Raster geometry sphere not working as expected

Question

I'm trying to use raster geometry to make a sphere-shaped mask (found in How to generate a sphere in 3D Numpy array made by user @norok2). Code is as following:

import raster_geometry as rg
import numpy as np

sphere_mask = rg.sphere((224, 224, 160), 15,(112,112,80)) #rg.sphere takes(shape,radius,midpoint)
sphere_mask = sphere_mask.astype(np.int_) 

print(np.sum(sphere_mask))

When I print the sum of the sphere mask, it gives 0 so no sphere was created. Modifying the code to not include the midpoint however works fine:

import raster_geometry as rg
import numpy as np

sphere_mask = rg.sphere((224, 224, 160), 15) #rg.sphere takes(shape,radius,midpoint)
sphere_mask = sphere_mask.astype(np.int_) 

print(np.sum(sphere_mask))

I've adapted the midpoint to be contained well within the shape of the image. I'm not sure what's going wrong here?

Larisa

Answer 1

The position parameter of rg.sphere() is a float or (float, float, float) which indicates the position of the center of the sphere in relative units, originating from its lowest edge.

This means that a value of 0.5 will translate into the middle of the shape. If a single value is provided, this is propagated in all dimensions, otherwise a value for each dimension must be provided.

import numpy as np
import raster_geometry as rg


m0 = rg.sphere((224, 224, 160), 15).astype(np.int_)
m1 = rg.sphere((224, 224, 160), 15, 0.5).astype(np.int_)
m2 = rg.sphere((224, 224, 160), 15, (0.5, 0.5, 0.5)).astype(np.int_)


print(np.sum(m0) > 0, np.allclose(m0, m1), np.allclose(m0, m2))
# True True True

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If you provide a value outside of the (0.0, 1.0) interval, this will place the center outside of the shape, and unless the radius is large enough, it will produce an empty mask.

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If you want to specify absolute values, you should use the more powerful rg.nd_superellipsoid() (which is what rg.sphere() uses internally anyway) where you can control how the position parameter is interpreted via the rel_position parameter.

Lucy

Thank you so much! rg.nd_superellipsoid() works like a charm. – Larisa

I am pretty confused about the package and can not find any documentation. In my case, I'd like to get a sphere mask of radius 5 for every voxel within a (100, 100, 50) array. How would I do that? – Loos

@BertGayus have you checked the original question? There is much more info in there – Lucy

@Lucy yes I did. Since I was not able to use your library properly, I have just used the sphere()-function you provided in your answer. – Loos