From 29f4984b978352fc2af619309be84be31482b6e7 Mon Sep 17 00:00:00 2001
From: "Hein, Simon" <simon.hein@dlr.de>
Date: Tue, 12 Mar 2024 09:27:35 +0100
Subject: [PATCH 1/2] Closes #917: points_to_spheres should now adds spheres in
 3D correctly

---
 src/porespy/tools/_sphere_insertions.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/porespy/tools/_sphere_insertions.py b/src/porespy/tools/_sphere_insertions.py
index 9b5d257ae..9bb489687 100644
--- a/src/porespy/tools/_sphere_insertions.py
+++ b/src/porespy/tools/_sphere_insertions.py
@@ -35,7 +35,7 @@ def points_to_spheres(im):
     from scipy.spatial import distance_matrix
     if im.ndim == 3:
         x, y, z = np.where(im > 0)
-        coords = np.vstack((x, y, z)).T
+        coords = np.vstack((x, y, z))
     else:
         x, y = np.where(im > 0)
         coords = np.vstack((x, y))
@@ -45,7 +45,10 @@ def points_to_spheres(im):
         dmap[mask] = np.inf
         r = np.around(dmap.min(axis=0)/2, decimals=0).astype(int)
     else:
-        r = im[x, y].flatten()
+        if im.ndim == 3:
+            r = im[x, y, z].flatten()
+        else:
+            r = im[x, y].flatten()
     im_spheres = np.zeros_like(im, dtype=bool)
     im_spheres = _insert_disks_at_points_parallel(
         im_spheres,

From 5487fe58b33396837516f5235423137b0cb2bda6 Mon Sep 17 00:00:00 2001
From: "Hein, Simon" <simon.hein@dlr.de>
Date: Wed, 13 Mar 2024 15:34:57 +0100
Subject: [PATCH 2/2] Added test cases for points_to_spheres in 2D and 3D. !
 dtype=bool for im is still NOT TESTED !

---
 test/unit/test_tools.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/test/unit/test_tools.py b/test/unit/test_tools.py
index ce302352c..5380c7635 100644
--- a/test/unit/test_tools.py
+++ b/test/unit/test_tools.py
@@ -428,6 +428,18 @@ def test_tic_toc(self):
         t = toc(quiet=True)
         assert t > 1
 
+    def test_points_to_spheres_3D(self):
+        im=np.full((41,41,41),0)
+        im[20,20,20]=10
+        res_ps_3D=ps.tools.points_to_spheres(im=im)
+        assert np.sum(res_ps_3D) == 4169
+        
+    def test_points_to_spheres_2D(self):
+        im=np.full((41,41),0)
+        im[20,20]=10
+        res_ps_2D=ps.tools.points_to_spheres(im=im)
+        assert np.sum(res_ps_2D) == 317
+
 
 if __name__ == '__main__':
     t = ToolsTest()