Visual centering

src/ttmask/box_setup.py

@@ -2,9 +2,12 @@
 import einops
 
 
-def box_setup(sidelength: int) -> np.ndarray:
+def box_setup(sidelength: int, centering: str) -> np.ndarray:
     c = sidelength // 2
-    center = np.array([c, c, c])
+    if centering == "visual" and sidelength % 2 == 0:
+        center = np.array([c, c, c]) - 0.5
+    else:
+        center = np.array([c, c, c])
     mask = np.zeros(shape=(sidelength, sidelength, sidelength), dtype=np.float32)
 
     # 3d coordinates of all voxels

src/ttmask/cone.py

@@ -13,10 +13,11 @@ def cone(
     cone_height: float, 
     cone_base_diameter: float, 
     soft_edge_width: int, 
-    pixel_size: float
+    pixel_size: float,
+    centering: str
 ) -> np.ndarray:
     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    coordinates_centered, mask = box_setup(sidelength, centering)
     # distances between each pixel and center :
     magnitudes = np.linalg.norm(coordinates_centered, axis=-1)
     magnitudes = einops.rearrange(magnitudes, 'd h w -> d h w 1')
@@ -61,8 +62,9 @@ def cone_cli(
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("cone.mrc")),
+    centering: str = typer.Option("standard"),
 ):
-    mask = cone(sidelength, cone_height, cone_base_diameter, soft_edge_width, pixel_size)
+    mask = cone(sidelength, cone_height, cone_base_diameter, soft_edge_width, pixel_size, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

src/ttmask/cube.py

@@ -12,10 +12,11 @@ def cube(
     cube_sidelength: float, 
     soft_edge_width: float, 
     pixel_size: float,
-    wall_thickness: float
+    wall_thickness: float,
+    centering: str
 ) -> np.ndarray:
-     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    # establish our coordinate system and empty mask
+    coordinates_centered, mask = box_setup(sidelength, centering)
     #converting relative coordinates to xyz distances (i.e. not a negative number) :
     xyz_distances = np.abs(coordinates_centered)
 
@@ -42,8 +43,9 @@ def cube_cli(
     pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("cube.mrc")),
     wall_thickness: float = typer.Option(0),
+    centering: str = typer.Option("standard"),
 ):
-    mask = cube(sidelength, cube_sidelength, soft_edge_width, pixel_size)
+    mask = cube(sidelength, cube_sidelength, soft_edge_width, pixel_size, wall_thickness, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

src/ttmask/cuboid.py

@@ -14,10 +14,11 @@ def cuboid(
     cuboid_sidelengths: Tuple[float, float, float], 
     soft_edge_width: float, 
     pixel_size: float,
-    wall_thickness: float
+    wall_thickness: float,
+    centering: str
 ) -> np.ndarray:
     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    coordinates_centered, mask = box_setup(sidelength, centering)
     #converting relative coordinates to xyz distances (i.e. not a negative number) :
     xyz_distances = np.abs(coordinates_centered)
 
@@ -44,8 +45,9 @@ def cuboid_cli(
     pixel_size: float = typer.Option(1),
     wall_thickness: float = typer.Option(0),
     output: Path = typer.Option(Path("cuboid.mrc")),
+    centering: str = typer.Option("standard"),
 ):
-    mask = cuboid(sidelength, cuboid_sidelengths, soft_edge_width, pixel_size,wall_thickness)
+    mask = cuboid(sidelength, cuboid_sidelengths, soft_edge_width, pixel_size,wall_thickness, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

src/ttmask/curved_surface.py

@@ -12,12 +12,13 @@ def curved_surface(
     fit_sphere_diameter: float, 
     soft_edge_width: int, 
     pixel_size: float,
-    surface_thickness: float 
+    surface_thickness: float,
+    centering: str
 ) -> np.ndarray:
     sphere_radius = fit_sphere_diameter / 2
 
     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    coordinates_centered, mask = box_setup(sidelength, centering)
     coordinates_shifted = coordinates_centered - ([0, sphere_radius, 0])
 
 
@@ -47,8 +48,9 @@ def curved_surface_cli(
     pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("curved_surface.mrc")),
     surface_thickness: float = typer.Option(...),
+    centering: str = typer.Option("standard"),
 ):
-    mask = curved_surface(sidelength, fit_sphere_diameter, soft_edge_width, pixel_size, surface_thickness)
+    mask = curved_surface(sidelength, fit_sphere_diameter, soft_edge_width, pixel_size, surface_thickness, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

src/ttmask/cylinder.py

@@ -15,12 +15,13 @@ def cylinder(
     cylinder_diameter: float, 
     wall_thickness: float, 
     soft_edge_width: int,
-    pixel_size: float
+    pixel_size: float,
+    centering: str
 ) -> np.ndarray:
     cylinder_radius = cylinder_diameter / 2
 
     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    coordinates_centered, mask = box_setup(sidelength, centering)
 
     # converting relative coordinates to xyz distances (i.e. not a negative number) :
     xyz_distances = np.abs(coordinates_centered)
@@ -53,8 +54,9 @@ def cylinder_cli(
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("cylinder.mrc")),
+    centering: str = typer.Option("standard"),
 ):
-    mask = cylinder(sidelength, cylinder_height, cylinder_diameter, wall_thickness, soft_edge_width, pixel_size)
+    mask = cylinder(sidelength, cylinder_height, cylinder_diameter, wall_thickness, soft_edge_width, pixel_size, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

src/ttmask/ellipsoid.py

@@ -15,10 +15,11 @@ def ellipsoid(
     ellipsoid_dimensions: Tuple[float, float, float], 
     soft_edge_width: float,
     pixel_size: float,
-    wall_thickness: float
+    wall_thickness: float,
+    centering: str
 ) -> np.ndarray:
     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    coordinates_centered, mask = box_setup(sidelength, centering)
     #converting relative coordinates to xyz distances (i.e. not a negative number) :
     xyz_distances = np.abs(coordinates_centered)
 
@@ -56,8 +57,9 @@ def ellipsoid_cli(
     soft_edge_width: float = typer.Option(0),
     pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("ellipsoid.mrc")),
+    centering: str = typer.Option("standard"),
 ):
-    mask = ellipsoid(sidelength, ellipsoid_dimensions, soft_edge_width, pixel_size)
+    mask = ellipsoid(sidelength, ellipsoid_dimensions, soft_edge_width, pixel_size, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

src/ttmask/sphere.py

@@ -12,12 +12,13 @@ def sphere(
     sphere_diameter: float, 
     soft_edge_width: int, 
     pixel_size: float, 
-    wall_thickness: float
+    wall_thickness: float,
+    centering: str
 ) -> np.ndarray:
     sphere_radius = sphere_diameter / 2
 
     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    coordinates_centered, mask = box_setup(sidelength, centering)
 
     # determine distances of each pixel to the center
     distance_to_center = np.linalg.norm(coordinates_centered, axis=-1)
@@ -44,8 +45,9 @@ def sphere_cli(
     pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("sphere.mrc")),
     wall_thickness: float = typer.Option(0),
+    centering: str = typer.Option("standard"),
 ):
-    mask = sphere(sidelength, sphere_diameter, soft_edge_width, pixel_size, wall_thickness)
+    mask = sphere(sidelength, sphere_diameter, soft_edge_width, pixel_size, wall_thickness, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

src/ttmask/tube.py

@@ -15,11 +15,12 @@ def tube(
     wall_thickness: float,
     soft_edge_width: int,
     pixel_size: float,
+    centering: str
 ) -> np.ndarray:
     tube_radius = tube_diameter / 2
 
     # establish our coordinate system and empty mask
-    coordinates_centered, mask = box_setup(sidelength)
+    coordinates_centered, mask = box_setup(sidelength, centering)
     #converting relative coordinates to xyz distances (i.e. not a negative number) :
     xyz_distances = np.abs(coordinates_centered)
 
@@ -46,8 +47,9 @@ def tube_cli(
     tube_diameter: float = typer.Option(...),
     wall_thickness: float = typer.Option(0),
     output: Path = typer.Option(Path("tube.mrc")),
+    centering: str = typer.Option("standard"),
 ):
-    mask = tube(sidelength, tube_height, tube_diameter, wall_thickness)
+    mask = tube(sidelength, tube_height, tube_diameter, wall_thickness, centering)
 
     # Save the mask to an MRC file
     with mrcfile.new(output, overwrite=True) as mrc:

tests/test_functions.py

@@ -2,20 +2,20 @@
 import numpy as np
 
 def test_cone():
-    mask = cone(100, 50, 50, 0, 1)
+    mask = cone(100, 50, 50, 0, 1, "standard")
     assert mask.shape == (100, 100, 100)
     assert mask.sum() > np.pi * 24**2 * (50 / 3) # Volume of cone
     assert mask.sum() < np.pi * 25**2 * 50 # Volume of cylinder
 
 def test_cube():
-    mask = cube(100, 50, 0, 1, 0)
+    mask = cube(100, 50, 0, 1, 0, "standard")
     assert mask.shape == (100, 100, 100)
     # Test against volume of cube +- center and subpixel issues
     assert mask.sum() > 48**3
     assert mask.sum() < 52**3
 
 def test_cuboid():
-    mask = cuboid(100, (50,40,30), 0, 1, 0)
+    mask = cuboid(100, (50,40,30), 0, 1, 0, "standard")
     assert mask.shape == (100, 100, 100)
     # Test against volume of cuboid +- center and subpixel issues
     assert mask.sum() > 48 * 38 * 28
@@ -28,26 +28,26 @@ def test_cuboid():
 #    assert mask.sum() < 2 * np.pi * 25 * 50 # Area of cylinder
 
 def test_cylinder():
-    mask = cylinder(100, 50, 50, 0, 0, 1)
+    mask = cylinder(100, 50, 50, 0, 0, 1, "standard")
     assert mask.shape == (100, 100, 100)
     assert mask.sum() > np.pi * 25**2 * 48 # Volume of cylinder
     assert mask.sum() < np.pi * 25**2 * 51 # Volume of cylinder
 
 def test_ellipsoid():
-    mask = ellipsoid(100, (50,40,30), 0, 1,0)
+    mask = ellipsoid(100, (50,40,30), 0, 1,0, "standard")
     assert mask.shape == (100, 100, 100)
     # Test against volume of ellipsoid +- center and subpixel issues
     assert mask.sum() > 24 * 19 * 14 * 4/3 * np.pi
     assert mask.sum() < 26 * 21 * 16 * 4/3 * np.pi
 
 def test_sphere():
-    mask = sphere(100, 50, 0, 1,0)
+    mask = sphere(100, 50, 0, 1,0, "standard")
     assert mask.shape == (100, 100, 100)
     assert mask.sum() > 4/3 * np.pi * 24**3 # Volume of sphere
     assert mask.sum() < 4/3 * np.pi * 26**3 # Volume of sphere
 
 def test_tube():
-    mask = tube(100, 50, 50, 0, 0, 1)
+    mask = tube(100, 50, 50, 0, 0, 1, "standard")
     assert mask.shape == (100, 100, 100)
     assert mask.sum() > np.pi * 24**2 * 48 # Volume of tube
     assert mask.sum() < np.pi * 26**2 * 52 # Volume of tube