Contouring

Contouring can be used to create meshes from images, implicit functions, or other scalar fields. It can also be used to modify existing meshes, for example by evaluating implicit functions at the nodes of the mesh.

See also: Contour, mymesh.contour, Constructive Solid Geometry

from mymesh import primitives, implicit, image, demo_image

Starting with a cube, an implicit function of a sphere can be evaluated at all nodes

cube = primitives.Grid([-0.9,0.9,-0.9,0.9,-0.9,0.9], .05)
func = implicit.sphere([0,0,0],1.1)

cube.NodeData['sphere'] = func(cube.NodeCoords[:,0],
                               cube.NodeCoords[:,1],
                               cube.NodeCoords[:,2])

cube.plot(scalars='sphere', clim=(-1.25, 1.25))

RFBOutputContext()

Identifying mesh nodes...Done

Choosing a threshold of 0, which corresponds to the surface of our implicit sphere, we can then use the Contour() method to “cut out” the sphere from the cube. Alternatively, one of several functions in the contour module can be used directly.

threshold = 0
contoured = cube.Contour('sphere', threshold)
contoured.plot()

RFBOutputContext()

Identifying mesh nodes...Done

The same approach can be used with more complicated shapes, for example we can take the Stanford bunny. and pattern it with a triply periodic minimal surface.

bunny_img = demo_image('bunny')

voxelsize = (0.337891, 0.337891, 0.5) # mm
threshold = 100
bunny_tet = image.TetMesh(bunny_img, voxelsize, threshold, scalefactor=0.35, interpolation='linear', voxel_mode='elem')
bunny_tet.plot(view='-x-z')

fischer_koch_S = implicit.wrapfunc(implicit.thicken(implicit.tpms('S', 20), 1))
bunny_tet.NodeData['f'] = fischer_koch_S(*bunny_tet.NodeCoords.T)
bunny_tet.plot(scalars='f', view='-x-z')

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RFBOutputContext()

Identifying mesh nodes...Done
        RFBOutputContext()

bunny_tetS = bunny_tet.Contour('f', 0, threshold_direction=-1)
bunny_tetS.plot(view='-x-z')

RFBOutputContext()

Identifying mesh nodes...Done