"""
Library of SPAM functions for generating partial volume balls, see Tengattini et al. 2015
Copyright (C) 2020 SPAM Contributors
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option)
any later version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see <http://www.gnu.org/licenses/>.
"""
import numpy
from . import kalispheraToolkit
real_t = '<f8'
# also need to select double or float in kalisphera C call
[docs]
def makeSphere(vol, centre, radius):
"""
This function creates a sphere in a given 3D volume,
with analytically-calculated partial-volume effects.
Background is assumed to have a greyvalue of zero,
and a fully-occupied sphere voxel is considered to
have a greyvalue of 1.
Greyvalues are added to the volume, so spheres can be
added to an existing background.
Parameters
----------
vol : 3D numpy array of doubles
A 3D image of greylevels (typically zeros) into which sphere(s) should be added
centre : 1D or 2D numpy array
Either a 3-component vector, or an Nx3 matrix of sphere centres to draw with respect to 0,0,0 in `vol`
radius : float or 1D numpy array
Raduis(ii) of spheres to draw in `vol`
Returns
-------
None : function updates vol
"""
if len(vol.shape) != 3:
print("\tkalisphera.makeSphere(), need 3D vol array")
return -1
centre = numpy.array(centre, dtype=real_t)
# Turn centre into a numpy array in case it is passed as a list-of-lists
if len(centre.shape) == 1:
centre = numpy.array([centre])
if len(centre.shape) == 2:
if type(radius) == float or type(radius) == int:
# print("\tkalisphera.makeSphere.run(), Got single radius for multiple spheres... fine")
radius = [radius] * centre.shape[0]
if len(radius) == centre.shape[0]:
for centre, radius in zip(centre, radius):
volTemp = numpy.zeros_like(vol, dtype=real_t)
# For compatibility with scipy centre of mass
# centre+=0.5
# print centre, radius
# print vol.sum()
kalispheraToolkit.kalisphera(volTemp, numpy.array(centre).astype(real_t), float(radius))
# print vol.sum()
vol += volTemp # .copy()
return 0
else:
print("\tkalisphera.makeSphere(), Got multiple radii, but different number from number of centres")
return -1
[docs]
def makeBlurryNoisySphere(dims, centre, radius, blur=0, noise=0, flatten=True, background=0.25, foreground=0.75):
"""
This function creates a sphere or series of spheres in a 3D volume,
with analytically-calculated partial-volume effects.
This function can flattens overlaps, then adds gaussian blur
and then gaussian noise to `makeSphere`.
Parameters
----------
dims : 3-component list
Dimensions of volume to create
centre : 1D or 2D numpy array
Either a 3-component vector, or an Nx3 array of sphere centres to draw with respect to 0,0,0 in `vol`
radius : float or 1D numpy array
Radius(ii) of spheres to draw in `vol`
blur : float, optional
Standard deviation of the blur kernel (in ~pixels)
Default = 0
noise : float, optional
Standard devitaion of the noise (in greylevels), noise is on the scale: background=0 and sphere=1
Default = 0
flatten : bool, optional
Flatten greyvalues >1 to 1 (caused by overlaps)?
Default = True
background : float, optional
Desired mean greyvalue of the background
Default = 0.25
foreground : float, optional
Desired mean greyvalue of the background
Default = 0.75
Returns
-------
vol : the input array
Note this is different return behaviour than makeSphere, which doesn't return anything!!
"""
assert(foreground > background)
vol = numpy.zeros(dims, dtype=real_t)
makeSphere(vol, centre, radius)
if flatten: vol[vol>1]=1
if blur != 0:
import scipy.ndimage
vol = scipy.ndimage.gaussian_filter(vol, sigma=blur)
if noise != 0:
vol += numpy.random.normal(size=dims, scale=noise)
vol *= float(foreground)-float(background)
vol += float(background)
return vol
