Merge pull request #884 from PMEAL/speedup_cylinders

Improved speed of cylinders 5x by using _insert_disk_at_points_parallel method instead of dilating using edt #enh
PMEAL · Aug 23, 2023 · d008465 · d008465
2 parents e78aa70 + ef53ba8
commit d008465
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Showing 2 changed files with 12 additions and 11 deletions.
diff --git a/porespy/filters/_funcs.py b/porespy/filters/_funcs.py
@@ -1218,7 +1218,7 @@ def trim_disconnected_blobs(im, inlets, strel=None):
     to view online example.
 
     """
-    if type(inlets) == tuple:
+    if isinstance(inlets, tuple):
         temp = np.copy(inlets)
         inlets = np.zeros_like(im, dtype=bool)
         inlets[temp] = True
@@ -1516,7 +1516,7 @@ def apply_func(func, **kwargs):
         return func(**kwargs)
 
     # Determine the value for im_arg
-    if type(im_arg) == str:
+    if isinstance(im_arg, str):
         im_arg = [im_arg]
     for item in im_arg:
         if item in kwargs.keys():
@@ -1533,7 +1533,7 @@ def apply_func(func, **kwargs):
     if overlap is not None:
         overlap = overlap * (divs > 1)
     else:
-        if type(strel_arg) == str:
+        if isinstance(strel_arg, str):
             strel_arg = [strel_arg]
         for item in strel_arg:
             if item in kwargs.keys():

diff --git a/porespy/generators/_imgen.py b/porespy/generators/_imgen.py
@@ -11,7 +11,7 @@
 from porespy.tools import norm_to_uniform, ps_ball, ps_disk, get_border, ps_round
 from porespy.tools import extract_subsection
 from porespy.tools import insert_sphere
-from porespy.tools import _insert_disk_at_points
+from porespy.tools import _insert_disk_at_points, _insert_disk_at_points_parallel
 from porespy import settings
 from typing import List
 
@@ -1216,12 +1216,12 @@ def _cylinders(
             upper = ~np.any(np.vstack(crds).T >= shape + L, axis=1)
             valid = upper * lower
             if np.any(valid):
-                im[crds[0][valid] - L, crds[1][valid] - L, crds[2][valid] - L] = 1
+                coords = np.vstack(crds).T[valid] - L
+                _insert_disk_at_points_parallel(im, coords=coords.T, r=r, v=1,
+                                                smooth=True, overwrite=False)
                 n += 1
                 pbar.update()
-    im = np.array(im, dtype=bool)
-    dt = edt(~im) < r
-    return ~dt
+    return ~im
 
 
 def cylinders(
@@ -1365,9 +1365,10 @@ def get_num_pixels(porosity):
         n_fibers_total = n_pixels_to_add / vol_fiber
         n_fibers = int(np.ceil(frac * n_fibers_total) - n_fibers_added)
         if n_fibers > 0:
-            im = im & _cylinders(shape, r, n_fibers,
-                                 phi_max, theta_max, length,
-                                 verbose=False)
+            tmp = _cylinders(shape, r, n_fibers,
+                             phi_max, theta_max, length,
+                             verbose=False)
+            im = im * tmp
         n_fibers_added += n_fibers
         # Update parameters for next iteration
         porosity = ps.metrics.porosity(im)