellPopulation")
        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 = (0.0, 0.0, 1.0)
        radius = 1.0
        boundary_condition = chaste.cell_based.SphereGeometryBoundaryCondition3(cell_population, centre, radius)
        simulator.AddCellPopulationBoundaryCondition(boundary_condition)

To run the simulation, we call Solve().

        simulator.Solve();

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)

Note that you cannot view the results of a 3D simulation using the Java visualiser but to visualize the results, use Paraview. See the UserTutorials/VisualizingWithParaview tutorial for more information.

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

Code

The full code is given below

File name TestNodeBasedCellSimulationsPythonLiteratePaper.py 

import unittest
import chaste.core
chaste.init()
import chaste.cell_based
import chaste.mesh
import chaste.visualization

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

        generator = chaste.mesh.HoneycombMeshGenerator(2, 2)
        generating_mesh = generator.GetMesh()

        mesh = chaste.mesh.NodesOnlyMesh2()

        mesh.ConstructNodesWithoutMesh(generating_mesh, 1.5)

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

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

        simulator = chaste.cell_based.OffLatticeSimulation2_2(cell_population)
        simulator.SetOutputDirectory("Python/TestNodeBasedCellPopulation")
        simulator.SetSamplingTimestepMultiple(12)
        simulator.SetEndTime(10.0)

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

        simulator.Solve();

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

    def test_spheroid(self):

        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)

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

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

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

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

        simulator.Solve();

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

    def test_spheroid_on_sphere(self):

        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)

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

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

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

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

        centre = (0.0, 0.0, 1.0)
        radius = 1.0
        boundary_condition = chaste.cell_based.SphereGeometryBoundaryCondition3(cell_population, centre, radius)
        simulator.AddCellPopulationBoundaryCondition(boundary_condition)

        simulator.Solve();

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

if __name__ == '__main__':
    unittest.main(verbosity=2)
Clone this wiki locally