diff --git a/src/ttmask/sphere.py b/src/ttmask/sphere.py index 19dd82b..ddf854d 100644 --- a/src/ttmask/sphere.py +++ b/src/ttmask/sphere.py @@ -4,6 +4,8 @@ import napari import typer from scipy.ndimage import distance_transform_edt +import mrcfile + @cli.command(name='sphere') def sphere( @@ -11,12 +13,12 @@ def sphere( sphere_diameter: float = typer.Option(...), soft_edge_size: int = typer.Option(...), ): - sphere_radius = sphere_diameter / 2 + c = boxsize // 2 + center = np.array([c, c, c]) + mask = np.zeros(shape=(boxsize, boxsize, boxsize), dtype=np.float32) - center = np.array([boxsize // 2, boxsize // 2, - boxsize // 2]) - mask = np.zeros(shape=(boxsize, boxsize, boxsize)) + print(mask.dtype) # 2d positions of all pixels positions = np.indices([boxsize, boxsize, boxsize]) @@ -37,7 +39,5 @@ def sphere( mask[boundary_pixels] = (0.5 * np.cos(normalised_distance_from_edge) + 0.5) - viewer = napari.Viewer(ndisplay=3) - viewer.add_image(mask) - napari.run() - + # mrcfile.read("bla.mrc") + mrcfile.write("sphere.mrc", mask, voxel_size=4, overwrite=True)