def ao_optimize(om,
dm,
mf,
modes=N.arange(4, 11, 1),
amprange=N.arange(-0.12, 0.12, 0.02),
S=None,
gain=50,
blaser=False,
rlaser=True,
LED=1):
center = om.zst.getPosition()
results = []
results.append(('Mode', 'Amp', 'Metric'))
dm.Send(cmd_best)
dt = N.zeros(amprange.shape)
om.open_Acq(exposure=0.1,
emgain=gain,
laser=blaser,
Rlaser=rlaser,
cntLaser=False,
LED12=LED,
FTM=False,
conv=0,
ccd=True,
trig=1,
regen=False)
om.get_img()
for mode in modes:
for k, amp in enumerate(amprange):
print(k, amp)
phiin = amp * zernike.Zm(mode, rad=17, orig=None, Nx=33) # was 28
# set mirror with new dm shape
dmarr = 0.5 * N.dot(S, phiin.reshape(33 * 33))
cmd = [0.] * 69
for i in range(69):
cmd[i] = dmarr[i] + cmd_best[i]
if (all(i <= 1.0 for i in cmd)):
dm.Send(cmd)
else:
raise Exception(' Error: push value greater than 1.0 ')
time.sleep(0.02)
om.zst.setPositionf(center)
om.get_img()
dt[k] = mf(om.data) # metric is peak intensity
results.append((mode, amp, dt[k]))
pmax = peak(amprange, dt)
zmv[mode] += pmax
print('setting mode %d at value of %f' % (mode, pmax))
phiin = pmax * zernike.Zm(mode, rad=17, orig=None, Nx=33) # was 28
# set mirror with new dm shape
dmarr = 0.5 * N.dot(S, phiin.reshape(33 * 33))
for i in range(69):
cmd_best[i] = cmd_best[i] + dmarr[i]
if (all(i <= 1.0 for i in cmd_best)):
dm.Send(cmd_best)
else:
raise Exception(' Error: push value greater than 1.0 ')
om.ccd.AbortAcquisition()
om.ccd.SetShutterMode(2)
return results, cmd_best
def testSm(mode):
S = Sm.S
phiin = zernike.Zm(mode, rad=17, orig=None, Nx=33) # was 28
# set mirror with new dm shape
dmarr = 0.5 * N.dot(S, phiin.reshape(33 * 33))
phiout = N.dot(Sm.R, dmarr).reshape(33 * 33)
return phiout
def setZernikeMode(om, dm, mode, amp, S):
phiin = amp * zernike.Zm(mode, rad=17, orig=None, Nx=33) # was 28
# set mirror with new dm shape
dmarr = 0.5 * N.dot(S, phiin.reshape(33 * 33))
for i in range(69):
cmd_best[i] = dmarr[i] + cmd_best[i]
if (all(i <= 1.0 for i in dmarr)):
dm.Send(cmd_best)
else:
raise Exception(' Error: push value greater than 1.0 ')
return cmd_best
def scanzernikemode(self):
n = self.ZernikeModeBox.value()
h = self.PushSpinBox.value()
phiin = h * zernike.Zm(n, rad=17, orig=None, Nx=33)
dmarr = 0.1 * np.dot(Sm.S, phiin.reshape(33 * 33))
dmfile = [0.] * 69
for i in range(69):
dmfile[i] = dmarr[i]
if (all(i <= 1.0 for i in dmfile)):
self.dm.Send(dmfile)
else:
raise Exception(' Error: push value greater than 1.0 ')
def setZernike(om, dm, mode, amp, S):
phiin = N.zeros((33, 33))
cmd = [0.] * 69
for j, m in enumerate(mode):
phiin += amp[j] * zernike.Zm(m, rad=17, orig=None, Nx=33)
# phiin = amp*zernike.Zm(mode,rad=17, orig=None,Nx=33) # was 28
# set mirror with new dm shape
dmarr = 0.5 * N.dot(S, phiin.reshape(33 * 33))
for i in range(69):
cmd[i] = dmarr[i] + cmd_best[i]
if (all(i <= 1.0 for i in dmarr)):
dm.Send(cmd)
print('PushDM_DONE')
else:
raise Exception(' Error: push value greater than 1.0 ')
return cmd_best
def getaberr(self):
wl = self.wl
na = self.na
n2 = 1.512
dp = 1 / (self.nx * self.dx)
radius = (na / wl) / dp
## prepare for focus mode
x = N.arange(-self.nx / 2, self.nx / 2, 1)
X, Y = N.meshgrid(x, x)
rho = N.sqrt(X**2 + Y**2) / radius
msk = (rho <= 1.0).astype(N.float64)
self.defoc = msk * (2 * pi) * (n2 /
wl) * N.sqrt(1 -
(na * msk * rho / n2)**2)
#########################
#msk = U.shift(U.discArray((self.nx,self.nx),radius))/(pi*radius**2)
msk = U.shift(U.discArray(
(self.nx, self.nx), radius)) / N.sqrt(pi * radius**2) / self.nx
phi = N.zeros((self.nx, self.nx))
for m in range(1, self.nzarr):
phi = phi + self.zarr[m] * Z.Zm(m, radius, [0, 0], self.nx)
self.wf = msk * N.exp(1j * phi).astype(N.complex64)
def scan_zermode(om, dm, mode=10, amp=0.1, S=Sm.S, path=None, center=None):
if path == None:
path = om.path
if center == None:
center = om.zst.getPosition()
# cmd_flat = dm.cmd #dm.read_command_file(dm.flat_file)
cmd = [0.] * 69
# flat
dm.Send(cmd)
time.sleep(0.1)
om.StackExt(center - 3.0, center + 3.0, 0.2, verbose=False)
filename = path + '\\stack_flat_start.tif'
om.saveTiff(fn=filename)
#zernike mode
phiin = amp * zernike.Zm(mode, rad=17, orig=None, Nx=33) # was 28
dmarr = 0.5 * N.dot(S, phiin.reshape(33 * 33))
for i in range(69):
cmd[i] = dmarr[i]
if (all(i <= 1.0 for i in dmarr)):
dm.Send(cmd)
else:
raise Exception(' Error: push value greater than 1.0 ')
time.sleep(0.1)
om.StackExt(center - 3.0, center + 3.0, 0.2, verbose=False)
filename = path + '\\stack_act_zernikemode_%02d.tif' % mode
om.saveTiff(fn=filename)
# flat
cmd = [0.] * 69
dm.Send(cmd)
time.sleep(0.1)
om.StackExt(center - 3.0, center + 3.0, 0.2, verbose=False)
filename = path + '\\stack_flat_end.tif'
om.saveTiff(fn=filename)
return True
def buildphiZ(phi, shape, radius):
nx = shape[0]
pupil = N.zeros(shape)
for m, amp in enumerate(phi):
pupil = pupil + amp * Z.Zm(m, radius, None, nx)
return pupil
def get_phi(self, gene):
phi = N.zeros((64, 64))
for m in range(1, self.Nz):
phi = phi + gene[m] * zernike.Zm(m, rad=32, orig=None, Nx=64)
return phi
def ao_optimize_pr(om, dm, S, center=None, path=None):
''' use phase retrieval to correct wavefront '''
rad = 32 # radius for S matrix
offset = 110 #125
if path == None:
path = om.path
if center == None:
center = om.zst.getPosition()
# if S == None:
# raise Exception('No S matrix')
# start
# cmd_flat = dm.cmd
# take stack
om.setCCD_EM_ext(exposure=0.1,
emgain=100,
laser=False,
Rlaser=False,
LED12=2)
om.StackExt(center - 1.6, center + 1.6, 0.2, verbose=False)
# do phase retrieval
p = phaseret.mre(stack_cut(om.data))
p.zcenter = 2.0
p.dz = 0.2
p.offset = offset
p.run(64)
if p.geterr() > 300:
print('convergence of phase retrieval is not great')
# determine new dm settings
amp, phase = p.get_amp_phase()
pylab.figure()
pylab.imshow(phase, interpolation='nearest')
ph0 = phase[32:96, 32:96]
if False:
amp0 = amp[32:96, 32:96]
msk = (amp0 > 0)
target = 1.0 * zernike.Zm(4, rad=30, orig=None, Nx=64)
ph0 = (ph0 - target) * msk
pylab.imshow(ph0, interpolation='nearest')
dmarr = 0.5 * N.dot(S, ph0.reshape(4 * rad**2))
# cmd = cmd_flat - dmarr
cmd = [0.] * 69
for i in range(69):
cmd[i] = dmarr[i] + cmd_best[i]
if (all(i <= 1.0 for i in cmd)):
dm.Send(cmd)
else:
raise Exception(' Error: push value greater than 1.0 ')
# dm.set_mirror(cmd)
# take stack
#om.setCCD_Conv_ext(exposure=0.100,laser=False,Rlaser=False,LED12=1)
om.StackExt(center - 2.0, center + 2.0, 0.2, verbose=False)
# do phase retrieval
p = phaseret.mre(stack_cut(om.data))
p.zcenter = 2.0
p.dz = 0.2
p.offset = offset
p.run(32)
if p.geterr() > 300:
print('convergence of phase retrieval is not great')
amp, phase = p.get_amp_phase()
pylab.figure()
pylab.imshow(phase, interpolation='nearest')
return (cmd, cmd_best, p)