example of differential geometry tools in slam

# Authors: Guillaume Auzias <guillaume.auzias@univ-amu.fr>

# License: BSD (3-clause)
# sphinx_gallery_thumbnail_number = 2

importation of slam modules

import slam.io as sio
import slam.differential_geometry as sdg
import slam.plot as splt

loading an examplar mesh and corresponding texture and show it

mesh_file = "../examples/data/example_mesh.gii"
texture_file = "../examples/data/example_texture.gii"
mesh = sio.load_mesh(mesh_file)
tex = sio.load_texture(texture_file)

visb_sc = splt.visbrain_plot(
    mesh=mesh, tex=tex.darray[0], caption="mesh with curvature", cblabel="curvature"
)
visb_sc.preview()

compute various types of Laplacian of the mesh

lap, lap_b = sdg.compute_mesh_laplacian(mesh, lap_type="fem")
print(mesh.vertices.shape)
print(lap.shape)
lap, lap_b = sdg.compute_mesh_laplacian(mesh, lap_type="conformal")
lap, lap_b = sdg.compute_mesh_laplacian(mesh, lap_type="meanvalue")
lap, lap_b = sdg.compute_mesh_laplacian(mesh, lap_type="authalic")

Out:

  Computing Laplacian
    Computing mesh weights of type fem
    -edge length threshold needed for  0  values =  0.0  %
    -number of Nan in weights:  0  =  0.0  %
    -number of Negative values in weights:  936  =  6.706792777300086  %
    -nb Nan in Laplacian :  0
    -nb Inf in Laplacian :  0
(2328, 3)
(2328, 2328)
  Computing Laplacian
    Computing mesh weights of type conformal
    -edge length threshold needed for  0  values =  0.0  %
    -number of Nan in weights:  0  =  0.0  %
    -number of Negative values in weights:  936  =  6.706792777300086  %
    -nb Nan in Laplacian :  0
    -nb Inf in Laplacian :  0
  Computing Laplacian
    Computing mesh weights of type meanvalue
    -number of Nan in weights:  0  =  0.0  %
    -number of Negative values in weights:  0  =  0.0  %
    -nb Nan in Laplacian :  0
    -nb Inf in Laplacian :  0
  Computing Laplacian
    Computing mesh weights of type authalic
    -number of Nan in weights:  0  =  0.0  %
    -number of Negative values in weights:  0  =  0.0  %
    -nb Nan in Laplacian :  0
    -nb Inf in Laplacian :  0

smooth the mesh using Laplacian

s_mesh = sdg.laplacian_mesh_smoothing(mesh, nb_iter=100, dt=0.1)

Out:

    Smoothing mesh
  Computing Laplacian
    Computing mesh weights of type fem
    -edge length threshold needed for  0  values =  0.0  %
    -number of Nan in weights:  0  =  0.0  %
    -number of Negative values in weights:  936  =  6.706792777300086  %
    -nb Nan in Laplacian :  0
    -nb Inf in Laplacian :  0
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    OK

show it

visb_sc = splt.visbrain_plot(mesh=s_mesh, caption="smoothed mesh")
visb_sc.preview()

compute the gradient of texture tex

triangle_grad = sdg.triangle_gradient(mesh, tex.darray[0])
print(triangle_grad)
grad = sdg.gradient(mesh, tex.darray[0])
print(grad)
norm_grad = sdg.norm_gradient(mesh, tex.darray[0])
print(norm_grad)

Out:

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[[ 0.00094788 -0.01505408  0.00434682]
 [ 0.00038984 -0.00959341  0.00294091]
 [-0.010571   -0.01175931 -0.0190667 ]
 ...
 [ 0.00327109  0.01139427  0.0021132 ]
 [ 0.00282758  0.01242133  0.00167353]
 [ 0.00266182  0.01337094  0.00175571]]
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[[-3.16016138e-03 -1.21617037e-02 -7.56323397e-03]
 [ 6.37035386e-05 -1.23221759e-02 -7.34847031e-03]
 [ 1.88016554e-03 -3.03642985e-03  2.32632729e-03]
 ...
 [ 2.24089885e-03  1.09245023e-02  4.04642855e-03]
 [-1.08939493e-04  4.64315729e-03  1.60189335e-03]
 [-5.57641899e-04  6.48352716e-04 -1.52567188e-03]]
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[0.01466616 0.01434713 0.00426224 ... 0.01186339 0.00491293 0.001749  ]

show it

visb_sc = splt.visbrain_plot(
    mesh=mesh,
    tex=norm_grad,
    caption="norm of the gradient of curvature",
    cblabel="gradient magnitude",
)
visb_sc.preview()

compute the depth potential function

dpf = sdg.depth_potential_function(mesh, tex.darray[0], [0.3])

Out:

Computing Laplacian
  Computing mesh weights of type fem
  -edge length threshold needed for  0  values =  0.0  %
  -number of Nan in weights:  0  =  0.0  %
  -number of Negative values in weights:  936  =  6.706792777300086  %
  -nb Nan in Laplacian :  0
  -nb Inf in Laplacian :  0

show it

visb_sc = splt.visbrain_plot(
    mesh=mesh, tex=dpf[0], caption="depth potential function", cblabel="dpf"
)
visb_sc.preview()