PyTom: generate a spherical mask

If you do not have a mask for your particles, you can generate one using this script.

$ipytom
from pytom.basic.functions import initSphere

sphere = initSphere(32,32,32,radius=10)
#initializes a sphere into a volume with a size of 32x32x32 and a radius of 10

sphere2 = initSphere(32,32,32,radius=10,smooth=4)
#initializes a sphere into a volume with a size of 32x32x32 and a radius of 10 and a gaussian smoothing of 4 pixels

sphere3 = initSphere(32,32,32,radius=10,smooth=4,filename='sphereMask.em')
#initializes a sphere into a volume with a size of 32x32x32 and a radius of 10 and a gaussian smoothing of 4 pixels. Writes mask to disk.

Please note: with the radius parameter you should cover the whole, significant area around the particle. Also, the size of the mask should be the same as the size of your subtomograms.