TestVertexBasedCellPopulationPython.py

"""Copyright (c) 2005-2019, University of Oxford.
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"""

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


class TestCell(chaste.cell_based.AbstractCellBasedTestSuite):

    def test_construct(self):

        file_handler = chaste.core.OutputFileHandler("Python/TestVertexBasedCellPopulation")

        # Set up the mesh
        mesh_generator = chaste.mesh.HoneycombVertexMeshGenerator(2, 2)
        mesh = mesh_generator.GetMesh()

        # Make the cells
        proliferative_type = chaste.cell_based.DefaultCellProliferativeType()
        cell_generator = chaste.cell_based.CellsGeneratorUniformCellCycleModel_2()
        cells = cell_generator.GenerateBasicRandom(mesh.GetNumElements(),
                                                   proliferative_type)

        # Make the cell population
        cell_population = chaste.cell_based.VertexBasedCellPopulation2(mesh,
                                                                       cells)

        # Set up the visualizer
        scene = chaste.visualization.VtkScene2()
        scene.SetCellPopulation(cell_population)
        scene.SetSaveAsAnimation(True)
        scene.SetOutputFilePath(file_handler.GetOutputDirectoryFullPath() +
                                "/cell_population")

        modifier = chaste.cell_based.VtkSceneModifier2()
        modifier.SetVtkScene(scene)

        force = chaste.cell_based.NagaiHondaForce2()
        target_area_modifier = chaste.cell_based.SimpleTargetAreaModifier2()
        target_area_modifier.SetGrowthDuration(1.0)

        # Set up the simulation
        simulator = chaste.cell_based.OffLatticeSimulation2_2(cell_population)
        simulator.SetOutputDirectory("Python/TestVertexBasedCellPopulation")
        simulator.SetEndTime(0.2)
        simulator.AddForce(force)
        simulator.SetSamplingTimestepMultiple(200)
        simulator.AddSimulationModifier(modifier)
        simulator.AddSimulationModifier(target_area_modifier)

        simulator.Solve()


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