hollowness for cube, cuboid, cylinder, ellipsoid and sphere (#27)

src/ttmask/cube.py

@@ -12,7 +12,8 @@ def cube(
     cube_sidelength: float =typer.Option(...),
     soft_edge_width: float = typer.Option(0),
     pixel_size: float = typer.Option(...),
-    output: str = typer.Option("cube.mrc")
+    output: str = typer.Option("cube.mrc"),
+    wall_thickness: float = typer.Option(0),
 ):
     c = sidelength // 2
     center = np.array([c, c, c])
@@ -29,10 +30,13 @@ def cube(
     print('calculating distance')
     difference = np.abs(positions - center)  # (100, 100, 100, 3)
 
-    in_cube = np.all(difference < (np.array(cube_sidelength / pixel_size) / 2), axis=-1)
-
+    in_cube = np.all(difference < np.array(cube_sidelength) / (pixel_size * 2), axis=-1)
     mask[in_cube] = 1
 
+    if wall_thickness != 0:
+        within_hollowing = np.all(difference < ((np.array(cube_sidelength) / (pixel_size * 2)) - wall_thickness), axis=-1)
+        mask[within_hollowing] = 0
+
     distance_from_edge = distance_transform_edt(mask == 0)
     boundary_pixels = (distance_from_edge <= soft_edge_width) & (distance_from_edge != 0)
     normalised_distance_from_edge = (distance_from_edge[boundary_pixels] / soft_edge_width) * np.pi

src/ttmask/cuboid.py

@@ -15,6 +15,7 @@ def cuboid(
     soft_edge_width: float = typer.Option(0),
     pixel_size: float = typer.Option(...),
     output: str = typer.Option("cuboid.mrc"),
+    wall_thickness: float = typer.Option(0),
 ):
     c = sidelength // 2
     center = np.array([c, c, c])
@@ -43,6 +44,10 @@ def cuboid(
 
     mask[inside_cuboid] = 1
 
+    if wall_thickness != 0:
+        within_hollowing = np.all(difference < ((np.array(cuboid_sidelengths) / (2 * pixel_size)) - wall_thickness), axis=-1)
+        mask[within_hollowing] = 0
+
     distance_from_edge = distance_transform_edt(mask == 0)
     boundary_pixels = (distance_from_edge <= soft_edge_width) & (distance_from_edge != 0)
     normalised_distance_from_edge = (distance_from_edge[boundary_pixels] / soft_edge_width) * np.pi

src/ttmask/cylinder.py

@@ -10,14 +10,13 @@
 def cylinder(
     sidelength: int = typer.Option(...),
     cylinder_height: float = typer.Option(...),
-    cylinder_outer_diameter: float = typer.Option(...),
-    cylinder_inner_diameter: float = typer.Option(0),
+    cylinder_diameter: float = typer.Option(...),
+    wall_thickness: float = typer.Option(0),
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(...),
     output: str = typer.Option("cylinder.mrc")
 ):
-    cylinder_outer_radius = cylinder_outer_diameter / 2
-    cylinder_inner_radius = cylinder_inner_diameter / 2
+    cylinder_radius = cylinder_diameter / 2
 
     c = sidelength // 2
     center = np.array([c, c, c])
@@ -29,15 +28,17 @@ def cylinder(
 
     print('calculating distance')
     difference = np.abs(positions - center)  # (100, 100, 100, 3)
-
     xy_distance = np.sum(difference[:, :, :, [1, 2]] ** 2, axis=-1) ** 0.5
+    within_z = difference[:, :, :, 0] < (cylinder_height / (2 * pixel_size))
+    within_xy = xy_distance < (cylinder_radius / pixel_size)
+
 
-    idx_z = difference[:, :, :, 0] < (cylinder_height / (2 * pixel_size))
-    idx_xy_outer = xy_distance < (cylinder_outer_radius / pixel_size)
-    idx_xy_inner = xy_distance < (cylinder_inner_radius / pixel_size)
+    mask[np.logical_and(within_z, within_xy)] = 1
 
-    mask[np.logical_and(idx_z, idx_xy_outer)] = 1
-    mask[np.logical_and(idx_z, idx_xy_inner)] = 0
+    if wall_thickness != 0:
+        within_z_hollowing = difference[:, :, :, 0] < (cylinder_height - wall_thickness) / (2 * pixel_size)
+        within_xy_hollowing = xy_distance < ((cylinder_radius - wall_thickness) / pixel_size)
+        mask[np.logical_and(within_z_hollowing, within_xy_hollowing)] = 0
 
     distance_from_edge = distance_transform_edt(mask == 0)
     boundary_pixels = (distance_from_edge <= soft_edge_width) & (distance_from_edge != 0)

src/ttmask/ellipsoid.py

@@ -15,6 +15,7 @@ def ellipsoid(
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(...),
     output: str = typer.Option("ellipsoid.mrc"),
+    wall_thickness: float = typer.Option(0),
 ):
     c = sidelength // 2
     center = np.array([c, c, c])
@@ -39,6 +40,11 @@ def ellipsoid(
             (z_magnitude ** 2) / (z_axis_length ** 2)) <= 1
     mask[in_ellipsoid] = 1
 
+    if wall_thickness != 0:
+        in_hollowing = (((x_magnitude) ** 2) / ((x_axis_length - wall_thickness) ** 2)) + ((y_magnitude ** 2) / ((y_axis_length - wall_thickness) ** 2)) + (
+            (z_magnitude ** 2) / ((z_axis_length - wall_thickness) ** 2)) <= 1
+        mask[in_hollowing] = 0
+
     distance_from_edge = distance_transform_edt(mask == 0)
     boundary_pixels = (distance_from_edge <= soft_edge_width) & (distance_from_edge != 0)
     normalised_distance_from_edge = (distance_from_edge[boundary_pixels] / soft_edge_width) * np.pi

src/ttmask/sphere.py

@@ -13,6 +13,7 @@ def sphere(
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(...),
     output: str = typer.Option("sphere.mrc"),
+    wall_thickness: float = typer.Option(0),
 ):
     sphere_radius = sphere_diameter / 2
     c = sidelength // 2
@@ -34,6 +35,10 @@ def sphere(
     idx = distance < (sphere_radius / pixel_size)
     mask[idx] = 1
 
+    if wall_thickness != 0:
+        within_hollowing = distance < ((sphere_radius - wall_thickness) / pixel_size)
+        mask[within_hollowing] = 0
+
     distance_from_edge = distance_transform_edt(mask == 0)
     boundary_pixels = (distance_from_edge <= soft_edge_width) & (distance_from_edge != 0)
     normalised_distance_from_edge = (distance_from_edge[boundary_pixels] / soft_edge_width) * np.pi