diff --git a/src/ttmask/cuboid.py b/src/ttmask/cuboid.py index e1f8a2e..ca6f56c 100644 --- a/src/ttmask/cuboid.py +++ b/src/ttmask/cuboid.py @@ -13,6 +13,7 @@ def cuboid( boxsize: int = typer.Option(...), cuboid_sidelengths: Annotated[Tuple[float, float, float], typer.Option()] = (None, None, None), soft_edge_size: float = typer.Option(...), + mrc_voxel_size: float = typer.Option(...), ): c = boxsize // 2 center = np.array([c, c, c]) @@ -47,4 +48,4 @@ def cuboid( mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5) - mrcfile.write("cuboid.mrc", mask, voxel_size=4, overwrite=True) + mrcfile.write("cuboid.mrc", mask, voxel_size= mrc_voxel_size, overwrite=True) diff --git a/src/ttmask/cylinder.py b/src/ttmask/cylinder.py index 2a64311..d7c9fbd 100644 --- a/src/ttmask/cylinder.py +++ b/src/ttmask/cylinder.py @@ -13,6 +13,7 @@ def cylinder( cylinder_outer_diameter: float = typer.Option(...), cylinder_inner_diameter: float = typer.Option(0), soft_edge_size: int = typer.Option(...), + mrc_voxel_size: float = typer.Option(...), ): cylinder_outer_radius = cylinder_outer_diameter / 2 cylinder_inner_radius = cylinder_inner_diameter / 2 @@ -43,4 +44,5 @@ def cylinder( mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5) - mrcfile.write("cylinder.mrc", mask, voxel_size=4, overwrite=True) + mrcfile.write("cylinder.mrc", mask, voxel_size= mrc_voxel_size, overwrite=True) + diff --git a/src/ttmask/sphere.py b/src/ttmask/sphere.py index 8fdf5b3..8e7eda9 100644 --- a/src/ttmask/sphere.py +++ b/src/ttmask/sphere.py @@ -11,6 +11,7 @@ def sphere( boxsize: int = typer.Option(...), sphere_diameter: float = typer.Option(...), soft_edge_size: int = typer.Option(...), + mrc_voxel_size: float = typer.Option(...), ): sphere_radius = sphere_diameter / 2 c = boxsize // 2 @@ -38,4 +39,4 @@ def sphere( mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5) - mrcfile.write("sphere.mrc", mask, voxel_size=4, overwrite=True) + mrcfile.write("sphere.mrc", mask, voxel_size= mrc_voxel_size, overwrite=True)