def Stack_Sectioning(self,start,stop,step=0.2, verbose=True):
no = int((stop-start)/step)+1
pos = start
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
# psz = qx.getordernum()
psz = 3
self.data = N.zeros((psz*no,xs,ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
self.pol.MoveAbs(0)
time.sleep(0.4)
for p in range(no):
self.zst.setPositionf(pos)
for m in range(psz):
qx.selecteorder(15+m)
qx.activate()
time.sleep(0.02)
daq.CCDTrig_run(self.handleA,self.handleB)
q = self.ccd.WaitForNewData()
print (p,q)
self.data[psz*p + m] = self.ccd.images
qx.deactivate()
time.sleep(0.02)
pos += step
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.zst.getPosition()
self.stackTags(cur_pos,start,stop,step,function='Z-Stack patterns')
return True
def si_2d_pattern(self,start,stop,step=0.2, verbose=True):
rots = self.pol_array
no = int((stop-start)/step)+1
pos = start
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
# psz = qx.getordernum()
psz = 9
phs = int(psz/3)
self.data = N.zeros((psz*no,xs,ys), dtype=N.uint16)
# self.slm.SLM_on()
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
time.sleep(0.1) # was 0.2, changed 20141114
for p in range(no):
self.zst.setPositionf(pos)
for w in range(3):
self.pol.MoveAbs(rots[w])
time.sleep(0.8)
for m in range(phs):
#self.pr.setVoltage(rots[m])
qx.selecteorder(19+phs*w+m)
qx.activate()
time.sleep(0.02)
#print self.pr.getVoltage()
#self.dmd.set_image(patt)
#self.slm.show_next_patt()
#self.slm.show_patt(m)
daq.CCDTrig_run(self.handleA,self.handleB)
q = self.ccd.WaitForNewData()
print (p,q)
self.data[psz*p + 5*w + m] = self.ccd.images
qx.deactivate()
# time.sleep(0.02)
pos += step
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
# self.slm.SLM_off()
#self.pr.setVoltage(0.0)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.zst.getPosition()
self.stackTags(cur_pos,start,stop,step,function='Z-Stack patterns')
return True
def Image_Patterns(self, angle=0, no=200, pol=0, verbose=True):
pos = self.zst.getPosition()
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
# psz = self.slm.ni
psz = 5
self.data = N.zeros((psz*no,xs,ys), dtype=N.uint16)
# self.slm.SLM_on()
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
time.sleep(0.01) # was 0.2, changed 20141114
self.zst.setPositionf(pos)
for p in range(no):
for m in range(angle*5,psz+angle*5):
#self.pr.setVoltage(rots[m])
self.pol.MoveAbs(pol)
qx.selecteorder(m)
qx.activate()
#time.sleep(.50)
#print self.pr.getVoltage()
#self.dmd.set_image(patt)
#self.slm.show_next_patt()
# self.slm.show_patt(m)
daq.CCDTrig_run(self.handleA,self.handleB)
q = self.ccd.WaitForNewData()
print (p,q)
self.data[psz*p+m%5] = self.ccd.images
qx.deactivate()
time.sleep(self.delay)
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
# self.slm.SLM_off()
#self.pr.setVoltage(0.0)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.prior.getPosition()
self.stackTags(cur_pos[0],cur_pos[1],function='Z-Stack patterns')
return True
def run(self):
self.is_videomode = True
if (self.normal_mode==True):
while (self.is_videomode):
self.get_img()
self.emit(SIGNAL('update'))
else:
while (self.is_videomode):
#self.slm.show_next_patt()
# psz = qx.getordernum()
psz =15
phs = int(psz/3)
for m in range(3):
self.pol.MoveAbs(self.pol_array[m])
time.sleep(0.02)
for n in range(phs):
qx.selecteorder(m*phs+n)
qx.activate()
self.get_img()
self.emit(SIGNAL('update'))
qx.deactivate()
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
def ao_optimize_si(om,
dm,
mf,
modes=[4],
amprange=N.arange(-1.0, 1.25, 0.25),
S=None,
gain=50,
blaser=False,
rlaser=True):
center = om.zst.getPosition()
dm.Send(cmd_best)
dt = N.zeros(amprange.shape)
results = []
om.open_Acq(exposure=0.1,
emgain=gain,
laser=blaser,
Rlaser=rlaser,
cntLaser=False,
LED12=1,
FTM=False,
conv=0,
ccd=True,
trig=1,
regen=False)
om.get_img()
slm.selecteorder(16)
slm.activate()
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 ')
slm.deactivate()
om.ccd.AbortAcquisition()
om.ccd.SetShutterMode(2)
return results, cmd_best
def deactivateSLM(self):
qx.deactivate()
return True