def gainscan(idx):
gainnum = 1
#where_i_was=acsc.getRPosition(hcomm,0)
acsc.toPoint(hcomm, None, 0, gain_z_out_of_beam)
# while(abs(acsc.getFVelocity(hcomm, 0))>wait_ms):
# 1+1
while (not acsc.getMotorState(hcomm, 0)['in position']
): #check for stop event using other API call?
time.sleep(.1)
while (gainnum < num_gain_per_scan):
mmc.snapImage()
image_npy = mmc.getImage()
image_itk = sitk.GetImageFromArray(image_npy)
sitk.WriteImage(
image_itk, output_dir + "\\gain\\gain_" + str(idx) + "_" +
str(gainnum) + ".tiff"
) #Change this to Gainscan_"+str(idx)+".tiff" if you would rather sort by time and not filename
dt = datetime.now()
micro = dt.microsecond
time_temp = time.strftime("%Y%m%d-%H%M%S") + ":" + str(micro)
file_output.write("gain_%d\t%f\t%f\t%f\t%s\t%s\t%d\n" %
(idx, 0, acsc.getRPosition(hcomm, 1),
acsc.getFPosition(hcomm, 1), time_temp,
(datetime.now() - startTime), exposure_inpt))
gainnum = gainnum + 1
acsc.toPoint(hcomm, None, 0, where_i_was)
# while(abs(acsc.getFVelocity(hcomm, 0))>wait_ms):
# 1+1
while (not acsc.getMotorState(hcomm, 0)['in position']
): #check for stop event using other API call?
time.sleep(.1)
def run(self):
"""Start the run. Comms should be open already with the controller."""
if acsc.getOutput(self.hc, 1, 16):
acsc.setOutput(self.hc, 1, 16, 0)
if self.vectrino:
acsc.enable(self.hc, 0)
acsc.enable(self.hc, 1)
while not acsc.getMotorState(self.hc, 0)["enabled"] or not \
acsc.getMotorState(self.hc, 1)["enabled"]:
self.msleep(100)
acsc.toPoint(self.hc, None, 0, self.y_R * self.R)
acsc.toPoint(self.hc, None, 1, self.z_H * self.H)
while not acsc.getMotorState(self.hc, 0)["in position"] or not \
acsc.getMotorState(self.hc, 1)["in position"]:
self.msleep(300)
print("y- and z-axes in position")
acsc.disable(self.hc, 0)
acsc.disable(self.hc, 1)
self.vec.serial_port = "COM2"
self.vec.connect()
tstart = time.time()
self.timeout = False
self.vecstatus = "Connecting to Vectrino..."
while not self.vec.connected:
self.msleep(300)
if time.time() - tstart > 10:
print("Vectrino timed out")
self.timeout = True
break
if not self.timeout:
self.vec.stop()
self.setvecconfig()
if self.recordvno:
self.vec.start_disk_recording(self.vecsavepath)
self.vec.start()
self.vecstatus = "Vectrino connected "
while self.vec.state != "Confirmation mode":
self.msleep(100)
print("Vectrino in data collection mode")
print("Waiting 6 seconds")
self.sleep(6)
self.daqthread.start()
if self.fbg:
self.fbgthread.start()
self.start_motion()
elif self.nidaq:
self.daqthread.start()
if self.fbg:
self.fbgthread.start()
self.start_motion()
else:
# Start motion
self.start_motion()
def run(self):
"""Start the run. Comms should be open already with the controller."""
if acsc.getOutput(self.hc, 1, 16):
acsc.setOutput(self.hc, 1, 16, 0)
if self.vectrino:
acsc.enable(self.hc, 0)
acsc.enable(self.hc, 1)
while not acsc.getMotorState(self.hc, 0)["enabled"] or not \
acsc.getMotorState(self.hc, 1)["enabled"]:
self.msleep(100)
acsc.toPoint(self.hc, None, 0, self.y_R*self.R)
acsc.toPoint(self.hc, None, 1, self.z_H*self.H)
while not acsc.getMotorState(self.hc, 0)["in position"] or not \
acsc.getMotorState(self.hc, 1)["in position"]:
self.msleep(300)
print("y- and z-axes in position")
acsc.disable(self.hc, 0)
acsc.disable(self.hc, 1)
self.vec.serial_port = "COM2"
self.vec.connect()
tstart = time.time()
self.timeout = False
self.vecstatus = "Connecting to Vectrino..."
while not self.vec.connected:
self.msleep(300)
if time.time() - tstart > 10:
print("Vectrino timed out")
self.timeout = True
break
if not self.timeout:
self.vec.stop()
self.setvecconfig()
if self.recordvno:
self.vec.start_disk_recording(self.vecsavepath)
self.vec.start()
self.vecstatus = "Vectrino connected "
while self.vec.state != "Confirmation mode":
self.msleep(100)
print("Vectrino in data collection mode")
print("Waiting 6 seconds")
self.sleep(6)
self.daqthread.start()
if self.fbg:
self.fbgthread.start()
self.start_motion()
elif self.nidaq:
self.daqthread.start()
if self.fbg:
self.fbgthread.start()
self.start_motion()
else:
# Start motion
self.start_motion()
then uploading it to the controller and running it.
"""
from __future__ import division, print_function
from acspy import acsc
import time
#file = open("test/test.prg", "w+")
acs_prg = """
ENABLE 1""" + \
"""
VEL(1) = 1000
PTP/r 1, -900
STOP
"""
#file.write(acs_prg)
#file.close()
print(acs_prg)
hc = acsc.openCommDirect()
acsc.loadBuffer(hc, 0, acs_prg, 512)
acsc.enable(hc, 0)
#acsc.LoadBuffersFromFile(hc, "test/test.prg")
acsc.runBuffer(hc, 0)
time.sleep(1)
print(acsc.getRPosition(hc, 1))
print(acsc.getMotorState(hc, 1))
acsc.closeComm(hc)
#exposure=60
mmc.setExposure(exposure_inpt)
mmc.setProperty(device_id, "Binning", binning_value)
print(mmc.getProperty(device_id, "Binning"))
os.chdir(prev_dir)
##################
###camera calls###
##################
#load in 10k devices
if load_camera10k:
camefile_path = "C:\\Users\\ChengLab\\Desktop\\MP71Camera\\VP-71MC-M5_P200SC_4tap(H)_12bit_RG (VST Y12).cam"
#Actually do the imaging
if do_scan:
while (not acsc.getMotorState(hcomm, 1)['in position']
): #check for stop event using other API call?
time.sleep(.1)
for focal_idx, focal_position in enumerate(focal_step_mtx):
projection_fill[focal_idx] = take_photo(1, 1, focal_position)
print("projecting at " + str(focal_position))
where_i_was = acsc.getRPosition(hcomm, 0)
acsc.toPoint(hcomm, None, 0, gain_z_out_of_beam)
while (not acsc.getMotorState(hcomm, 0)['in position']
): #check for stop event using other API call?
time.sleep(.1)
if scan_gain:
for focal_idx, focal_position in enumerate(focal_step_mtx):
gain_fill[focal_idx] = gainscan(1, focal_position)
print("projecting at " + str(focal_position))
def motor_state(self):
"""Returns motor state dict."""
return acsc.getMotorState(self.controller.hc, self.axisno)
def motor_state(self):
"""Returns motor state dict."""
return acsc.getMotorState(self.controller.hc, self.axisno)
def take_drift_correction_photo(deg):
move_stage(0)
moving = True
# while(abs(acsc.getFVelocity(hcomm, 1))>wait_ms): #check for stop event using other API call?
# 1+1
while (not acsc.getMotorState(hcomm, 1)['in position']
): #check for stop event using other API call?
time.sleep(.1)
for projnum in range(num_exposures_per_projection):
print("Projection average %d out of %d" %
(projnum + 1, num_exposures_per_projection))
if load_camera10k:
print("Projection %d out of %d" %
(projnum + 1, num_exposures_per_projection))
# image_npy,channel_temp=GrabOneImage(channel)
s2 = datetime.now()
MC.SetParamStr(channel, 'ChannelState', 'ACTIVE')
gotEndOfChannelActivity = False
gotAcquisitionFailure = False
while not gotEndOfChannelActivity:
signalInfo = MC.WaitSignal(
channel, MC.SIG_ANY, 15000
) #Attempt to make this call shorter (1.5 second overhead as written....)
# signalInfo = MC.WaitSignal(channel, MC.SIG_ANY, 1000)
if signalInfo.Signal == MC.SIG_END_CHANNEL_ACTIVITY:
gotEndOfChannelActivity = True
elif signalInfo.Signal == MC.SIG_ACQUISITION_FAILURE:
gotAcquisitionFailure = True
elif signalInfo.Signal == MC.SIG_SURFACE_PROCESSING:
MC.SetParamStr(signalInfo.SignalInfo, 'SurfaceState',
'FREE')
else:
raise MC.MultiCamError('Unexpected signal: %d' %
signalInfo.Signal)
# MC.SetParamStr(channel, "ForceTrig", "TRIG");
if gotAcquisitionFailure:
raise MC.MultiCamError('Acquisition failure!')
surface = MC.GetParamInst(channel, 'Cluster:0')
width = MC.GetParamInt(surface, 'SurfaceSizeX')
height = MC.GetParamInt(surface, 'SurfaceSizeY')
# image = ConvertSurfaceIntoImage(surface)
surfaceAddress = MC.GetParamPtr(surface,
'SurfaceAddr:%d' % planeIndex)
surfaceSize = MC.GetParamInt(surface,
'SurfaceSize:%d' % planeIndex)
imageBuffer = ctypes.string_at(surfaceAddress, surfaceSize)
MC.SetParamStr(channel, 'ChannelState', 'READY')
data = np.fromstring(imageBuffer, np.uint16)
image_npy = np.reshape(data, (height, width))
# image = ConvertBufferIntoImage(width, height, imageBuffer)
# print(image.shape)
# print(image[0].shape)
# channel_temp=channel
print(str(datetime.now() - s2) + " single proj")
else:
mmc.snapImage()
image_npy = mmc.getImage()
projection_fill[projnum] = image_npy
proj = np.mean(projection_fill, axis=0)
# image_itk = sitk.GetImageFromArray(proj)
#sitk.WriteImage(image_itk, output_dir+"/Projection_"+str(idx)+".tiff")
dx.write_tiff(proj,
output_dir +
"//Drift_Projections_at_0deg/Correction_Projection_from_" +
str(int(np.where(degrees_array == deg)[0][0])) + ".tiff",
dtype=np.uint16)
move_stage(deg)
# while(abs(acsc.getFVelocity(hcomm, 1))>wait_ms): #check for stop event using other API call?
# 1+1
while (not acsc.getMotorState(hcomm, 1)['in position']
): #check for stop event using other API call?
time.sleep(.1)
"""
This is a test for generating an ACSPL+ program
then uploading it to the controller and running it.
"""
from acspy import acsc
import time
#file = open("test/test.prg", "w+")
acs_prg = """
ENABLE 1""" + \
"""
VEL(1) = 1000
PTP/r 1, -900
STOP
"""
#file.write(acs_prg)
#file.close()
print acs_prg
hc = acsc.openCommDirect()
acsc.loadBuffer(hc, 0, acs_prg, 512)
acsc.enable(hc, 0)
#acsc.LoadBuffersFromFile(hc, "test/test.prg")
acsc.runBuffer(hc, 0)
time.sleep(1)
print acsc.getRPosition(hc, 1)
print acsc.getMotorState(hc, 1)
acsc.closeComm(hc)
