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 porespy as ps
import numpy as np
import matplotlib.pyplot as plt
import scipy.ndimage as spim
im = ps.generators.rsa([80, 80, 80], r=10, clearance=3)
plt.imshow(im[20, ...], origin='lower', interpolation='none');
../../../_images/d4e53c4fb94f596039242587319858fda53036c48e3e89163d9e4f3c2f7aa10a.png

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

regions = spim.label(im)[0]
plt.imshow(regions[20, ...], origin='lower', interpolation='none');
../../../_images/f72ee2fec25434c7b64dd50ad4fdaabd96f8532cbe5394de68bac4eedd2cdb2a.png
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 0x7feb8fc6ca30>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc787c0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc78be0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc78b50>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc789d0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8f0d3700>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fd989d0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fd98220>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c310>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6cc70>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6cf10>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c850>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c880>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c8b0>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c730>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c790>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c760>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c610>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c640>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6c670>,
 <porespy.metrics._regionprops.RegionPropertiesPS at 0x7feb8fc6cd00>]

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
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
label
mask
moments
moments_central
moments_hu
moments_normalized
moments_weighted
moments_weighted_central
moments_weighted_hu
moments_weighted_normalized
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)
4139

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)
4139

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

print(props[0].surface_area)
1165.306396484375

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

plt.imshow(props[0].dt[5, ...]);
../../../_images/0a7ae68ae12d536e0fa7c213da5183668bf2197c442d3719e38ad6a84791d14d.png