Index

A

add_glyph() (microvessel_chaste.visualization.mpl_scene.Scene method) add_image() (microvessel_chaste.visualization.mpl_scene.Scene method) add_series() (microvessel_chaste.visualization.mpl_scene.Scene method) add_tiff() (microvessel_chaste.visualization.mpl_scene.Scene method) AddCircle() (microvessel_chaste.geometry.Part3 method) AddContourPlot() (in module microvessel_chaste.mesh.numpy_tools) AddCuboid() (microvessel_chaste.geometry.Part3 method) AddCylinder() (microvessel_chaste.geometry.Part3 method)

AddHoleMarker() (microvessel_chaste.geometry.Part3 method) AddPolygon() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Part3 method) AddPolygons() (microvessel_chaste.geometry.Facet3 method) AddRectangle() (microvessel_chaste.geometry.Part3 method) AddVertex() (microvessel_chaste.geometry.Polygon3 method) AddVertices() (microvessel_chaste.geometry.Polygon3 method) AddVesselNetwork() (microvessel_chaste.geometry.Part3 method)

B

BooleanWithNetwork() (microvessel_chaste.geometry.Part3 method)

BoundaryExtractor (class in microvessel_chaste.geometry)

C

ContainsPoint() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Polygon3 method) Create() (microvessel_chaste.geometry.BoundaryExtractor static method) (microvessel_chaste.geometry.Facet3 static method) (microvessel_chaste.geometry.GeometryWriter static method) (microvessel_chaste.geometry.Part3 static method) (microvessel_chaste.geometry.Polygon3 static method) (microvessel_chaste.geometry.SurfaceCleaner static method)

D

dir_maker() (in module microvessel_chaste.utility.readwrite)

E

Extrude() (microvessel_chaste.geometry.Part3 method)

F

Facet3 (class in microvessel_chaste.geometry)

G

GeometryWriter (class in microvessel_chaste.geometry) get_class() (in module microvessel_chaste.utility.recursion) GetBoundingBox() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Part3 method) (microvessel_chaste.geometry.Polygon3 method) GetCentroid() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Polygon3 method) GetContainingGridIndices() (microvessel_chaste.geometry.Part3 method) GetDistance() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Polygon3 method) GetDistanceToEdges() (microvessel_chaste.geometry.Polygon3 method) GetFacet() (microvessel_chaste.geometry.Part3 method) GetFacets() (microvessel_chaste.geometry.Part3 method) GetHoleMarkers() (microvessel_chaste.geometry.Part3 method) GetLabel() (microvessel_chaste.geometry.Facet3 method) GetLineSolution() (in module microvessel_chaste.mesh.numpy_tools) GetMeshGrid2d() (in module microvessel_chaste.mesh.numpy_tools) GetMeshGridSolution() (in module microvessel_chaste.mesh.numpy_tools) GetNormal() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Polygon3 method)

GetOutput() (microvessel_chaste.geometry.BoundaryExtractor method) (microvessel_chaste.geometry.SurfaceCleaner method) GetPlane() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Polygon3 method) GetPlaneSolution() (in module microvessel_chaste.mesh.numpy_tools) GetPolygons() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Part3 method) GetReferenceLengthScale() (microvessel_chaste.geometry.Part3 method) GetSegmentIndices() (microvessel_chaste.geometry.Part3 method) GetVertex() (microvessel_chaste.geometry.Polygon3 method) GetVertexLocations() (microvessel_chaste.geometry.Part3 method) GetVertices() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Part3 method) (microvessel_chaste.geometry.Polygon3 method) GetVtk() (microvessel_chaste.geometry.Part3 method) GetVtkPolygon() (microvessel_chaste.geometry.Polygon3 method) GetVtkVertices() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Polygon3 method) GetXPoints() (in module microvessel_chaste.mesh.numpy_tools)

I

Image2d (class in microvessel_chaste.visualization.viewer)

IsPointInPart() (microvessel_chaste.geometry.Part3 method)

M

MergeCoincidentVertices() (microvessel_chaste.geometry.Part3 method) Mesh2d (class in microvessel_chaste.visualization.viewer) microvessel_chaste (module) microvessel_chaste.geometry (module) microvessel_chaste.mesh (module) microvessel_chaste.mesh.numpy_tools (module) microvessel_chaste.pde (module) microvessel_chaste.population (module)

microvessel_chaste.population.cell (module) microvessel_chaste.population.vessel (module) microvessel_chaste.simulation (module) microvessel_chaste.utility (module) microvessel_chaste.utility.readwrite (module) microvessel_chaste.utility.recursion (module) microvessel_chaste.visualization (module) microvessel_chaste.visualization.mpl_scene (module) microvessel_chaste.visualization.viewer (module)

P

Part3 (class in microvessel_chaste.geometry)

PolyData2d (class in microvessel_chaste.visualization.viewer) Polygon3 (class in microvessel_chaste.geometry)

R

read() (in module microvessel_chaste.utility.readwrite) read_pickle() (in module microvessel_chaste.utility.readwrite) read_vtk_surface() (in module microvessel_chaste.utility.readwrite)

ReplaceVertex() (microvessel_chaste.geometry.Polygon3 method) RotateAboutAxis() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Polygon3 method)

S

Scene (class in microvessel_chaste.visualization.mpl_scene) SetDecimateFeatureAngle() (microvessel_chaste.geometry.SurfaceCleaner method) SetDecimateTargetReduction() (microvessel_chaste.geometry.SurfaceCleaner method) SetDoSmoothing() (microvessel_chaste.geometry.BoundaryExtractor method) SetFileName() (microvessel_chaste.geometry.GeometryWriter method) SetInput() (microvessel_chaste.geometry.BoundaryExtractor method) (microvessel_chaste.geometry.GeometryWriter method) (microvessel_chaste.geometry.SurfaceCleaner method) SetLabel() (microvessel_chaste.geometry.Facet3 method)

SetLinearSubdivisionNumber() (microvessel_chaste.geometry.SurfaceCleaner method) SetOutputFormat() (microvessel_chaste.geometry.GeometryWriter method) SetReferenceLengthScale() (microvessel_chaste.geometry.Part3 method) SetSmoothingLength() (microvessel_chaste.geometry.BoundaryExtractor method) show() (microvessel_chaste.visualization.mpl_scene.Scene method) (microvessel_chaste.visualization.viewer.Image2d method) (microvessel_chaste.visualization.viewer.Mesh2d method) (microvessel_chaste.visualization.viewer.PolyData2d method) SurfaceCleaner (class in microvessel_chaste.geometry)

T

Translate() (microvessel_chaste.geometry.Facet3 method) (microvessel_chaste.geometry.Part3 method) (microvessel_chaste.geometry.Polygon3 method)

U

Update() (microvessel_chaste.geometry.BoundaryExtractor method) (microvessel_chaste.geometry.SurfaceCleaner method)

UpdateVertices() (microvessel_chaste.geometry.Facet3 method)

W

write() (in module microvessel_chaste.utility.readwrite) Write() (microvessel_chaste.geometry.GeometryWriter method) (microvessel_chaste.geometry.Part3 method)

write_pickle() (in module microvessel_chaste.utility.readwrite)