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 ptp(self, target, coordinates="absolute", wait=acsc.SYNCHRONOUS):
"""Performs a point to point move in either relative or absolute
(default) coordinates."""
if coordinates == "relative":
flags = acsc.AMF_RELATIVE
else:
flags = None
acsc.toPoint(self.controller.hc, flags, self.axisno, target, wait)
def on_goPlatform(self):
vel = self.ui.velSpinBox.value()
acc = self.ui.accSpinBox.value()
acsc.setVelocity(self.hcomm, self.axis, vel)
acsc.setAcceleration(self.hcomm, self.axis, acc)
acsc.setDeceleration(self.hcomm, self.axis, acc)
acsc.setJerk(self.hcomm, self.axis, acc*10)
acsc.toPoint(self.hcomm, None, self.axis, self.platform)
def ptp(self, target, coordinates="absolute", wait=acsc.SYNCHRONOUS):
"""Performs a point to point move in either relative or absolute
(default) coordinates."""
if coordinates == "relative":
flags = acsc.AMF_RELATIVE
else:
flags = None
acsc.toPoint(self.controller.hc, flags, self.axisno, target, wait)
def autoabort(self):
"""This should stop everything and return carriage and turbine back
to zero."""
self.autoaborted = True
acsc.stopBuffer(self.hc, 19)
acsc.halt(self.hc, 0)
acsc.halt(self.hc, 1)
acsc.halt(self.hc, 4)
acsc.halt(self.hc, 5)
acsc.toPoint(self.hc, None, 4, 0.0)
acsc.setVelocity(self.hc, 5, 0.5)
acsc.toPoint(self.hc, None, 5, 0.0)
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 autoabort(self):
"""This should stop everything and return carriage and turbine back
to zero."""
self.autoaborted = True
acsc.stopBuffer(self.hc, 19)
acsc.halt(self.hc, 0)
acsc.halt(self.hc, 1)
acsc.halt(self.hc, 4)
acsc.halt(self.hc, 5)
acsc.toPoint(self.hc, None, 4, 0.0)
acsc.setVelocity(self.hc, 5, 0.5)
acsc.toPoint(self.hc, None, 5, 0.0)
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 on_go(self):
target = self.ui.posSpinBox.value()
vel = self.ui.velSpinBox.value()
acc = self.ui.accSpinBox.value()
acsc.setVelocity(self.hcomm, self.axis, vel)
acsc.setAcceleration(self.hcomm, self.axis, acc)
acsc.setDeceleration(self.hcomm, self.axis, acc)
acsc.setJerk(self.hcomm, self.axis, acc*10)
if self.ui.rbRelative.isChecked() == True:
flags = acsc.AMF_RELATIVE
else:
flags = None
acsc.toPoint(self.hcomm, flags, self.axis, target)
def move(self, axis, distance, relative_or_absolute='r'):
"""
'r' for relative, 'a' for absolute
distance in [mm]
"""
if relative_or_absolute == 'r':
flags = acsc.AMF_RELATIVE
else:
flags = 0
acsc.getLastError()
if not acsc.toPoint(self.hc, flags, axis, float(distance)):
print "Transaction error: %d\n" % (acsc.getLastError())
def ptp(self, axis, target, flags=None, wait=acsc.SYNCHRONOUS):
if axis in self.axisdefs:
axis = self.axisdefs[axis]
acsc.toPoint(self.hc, flags, axis, target, wait)
def move_stage(set_degree):
acsc.toPoint(hcomm, None, 1, set_degree)
###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))
acsc.toPoint(hcomm, None, 0, where_i_was)
while (not acsc.getMotorState(hcomm, 0)['in position']
): #check for stop event using other API call?
time.sleep(.1)
if load_stages:
while (not acsc.getMotorState(hcomm, 1)['in position']
def initialization(self):
print "Waiting for Motorized Stage (ACS) Initialization"
self.hc = acsc.openCommEthernetTCP(address="10.0.0.100",
port=701) ## craete comminucation
acsc.runBuffer(self.hc, 0)
acsc.runBuffer(self.hc, 1)
acsc.runBuffer(self.hc, 2)
acsc.runBuffer(self.hc, 4)
acsc.runBuffer(self.hc, 5)
acsc.runBuffer(self.hc, 6)
time.sleep(30)
## Homing process
## Axis 6
acsc.waitMotionEnd(self.hc, axis=6) ## stop at left limit
if acsc.setFPosition(self.hc, axis=6, fposition=0) != 0:
print 'Axis 6 (Receiver Z): Homing completed'
else:
print 'Axis 6 (Receiver Z): Homing failed'
## Axis 0
acsc.waitMotionEnd(self.hc, axis=0)
acsc.toPoint(self.hc, flags=acsc.AMF_RELATIVE, axis=0, target=47.5)
acsc.waitMotionEnd(self.hc, axis=0)
if acsc.setFPosition(self.hc, axis=0, fposition=0) == 1:
print 'Axis 0 (Sample X): Homing completed'
else:
print 'Axis 0 (Sample X): Homing failed'
## Axis 1
acsc.waitMotionEnd(self.hc, axis=1)
acsc.toPoint(self.hc, flags=acsc.AMF_RELATIVE, axis=1, target=19.51)
acsc.waitMotionEnd(self.hc, axis=1)
if acsc.setFPosition(self.hc, axis=1, fposition=0) == 1:
print 'Axis 1 (Sample Y): Homing completed'
else:
print 'Axis 1 (Sample Y): Homing failed'
## Axis 2
acsc.waitMotionEnd(self.hc, axis=2) ## stop at left limit
acsc.toPoint(self.hc, flags=0, axis=2, target=2.8915)
print 'Axis 2 (Lens array): Homing completed'
## Axis 4
acsc.waitMotionEnd(self.hc, axis=4) ## stop at left limit
acsc.toPoint(self.hc, flags=acsc.AMF_RELATIVE, axis=4, target=4.42)
acsc.waitMotionEnd(self.hc, axis=4)
if acsc.setFPosition(self.hc, axis=4, fposition=0) == 1:
print 'Axis 4 (Receiver X): Homing completed'
else:
print 'Axis 4 (Receiver X): Homing failed'
## Axis5
acsc.waitMotionEnd(self.hc, axis=5) ## stop at left limit
acsc.toPoint(self.hc, flags=acsc.AMF_RELATIVE, axis=5, target=23.8)
acsc.waitMotionEnd(self.hc, axis=5)
if acsc.setFPosition(self.hc, axis=5, fposition=0) == 1:
print 'Axis 5 (Receiver Y): Homing completed'
else:
print 'Axis 5 (Receiver Y): Homing failed'
## parameter setting
acsc.setVelocity(self.hc, 0, 30) ## axis 0 (linear X)
acsc.setAcceleration(self.hc, 0, 100)
acsc.setDeceleration(self.hc, 0, 100)
acsc.setJerk(self.hc, 0, 1000)
acsc.setVelocity(self.hc, 1, 30) ## axis1 (linear Y)
acsc.setAcceleration(self.hc, 1, 100)
acsc.setDeceleration(self.hc, 1, 100)
acsc.setJerk(self.hc, 1, 1000)
acsc.setVelocity(self.hc, 2, 30) ## axis 2 (revolver)
acsc.setAcceleration(self.hc, 2, 100)
acsc.setDeceleration(self.hc, 2, 100)
acsc.setJerk(self.hc, 2, 1000)
acsc.setVelocity(self.hc, 4, 30) ## axis4 (step X)
acsc.setAcceleration(self.hc, 4, 100)
acsc.setDeceleration(self.hc, 4, 100)
acsc.setJerk(self.hc, 4, 1000)
acsc.setVelocity(self.hc, 5, 30) ## axis 5 (step Y)
acsc.setAcceleration(self.hc, 5, 100)
acsc.setDeceleration(self.hc, 5, 100)
acsc.setJerk(self.hc, 5, 1000)
acsc.setVelocity(self.hc, 6, 5) ## axis 6 (step Z)
acsc.setAcceleration(self.hc, 6, 50)
acsc.setDeceleration(self.hc, 6, 50)
acsc.setJerk(self.hc, 1, 100)
print(device_id)
mmc.setExposure(exposure_inpt)
mmc.setProperty(device_id, "Binning", binning_value)
print(mmc.getProperty(device_id, "Binning"))
os.chdir(prev_dir)
##################
####stage calls###
##################
if load_stages:
#initiate connection
hcomm = acsc.openCommEthernetTCP(address="10.0.0.100", port=701)
#z
if scan_gain:
acsc.enable(hcomm, 0)
acsc.toPoint(hcomm, None, 0, 110) #YIFU CHECK THIS
acsc.setVelocity(hcomm, 0, 5) #velocity in mm/sec
#theta
acsc.enable(hcomm, 1)
acsc.setVelocity(hcomm, 1, 10) #velocity in degrees/sec
acsc.setJerk(hcomm, 1, 500) #jerk, normal is 9000
acsc.setDeceleration(hcomm, 1, 450) #jerk, normal is 9000
acsc.setAcceleration(hcomm, 1, 450) #Acceleration, normal is 9000
acsc.toPoint(hcomm, None, 1, 0)
#Actually do the imaging
if do_scan:
for idx in range(degrees_array.shape[0]):
q = time.time()
set_degree = degrees_array[idx]
move_stage(degrees_array[idx])
