def halton_cost_func_t(N, vol1, vol2, t, arg, mask=False):
'''
N: Number of Halton Sampling Points
vol1: original image
vol2: volume to be rotated
theta: rotation by degrees
t: list of translations to try
arg: string for plot titles
'''
cost_func = np.zeros(len(t))
t0 = time.time()
# generate Halton Sequence in the 32*32*32 grid
sequencer = ghalton.GeneralizedHalton(ghalton.EA_PERMS[:3])
sequencer.reset()
points = sequencer.get(N)
pts = np.array(points)
x1 = 31 * pts[:,0]
y1 = 31 * pts[:,1]
z1 = 31 * pts[:,2]
#x1, y1, z1 = np.meshgrid(x1, y1, z1)
for idx, th in enumerate(t):
v2 = translation(vol2, x1+th[0], y1+th[1], z1+th[2])
v1 = translation(vol1, x1, y1, z1)
#new_vol2 = translation(v2, th)
cost_func[idx] = cf_ssd(v2,v1)
t1 = time.time()
print 'Time for %s halton samples is %s seconds' % (N,t1-t0)
return cost_func
def bessel_cost_func(vol1_org, vol2_org, thetas, axis, mask=False, smooth = False, mode = 1):
'''
vol1: original image
vol2: volume to be rotated
thetas: list of degress to try
cf: cost function
arg: string for plot titles
'''
vol1 = vol1_org.copy()
vol2 = vol2_org.copy()
cost_func = np.zeros([len(thetas),])
if(mask):
for i in xrange(len(vol1)):
if(axis == 0):
vol1[i,:,:] = circle_mask(vol1[i,:,:], smooth, mode)
elif(axis == 1):
vol1[:,i,:] = circle_mask(vol1[:,i,:], smooth, mode)
else:
vol1[:,:,i] = circle_mask(vol1[:,:,i], smooth, mode)
for idx, t in enumerate(thetas):
print t,
new_vol2 = np.zeros(vol2.shape)
for i in xrange(len(vol2)):
if(axis == 0):
new_vol2[i,:,:] = bessel_rotate(vol2[i,:,:], t, mask, smooth, mode)
elif(axis == 1):
new_vol2[:,i,:] = bessel_rotate(vol2[:,i,:], t, mask, smooth, mode)
else:
new_vol2[:,:,i] = bessel_rotate(vol2[:,:,i], t, mask, smooth, mode)
cost_func[idx] = cf_ssd(new_vol2, vol1)
return cost_func
def rot_cost_func_3d(vol1, vol2, thetas, mask=False):
'''
vol1: original image
vol2: volume to be rotated
thetas: list of degress to try
arg: string for plot titles
'''
cost_func = np.zeros([len(thetas),3])
for idx, t in enumerate(thetas):
new_vol2 = volrotate(vol2, t[0],t[1],t[2], mask)
cost_func[idx,0] = cf_ssd(new_vol2,vol1)
cost_func[idx,1] = cf_L1(new_vol2,vol1)
cost_func[idx,2] = cf_L2(new_vol2,vol1)
return cost_func
def rot_halton_cost_func(vol1_org, vol2_org, N, thetas, axis, interpolation='bilinear', smooth = True, mode = 1):
'''
vol1: original image
vol2: volume to be rotated
thetas: list of degress to try
cf: cost function
arg: string for plot titles
'''
vol1 = vol1_org.copy()
vol2 = vol2_org.copy()
cost_func = np.zeros([len(thetas),])
# generate Halton sample points
s = (len(vol1)-1)/2.
sequencer = ghalton.GeneralizedHalton(ghalton.EA_PERMS[:3])
sequencer.reset()
points = sequencer.get(N)
pts = np.array(points)
xx1 = (len(vol1)-1) * pts[:,0] - s
yy1 = (len(vol1)-1) * pts[:,1] - s
mask = np.sqrt(xx1**2+yy1**2) < s*0.7
x1 = xx1[mask]
y1 = yy1[mask]
new_vol1 = np.zeros([len(vol1),len(x1)])
print len(x1),
for i in xrange(len(vol1)):
if(axis == 0):
sub1 = circle_mask(vol1[i,:,:], smooth = True, mode = 1)
elif(axis == 1):
sub1 = circle_mask(vol1[:,i,:], smooth = True, mode = 1)
else:
sub1 = circle_mask(vol1[:,:,i], smooth = True, mode = 1)
rot = imrotate(sub1, 0, interpolation, True, smooth, mode, x1, y1)
new_vol1[i] = rot
for idx, t in enumerate(thetas):
new_vol2 = np.empty([len(vol2),len(x1)])
for i in xrange(len(vol2)):
if(axis==0):
sub2 = circle_mask(vol2[i,:,:], smooth = True, mode = 1)
elif(axis==1):
sub2 = circle_mask(vol2[:,i,:], smooth = True, mode = 1)
else:
sub2 = circle_mask(vol2[:,:,i], smooth = True, mode = 1)
rot = imrotate(sub2, t, interpolation, True, smooth, mode, x1, y1)
new_vol2[i] = rot
cost_func[idx] = cf_ssd(new_vol2,new_vol1)
return cost_func
def bessel_halton_cost_func(vol1_org, vol2, N, thetas, axis):
'''
vol1: original image
vol2: volume to be rotated
thetas: list of degress to try
cf: cost function
arg: string for plot titles
'''
vol1 = vol1_org.copy()
# initialize vector to store cost
cost_func = np.zeros([len(thetas),])
# generate Halton sample points
s = (len(vol1)-1)/2.
sequencer = ghalton.GeneralizedHalton(ghalton.EA_PERMS[:3])
sequencer.reset()
points = sequencer.get(N)
pts = np.array(points)
x1 = (len(vol1)-1) * pts[:,0] - s
y1 = (len(vol1)-1) * pts[:,1] - s
new_vol1 = np.empty([len(vol1),N])
for i in xrange(len(vol1)):
if(axis == 0):
sub1 = circle_mask(vol1[i,:,:])
elif(axis == 1):
sub1 = circle_mask(vol1[:,i,:])
else:
sub1 = circle_mask(vol1[:,:,i])
rot = bessel_rotate_halton(sub1, 0, x1, y1)
new_vol1[i] = rot
for idx, t in enumerate(thetas):
print t,
new_vol2 = np.empty([len(vol2),N])
for i in xrange(len(vol2)):
if(axis==0):
sub2 = circle_mask(vol2[i,:,:])
elif(axis==1):
sub2 = circle_mask(vol2[:,i,:])
else:
sub2 = circle_mask(vol2[:,:,i])
new_vol2[i] = bessel_rotate_halton(sub2, t, x1, y1)
cost_func[idx] = cf_ssd(new_vol2,new_vol1)
return cost_func
def vol_cost_func_t(vol1, vol2, t):
'''
vol1: original image
vol2: volume to be rotated
thetas: list of degress to try
t: list of translation to try
cf: cost function
arg: string for plot titles
'''
x = np.linspace(0, vol1.shape[1]-1, vol1.shape[1]).astype(int)
y = np.linspace(0, vol1.shape[0]-1, vol1.shape[0]).astype(int)
z = np.linspace(0, vol1.shape[2]-1, vol1.shape[2]).astype(int)
xx, yy, zz = np.meshgrid(x, y, z)
cost_func = np.zeros(len(t))
for idx, th in enumerate(t):
new_vol2 = translation(vol2, xx-th[1], yy-th[0], zz-th[2])
#new_vol2 = translation1(vol2, th)
cost_func[idx] = cf_ssd(new_vol2,vol1)
return cost_func
def rot_cost_func(vol1_org, vol2_org, thetas, axis, interpolation='bilinear', mask=False, smooth=False, mode=1, x=None, y=None):
'''
vol1: original image
vol2: volume to be rotated
thetas: list of degress to try
arg: string for plot titles
'''
vol1 = vol1_org.copy()
vol2 = vol2_org.copy()
if(mask):
for i in xrange(len(vol1)):
if(axis == 0):
vol1[i,:,:] = circle_mask(vol1[i,:,:], smooth, mode)
elif(axis == 1):
vol1[:,i,:] = circle_mask(vol1[:,i,:], smooth, mode)
else:
vol1[:,:,i] = circle_mask(vol1[:,:,i], smooth, mode)
cost_func = np.zeros([len(thetas),])
for idx, t in enumerate(thetas):
new_vol2 = np.ones(vol2.shape)
for i in xrange(len(vol2)):
if(axis == 0):
sub = vol2[i,:,:]
elif(axis == 1):
sub = vol2[:,i,:]
else:
sub = vol2[:,:,i]
rot = imrotate(sub, t, interpolation, mask, smooth, mode, x, y)
if(axis == 0):
new_vol2[i,:,:] = rot
elif(axis == 1):
new_vol2[:,i,:] = rot
else:
new_vol2[:,:,i] = rot
cost_func[idx] = cf_ssd(new_vol2,vol1)
return cost_func