speedup and count unlinked voxels

voxelise.py

@@ -136,6 +136,7 @@ def vox_section_area(voxels, mesh_file_name, vox_dim=3):
     tu.transform_to_z0(mesh)
     tm_mesh = to_trimesh(mesh)
     SecArea = np.zeros(len(voxels))
+    default_high = 1e7
 
     z = 0
     i = 0
@@ -147,11 +148,19 @@ def vox_section_area(voxels, mesh_file_name, vox_dim=3):
         if c[2] != z:
             sl = tm_mesh.section(plane_origin=c, plane_normal=[0,0,1])
             if sl is None:
-                SecArea[i] = 1e7
+                SecArea[i] = default_high
                 continue
             sl2d,_ =sl.to_planar()
             z = c[2]
 
+        # if neighbour is adjacent and completed, can simply copy over info
+        if SecArea[i-1] != 0 and SecArea[i-1]!= default_high:
+            c1 = voxels.iloc[i-1,1:4].to_numpy()
+            d1 = abs(sum(c-c1))/vox_dim
+            if d1 <1.001:
+                SecArea[i] = SecArea[i-1]
+                continue
+
         for e in sl2d.split():
             e.apply_translation(-sl2d.centroid)
             e.apply_translation(sl.centroid[0:2])
@@ -159,23 +168,23 @@ def vox_section_area(voxels, mesh_file_name, vox_dim=3):
 
             if poly.contains(Point(c[:2])):
                 SecArea[i] = poly.area
-     
+
+                if abs(SecArea[i-1] - default_high) < 1:
+                    c1 = voxels.iloc[i-1,1:4].to_numpy()
+                    d1 = abs(sum(c-c1))/vox_dim
+                    print("Trying to fix voxel " + str(i-1) + ", dist: " + str(d1))
+                    if d1 <1.001:
+                        SecArea[i-1] = SecArea[i]
+                        print("voxel " + str(i-1) + " fixed")
+
         if SecArea[i] == 0:
-            c1 = voxels.iloc[i-1,1:4].to_numpy()
-            d1 = abs(sum(c-c1))/vox_dim
-            c2 = voxels.iloc[i+1,1:4].to_numpy()
-            d2 = abs(sum(c-c2))/vox_dim
-            if d1 <1.001:
-                SecArea[i] = SecArea[i-1]
-            elif d2 < 1.001:
-                SecArea[i] = SecArea[i+1]
-            else:
-                print("Uh OH rogue voxel")
-                SecArea[i] = 1e7
-
-        if z>20:
-            print(set(SecArea))
-            break
+            print("Uh OH unlinked voxel " + str(i))
+            SecArea[i] = default_high
+
+        #if z>40:
+        #    print(set(SecArea))
+        #    break
+    print("Unlinked Voxels: {}/{}".format(sum(SecArea==default_high), len(SecArea)))
 
 
 if __name__ == '__main__':