def __init__(self):
sys.path.append(os.path.dirname(__file__))
from asdk import DM
super(MirrorControllerPython,self).__init__()
self.mirror_id = ccfg.mirror_id
#self.dm = DM(os.path.join(ccfg.dm_directory,self.mirror_id))
self.dm = DM(self.mirror_id)
n_actuators_queried = int( self.dm.Get('NBOfActuator') )
try:
assert n_actuators_queried==ccfg.mirror_n_actuators
except AssertionError as ae:
print 'Number of actuator disagreement.'
self.command[:] = 0.0 # this doesn't really matter
def __init__(self,):
self.seri_num = "BOL115"
self.alpao = DM(self.seri_num)
self.nba = int(alpao.Get('NBOfActuator'))
self.alpao.Send([0.] * nbAct) # init the DM: zeroes everywhere
self.dms = 11 # DM size
dms = self.dms
xdm, ydm = np.meshgrid(np.arange(dms)-dms/2, np.arange(dms)-dms/2)
self.xdm = xdm.T.astype('float32')
self.ydm = ydm.T.astype('float32')
self.dmmask = np.ones((dms, dms), dtype=np.int) # corner mask
self.dmmask[np.abs(self.xdm) + np.abs(self.ydm) > 7] = 0.0
self.flat_mask = self.dmmask.flatten()
self.nch = 8 # number of DM channels
self.dmd0 = np.zeros((dms,dms), dtype=np.float32)
self.cntrs = np.zeros(self.nch+1) - 1 # shared mem counters for channels
for ii in range(self.nch):
exec "disp%d = shm(fname='/tmp/dmdisp%d.im.shm', data=self.dmd0, verbose=False)" % (ii,ii)
def __init__(self,parent=None):
super(scope, self).__init__()
self.delay = 0.02 # delay in loops (StackExt)
self.handleA = None
self.handleB = None
self.QUIT = False
self.stackparams = {'Date/Time':0,'X':0,'Y':0,'Z1':0,'Z2':0,'Zstep':0,'Exposure(s)':0,'CCD Temperature':0,'Pixel Size(nm)':89,'CCD setting':'','User':''}
# camera
self.ccd = pyAndor_P271_slm.ccd()
self.ccd.CoolerON()
self.ccd.SetCoolerMode(COOLER_MODE)
self.ccd.SetTemperature(TEMPERATURE_SETPOINT)
self.data = N.zeros(self.ccd.image_size, dtype=N.uint16)
# piezo
self.zst = zstage.zstage()
self.zst.setPositionf(50)
self.zpos = 0
# Filter wheel
self.fw = filterWheel.filter_wheel()
# deformable mirror
self.serialName = 'BAX228'
self.dm = DM( self.serialName )
self.nbAct = int( self.dm.Get('NBOfActuator') )
# self.values = [0.] * self.nbAct
# self.dm.Send( self.values )
with open(FLAT_FILE, "r") as file:
self.dmfile = eval(file.readline())
if (all(i <= 1.0 for i in self.dmfile)):
self.dm.Send(self.dmfile)
else:
raise Exception(' Error: push value greater than 1.0 ')
#motorized polarizer
print('Initializing Polarizer')
self.pol = mp2.A8MRU()
self.pol.MotorOn()
self.pol.setSpeed(1000,1)
self.pol_array = N.array([50.,20.,-10.]) #3D
print(self.pol.getState())
# priorxy
self.prior = priorxyP27.prior()
self.xpos = 0
self.ypos = 0
self.prior.limits=[-10000, 10000, -10000, 10000]
# qxga
qx.initiate()
qx.open_usb_port()
#Coherent 647 laser
try:
self.ll647 = Coherent_P33.obis('COM16')
self.ll647.SetLaserOn()
self.ll647.SetDigitalModMode()
except:
self.ll647 = None
print('647nm Laser not on') #raise Exception('647nm Laser not on')
#set save path
t=time.localtime()
self.is_videomode = False
dpth=str(int(t[0]*1e4+t[1]*1e2+t[2]))+'_'+getuser()
self.path=os.path.join(datapath,dpth)
try:
os.mkdir(self.path)
except:
print('Directory already exists')
# defaults
self.coord=(200,400,200,400)
self.Name='default'
###
self.Name = 'default'
self.coordVal = self.ccd.GetImageCoordinates()
self.old_Cval = self.ccd.GetImageCoordinates()
self.normal_mode = False
class scope(QThread):
def __init__(self,parent=None):
super(scope, self).__init__()
self.delay = 0.02 # delay in loops (StackExt)
self.handleA = None
self.handleB = None
self.QUIT = False
self.stackparams = {'Date/Time':0,'X':0,'Y':0,'Z1':0,'Z2':0,'Zstep':0,'Exposure(s)':0,'CCD Temperature':0,'Pixel Size(nm)':89,'CCD setting':'','User':''}
# camera
self.ccd = pyAndor_P271_slm.ccd()
self.ccd.CoolerON()
self.ccd.SetCoolerMode(COOLER_MODE)
self.ccd.SetTemperature(TEMPERATURE_SETPOINT)
self.data = N.zeros(self.ccd.image_size, dtype=N.uint16)
# piezo
self.zst = zstage.zstage()
self.zst.setPositionf(50)
self.zpos = 0
# Filter wheel
self.fw = filterWheel.filter_wheel()
# deformable mirror
self.serialName = 'BAX228'
self.dm = DM( self.serialName )
self.nbAct = int( self.dm.Get('NBOfActuator') )
# self.values = [0.] * self.nbAct
# self.dm.Send( self.values )
with open(FLAT_FILE, "r") as file:
self.dmfile = eval(file.readline())
if (all(i <= 1.0 for i in self.dmfile)):
self.dm.Send(self.dmfile)
else:
raise Exception(' Error: push value greater than 1.0 ')
#motorized polarizer
print('Initializing Polarizer')
self.pol = mp2.A8MRU()
self.pol.MotorOn()
self.pol.setSpeed(1000,1)
self.pol_array = N.array([50.,20.,-10.]) #3D
print(self.pol.getState())
# priorxy
self.prior = priorxyP27.prior()
self.xpos = 0
self.ypos = 0
self.prior.limits=[-10000, 10000, -10000, 10000]
# qxga
qx.initiate()
qx.open_usb_port()
#Coherent 647 laser
try:
self.ll647 = Coherent_P33.obis('COM16')
self.ll647.SetLaserOn()
self.ll647.SetDigitalModMode()
except:
self.ll647 = None
print('647nm Laser not on') #raise Exception('647nm Laser not on')
#set save path
t=time.localtime()
self.is_videomode = False
dpth=str(int(t[0]*1e4+t[1]*1e2+t[2]))+'_'+getuser()
self.path=os.path.join(datapath,dpth)
try:
os.mkdir(self.path)
except:
print('Directory already exists')
# defaults
self.coord=(200,400,200,400)
self.Name='default'
###
self.Name = 'default'
self.coordVal = self.ccd.GetImageCoordinates()
self.old_Cval = self.ccd.GetImageCoordinates()
self.normal_mode = False
def __del__(self):
if (self.handleA != None):
daq.CCDTrig_close(self.handleA,self.handleB)
x = self.dm.Reset()
if (x==0):
print('DM Reset')
else:
print('DM cannot reset')
qx.close()
# self.dm.close()
#
def get_img(self):
daq.CCDTrig_run(self.handleA,self.handleB)
self.ccd.WaitForNewData()
self.data[:,:] = self.ccd.images
def open_Acq(self,exposure=0.1,emgain=200,laser=False,Rlaser=False,cntLaser=False,LED12=1,FTM=False,conv=False,ccd=True,trig=1,regen=False):
# setup camera
self.ccd.SetTriggerMode(trig) #0:internal, 1:External
self.ccd.SetShutterMode(2) #auto
self.ccd.SetReadMode(4) #image
self.ccd.SetADChannel(0) # 14-bit channel
self.ccd.SetOutputAmplifier(int(conv))
self.ccd.SetHSSpeed(0)
self.ccd.SetEMCCDGain(emgain)
if FTM: # Frame transfer mode
self.ccd.SetExposureTime(0)
self.ccd.SetFrameTransferMode(1)
self.ccd.SetAcquisitionMode(7) # run until abort
else:
self.ccd.SetExposureTime(exposure)
self.ccd.SetFrameTransferMode(0)
self.ccd.SetAcquisitionMode(5) # run until abort
q,w,e = self.ccd.GetAcquisitionTimings()
# setup triggers
if not self.handleA == None:
daq.CCDTrig_close(self.handleA,self.handleB)
if cntLaser:
digsig = self.getTiming3(FREQ,1e3*exposure,1e3*exposure,1,laser,Rlaser,LED=LED12,CCD=ccd)
elif regen:
digsig = self.getTiming2(FREQ,1e3*exposure,1e3*exposure,1,laser,Rlaser,LED=LED12,CCD=ccd)
else:
digsig = self.getTiming(FREQ,1e3*exposure,1e3*exposure,1,laser,Rlaser,LED=LED12,CCD=ccd)
b = daq.CCDTrig_open(FREQ,digsig)
self.handleA = b[0]
self.handleB = b[1]
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
self.data = N.zeros((xs,ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
self.ccd.Acquire()
#self.slm.SLM_on()
print(q,w,e)
return (q,w,e)
def close_Acq(self):
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
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)
#self.slm.SLM_off()
############## External ######################################################
def StackExt(self,start,stop,step=0.2,verbose=True):
init_loc=self.zst.getPosition()
no = int((stop-start)/step)+1
pos = start
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
self.data = N.zeros((no,xs,ys), N.uint16)
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
time.sleep(0.2) # was 0.05
for p in range(no):
self.zst.setPositionf(pos)
daq.CCDTrig_run(self.handleA,self.handleB)
q = self.ccd.WaitForNewData()
print(p,q)
self.data[p] = self.ccd.images
pos += step
time.sleep(self.delay)
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
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],start,stop,step,function='Z-Stack')
self.zst.setPositionf(init_loc)
return True
def Stack_Patterns(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 = 15
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(0.4)
for m in range(phs):
#self.pr.setVoltage(rots[m])
qx.selecteorder(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 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 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 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 setlaserpower(self,power):
self.ll647.SetPowerLevel(power)
out = self.ll647.GetPower()
return out
def singleSnapExt(self,verbose=True):
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
self.data = N.zeros((xs,ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
self.ccd.Acquire()
time.sleep(0.2) # was 0.05
daq.CCDTrig_run(self.handleA,self.handleB)
self.ccd.WaitForNewData()
self.data[:,:] = self.ccd.images
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
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],self.zst.getPosition(),0,0,function='Single snap')
return True
def setCCD_Conv_ext(self,exposure=0.100,laser=False,Rlaser=False,LED12=1):
self.is_videMode = False
# setup camera
self.ccd.SetTriggerMode(1) #0: internal
self.ccd.SetShutterMode(2) #0: auto
self.ccd.SetFrameTransferMode(0)
self.ccd.SetAcquisitionMode(5) # run until abort
self.ccd.SetReadMode(4) #image
self.ccd.SetADChannel(0) # 14-bit channel
# this sets camera to 1.8us vs speed, and 3MHz readout which doesn't have a lot of pattern
# to get rid of patterns entirely in conventional mode, go to 1Mhz readout
self.ccd.SetVSSpeed(3)
self.ccd.SetHSSpeed(0)
self.ccd.SetOutputAmplifier(1)
self.ccd.SetExposureTime(exposure)
q,w,e = self.ccd.GetAcquisitionTimings()
# setup triggers
if not self.handleA == None:
daq.CCDTrig_close(self.handleA,self.handleB)
digsig = self.getTiming(FREQ,1e3*exposure,1e3*exposure,1,laser,Rlaser,LED=LED12)
b = daq.CCDTrig_open(FREQ,digsig)
self.handleA = b[0]
self.handleB = b[1]
return (q,w,e)
def setCCD_EM_ext(self,exposure=0.1,emgain=200,laser=False,Rlaser=False,LED12=1):
self.is_videMode = False
# setup camera
self.ccd.SetTriggerMode(1) #0:internal, 1:External
self.ccd.SetShutterMode(2) #0: auto
self.ccd.SetFrameTransferMode(0)
self.ccd.SetAcquisitionMode(5) # run until abort
self.ccd.SetReadMode(4) #image
self.ccd.SetADChannel(0) # 14-bit channel
self.ccd.SetOutputAmplifier(0)
self.ccd.SetHSSpeed(0)
self.ccd.SetEMCCDGain(emgain)
self.ccd.SetExposureTime(exposure)
q,w,e = self.ccd.GetAcquisitionTimings()
# setup triggers
if not self.handleA.value == 0:
daq.CCDTrig_close(self.handleA,self.handleB)
digsig = self.getTiming(FREQ,1e3*exposure,1e3*exposure,1,laser,Rlaser,LED=LED12)
b = daq.CCDTrig_open(FREQ,digsig)
self.handleA = b[0]
self.handleB = b[1]
return (q,w,e)
def getTiming(self,freq,exposure,pulse,delay,laser=False,Rlaser=False,LED=1,CCD=True):
''' frequency is in Hertz, exposure and delay are in ms
bit 1: CCD Trigger
bit 2: LED pulse
bit 3: Laser shutter
bit 4: Red Laser
bit 5: LED 1/2'''
# laser shutter is active
count = int(1.1*(exposure+delay)*0.001*freq)
td = int(delay*0.001*freq)
texp = int(exposure*0.001*freq)
tpulse = int(pulse*0.001*freq)
trigpulse = int(0.004*freq)
p = range(count)
laser_arr = N.zeros(count)
led_arr = N.zeros(count)
Rlaser_arr = N.zeros(count)
if LED==1:
LED12_arr = N.zeros(count)
else:
LED12_arr = N.ones(count)
if laser:
laser_arr = N.array([(i>td) & (i<(td+texp)) for i in p])
elif Rlaser:
Rlaser_arr = N.array([(i>td) & (i<(td+texp)) for i in p])
else:
led_arr = N.array([(i>td) & (i<(td+tpulse)) for i in p])
if (CCD):
ccdtrig = N.array([(i<=(trigpulse)) for i in p])
else:
ccdtrig = N.array([(0) for i in p])
#out = N.add(N.add(1.*ccdtrig,2.*lha),4.*shutt2).astype(N.int)
## out = (ccdtrig+2*led+4*laser).astype(N.int)
out = (ccdtrig+2*led_arr+4*laser_arr+8*Rlaser_arr+16*LED12_arr).astype(N.int)
return out
def getTiming2(self,freq,exposure,pulse,delay,laser=False,Rlaser=False,LED=2,CCD=True):
''' Regen with every pulse with LED
exposure time is for laser, followed by pulse time that is for LED.
'''
# laser shutter is active
count = int(1.1*(exposure+pulse+2*delay)*0.001*freq)
td = int(delay*0.001*freq)
texp = int(exposure*0.001*freq)
tpulse = int(pulse*0.001*freq)
trigpulse = int(0.004*freq)
p = range(count)
laser_arr = N.zeros(count)
led_arr = N.zeros(count)
Rlaser_arr = N.zeros(count)
if LED==1:
LED12_arr = N.zeros(count)
else:
LED12_arr = N.ones(count)
if laser:
laser_arr = N.array([(i>td) & (i<(td+texp)) for i in p])
elif Rlaser:
Rlaser_arr = N.array([(i>td) & (i<(td+texp)) for i in p])
else:
led_arr = N.array([(i>(2*td+texp)) & (i<(2*td+texp+tpulse)) for i in p])
if (CCD):
ccdtrig = N.array([(i<=(trigpulse)) for i in p])
else:
ccdtrig = N.array([(0) for i in p])
out = (ccdtrig+2*led_arr+4*laser_arr+8*Rlaser_arr+16*LED12_arr).astype(N.int)
return out
def getTiming3(self,freq,exposure,pulse,delay,laser=False,Rlaser=False,LED=1,CCD=True):
## def getTiming(self,freq,exposure,pulse,delay,laser=False):
''' frequency is in Hertz, exposure and delay are in ms
bit 1: CCD Trigger
bit 2: LED pulse
bit 3: Laser shutter Contineous
bit 4: Red Laser contineous
bit 5: LED 1/2'''
# laser shutter is active
count = int(1.1*(exposure+delay)*0.001*freq)
td = int(delay*0.001*freq)
texp = int(exposure*0.001*freq)
tpulse = int(pulse*0.001*freq)
trigpulse = int(0.004*freq)
p = range(count)
led_arr = N.zeros(count)
ccdtrig = N.zeros(count)
laser_arr = N.zeros(count)
Rlaser_arr = N.zeros(count)
LED12_arr = N.ones(count)
if LED==1:
LED12_arr = N.zeros(count)
if laser:
laser_arr = N.ones(count)
if Rlaser:
Rlaser_arr = N.ones(count)
if not (laser | Rlaser):
# led_arr = N.array([(i>td) & (i<(td+tpulse)) for i in p])
led_arr = N.ones(count)
if (CCD):
ccdtrig = N.array([(i<=(trigpulse)) for i in p])
out = (ccdtrig+2*led_arr+4*laser_arr+8*Rlaser_arr+16*LED12_arr).astype(N.int)
return out
####### Internal Trigger ###################################################
def setCCD_Conv_Int(self,exposure=0.100):
self.ccd.SetAcquisitionMode(1) # single exposure
self.ccd.SetOutputAmplifier(1)
self.ccd.SetTriggerMode(0) #0: internal
self.ccd.SetShutterMode(2) #0: auto
self.ccd.SetExposureTime(exposure)
q = self.ccd.GetAcquisitionTimings()
return q
def StackInt(self,start,stop,step=0.2):
no = int((stop-start)/step)+1
pos = start
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
self.data = N.zeros((no,xs,ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
for p in range(no):
self.zst.setPositionf(pos)
q = self.ccd.Acquire()
q = self.ccd.WaitForNewData()
q = self.ccd.AbortAcquisition()
self.data[p] = self.ccd.images
pos += step
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
cur_pos = self.prior.getPosition()
self.stackTags(cur_pos[0],cur_pos[1],start,stop,step,function='Z-Stack')
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
return True
###########################################################################
def saveTifA(self,slideName='',comments='',Upload=False):
t=time.localtime()
x = N.array([1e4,1e2,1])
t1 = int((t[0:3]*x).sum())
t2 = int((t[3:6]*x).sum())
if slideName=='':
slideName=self.Name
else:
self.Name=slideName
self.stackparams['Comments']=comments
self.stackparams['Slide Name']=slideName
fn = "%s-%s_%s_%s" %(t1,t2,slideName,comments)
fn1 = os.path.join(self.path,fn+'.tif')
fn2 = os.path.join(self.path,fn+'_ps.txt')
T.imsave(fn1,self.data)
self._SaveText(fn2)
return fn
def saveTiff(self,comments='',fn=None,Upload=False):
if fn==None:
return None
t = fn.partition('.')
fn1 = t[0]+'.tif'
fn2 = t[0]+'_ps.txt'
T.imsave(fn1,self.data)
if comments:
self.stackparams['Comments']=comments
self._SaveText(fn2)
return fn
def _SaveText(self,fn=None):
if fn==None:
return False
s = []
for parts in self.stackparams:
s.append('%s : %s \n' % (parts, self.stackparams[parts]))
s.sort()
fid = open(fn,'w')
fid.writelines(s)
fid.close()
return True
def stackTags(self,xx,yy,z1,z2,zs,function='',ps=89):
'''Date/Time,X,Y,Z1,Z2,Zstep,Exposure(s),CCD Temperature,
Pixel Size(nm),CCD setting',User
'''
self.stackparams.clear()
self.stackparams['00 function']=function
self.stackparams['01 Date/Time']=time.asctime()
self.stackparams['05 X']=xx
self.stackparams['06 Y']=yy
self.stackparams['07 Z1']=z1
self.stackparams['08 Z2']=z2
self.stackparams['09 Zstep']=zs
self.stackparams['02 Exposure(s)']=self.ccd.GetExposureTime()
self.stackparams['03 CCD Temperature']=self.ccd.GetTemperature()
self.stackparams['10 User']=getuser()
self.stackparams['11 Coordinates']=self.ccd.GetImageCoordinates()
self.stackparams['12 Pixel size']=ps
ccdsett=self.ccd.SettingsString()
i=13
for item in ccdsett.splitlines():
try:
csi,csv=item.split(':')
ncsi=str(i)+' '+csi
self.stackparams[ncsi]=csv
except:
csi=0
i+=1
return True
def setCoord(self,xs,xe,ys,ye):
'''val=(xs,xe,ys,ye)'''
oxs,oxe,oys,oye = self.coordVal
self.old_Cval = (oxs,oxe,oys,oye)
self.coordVal=(xs,xe,ys,ye)
q=self.ccd.SetImageCoordinates(self.coordVal)
return q
def setCoord2(self,xs,ys,nn):
'''Gets one corner (xs,ys) to make (nn x nn) image size'''
oxs,oxe,oys,oye = self.coordVal
self.old_Cval = (oxs,oxe,oys,oye)
self.coordVal=(xs,xs+nn-1,ys,ys+nn-1)
q=self.ccd.SetImageCoordinates(self.coordVal)
return q
def reSetCoord(self,mode = 0):
'''mode 0: Full CCD:(1,512,1,512)
mode 1: return to previous coordinates: old_Cval
'''
if mode==0:
xs,xe,ys,ye = (1,512,1,512)
elif mode==1:
xs,xe,ys,ye = self.old_Cval
return self.setCoord(xs,xe,ys,ye)
class ALPAO_DM():
# -------------------------------------------------------------------------
def __init__(self,):
self.seri_num = "BOL115"
self.alpao = DM(self.seri_num)
self.nba = int(alpao.Get('NBOfActuator'))
self.alpao.Send([0.] * nbAct) # init the DM: zeroes everywhere
self.dms = 11 # DM size
dms = self.dms
xdm, ydm = np.meshgrid(np.arange(dms)-dms/2, np.arange(dms)-dms/2)
self.xdm = xdm.T.astype('float32')
self.ydm = ydm.T.astype('float32')
self.dmmask = np.ones((dms, dms), dtype=np.int) # corner mask
self.dmmask[np.abs(self.xdm) + np.abs(self.ydm) > 7] = 0.0
self.flat_mask = self.dmmask.flatten()
self.nch = 8 # number of DM channels
self.dmd0 = np.zeros((dms,dms), dtype=np.float32)
self.cntrs = np.zeros(self.nch+1) - 1 # shared mem counters for channels
for ii in range(self.nch):
exec "disp%d = shm(fname='/tmp/dmdisp%d.im.shm', data=self.dmd0, verbose=False)" % (ii,ii)
# -------------------------------------------------------------------------
def map2dm(self, cmap):
''' --------------------------------------------
Sends a 2D command to the DM, using the mapping
knowledge provided by the flat_mask array.
-------------------------------------------- '''
temp = cmap.flatten()
values = [0.0] * self.nba # data to be uploaded to the DM
jj = 0
for ii in xrange(cmap.size):
if not np.isnan(self.flat_mask[ii]):
values[jj] = temp[i]
jj += 1
self.alpao.Send(values)
# -------------------------------------------------------------------------
def reset(self, chn=0):
''' ----------------------------------------------
Reset one or (default) all channels of the DM.
---------------------------------------------- '''
if chn == 0: # send the flat-map!
try:
data = np.loadtxt('/home/ciaodev/.config/ciao/zygo_flat.txt')
disp0.set_data(list2map2D(data))
except:
disp0.set_data(self.dmd0)
else:
try:
exec 'self.dmdisp%d.set_data(self.dmd0)' %
except:
print("error reset channel #%d" % (chn))
# -------------------------------------------------------------------------
def quit(self, chn=None):
# -------------------------------------------------------------------------
def quit(self, chn=None):
self.alpao.Reset()
sys.exit()
# =============================================================================
# =============================================================================
if __name__ == "__main__":
mydm = ALPAO_DM()
def __init__(self):
super(Form, self).__init__()
uic.loadUi('Gui_FLIR.ui', self)
self.connect(self.QuitButton, SIGNAL("clicked()"), self.shutdown)
self.connect(self.RunButton, SIGNAL("clicked()"), self.run)
# self.connect(self.StopButton, SIGNAL("clicked()"), self.stop)
self.connect(self.SaveButton, SIGNAL("clicked()"), self.Saveimg)
self.connect(self.SaveWFButton, SIGNAL("clicked()"), self.savedmwf)
self.connect(self.SaveZMWFButton, SIGNAL("clicked()"), self.savezmwf)
self.connect(self.AutoScanButton, SIGNAL("clicked()"), self.autoscandm)
self.connect(self.exposurebox, SIGNAL("returnPressed()"),
self.exposureupdate)
self.connect(self.thresholdbox, SIGNAL("returnPressed()"),
self.thresholdupdate)
self.connect(self.PushDMButton, SIGNAL("clicked()"), self.pushdm)
self.connect(self.ScanZernikeModeButton, SIGNAL("clicked()"),
self.scanzernikemode)
self.connect(self.LoadDMButton, SIGNAL("clicked()"), self.loaddmfile)
self.connect(self.InitiatePushButton, SIGNAL("clicked()"),
self.set_baseimage)
self.connect(self.Infl_func_pushButton, SIGNAL("clicked()"),
self.influencefunction)
self.ProgressBar.setRange(0, 100)
self.ProgressBar.setValue(0)
self.index = 0
#DM
self.serialName = 'BAX228'
self.dm = DM(self.serialName)
self.nbAct = int(self.dm.Get('NBOfActuator'))
self.values = [0.] * self.nbAct
self.dm.Send(self.values)
#Initial camera
self.system = PySpin.System.GetInstance()
self.cam_list = self.system.GetCameras()
self.cam = self.cam_list[0]
self.cam.Init()
self.nodemap = self.cam.GetNodeMap()
self.node_acquisition_mode = PySpin.CEnumerationPtr(
self.nodemap.GetNode('AcquisitionMode'))
self.node_acquisition_mode_continuous = self.node_acquisition_mode.GetEntryByName(
'Continuous')
self.acquisition_mode_continuous = self.node_acquisition_mode_continuous.GetValue(
)
self.node_acquisition_mode.SetIntValue(
self.acquisition_mode_continuous)
self.cam.ExposureAuto.SetValue(PySpin.ExposureAuto_Off)
self.exposure_time_to_set = 200.0
self.cam.ExposureTime.SetValue(self.exposure_time_to_set)
self.cam.BeginAcquisition()
self.image_result = self.cam.GetNextImage()
self.img = self.image_result.GetNDArray()
self.image = self.img.copy()
self.baseimage = self.img.copy()
self.image_result.Release()
self.cam.EndAcquisition()
self.ah = self.CCDImage.axes.imshow(self.image)
# setup the wavefront
self.WFS = shwfs.Wavefront_Sensor()
self.phi = self.WFS.GetAberration2img(self.baseimage, self.baseimage)
self.phi = self.phi * self.WFS.Zero_Mask
self.wah = self.WFimage.axes.imshow(self.phi,
interpolation='nearest',
vmin=-0.8,
vmax=0.8)
self.WFimage.figure.colorbar(self.wah)
class Form(QDialog):
def __init__(self):
super(Form, self).__init__()
uic.loadUi('Gui_FLIR.ui', self)
self.connect(self.QuitButton, SIGNAL("clicked()"), self.shutdown)
self.connect(self.RunButton, SIGNAL("clicked()"), self.run)
# self.connect(self.StopButton, SIGNAL("clicked()"), self.stop)
self.connect(self.SaveButton, SIGNAL("clicked()"), self.Saveimg)
self.connect(self.SaveWFButton, SIGNAL("clicked()"), self.savedmwf)
self.connect(self.SaveZMWFButton, SIGNAL("clicked()"), self.savezmwf)
self.connect(self.AutoScanButton, SIGNAL("clicked()"), self.autoscandm)
self.connect(self.exposurebox, SIGNAL("returnPressed()"),
self.exposureupdate)
self.connect(self.thresholdbox, SIGNAL("returnPressed()"),
self.thresholdupdate)
self.connect(self.PushDMButton, SIGNAL("clicked()"), self.pushdm)
self.connect(self.ScanZernikeModeButton, SIGNAL("clicked()"),
self.scanzernikemode)
self.connect(self.LoadDMButton, SIGNAL("clicked()"), self.loaddmfile)
self.connect(self.InitiatePushButton, SIGNAL("clicked()"),
self.set_baseimage)
self.connect(self.Infl_func_pushButton, SIGNAL("clicked()"),
self.influencefunction)
self.ProgressBar.setRange(0, 100)
self.ProgressBar.setValue(0)
self.index = 0
#DM
self.serialName = 'BAX228'
self.dm = DM(self.serialName)
self.nbAct = int(self.dm.Get('NBOfActuator'))
self.values = [0.] * self.nbAct
self.dm.Send(self.values)
#Initial camera
self.system = PySpin.System.GetInstance()
self.cam_list = self.system.GetCameras()
self.cam = self.cam_list[0]
self.cam.Init()
self.nodemap = self.cam.GetNodeMap()
self.node_acquisition_mode = PySpin.CEnumerationPtr(
self.nodemap.GetNode('AcquisitionMode'))
self.node_acquisition_mode_continuous = self.node_acquisition_mode.GetEntryByName(
'Continuous')
self.acquisition_mode_continuous = self.node_acquisition_mode_continuous.GetValue(
)
self.node_acquisition_mode.SetIntValue(
self.acquisition_mode_continuous)
self.cam.ExposureAuto.SetValue(PySpin.ExposureAuto_Off)
self.exposure_time_to_set = 200.0
self.cam.ExposureTime.SetValue(self.exposure_time_to_set)
self.cam.BeginAcquisition()
self.image_result = self.cam.GetNextImage()
self.img = self.image_result.GetNDArray()
self.image = self.img.copy()
self.baseimage = self.img.copy()
self.image_result.Release()
self.cam.EndAcquisition()
self.ah = self.CCDImage.axes.imshow(self.image)
# setup the wavefront
self.WFS = shwfs.Wavefront_Sensor()
self.phi = self.WFS.GetAberration2img(self.baseimage, self.baseimage)
self.phi = self.phi * self.WFS.Zero_Mask
self.wah = self.WFimage.axes.imshow(self.phi,
interpolation='nearest',
vmin=-0.8,
vmax=0.8)
self.WFimage.figure.colorbar(self.wah)
def set_baseimage(self, ):
self.cam.BeginAcquisition()
self.image_result = self.cam.GetNextImage()
self.baseimage = self.image_result.GetNDArray().copy()
self.image_result.Release()
self.cam.EndAcquisition()
def run(self):
self.cam.BeginAcquisition()
self.image_result = self.cam.GetNextImage()
self.image = self.image_result.GetNDArray().copy()
self.image_result.Release()
self.cam.EndAcquisition()
self.imageupdate()
def imageupdate(self):
# update ccd image
self.ah.set_data(self.image)
self.CCDImage.figure.canvas.draw()
# measure wavefront
self.phi = self.WFS.GetAberration2img(self.baseimage, self.image)
self.phi = self.phi * self.WFS.Zero_Mask
self.wah.set_data(self.phi)
self.wah.set_clim(self.phi.min(), self.phi.max())
self.WFimage.figure.canvas.draw()
self.ProgressBar.setValue(self.index)
self.index = (self.index + 1) % 100
def shutdown(self):
x = self.dm.Reset()
if (x == 0):
print('DM Reset')
else:
print('DM cannot reset')
del self.cam
self.cam_list.Clear()
self.system.ReleaseInstance()
self.close()
def pushdm(self):
push = self.PushdoubleSpinBox.value()
num = self.ActspinBox.value()
self.values[num] = push
self.dm.Send(self.values)
self.values[num] = 0.
return True
def influencefunction(self):
n = self.nbAct
push = self.PushdoubleSpinBox.value()
for i in range(n):
self.values[i] = push
self.dm.Send(self.values)
self.values[i] = 0.
self.run()
fn = 'act_%d' % i + '_v%f.tif' % push
tf.imsave(fn,
self.phi.astype(np.float32),
photometric='minisblack')
return True
def autoscandm(self):
for i in range(self.nbAct):
data = []
for p in range(19):
push = -0.9 + p * 0.1
self.values[i] = push
self.dm.Send(self.values)
self.cam.BeginAcquisition()
self.image_result = self.cam.GetNextImage()
self.image = self.image_result.GetNDArray().copy()
self.image_result.Release()
self.cam.EndAcquisition()
self.phi = self.WFS.GetAberration2img(self.baseimage,
self.image)
self.phi = self.phi * self.WFS.Zero_Mask
data[p] = self.phi
self.values[i] = 0.
time.sleep(0.1)
fn = 'act_%d.tif' % (i)
tf.imsave(join(fn),
data.astype(np.float32),
photometric='minisblack')
return True
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 loaddmfile(self):
fns = self.dmfilebox.text()
fn = r'%s' % fns
with open(fn, "r") as file:
cmd = eval(file.readline())
if (all(i <= 1.0 for i in cmd)):
self.dm.Send(cmd)
else:
raise Exception(' Error: push value greater than 1.0 ')
def savedmwf(self):
m = self.ActspinBox.value()
v = self.PushdoubleSpinBox.value()
fn = 'act_%d' % m + '_v%f.tif' % v
tf.imsave(fn, self.phi.astype(np.float32), photometric='minisblack')
def savezmwf(self):
m = self.ZernikeModeBox.value()
v = self.PushSpinBox.value()
fn = 'zernike_mode%d' % m + '_v%f.tif' % v
tf.imsave(fn, self.phi.astype(np.float32), photometric='minisblack')
def Saveimg(self):
tf.imsave('camera_image.tif',
self.img.astype(np.float32),
photometric='minisblack')
tf.imsave('wfs_image.tif',
self.phi.astype(np.float32),
photometric='minisblack')
def updatespacing(self):
text = self.Spacinglinebox.text()
self.px_spacing = float(text)
def updateXcenter(self):
xcenter = self.xCenterbox.text()
self.x_center = float(xcenter)
def updateYcenter(self):
ycenter = self.yCenterbox.text()
self.y_center = float(ycenter)
def exposureupdate(self):
exposure = self.exposurebox.text()
exposure = int(exposure)
self.cam.ExposureTime.SetValue(exposure)
def thresholdupdate(self):
threshold = self.thresholdbox.text()
self.theshold = float(threshold)
def high_pass_filter(self, data):
y, x = data.shape
data[data < self.threshold] = 0.0
return data
@author: snf56384
"""
import sys
import os
#import time
import struct
''' Add '/Lib' or '/Lib64' to path '''
if (8 * struct.calcsize("P")) == 32:
print("Use x86 libraries.")
sys.path.append(os.path.join(os.path.dirname(__file__), 'Lib'))
else:
print("Use x86_64 libraries.")
sys.path.append(os.path.join(os.path.dirname(__file__), 'Lib64'))
''' Import Alpao SDK class '''
from asdk import DM
dm1 = DM("BAX111")
dm2 = DM("BAX112")
#dm1.Send( check1on2 )
#dm2.Send( -Zplot )
dm1.Reset()
dm2.Reset()
import numpy as np
signal = np.loadtxt("mirror_command.csv", delimiter=",")
dm1.Send(signal)
