chaste.visualization package

Submodules

chaste.visualization.fortests module

Helper classes for running tests

class chaste.visualization.fortests.JupyterNotebookManager

container_id = 0

interactive_plot_init()

interactive_plot_show(width, height, file_name='temp_scene.wrl', increment=True)

interactive_plotting_loaded = False

three_js_dir = '/home/grogan/git/PyChaste/src/python/chaste/external'

vtk_show(scene, width=400, height=300, output_format='png', increment=True)

Takes vtkRenderer instance and returns an IPython Image with the rendering.

class chaste.visualization.fortests.JupyterSceneModifier2(plotting_manager)

Bases: chaste.cell_based._chaste_project_PyChaste_cell_based.VtkSceneModifier2

Class for real time plotting of output

UpdateAtEndOfTimeStep(cell_population)

Update the Jupyter notebook plot with the new scene

class chaste.visualization.fortests.JupyterSceneModifier3

Bases: chaste.cell_based._chaste_project_PyChaste_cell_based.VtkSceneModifier3

Class for real time plotting of output

UpdateAtEndOfTimeStep(cell_population)

Update the Jupyter notebook plot with the new scene

chaste.visualization.fortests.vtk_show_basic(scene, width=800, height=600)

Takes a Scene instance and returns an IPython Image with the rendering.

Module contents

Visualization Module

class chaste.visualization.VtkScene3

End((VtkScene3)arg1) → None :

C++ signature :

void End(VtkScene<3u> {lvalue})

GetCellPopulationActorGenerator((VtkScene3)arg1) → CellPopulationPyChasteActorGenerator3 :

C++ signature :

boost::shared_ptr<CellPopulationPyChasteActorGenerator<3u> > GetCellPopulationActorGenerator(VtkScene<3u> {lvalue})

GetRenderer((VtkScene3)arg1) → object :

C++ signature :

vtkSmartPointer<vtkRenderer> GetRenderer(VtkScene<3u> {lvalue})

GetSceneAsCharBuffer((VtkScene3)arg1) → object :

C++ signature :

vtkSmartPointer<vtkUnsignedCharArray> GetSceneAsCharBuffer(VtkScene<3u> {lvalue})

ResetRenderer((VtkScene3)arg1[, (int)timeStep=0]) → None :

C++ signature :

void ResetRenderer(VtkScene<3u> {lvalue} [,unsigned int=0])

ResetRenderer( (VtkScene3)arg1 [, (int)timeStep=0]) -> None :

C++ signature :

void ResetRenderer(VtkScene_less__3__greater__wrapper {lvalue} [,unsigned int=0])

SetCellPopulation((VtkScene3)arg1, (AbstractCellPopulation3_3)pCellPopulation) → None :

C++ signature :

void SetCellPopulation(VtkScene<3u> {lvalue},boost::shared_ptr<AbstractCellPopulation<3u, 3u> >)

SetIsInteractive((VtkScene3)arg1, (bool)isInteractive) → None :

C++ signature :

void SetIsInteractive(VtkScene<3u> {lvalue},bool)

SetOutputFilePath((VtkScene3)arg1, (str)rPath) → None :

C++ signature :

void SetOutputFilePath(VtkScene<3u> {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

SetSaveAsAnimation((VtkScene3)arg1, (bool)saveAsAnimation) → None :

C++ signature :

void SetSaveAsAnimation(VtkScene<3u> {lvalue},bool)

SetSaveAsImages((VtkScene3)arg1, (bool)saveAsImages) → None :

C++ signature :

void SetSaveAsImages(VtkScene<3u> {lvalue},bool)

Start((VtkScene3)arg1) → None :

C++ signature :

void Start(VtkScene<3u> {lvalue})

StartInteractiveEventHandler((VtkScene3)arg1) → None :

C++ signature :

void StartInteractiveEventHandler(VtkScene<3u> {lvalue})

class chaste.visualization.VtkScene2

End((VtkScene2)arg1) → None :

C++ signature :

void End(VtkScene<2u> {lvalue})

GetCellPopulationActorGenerator((VtkScene2)arg1) → CellPopulationPyChasteActorGenerator2 :

C++ signature :

boost::shared_ptr<CellPopulationPyChasteActorGenerator<2u> > GetCellPopulationActorGenerator(VtkScene<2u> {lvalue})

GetRenderer((VtkScene2)arg1) → object :

C++ signature :

vtkSmartPointer<vtkRenderer> GetRenderer(VtkScene<2u> {lvalue})

GetSceneAsCharBuffer((VtkScene2)arg1) → object :

C++ signature :

vtkSmartPointer<vtkUnsignedCharArray> GetSceneAsCharBuffer(VtkScene<2u> {lvalue})

ResetRenderer((VtkScene2)arg1[, (int)timeStep=0]) → None :

C++ signature :

void ResetRenderer(VtkScene<2u> {lvalue} [,unsigned int=0])

ResetRenderer( (VtkScene2)arg1 [, (int)timeStep=0]) -> None :

C++ signature :

void ResetRenderer(VtkScene_less__2__greater__wrapper {lvalue} [,unsigned int=0])

SetCellPopulation((VtkScene2)arg1, (AbstractCellPopulation2_2)pCellPopulation) → None :

C++ signature :

void SetCellPopulation(VtkScene<2u> {lvalue},boost::shared_ptr<AbstractCellPopulation<2u, 2u> >)

SetIsInteractive((VtkScene2)arg1, (bool)isInteractive) → None :

C++ signature :

void SetIsInteractive(VtkScene<2u> {lvalue},bool)

SetOutputFilePath((VtkScene2)arg1, (str)rPath) → None :

C++ signature :

void SetOutputFilePath(VtkScene<2u> {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

SetSaveAsAnimation((VtkScene2)arg1, (bool)saveAsAnimation) → None :

C++ signature :

void SetSaveAsAnimation(VtkScene<2u> {lvalue},bool)

SetSaveAsImages((VtkScene2)arg1, (bool)saveAsImages) → None :

C++ signature :

void SetSaveAsImages(VtkScene<2u> {lvalue},bool)

Start((VtkScene2)arg1) → None :

C++ signature :

void Start(VtkScene<2u> {lvalue})

StartInteractiveEventHandler((VtkScene2)arg1) → None :

C++ signature :

void StartInteractiveEventHandler(VtkScene<2u> {lvalue})

class chaste.visualization.AbstractPyChasteActorGenerator2

AddActor((AbstractPyChasteActorGenerator2)arg1, (object)pRenderer) → None :

C++ signature :

void AddActor(AbstractPyChasteActorGenerator<2u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddActor( (AbstractPyChasteActorGenerator2)arg1, (object)arg2) -> None :

C++ signature :

void AddActor(AbstractPyChasteActorGenerator_less__2__greater__wrapper {lvalue},vtkSmartPointer<vtkRenderer>)

GetColorTransferFunction((AbstractPyChasteActorGenerator2)arg1) → object :

C++ signature :

vtkSmartPointer<vtkColorTransferFunction> GetColorTransferFunction(AbstractPyChasteActorGenerator<2u> {lvalue})

GetDiscreteColorTransferFunction((AbstractPyChasteActorGenerator2)arg1) → object :

C++ signature :

vtkSmartPointer<vtkColorTransferFunction> GetDiscreteColorTransferFunction(AbstractPyChasteActorGenerator<2u> {lvalue})

SetDataLabel((AbstractPyChasteActorGenerator2)arg1, (str)rLabel) → None :

C++ signature :

void SetDataLabel(AbstractPyChasteActorGenerator<2u> {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

SetEdgeColor((AbstractPyChasteActorGenerator2)arg1, (object)rColor) → None :

C++ signature :

void SetEdgeColor(AbstractPyChasteActorGenerator<2u> {lvalue},boost::numeric::ublas::c_vector<double, 3ul>)

SetEdgeSize((AbstractPyChasteActorGenerator2)arg1, (float)size) → None :

C++ signature :

void SetEdgeSize(AbstractPyChasteActorGenerator<2u> {lvalue},double)

SetPointColor((AbstractPyChasteActorGenerator2)arg1, (object)rColor) → None :

C++ signature :

void SetPointColor(AbstractPyChasteActorGenerator<2u> {lvalue},boost::numeric::ublas::c_vector<double, 3ul>)

SetPointSize((AbstractPyChasteActorGenerator2)arg1, (float)size) → None :

C++ signature :

void SetPointSize(AbstractPyChasteActorGenerator<2u> {lvalue},double)

SetShowEdges((AbstractPyChasteActorGenerator2)arg1, (bool)show) → None :

C++ signature :

void SetShowEdges(AbstractPyChasteActorGenerator<2u> {lvalue},bool)

SetShowPoints((AbstractPyChasteActorGenerator2)arg1, (bool)show) → None :

C++ signature :

void SetShowPoints(AbstractPyChasteActorGenerator<2u> {lvalue},bool)

SetShowVolume((AbstractPyChasteActorGenerator2)arg1, (bool)show) → None :

C++ signature :

void SetShowVolume(AbstractPyChasteActorGenerator<2u> {lvalue},bool)

SetVolumeColor((AbstractPyChasteActorGenerator2)arg1, (object)rColor) → None :

C++ signature :

void SetVolumeColor(AbstractPyChasteActorGenerator<2u> {lvalue},boost::numeric::ublas::c_vector<double, 3ul>)

SetVolumeOpacity((AbstractPyChasteActorGenerator2)arg1, (float)opacity) → None :

C++ signature :

void SetVolumeOpacity(AbstractPyChasteActorGenerator<2u> {lvalue},double)

class chaste.visualization.AbstractPyChasteActorGenerator3

AddActor((AbstractPyChasteActorGenerator3)arg1, (object)pRenderer) → None :

C++ signature :

void AddActor(AbstractPyChasteActorGenerator<3u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddActor( (AbstractPyChasteActorGenerator3)arg1, (object)arg2) -> None :

C++ signature :

void AddActor(AbstractPyChasteActorGenerator_less__3__greater__wrapper {lvalue},vtkSmartPointer<vtkRenderer>)

GetColorTransferFunction((AbstractPyChasteActorGenerator3)arg1) → object :

C++ signature :

vtkSmartPointer<vtkColorTransferFunction> GetColorTransferFunction(AbstractPyChasteActorGenerator<3u> {lvalue})

GetDiscreteColorTransferFunction((AbstractPyChasteActorGenerator3)arg1) → object :

C++ signature :

vtkSmartPointer<vtkColorTransferFunction> GetDiscreteColorTransferFunction(AbstractPyChasteActorGenerator<3u> {lvalue})

SetDataLabel((AbstractPyChasteActorGenerator3)arg1, (str)rLabel) → None :

C++ signature :

void SetDataLabel(AbstractPyChasteActorGenerator<3u> {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

SetEdgeColor((AbstractPyChasteActorGenerator3)arg1, (object)rColor) → None :

C++ signature :

void SetEdgeColor(AbstractPyChasteActorGenerator<3u> {lvalue},boost::numeric::ublas::c_vector<double, 3ul>)

SetEdgeSize((AbstractPyChasteActorGenerator3)arg1, (float)size) → None :

C++ signature :

void SetEdgeSize(AbstractPyChasteActorGenerator<3u> {lvalue},double)

SetPointColor((AbstractPyChasteActorGenerator3)arg1, (object)rColor) → None :

C++ signature :

void SetPointColor(AbstractPyChasteActorGenerator<3u> {lvalue},boost::numeric::ublas::c_vector<double, 3ul>)

SetPointSize((AbstractPyChasteActorGenerator3)arg1, (float)size) → None :

C++ signature :

void SetPointSize(AbstractPyChasteActorGenerator<3u> {lvalue},double)

SetShowEdges((AbstractPyChasteActorGenerator3)arg1, (bool)show) → None :

C++ signature :

void SetShowEdges(AbstractPyChasteActorGenerator<3u> {lvalue},bool)

SetShowPoints((AbstractPyChasteActorGenerator3)arg1, (bool)show) → None :

C++ signature :

void SetShowPoints(AbstractPyChasteActorGenerator<3u> {lvalue},bool)

SetShowVolume((AbstractPyChasteActorGenerator3)arg1, (bool)show) → None :

C++ signature :

void SetShowVolume(AbstractPyChasteActorGenerator<3u> {lvalue},bool)

SetVolumeColor((AbstractPyChasteActorGenerator3)arg1, (object)rColor) → None :

C++ signature :

void SetVolumeColor(AbstractPyChasteActorGenerator<3u> {lvalue},boost::numeric::ublas::c_vector<double, 3ul>)

SetVolumeOpacity((AbstractPyChasteActorGenerator3)arg1, (float)opacity) → None :

C++ signature :

void SetVolumeOpacity(AbstractPyChasteActorGenerator<3u> {lvalue},double)

class chaste.visualization.CellPopulationPyChasteActorGenerator2

AddActor((CellPopulationPyChasteActorGenerator2)arg1, (object)pRenderer) → None :

C++ signature :

void AddActor(CellPopulationPyChasteActorGenerator<2u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddActor( (CellPopulationPyChasteActorGenerator2)arg1, (object)pRenderer) -> None :

C++ signature :

void AddActor(CellPopulationPyChasteActorGenerator_less__2__greater__wrapper {lvalue},vtkSmartPointer<vtkRenderer>)

AddCaBasedCellPopulationActor((CellPopulationPyChasteActorGenerator2)arg1, (object)pRenderer) → None :

C++ signature :

void AddCaBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<2u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddMeshBasedCellPopulationActor((CellPopulationPyChasteActorGenerator2)arg1, (object)pRenderer) → None :

C++ signature :

void AddMeshBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<2u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddPottsBasedCellPopulationActor((CellPopulationPyChasteActorGenerator2)arg1, (object)pRenderer) → None :

C++ signature :

void AddPottsBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<2u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddVertexBasedCellPopulationActor((CellPopulationPyChasteActorGenerator2)arg1, (object)pRenderer) → None :

C++ signature :

void AddVertexBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<2u> {lvalue},vtkSmartPointer<vtkRenderer>)

SetCellPopulation((CellPopulationPyChasteActorGenerator2)arg1, (AbstractCellPopulation2_2)pCellPopulation) → None :

C++ signature :

void SetCellPopulation(CellPopulationPyChasteActorGenerator<2u> {lvalue},boost::shared_ptr<AbstractCellPopulation<2u, 2u> >)

SetColorByCellData((CellPopulationPyChasteActorGenerator2)arg1, (bool)colorByCellData) → None :

C++ signature :

void SetColorByCellData(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

SetColorByCellType((CellPopulationPyChasteActorGenerator2)arg1, (bool)colorByCellType) → None :

C++ signature :

void SetColorByCellType(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

SetColorByUserDefined((CellPopulationPyChasteActorGenerator2)arg1, (bool)colorByCellUserDefined) → None :

C++ signature :

void SetColorByUserDefined(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

SetShowCellCentres((CellPopulationPyChasteActorGenerator2)arg1, (bool)showCentres) → None :

C++ signature :

void SetShowCellCentres(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

SetShowMutableMeshEdges((CellPopulationPyChasteActorGenerator2)arg1, (bool)showEdges) → None :

C++ signature :

void SetShowMutableMeshEdges(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

SetShowPottsMeshEdges((CellPopulationPyChasteActorGenerator2)arg1, (bool)showEdges) → None :

C++ signature :

void SetShowPottsMeshEdges(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

SetShowPottsMeshOutlines((CellPopulationPyChasteActorGenerator2)arg1, (bool)showOutlines) → None :

C++ signature :

void SetShowPottsMeshOutlines(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

SetShowVoronoiMeshEdges((CellPopulationPyChasteActorGenerator2)arg1, (bool)showEdges) → None :

C++ signature :

void SetShowVoronoiMeshEdges(CellPopulationPyChasteActorGenerator<2u> {lvalue},bool)

class chaste.visualization.CellPopulationPyChasteActorGenerator3

AddActor((CellPopulationPyChasteActorGenerator3)arg1, (object)pRenderer) → None :

C++ signature :

void AddActor(CellPopulationPyChasteActorGenerator<3u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddActor( (CellPopulationPyChasteActorGenerator3)arg1, (object)pRenderer) -> None :

C++ signature :

void AddActor(CellPopulationPyChasteActorGenerator_less__3__greater__wrapper {lvalue},vtkSmartPointer<vtkRenderer>)

AddCaBasedCellPopulationActor((CellPopulationPyChasteActorGenerator3)arg1, (object)pRenderer) → None :

C++ signature :

void AddCaBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<3u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddMeshBasedCellPopulationActor((CellPopulationPyChasteActorGenerator3)arg1, (object)pRenderer) → None :

C++ signature :

void AddMeshBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<3u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddPottsBasedCellPopulationActor((CellPopulationPyChasteActorGenerator3)arg1, (object)pRenderer) → None :

C++ signature :

void AddPottsBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<3u> {lvalue},vtkSmartPointer<vtkRenderer>)

AddVertexBasedCellPopulationActor((CellPopulationPyChasteActorGenerator3)arg1, (object)pRenderer) → None :

C++ signature :

void AddVertexBasedCellPopulationActor(CellPopulationPyChasteActorGenerator<3u> {lvalue},vtkSmartPointer<vtkRenderer>)

SetCellPopulation((CellPopulationPyChasteActorGenerator3)arg1, (AbstractCellPopulation3_3)pCellPopulation) → None :

C++ signature :

void SetCellPopulation(CellPopulationPyChasteActorGenerator<3u> {lvalue},boost::shared_ptr<AbstractCellPopulation<3u, 3u> >)

SetColorByCellData((CellPopulationPyChasteActorGenerator3)arg1, (bool)colorByCellData) → None :

C++ signature :

void SetColorByCellData(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)

SetColorByCellType((CellPopulationPyChasteActorGenerator3)arg1, (bool)colorByCellType) → None :

C++ signature :

void SetColorByCellType(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)

SetColorByUserDefined((CellPopulationPyChasteActorGenerator3)arg1, (bool)colorByCellUserDefined) → None :

C++ signature :

void SetColorByUserDefined(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)

SetShowCellCentres((CellPopulationPyChasteActorGenerator3)arg1, (bool)showCentres) → None :

C++ signature :

void SetShowCellCentres(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)

SetShowMutableMeshEdges((CellPopulationPyChasteActorGenerator3)arg1, (bool)showEdges) → None :

C++ signature :

void SetShowMutableMeshEdges(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)

SetShowPottsMeshEdges((CellPopulationPyChasteActorGenerator3)arg1, (bool)showEdges) → None :

C++ signature :

void SetShowPottsMeshEdges(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)

SetShowPottsMeshOutlines((CellPopulationPyChasteActorGenerator3)arg1, (bool)showOutlines) → None :

C++ signature :

void SetShowPottsMeshOutlines(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)

SetShowVoronoiMeshEdges((CellPopulationPyChasteActorGenerator3)arg1, (bool)showEdges) → None :

C++ signature :

void SetShowVoronoiMeshEdges(CellPopulationPyChasteActorGenerator<3u> {lvalue},bool)