def speed_test3(imshape=(128,128,128), gshape=(4,4,4)):
im = np.zeros(imshape)
hs = np.ones(gshape+imshape)
out, plan = convolve_spatial3(im, hs, return_plan=True)
t = time()
out = convolve_spatial3(im, hs, plan=plan)
t = time()-t
print "imshape: %s \tgshape: %s \ttime = %.2gs"%(imshape, gshape, t)
return t
def speed_test3(imshape=(128, 128, 128), gshape=(4, 4, 4)):
im = np.zeros(imshape)
hs = np.ones(gshape + imshape)
out, plan = convolve_spatial3(im, hs, return_plan=True)
t = time()
out = convolve_spatial3(im, hs, plan=plan)
t = time() - t
print("imshape: %s \tgshape: %s \ttime = %.2gs" % (imshape, gshape, t))
return t
def test_conv3():
im = np.zeros((128, 64, 32))
Gx = 8
Gy = 4
Gz = 2
hs = psf_grid_linear3(Gx, Gy, Gz, 10)
out = convolve_spatial3(im, hs)
return im, out, hs
def test_conv3():
im = np.zeros((128,64,32))
Gx = 8
Gy = 4
Gz = 2
hs = psf_grid_linear3(Gx,Gy,Gz,10)
out = convolve_spatial3(im, hs)
return im,out, hs
def test_conv3_psfs():
im = np.zeros((128, 128, 128))
im[::16, ::16, ::16] = 1.
Gx = 16
Gy = 16
Gz = 16
hs = psf_grid_motion3(Gx, Gy, Gz, 20)
out = convolve_spatial3(im, hs)
return im, out, hs
def test_conv3_psfs():
im = np.zeros((128,64,32))
im[::16,::16,::16] = 1.
Gx = 16
Gy = 16
Gz = 16
hs = psf_grid_motion3(Gx,Gy,Gz,20)
out = convolve_spatial3(im, hs)
return im,out, hs
def test_single_z():
Ng = 32
Nx = 512
Nh = 3
im = np.zeros((16, Nx, Nx))
im[4:-4, 4::16, 4::16] = 1.
hs = np.zeros((16, Nx, Nx))
for i in range(Ng):
for j in range(Ng):
si = slice(i * (Nx // Ng) - Nh + (Nx // Ng) // 2,
i * (Nx // Ng) + Nh + 1 + (Nx // Ng) // 2)
sj = slice(j * (Nx // Ng) - Nh + (Nx // Ng) // 2,
j * (Nx // Ng) + Nh + 1 + (Nx // Ng) // 2)
hs[:, sj, si] = np.ones((16, 2 * Nh + 1, 2 * Nh + 1))
hs[:, Nx // Ng // 2::Nx // Ng, Nx // Ng // 2::Nx // Ng] = 1.
out = convolve_spatial3(im, hs, grid_dim=(1, Ng, Ng), pad_factor=2)
return im, out, hs
def simulate_image_z(self,
cz=0,
signal=None,
psf_grid_dim=(8, 8),
zslice=16,
conv_sub_blocks=(1, 1),
conv_pad_factor=2,
conv_mode="wrap",
mode="product",
with_sheet=True,
**bpm_kwargs):
"""
mode = ["product","illum"]
"""
if not mode in ["product", "illum"]:
raise KeyError("unknown mode: %s" % mode)
if signal is None:
signal = self.signal
if signal is None:
raise ValueError("no signal defined (signal)!")
# illumination
psfs = self.psf_grid_z(cz=cz,
grid_dim=psf_grid_dim,
zslice=zslice,
**bpm_kwargs)
offset_z = int(np.round(cz / self._bpm_detect.units[-1]))
assert offset_z + zslice < self.Nz and self.Nz // 2 + offset_z - zslice >= 0
s = slice(self.Nz // 2 + offset_z - zslice,
self.Nz // 2 + offset_z + zslice)
signal = 1. * signal[s].copy()
if with_sheet:
print("illuminating at z= %s mu with psf mode %s" % (cz, mode))
u = self.propagate_illum(cz=cz, **bpm_kwargs)
if mode == "psf_product":
psfs = psfs * u[s]
else:
signal = signal * u[s]
print("spatially varying convolution: %s %s" %
(signal.shape, psfs.shape))
#convolve
conv = convolve_spatial3(signal.copy(),
psfs.copy(),
grid_dim=(1, ) + psf_grid_dim,
sub_blocks=(1, ) + conv_sub_blocks,
pad_factor=conv_pad_factor,
mode=conv_mode,
verbose=True)
#return u, self.signal[s].copy(), signal, psfs, conv
return conv
def test_conv3_reflect():
im = np.zeros((128, 64, 32))
Gx, Gy, Gz = 8, 4, 2
hs = psf_grid_linear3(Gx, Gy, Gz, 10)
out = convolve_spatial3(im, hs, mode='reflect')
return im, out, hs
def simulate_image_z(self, cz = 0,
signal = None,
psf_grid_dim = (8,8),
zslice = 16,
conv_sub_blocks = (1,1),
conv_pad_factor = 2,
conv_mode = "wrap",
mode = "product",
with_sheet = True,
**bpm_kwargs):
"""
mode = ["product","illum"]
"""
if not mode in ["product","illum"]:
raise KeyError("unknown mode: %s"%mode)
if signal is None:
signal = self.signal
if signal is None:
raise ValueError("no signal defined (signal)!")
# illumination
psfs = self.psf_grid_z(cz = cz,
grid_dim=psf_grid_dim,
zslice=zslice,
**bpm_kwargs)
offset_z = int(np.round(cz/self._bpm_detect.units[-1]))
assert offset_z+zslice<self.Nz and self.Nz//2+offset_z-zslice>=0
s = slice(self.Nz//2+offset_z-zslice,self.Nz//2+offset_z+zslice)
signal = 1.*signal[s].copy()
if with_sheet:
print("illuminating at z= %s mu with psf mode %s" % (cz, mode))
u = self.propagate_illum(cz = cz,**bpm_kwargs)
if mode =="psf_product":
psfs = psfs*u[s]
else:
signal = signal*u[s]
print("spatially varying convolution: %s %s"%(signal.shape,psfs.shape))
#convolve
conv = convolve_spatial3(signal.copy(), psfs.copy(),
grid_dim = (1,)+psf_grid_dim,
sub_blocks=(1,)+conv_sub_blocks,
pad_factor=conv_pad_factor,
mode = conv_mode, verbose = True)
#return u, self.signal[s].copy(), signal, psfs, conv
return conv
