apply_padded
#
Applies padding to an image before passing through specified function
Import packages#
import numpy as np
import porespy as ps
import scipy.ndimage as spim
import matplotlib.pyplot as plt
import skimage
from edt import edt
ps.visualization.set_mpl_style()
im
#
Generate a test image. Can be 2D or 3D image.
im = np.zeros([300, 300])
im = ps.generators.rsa(im, r=20, volume_fraction=0.4) == 0
plt.figure(figsize=[6, 6])
plt.axis(False)
plt.imshow(im);

func
#
A good use case is skeletonize_3d
, which has edge artifacts that can be reduced if the image is pre-padded. It works on 2D or 3D images.
func = skimage.morphology.skeletonize_3d
pad_width
#
The amount of padding to add to each axis
x1 = ps.filters.apply_padded(im=im, pad_width=1, func=func, pad_val=1)
x2 = ps.filters.apply_padded(im=im, pad_width=100, func=func, pad_val=1)
fig, ax = plt.subplots(1, 2, figsize=[12, 12]);
ax[0].imshow(x1);
ax[0].axis(False)
ax[0].set_title('pad_width = 1')
ax[1].imshow(x2);
ax[1].axis(False)
ax[1].set_title('pad_width = 100');

It’s also useful for morphological operations such as binary_opening
func = skimage.morphology.binary_opening
x3 = ps.filters.apply_padded(im=im, pad_width=0, func=func, pad_val=1, selem=ps.tools.ps_disk(15))
x4 = ps.filters.apply_padded(im=im, pad_width=50, func=func, pad_val=1, selem=ps.tools.ps_disk(15))
fig, ax = plt.subplots(1, 2, figsize=[12, 12]);
ax[0].imshow(x3)
ax[0].axis(False)
ax[0].set_title('With no padding')
ax[1].imshow(x4)
ax[1].axis(False)
ax[1].set_title('With padding');
/home/runner/work/porespy/porespy/porespy/filters/_funcs.py:142: FutureWarning: `selem` is a deprecated argument name for `binary_opening`. It will be removed in version 1.0. Please use `footprint` instead.
temp = func(padded, **kwargs)

pad_val
#
The value to be placed in padded voxels. It is almost always 1 but setting to 0 may be useful for applying a distance transform.
func = edt
x5 = ps.filters.apply_padded(im=im, pad_width=10, func=func, pad_val=1)
x6 = ps.filters.apply_padded(im=im, pad_width=10, func=func, pad_val=0)
fig, ax = plt.subplots(1, 2, figsize=[12, 12]);
ax[0].imshow(x5);
ax[0].axis(False)
ax[0].set_title('pad_val = 1')
ax[1].imshow(x6);
ax[1].axis(False)
ax[1].set_title('pad_val = 0');
