Surface quality measurements using vedo in napari

Surface quality measurements using vedo in napari#

This notebook shows how to visualize quantitatvie measurements on surface data in napari.

See also

import napari_process_points_and_surfaces as nppas

import napari
import numpy as np
import pandas as pd
from skimage.measure import label
from skimage.data import cells3d

viewer = napari.Viewer(ndisplay=3)

def hide_all(viewer):
    for layer in viewer.layers:
        layer.visible = False
        
def show_all(viewer):
    for layer in viewer.layers:
        layer.visible = True

surface = nppas.gastruloid()

surface_layer = viewer.add_surface(surface, blending='translucent', shading='flat')
surface = surface_layer.data

napari.utils.nbscreenshot(viewer)

The nppas gastruloid example is derived from AV Luque and JV Veenvliet (2023) which is licensed CC-BY (https://creativecommons.org/licenses/by/4.0/legalcode) and can be downloaded from here: https://zenodo.org/record/7603081

hide_all(viewer)

area_surface = nppas.add_quality(surface, quality_id=nppas.Quality.AREA)
viewer.add_surface(area_surface, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

aspect_ratio_surface = nppas.add_quality(surface, quality_id=nppas.Quality.ASPECT_RATIO)
viewer.add_surface(aspect_ratio_surface, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

distortion_surface = nppas.add_quality(surface, quality_id=nppas.Quality.DISTORTION)
viewer.add_surface(distortion_surface, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

min_angle_surface = nppas.add_quality(surface, quality_id=nppas.Quality.MIN_ANGLE)
viewer.add_surface(min_angle_surface, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

condition_surface = nppas.add_quality(surface, quality_id=nppas.Quality.CONDITION)
viewer.add_surface(condition_surface, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

max_angle_surface = nppas.add_quality(surface, quality_id=nppas.Quality.MAX_ANGLE)
viewer.add_surface(max_angle_surface, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

curvature1 = nppas.add_quality(surface, quality_id=nppas.Quality.MEAN_CURVATURE)
viewer.add_surface(curvature1, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

curvature2 = nppas.add_quality(surface, quality_id=nppas.Quality.SPHERE_FITTED_CURVATURE_DECA_VOXEL)
viewer.add_surface(curvature2, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

curvature3 = nppas.add_quality(surface, quality_id=nppas.Quality.SPHERE_FITTED_CURVATURE_HECTA_VOXEL)
viewer.add_surface(curvature3, colormap='jet')

napari.utils.nbscreenshot(viewer)

hide_all(viewer)

curvature4 = nppas.add_quality(surface, quality_id=nppas.Quality.SPHERE_FITTED_CURVATURE_KILO_VOXEL)
viewer.add_surface(curvature4, colormap='jet')

napari.utils.nbscreenshot(viewer)

Reading out values#

After measurements have been visualized, you can read them out:

vertices, faces, values = viewer.layers[-1].data

table = {
    "X": vertices[:,2],
    "Y": vertices[:,1],
    "Z": vertices[:,0],
    "value":values
}

pd.DataFrame(table)
X Y Z value
0 224.082855 220.405991 14.174363 0.000019
1 220.321533 208.158768 13.983076 0.000019
2 229.455795 219.060226 14.819012 0.000019
3 209.542557 150.734894 14.348864 0.000019
4 214.309753 145.722107 14.344353 0.000019
... ... ... ... ...
3319 428.314514 349.007416 112.390945 0.000019
3320 412.195129 354.458801 112.101349 0.000019
3321 430.368317 356.983643 112.182083 0.000019
3322 421.842499 360.458557 112.378403 0.000019
3323 422.173492 352.256104 112.865425 0.000019

3324 rows × 4 columns

Other mesh quality measurements#

There are more mesh quality measurements available. Not all work on all meshes. Watch out for an error message in a grey window.

for q in nppas.Quality:
    print(q)

Quality.EDGE_RATIO
Quality.ASPECT_RATIO
Quality.RADIUS_RATIO
Quality.ASPECT_FROBENIUS
Quality.MED_ASPECT_FROBENIUS
Quality.MAX_ASPECT_FROBENIUS
Quality.MIN_ANGLE
Quality.COLLAPSE_RATIO
Quality.MAX_ANGLE
Quality.CONDITION
Quality.SCALED_JACOBIAN
Quality.SHEAR
Quality.RELATIVE_SIZE_SQUARED
Quality.SHAPE
Quality.SHAPE_AND_SIZE
Quality.DISTORTION
Quality.MAX_EDGE_RATIO
Quality.SKEW
Quality.TAPER
Quality.VOLUME
Quality.STRETCH
Quality.DIAGONAL
Quality.DIMENSION
Quality.ODDY
Quality.SHEAR_AND_SIZE
Quality.JACOBIAN
Quality.WARPAGE
Quality.ASPECT_GAMMA
Quality.AREA
Quality.ASPECT_BETA
Quality.GAUSS_CURVATURE
Quality.MEAN_CURVATURE
Quality.MAXIMUM_CURVATURE
Quality.MINIMUM_CURVATURE
Quality.SPHERE_FITTED_CURVATURE_1_PERCENT
Quality.SPHERE_FITTED_CURVATURE_2_PERCENT
Quality.SPHERE_FITTED_CURVATURE_5_PERCENT
Quality.SPHERE_FITTED_CURVATURE_10_PERCENT
Quality.SPHERE_FITTED_CURVATURE_25_PERCENT
Quality.SPHERE_FITTED_CURVATURE_50_PERCENT
Quality.SPHERE_FITTED_CURVATURE_MICRO_VOXEL
Quality.SPHERE_FITTED_CURVATURE_MILLI_VOXEL
Quality.SPHERE_FITTED_CURVATURE_CENTI_VOXEL
Quality.SPHERE_FITTED_CURVATURE_DECI_VOXEL
Quality.SPHERE_FITTED_CURVATURE_VOXEL
Quality.SPHERE_FITTED_CURVATURE_DECA_VOXEL
Quality.SPHERE_FITTED_CURVATURE_HECTA_VOXEL
Quality.SPHERE_FITTED_CURVATURE_KILO_VOXEL
Quality.SPHERE_FITTED_CURVATURE_MEGA_VOXEL

show_all(viewer)
viewer.grid.enabled = True
viewer.grid.stride = -1
napari.utils.nbscreenshot(viewer)
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