trim_extrema

Trims local extremes in the greyscale values of an image. It is useful for flattening peaks.

Import Packages

import numpy as np
import porespy as ps
from edt import edt 
import matplotlib.pyplot as plt
ps.visualization.set_mpl_style()

/opt/hostedtoolcache/Python/3.8.16/x64/lib/python3.8/site-packages/openpnm/algorithms/_invasion_percolation.py:358: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _find_trapped_pores(inv_seq, indices, indptr, outlets):  # pragma: no cover

im

The function works on 2D or 3D image with greyscale values, such as a distance transform:

im = ps.generators.blobs(shape=[50, 50], porosity=0.7)
dt = edt(im)

plt.figure(figsize=[6, 6])
plt.imshow(dt/im)
plt.axis(False);

dt1 = ps.filters.trim_extrema(im=dt, h=1, mode='maxima')
dt2 = ps.filters.trim_extrema(im=dt, h=2, mode='maxima')

fig, ax = plt.subplots(2, 2, figsize=[12, 12])

stripe = np.zeros_like(dt)
stripe[10, :] = dt.max()/2

ax[0][0].imshow(dt1 + stripe)
ax[0][0].set_title('h = 25')
ax[0][0].axis(False)
ax[0][1].plot(dt[10, :])
ax[0][1].plot(dt1[10, :])
ax[0][1].set_title('Line Profile')

ax[1][0].imshow(dt2 + stripe)
ax[1][0].axis(False)
ax[1][0].set_title('h = 10')
ax[1][1].plot(dt[10, :])
ax[1][1].plot(dt2[10, :])
ax[1][1].set_title('Line Profile');

mode

The available modes are maxima, minima, and extrema. These modes specify which extremes to remove. Minima and maxima modes trim the maximum and minimum extremes respectively. The extrema mode trims both extremes.

dt1 = ps.filters.trim_extrema(im=dt, h=1, mode='minima')
dt2 = ps.filters.trim_extrema(im=dt, h=2, mode='minima')

fig, ax = plt.subplots(2, 2, figsize=[12, 12])

ax[0][0].imshow(dt1 + stripe)
ax[0][0].set_title('h = 25')
ax[0][0].axis(False)
ax[0][1].plot(dt[10, :])
ax[0][1].plot(dt1[10, :])
ax[0][1].set_title('Line Profile')

ax[1][0].imshow(dt2 + stripe)
ax[1][0].axis(False)
ax[1][0].set_title('h = 10')
ax[1][1].plot(dt[10, :])
ax[1][1].plot(dt2[10, :])
ax[1][1].set_title('Line Profile');

dt1 = ps.filters.trim_extrema(im=dt, h=1, mode='extrema')
dt2 = ps.filters.trim_extrema(im=dt, h=2, mode='extrema')

fig, ax = plt.subplots(2, 2, figsize=[12, 12])

ax[0][0].imshow(dt1 + stripe)
ax[0][0].set_title('h = 25')
ax[0][0].axis(False)
ax[0][1].plot(dt[10, :])
ax[0][1].plot(dt1[10, :])
ax[0][1].set_title('Line Profile')

ax[1][0].imshow(dt2 + stripe)
ax[1][0].axis(False)
ax[1][0].set_title('h = 10')
ax[1][1].plot(dt[10, :])
ax[1][1].plot(dt2[10, :])
ax[1][1].set_title('Line Profile');