This page was generated from: notebooks/nanopores/how_to_calculate_cell_quality_metrics.ipynb

[1]:

%load_ext autoreload
%autoreload 2
%config InlineBackend.rc = {'figure.figsize': (10,6)}
%matplotlib inline

Calculate mesh quality metrics

This notebook reads a mesh and plots different quality indicators:

  • Minimum/maximum angle

  • Ratio min/max edge length

  • Ratio circumscribed to inscribed circle (largest circle fitting inside vs smallest circle fitting around a triangle)

The indicators are plotted on the mesh and as a histogram.

You can use your own mesh by supplying it to MeshContainer.read().

[2]:

from nanomesh import metrics
from nanomesh import MeshContainer

[3]:

mesh = MeshContainer.read('out.msh')
triangle_mesh = mesh.get('triangle')

triangle_mesh.plot()

[3]:

<AxesSubplot:title={'center':'triangle mesh'}>
../_images/examples_nanopores_calculate_mesh_quality_metrics_3_1.png

Metrics

Quality metrics are available through the metrics submodule, for example to access the area for each face:

[4]:

metrics.area(triangle_mesh)

[4]:

array([39.65259243, 45.70571101, 17.81927029, ..., 38.98781136,
       43.35816492, 41.13174034])

Minumum and maximum cell angles

nanomesh.metrics includes convenience functions for plotting histograms and colored 2d meshes. The ax object can be re-used to overlay the mesh triangles.

[5]:

plot_kwargs = {
    'linewidth': 1,
    'show_labels': ('Pore', ),
    'colors': ('tab:orange', ),
    'flip_xy': False,
    'legend': 'all',
}

metrics.histogram(triangle_mesh, metric='min_angle')
ax = metrics.plot2d(triangle_mesh, metric='min_angle')
triangle_mesh.plot_mpl(ax, **plot_kwargs)

[5]:

<AxesSubplot:title={'center':'triangle mesh'}>
../_images/examples_nanopores_calculate_mesh_quality_metrics_7_1.png
../_images/examples_nanopores_calculate_mesh_quality_metrics_7_2.png 
[6]:

metrics.histogram(triangle_mesh, metric='max_angle')
ax = metrics.plot2d(triangle_mesh, metric='max_angle')
triangle_mesh.plot_mpl(ax, **plot_kwargs)

[6]:

<AxesSubplot:title={'center':'triangle mesh'}>
../_images/examples_nanopores_calculate_mesh_quality_metrics_8_1.png
../_images/examples_nanopores_calculate_mesh_quality_metrics_8_2.png

Ratio between radii

Another useful metric is the ratio between the inner and outer radius. For more info, see this link.

[7]:

metrics.histogram(triangle_mesh, metric='radius_ratio')
ax = metrics.plot2d(triangle_mesh, metric='radius_ratio')
triangle_mesh.plot_mpl(ax, **plot_kwargs)

[7]:

<AxesSubplot:title={'center':'triangle mesh'}>
../_images/examples_nanopores_calculate_mesh_quality_metrics_10_1.png
../_images/examples_nanopores_calculate_mesh_quality_metrics_10_2.png

Ratio between longest and shortest edge

[8]:

metrics.histogram(triangle_mesh, metric='max_min_edge_ratio')
ax = metrics.plot2d(triangle_mesh, metric='max_min_edge_ratio')
triangle_mesh.plot_mpl(ax, **plot_kwargs)

[8]:

<AxesSubplot:title={'center':'triangle mesh'}>
../_images/examples_nanopores_calculate_mesh_quality_metrics_12_1.png
../_images/examples_nanopores_calculate_mesh_quality_metrics_12_2.png

Calculate and export all metrics

This way they can be viewed in another program like Paraview.

[9]:

metrics.calculate_all_metrics(triangle_mesh, inplace=True)
triangle_mesh.write("mesh_quality.msh", file_format='gmsh22', binary=False)

Warning: Appending zeros to replace the missing physical tag data.

Warning: Appending zeros to replace the missing geometrical tag data.

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