Creating And Using New Cell Based Writers

This tutorial is automatically generated from TestCreatingAndUsingNewCellBasedWritersTutorial.hpp at revision 409e06cb314b. Note that the code is given in full at the bottom of the page.

An example showing how to create a new cell writer and use it in a cell-based simulation

Introduction

This tutorial assumes you have already read the tutorial Creating And Using A New Cell Property.

In Creating And Using A New Cell Property we showed how to create a new cell property class, MotileCellProperty, and how this can be used in a cell-based simulation. In this tutorial, we show how to create a new cell writer class, which can be used to output different data from a cell-based simulation. Our example will be a writer class for outputting information about those cells in a simulation that have the MotileCellProperty.

1. Including header files

As in previous cell-based Chaste tutorials, we begin by including the necessary header file and archiving headers. For simplicity, we duplicate the code presented in Creating And Using A New Cell Property that defines the MotileCellProperty class. As before, note that usually this code would be separated out into a declaration in a .hpp file and a definition in a .cpp file. We also include some header files defining classes to be used in the cell-based simulation test. We have encountered each of these header files in previous cell-based Chaste tutorials.

#include <cxxtest/TestSuite.h>
#include "CheckpointArchiveTypes.hpp"
#include "AbstractCellBasedTestSuite.hpp"
#include "AbstractCellProperty.hpp"
#include "AbstractForce.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "NodesOnlyMesh.hpp"
#include "WildTypeCellMutationState.hpp"
#include "DifferentiatedCellProliferativeType.hpp"
#include "CellLabel.hpp"
#include "FixedG1GenerationalCellCycleModel.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "CellMutationStatesCountWriter.hpp"
#include "OffLatticeSimulation.hpp"
#include "SmartPointers.hpp"
#include "PetscSetupAndFinalize.hpp"

class MotileCellProperty : public AbstractCellProperty
{
private:
    unsigned mColour;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellProperty>(*this);
        archive & mColour;
    }

public:

    MotileCellProperty(unsigned colour=5)
        : AbstractCellProperty(),
          mColour(colour)
    {}

    ~MotileCellProperty()
    {}

    unsigned GetColour() const
    {
        return mColour;
    }
};

Defining a cell writer class

We next define a class that writes information about each cell in the population, using the public methods of the population class. Note that usually this code would be separated out into a declaration in a .hpp file and definition in a .cpp file.

We inherit from the base class, AbstractCellWriter, whose header we must include. This abstract class encapsulates how files are written. To specify how this writer should act on each cell, we implement the VisitCell() method.

#include "AbstractCellWriter.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class CellMotilityWriter : public AbstractCellWriter<ELEMENT_DIM, SPACE_DIM>
{
private:

The serialize() method defines how a cell writer object itself can be written to file. In almost all cases it should just call the base class serializer, using the code below. If the new cell writer class has any data members, they should be serialized in this method after calling the base class serializer.

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> >(*this);
    }

public:

The constructor method calls the base class constructor, with the name of the output file as a parameter. In this case the filename written to will be “cellmotilityresults.dat”.

    CellMotilityWriter()
        : AbstractCellWriter<ELEMENT_DIM, SPACE_DIM>("cellmotilityresults.dat")
    {
    }

The next method provides functionality that will be used in future for outputting data to VTK.

    double GetCellDataForVtkOutput(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
    {
        return pCell->HasCellProperty<MotileCellProperty>();
    }

The implementation of the VisitCell() method defines the data this writer commits to the file. Data can be streamed into the member variable mpOutputStream using the << operator. These data are then written to file. In this example, for each cell pCell in pCellPopulation, we write its location index, followed by a space, followed by its location coordinates (space separated) followed by a 0 or 1 indicating whether the cell has the motile property. The base class handles writing the timestamp and newline for each simulation timestep, so we don’t need to worry about that.

    void VisitCell(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
    {
        *this->mpOutStream << pCellPopulation->GetLocationIndexUsingCell(pCell) << " ";

        c_vector<double, SPACE_DIM> cell_location = pCellPopulation->GetLocationOfCellCentre(pCell);
        for (unsigned i=0; i<SPACE_DIM; i++)
        {
            *this->mpOutStream << cell_location[i] << " ";
        }

        *this->mpOutStream << pCell->HasCellProperty<MotileCellProperty>() << " ";
    }
};

As mentioned in previous cell-based Chaste tutorials, we need to include the next block of code to be able to archive the cell property and writer objects in a cell-based simulation, and to obtain a unique identifier for our new classes for when writing results to file.

Identifiers for both classes are defined together here, since we can only have each #include once in this source file. Normally the first #include and export would go in each respective class’s header file, and the second include and export in its source file.

#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)
EXPORT_TEMPLATE_CLASS_ALL_DIMS(CellMotilityWriter)
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)
EXPORT_TEMPLATE_CLASS_ALL_DIMS(CellMotilityWriter)

This completes the code for MotileCellProperty and CellMotilityWriter.

We now define the test class, which inherits from AbstractCellBasedTestSuite and demonstrates how MotileCellProperty and CellMotilityWriter can be used in a cell-based simulation.

class TestCreatingAndUsingNewCellBasedWritersTutorial : public AbstractCellBasedTestSuite
{
public:

    void TestOffLatticeSimulationWithMotileCellPropertyAndWriters()
    {

We begin by creating a NodeBasedCellPopulation, just as in Creating And Using A New Cell Property. We add the MotileCellProperty to a random selection of cells. We also add the CellLabel to these cells so that we can easily visualize the different cell types.

        EXIT_IF_PARALLEL;

        HoneycombMeshGenerator generator(10, 10);
        boost::shared_ptr<MutableMesh<2,2> > p_generating_mesh = generator.GetCircularMesh(5);

        NodesOnlyMesh<2> mesh;
        mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);

        MAKE_PTR(MotileCellProperty, p_motile);
        MAKE_PTR(CellLabel, p_label);
        MAKE_PTR(WildTypeCellMutationState, p_state);
        MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);

        std::vector<CellPtr> cells;
        for (unsigned i=0; i<mesh.GetNumNodes(); i++)
        {
            FixedG1GenerationalCellCycleModel* p_model = new FixedG1GenerationalCellCycleModel();

            CellPropertyCollection collection;
            if (RandomNumberGenerator::Instance()->ranf() < 0.2)
            {
                collection.AddProperty(p_motile);
                collection.AddProperty(p_label);
            }

            CellPtr p_cell(new Cell(p_state, p_model, NULL, false, collection));
            p_cell->SetCellProliferativeType(p_diff_type);

            double birth_time = - RandomNumberGenerator::Instance()->ranf() *
                                    (p_model->GetStemCellG1Duration() + p_model->GetSG2MDuration());

            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

        NodeBasedCellPopulation<2> cell_population(mesh, cells);

In order to write cell motility data using our writer, we must add it to the list of writers used by the population. This is achieved using the AddCellWriter() method, which is templated.

        cell_population.AddCellWriter<CellMotilityWriter>();

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

        OffLatticeSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestOffLatticeSimulationWithMotileCellPropertyAndWriters");
        simulator.SetSamplingTimestepMultiple(12);
        simulator.SetEndTime(10.0);

Next we create a force law and pass it to the OffLatticeSimulation, and call Solve() to run the simulation.

        MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
        p_linear_force->SetCutOffLength(1.5);
        simulator.AddForce(p_linear_force);

        simulator.Solve();
    }
};

As in Creating And Using A New Cell Property, when you visualize the results with

java Visualize2dCentreCells $CHASTE_TEST_OUTPUT/TestOffLatticeSimulationWithMotileCellPropertyAndWriters/results_from_time_0

you should see a collection of cells with the MotileCellProperty (labelled dark blue) moving towards the origin.

Upon running this test, the output file cellmotilityresults.dat should be created in the folder tmp/$USER/testoutput/TestOffLatticeSimulationWithMotileCellPropertyAndWriters/results_from_time_0.

Full code

#include <cxxtest/TestSuite.h>
#include "CheckpointArchiveTypes.hpp"
#include "AbstractCellBasedTestSuite.hpp"
#include "AbstractCellProperty.hpp"
#include "AbstractForce.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "NodesOnlyMesh.hpp"
#include "WildTypeCellMutationState.hpp"
#include "DifferentiatedCellProliferativeType.hpp"
#include "CellLabel.hpp"
#include "FixedG1GenerationalCellCycleModel.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "CellMutationStatesCountWriter.hpp"
#include "OffLatticeSimulation.hpp"
#include "SmartPointers.hpp"
#include "PetscSetupAndFinalize.hpp"

class MotileCellProperty : public AbstractCellProperty
{
private:
    unsigned mColour;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellProperty>(*this);
        archive & mColour;
    }

public:

    MotileCellProperty(unsigned colour=5)
        : AbstractCellProperty(),
          mColour(colour)
    {}

    ~MotileCellProperty()
    {}

    unsigned GetColour() const
    {
        return mColour;
    }
};

#include "AbstractCellWriter.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class CellMotilityWriter : public AbstractCellWriter<ELEMENT_DIM, SPACE_DIM>
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> >(*this);
    }

public:

    CellMotilityWriter()
        : AbstractCellWriter<ELEMENT_DIM, SPACE_DIM>("cellmotilityresults.dat")
    {
    }

    double GetCellDataForVtkOutput(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
    {
        return pCell->HasCellProperty<MotileCellProperty>();
    }

    void VisitCell(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
    {
        *this->mpOutStream << pCellPopulation->GetLocationIndexUsingCell(pCell) << " ";

        c_vector<double, SPACE_DIM> cell_location = pCellPopulation->GetLocationOfCellCentre(pCell);
        for (unsigned i=0; i<SPACE_DIM; i++)
        {
            *this->mpOutStream << cell_location[i] << " ";
        }

        *this->mpOutStream << pCell->HasCellProperty<MotileCellProperty>() << " ";
    }
};

#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)
EXPORT_TEMPLATE_CLASS_ALL_DIMS(CellMotilityWriter)
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)
EXPORT_TEMPLATE_CLASS_ALL_DIMS(CellMotilityWriter)

class TestCreatingAndUsingNewCellBasedWritersTutorial : public AbstractCellBasedTestSuite
{
public:

    void TestOffLatticeSimulationWithMotileCellPropertyAndWriters()
    {
        EXIT_IF_PARALLEL;

        HoneycombMeshGenerator generator(10, 10);
        boost::shared_ptr<MutableMesh<2,2> > p_generating_mesh = generator.GetCircularMesh(5);

        NodesOnlyMesh<2> mesh;
        mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);

        MAKE_PTR(MotileCellProperty, p_motile);
        MAKE_PTR(CellLabel, p_label);
        MAKE_PTR(WildTypeCellMutationState, p_state);
        MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);

        std::vector<CellPtr> cells;
        for (unsigned i=0; i<mesh.GetNumNodes(); i++)
        {
            FixedG1GenerationalCellCycleModel* p_model = new FixedG1GenerationalCellCycleModel();

            CellPropertyCollection collection;
            if (RandomNumberGenerator::Instance()->ranf() < 0.2)
            {
                collection.AddProperty(p_motile);
                collection.AddProperty(p_label);
            }

            CellPtr p_cell(new Cell(p_state, p_model, NULL, false, collection));
            p_cell->SetCellProliferativeType(p_diff_type);

            double birth_time = - RandomNumberGenerator::Instance()->ranf() *
                                    (p_model->GetStemCellG1Duration() + p_model->GetSG2MDuration());

            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

        NodeBasedCellPopulation<2> cell_population(mesh, cells);

        cell_population.AddCellWriter<CellMotilityWriter>();

        OffLatticeSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestOffLatticeSimulationWithMotileCellPropertyAndWriters");
        simulator.SetSamplingTimestepMultiple(12);
        simulator.SetEndTime(10.0);

        MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
        p_linear_force->SetCutOffLength(1.5);
        simulator.AddForce(p_linear_force);

        simulator.Solve();
    }
};

Creating And Using A New Srn Model

Developer Install Guide

Creating And Using New Cell Based Writers

An example showing how to create a new cell writer and use it in a cell-based simulation#

Introduction#

1. Including header files#

Defining a cell writer class#

Full code#

An example showing how to create a new cell writer and use it in a cell-based simulation

Introduction

1. Including header files

Defining a cell writer class

Full code