implemented work around for some edge cases

voxelise.py

@@ -130,7 +130,7 @@ def contour2dict(c):
     return {'pos':c.pos, 'time':c.time}
 
 
-def vox_section_area(voxels, mesh_file_name):
+def vox_section_area(voxels, mesh_file_name, vox_dim=3):
     mesh = pv.read(mesh_file_name)
     tu.transform_to_bed_centre(mesh, [110, 110, 0])
     tu.transform_to_z0(mesh)
@@ -142,7 +142,6 @@ def vox_section_area(voxels, mesh_file_name):
     while 0 in SecArea:
         i = np.where(SecArea==0)[0][0]
         c = voxels.iloc[i,1:4].to_numpy()
-        print(c)
 
         # if new slice required
         if c[2] != z:
@@ -162,10 +161,20 @@ def vox_section_area(voxels, mesh_file_name):
                 SecArea[i] = poly.area
      
         if SecArea[i] == 0:
-            # TODO HACK so it uses neighbour's SecArea
-            SecArea[i] = 1e7
+            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>3:
+        if z>20:
+            print(set(SecArea))
             break