Fix visualisation crashes in notebooks

[kwabenantim]

Description
PyChaste visualisations crash routinely in notebooks.

To Do

• Reproduce problem.
• Fix problem (if possible).
• Recover gently from unavoidable crashes.
• Add additional tests if necessary.

[kwabenantim]

To Reproduce

import chaste
from chaste.cell_based import (
    CellsGeneratorNoCellCycleModel_2,
    ConstantTargetAreaModifier2,
    DifferentiatedCellProliferativeType,
    FarhadifarForce2,
    OffLatticeSimulation2_2,
    SetupNotebookTest, 
    VertexBasedCellPopulation2
)
from chaste.core import RandomNumberGenerator
from chaste.mesh import VoronoiVertexMeshGenerator
from chaste.visualization import JupyterNotebookManager, VtkScene2

chaste.init()
SetupNotebookTest()

RandomNumberGenerator.Instance().Reseed(1)
generator = chaste.mesh.VoronoiVertexMeshGenerator(6, 6, 1)
mesh = generator.GetMesh()
mesh.SetDistanceForT3SwapChecking(1.0)

cell_type = DifferentiatedCellProliferativeType()
cell_generator = CellsGeneratorNoCellCycleModel_2()
cells = cell_generator.GenerateBasicRandom(mesh.GetNumElements(), cell_type)

cell_population = VertexBasedCellPopulation2(mesh, cells)
cell_population.AddCellWriterCellVolumesWriter()

scene = VtkScene2()
scene.SetCellPopulation(cell_population)
nb_manager = JupyterNotebookManager()
nb_manager.vtk_show(scene, height=300)

Displays image in notebook here.

simulation = OffLatticeSimulation2_2(cell_population)

output_path = "Results"
file_handler = chaste.core.OutputFileHandler(output_path)
simulation.SetOutputDirectory(output_path)

simulation.SetEndTime(100)
simulation.SetDt(0.01)
simulation.SetSamplingTimestepMultiple(10)

force = FarhadifarForce2()
force.SetAreaElasticityParameter(1.0)
force.SetPerimeterContractilityParameter(0.04)
force.SetLineTensionParameter(0.12)
force.SetBoundaryLineTensionParameter(0.12)
simulation.AddForce(force)

target_area_modifier = ConstantTargetAreaModifier2()
simulation.AddSimulationModifier(target_area_modifier)

simulation.Solve()

nb_manager.vtk_show(scene, height=300)

Displays image in notebook here.

scene = VtkScene2()
scene.SetCellPopulation(simulation.rGetCellPopulation())
nb_manager.vtk_show(scene, height=300)

Jupyter kernel dies here. Colab displays image in notebook here.

scene = VtkScene2()
scene.SetCellPopulation(simulation.rGetCellPopulation())
nb_manager.vtk_show(scene, height=300)

Colab kernel dies here.

[kwabenantim]

Fix

Reset renderer list after each call to JupyterNotebookManager::vtk_show():

self.renderWindow.RemoveRenderer(renderer)