regionprops_3D

This is similar to the regionprops in scikit-image but has some extra features that are relevant to 3D images. Note that the scikit-image version has been adding 3D capabilities, make the PoreSpy version less useful.

import matplotlib.pyplot as plt
import scipy.ndimage as spim

import porespy as ps

ps.visualization.set_mpl_style()

im = ps.generators.random_spheres(shape=[80, 80, 80], r=10, clearance=3)

fig, ax = plt.subplots(figsize=[4, 4])
ax.imshow(im[20, ...], origin="lower", interpolation="none")
ax.axis(False);

We need to label each sphere so they are recognized as individual regions:

regions = spim.label(im)[0]

fig, ax = plt.subplots(figsize=[4, 4])
ax.imshow(regions[20, ...], origin="lower", interpolation="none")
ax.axis(False);

props = ps.metrics.regionprops_3D(regions)

props is a list of RegionProperties objects, subclassed from scikit-image. Each RegionProperties object possess the properties as attributes. Note that these are calculated on demand, so the regionsprops_3D function appears very quick, but the work has not yet been done.

props

[<porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306ff1f770>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa4fb10>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f307000e5d0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa703e0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa70180>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa583b0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa38af0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa388d0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f307017a550>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f30e8cc5550>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa29220>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa29040>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fdf52b0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fdf4f30>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f30700ee680>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa03a10>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa02150>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7f306fa037d0>]

The properties of regions 1 are on the RegionsProperties object located at position 0 in the props list:

for d in dir(props[0]):
    if not d.startswith("_"):
        print(d)

area
area_bbox
area_convex
area_filled
axis_major_length
axis_minor_length
bbox
bbox_volume
border
centroid
centroid_local
centroid_weighted
centroid_weighted_local
convex_volume
coords
coords_scaled
dt
eccentricity
equivalent_diameter_area
euler_number
extent
feret_diameter_max
image
image_convex
image_filled
image_intensity
inertia_tensor
inertia_tensor_eigvals
inscribed_sphere
intensity_max
intensity_mean
intensity_min
intensity_std
label
mask
moments
moments_central
moments_hu
moments_normalized
moments_weighted
moments_weighted_central
moments_weighted_hu
moments_weighted_normalized
num_pixels
orientation
perimeter
perimeter_crofton
skeleton
slice
slices
solidity
sphericity
surface_area
surface_mesh_simplices
surface_mesh_vertices
volume

Let’s check a few of the properties:

print(props[0].volume)

5497.0

Because the present function is meant for 3D images, we have added specific terminology, like volume, instead of allowing area to mean volume like the scikit-image version”

print(props[0].area)

5497.0

We do have a surface_area, which is also specific to 3D objects:

print(props[0].surface_area)

1407.9961

In addition to scalar metrics, we also provide access to useful images of the region:

fig, ax = plt.subplots(figsize=[4, 4])
ax.imshow(props[0].dt[5, ...])
ax.axis(False);