Labelled image toolkit advanced examples

Here we demonstrate some of the more advanced functions of the labelled toolkit, specifically at how space in a granular medium can be divided in different ways

Preparations as previous example

import spam.mesh
import matplotlib.pyplot as plt
import spam.label
import spam.plotting
import scipy.ndimage
import spam.datasets
import numpy

im = spam.datasets.loadConcreteNe()
midSlice = im.shape[0] // 2
binary = numpy.logical_and(im > 28000, im < 40000)
cyl = spam.mesh.createCylindricalMask(im.shape, 40)
binary = numpy.logical_and(binary, cyl)
pores = scipy.ndimage.binary_dilation(im < 26000, iterations=1)
binary[pores] = 0
labelled = spam.label.ITKwatershed.watershed(binary)
print("{} particles have been identified".format(labelled.max()))
plt.figure()
plt.title("Labelled volume")
plt.imshow(labelled[midSlice], cmap=spam.label.randomCmap)

540 particles have been identified

<matplotlib.image.AxesImage object at 0x7f15b0f35d10>

Label tookit: Make a Set Voronoi partition of the space

Here we use an approximate algorith for the computation of the set voronoi as described in Schaller et al., (2013) Since we have a cylindrical limit, we will set the Set Voronoi to zero outside the cylinder

setVoronoi = spam.label.setVoronoi(labelled, maxPoreRadius=5)
setVoronoi[numpy.logical_not(cyl)] = 0
plt.figure()
plt.title("Set Voronoi")
plt.imshow(setVoronoi[midSlice], cmap=spam.label.randomCmap)

<matplotlib.image.AxesImage object at 0x7f15b0b11290>

If you compare the labelled volume above and the Set Voronoi you can see that they correspond – i.e., in the Set Voronoi labels are correctly propagated so that they fill the pores space.

Local definition of porosity?

This means that the pore space is assigned to each label, meaning that a per-particle porosity can be easily calculated:

particleVolumes = spam.label.volumes(labelled).astype('<f4')
setVoronoiVolumes = spam.label.volumes(setVoronoi).astype('<f4')
voidVolumes = setVoronoiVolumes - particleVolumes
porosities = voidVolumes / setVoronoiVolumes
voidRatio = voidVolumes / particleVolumes

/home/roubin/repos/gitlab.com/spam-project/spam/examples/label/plot_labelToolkit02.py:63: RuntimeWarning: invalid value encountered in divide
  porosities = voidVolumes / setVoronoiVolumes
/home/roubin/repos/gitlab.com/spam-project/spam/examples/label/plot_labelToolkit02.py:64: RuntimeWarning: invalid value encountered in divide
  voidRatio = voidVolumes / particleVolumes

As in the example in the previous example, we can show this by colouring particles:

plt.figure()
plt.title("Per-particle dimensionless porosity")
plt.imshow(spam.label.convertLabelToFloat(labelled, porosities)[midSlice], vmin=0.0, vmax=1.0)
plt.colorbar()
plt.show()

Now let’s try to plot the direction of the minimum eigenvector of these particles to orient them in space. This eigen vector points down the axis of a grain of rice

MOIval, MOIvec = spam.label.momentOfInertia(labelled)
# We'll plot from 1 onwards (0 not a valid label)
spam.plotting.plotOrientations(MOIvec[1:, 6:9], numberOfRings=4)

Perhaps we can detect a slight concentration of orientations close to horizontal, although there are few points…