changed distances to angstrom (i.e. input for shape dimensions are no…

… longer in pixels) (#26)

also corrected depth, height, width of ellipsoid as I spotted I'd mislabelled them

src/ttmask/cone.py

@@ -12,7 +12,7 @@ def cone(
     cone_height: float = typer.Option(...),
     cone_base_diameter: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
-    mrc_voxel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(...),
     output: str = typer.Option("cone.mrc")
 ):
     c = sidelength // 2
@@ -41,10 +41,10 @@ def cone(
     z_distance = centered[:, :, :, 0]  # (100, 100, 100)
 
     # Calculate the angle from the tip of the cone to the edge of the base
-    cone_base_radius = cone_base_diameter / 2
+    cone_base_radius = (cone_base_diameter / 2) / pixel_size
     cone_angle = np.rad2deg(np.arctan(cone_base_radius / cone_height))
 
-    within_cone_height = z_distance < cone_height
+    within_cone_height = z_distance < (cone_height / pixel_size)
     within_cone_angle = angles < cone_angle
 
     # mask[within_cone_height] = 1
@@ -62,6 +62,6 @@ def cone(
     mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5)
 
 
-    mrcfile.write(output, mask, voxel_size= mrc_voxel_size, overwrite=True)
+    mrcfile.write(output, mask, voxel_size= pixel_size, overwrite=True)
 
 

src/ttmask/cube.py

@@ -11,7 +11,7 @@ def cube(
     sidelength: int = typer.Option(...),
     cube_sidelength: float =typer.Option(...),
     soft_edge_width: float = typer.Option(0),
-    mrc_voxel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(...),
     output: str = typer.Option("cube.mrc")
 ):
     c = sidelength // 2
@@ -29,14 +29,14 @@ def cube(
     print('calculating distance')
     difference = np.abs(positions - center)  # (100, 100, 100, 3)
 
-    idx = np.all(difference < (np.array(cube_sidelength) / 2), axis=-1)
+    in_cube = np.all(difference < (np.array(cube_sidelength / pixel_size) / 2), axis=-1)
 
-    mask[idx] = 1
+    mask[in_cube] = 1
 
     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
 
     mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5)
 
-    mrcfile.write(output, mask, voxel_size= mrc_voxel_size, overwrite=True)
+    mrcfile.write(output, mask, voxel_size= pixel_size, overwrite=True)

src/ttmask/cuboid.py

@@ -13,7 +13,7 @@ def cuboid(
     sidelength: int = typer.Option(...),
     cuboid_sidelengths: Annotated[Tuple[float, float, float], typer.Option()] = (None, None, None),
     soft_edge_width: float = typer.Option(0),
-    mrc_voxel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(...),
     output: str = typer.Option("cuboid.mrc"),
 ):
     c = sidelength // 2
@@ -39,14 +39,14 @@ def cuboid(
 
     # mask[np.logical_not(idx)] = 1 #if you wanted to do opposite for whatever reason
 
-    idx = np.all(difference < (np.array(cuboid_sidelengths) / 2), axis=-1)
+    inside_cuboid = np.all(difference < (np.array(cuboid_sidelengths) / (2 * pixel_size)), axis=-1)
 
-    mask[idx] = 1
+    mask[inside_cuboid] = 1
 
     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
 
     mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5)
 
-    mrcfile.write(output, mask, voxel_size= mrc_voxel_size, overwrite=True)
+    mrcfile.write(output, mask, voxel_size= pixel_size, overwrite=True)

src/ttmask/cylinder.py

@@ -13,7 +13,7 @@ def cylinder(
     cylinder_outer_diameter: float = typer.Option(...),
     cylinder_inner_diameter: float = typer.Option(0),
     soft_edge_width: int = typer.Option(0),
-    mrc_voxel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(...),
     output: str = typer.Option("cylinder.mrc")
 ):
     cylinder_outer_radius = cylinder_outer_diameter / 2
@@ -32,9 +32,9 @@ def cylinder(
 
     xy_distance = np.sum(difference[:, :, :, [1, 2]] ** 2, axis=-1) ** 0.5
 
-    idx_z = difference[:, :, :, 0] < cylinder_height / 2
-    idx_xy_outer = xy_distance < cylinder_outer_radius
-    idx_xy_inner = xy_distance < cylinder_inner_radius
+    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(idx_z, idx_xy_outer)] = 1
     mask[np.logical_and(idx_z, idx_xy_inner)] = 0
@@ -45,5 +45,5 @@ def cylinder(
 
     mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5)
 
-    mrcfile.write(output, mask, voxel_size= mrc_voxel_size, overwrite=True)
+    mrcfile.write(output, mask, voxel_size= pixel_size, overwrite=True)
 

src/ttmask/ellipsoid.py

@@ -13,7 +13,7 @@ def ellipsoid(
     height: float = typer.Option(...),
     depth: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
-    mrc_voxel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(...),
     output: str = typer.Option("ellipsoid.mrc"),
 ):
     c = sidelength // 2
@@ -31,9 +31,9 @@ def ellipsoid(
     y_magnitude = difference[:, :, :, 1]
     z_magnitude = difference[:, :, :, 0]
 
-    x_axis_length = depth / 2
-    y_axis_length = height / 2
-    z_axis_length = width / 2
+    z_axis_length = depth / (2 * pixel_size)
+    y_axis_length = height / (2 * pixel_size)
+    x_axis_length = width / (2 * pixel_size)
 
     in_ellipsoid = (((x_magnitude) ** 2) / (x_axis_length ** 2)) + ((y_magnitude ** 2) / (y_axis_length ** 2)) + (
             (z_magnitude ** 2) / (z_axis_length ** 2)) <= 1
@@ -45,4 +45,4 @@ def ellipsoid(
 
     mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5)
 
-    mrcfile.write(output, mask, voxel_size=mrc_voxel_size, overwrite=True)
+    mrcfile.write(output, mask, voxel_size=pixel_size, overwrite=True)

src/ttmask/sphere.py

@@ -11,7 +11,7 @@ def sphere(
     sidelength: int = typer.Option(...),
     sphere_diameter: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
-    mrc_voxel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(...),
     output: str = typer.Option("sphere.mrc"),
 ):
     sphere_radius = sphere_diameter / 2
@@ -31,7 +31,7 @@ def sphere(
 
     # calculate whether each pixel is inside or outside the circle
     print('calculating which pixels are in sphere')
-    idx = distance < sphere_radius
+    idx = distance < (sphere_radius / pixel_size)
     mask[idx] = 1
 
     distance_from_edge = distance_transform_edt(mask == 0)
@@ -40,5 +40,5 @@ def sphere(
 
     mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5)
 
-    mrcfile.write(output, mask, voxel_size= mrc_voxel_size, overwrite=True)
+    mrcfile.write(output, mask, voxel_size= pixel_size, overwrite=True)