def __init__(self,main_widget,data_base_path): # Call parent class constructor super(Experiment,self).__init__() self.exiting = False self.main_widget = main_widget self.setup = main_widget.setup self.cameraControl = main_widget.cameraWidget.cameraControl self.column_names = [ 'key INTEGER', 'time REAL', 'zPos REAL', 'molointensity REAL', 'bkgmean REAL', 'bkgstd REAL', 'exposure REAL', 'MIExpWeighted REAL' ] self.database_path = data_base_path print(self.database_path) db.create_sql_database(self.column_names,self.database_path) self.stop_thread = False self.pause_thread = False
def run(self):
# get cursor and connection to new SQL database
experiment_start_time = time.time()
# depending on stack type change image aquisition method
exposure = self.setup.camera.exposure
if self.stack_type == self.stack_type_list[0]:
# time stack
for i in range(self.num_captures):
# If stop button was pressed, exit loop
if self.stop_thread:
break
# If pause button was pressed, wait until it is pressed again
while self.pause_thread:
continue
z_position = self.setup.motors.z.pos('um')
time.sleep(0.2)
# Record start time
start_time = time.time()
# Determine file name for image
#self.cameraControl.update_exposure_slider(exposure*0.9)
image_name = self.setup.chip.file_name()
image_name += '_' + 'exposure-' + str(exposure) + '-ms'
image_name += '_' + str(i+1)
# Try a few times to capture/save
print('Capturing ( ' + image_name + ' ): ' + str(i+1))
num_attempts = 10
for j in range(num_attempts):
img,retval = self.setup.camera.get_raw_img()
curr_time = start_time - experiment_start_time
if retval:
if self.crop_image:
self.setup.camera.crop_and_save_img(self.image_path+'/'+image_name, img)
break
else:
self.setup.camera.save_img(self.image_path+'/'+image_name, img)
break
entry = mologram_processing.calc_datapoint_entry(i,curr_time,z_position,exposure,img,retval)
if retval:
if self.adjust_exposure:
if np.amax(img) > 3000:
print("Adjusted Exposure")
exposure = exposure*0.9
self.setup.camera.set_exposure(exposure)
db.add_entry(entry,self.database_path)
if self.update_plots:
print("lauched Signal to update GUI")
self.emit(QtCore.SIGNAL("database_updated"))
# Wait until delay is passed
while time.time() - start_time < self.time_interval:
continue
elif self.stack_type == self.stack_type_list[1]:
z_start = self.setup.motors.z.pos('um')
time.sleep(0.2)
for i in range(self.num_captures):
exposure = self.setup.camera.exposure
z_position = self.setup.motors.z.pos('um')
time.sleep(0.2)
image_name = self.setup.chip.file_name()
image_name += '_' + 'exposure-' + str(exposure) + '-ms'
image_name += 'z_' + str(z_position-z_start)
image_name += '_' + str(i+1)
for k in range(self.num_avg):
# If stop button was pressed, exit loop
if self.stop_thread:
break
# If pause button was pressed, wait until it is pressed again
while self.pause_thread:
continue
# Record start time
start_time = time.time()
# Try a few times to capture/save
print('Capturing ( ' + image_name + ' ): ' + str(i+1))
num_attempts = 10
for j in range(num_attempts):
img,retval = self.setup.camera.get_raw_img()
curr_time = start_time - experiment_start_time
if retval:
if k == 0:
avg_image = img
else:
avg_image += img
if k == (self.num_avg-1):
avg_image = avg_image/self.num_avg
if self.crop_image:
self.setup.camera.crop_and_save_img(self.image_path+'/'+image_name, avg_image)
break
else:
self.setup.camera.save_img(self.image_path+'/'+image_name, avg_image)
break
# Store data in SQL database
#update Database
entry = mologram_processing.calc_datapoint_entry(i,curr_time,z_position,exposure,img,retval)
db.add_entry(entry,self.database_path)
if self.update_plots:
self.emit(QtCore.SIGNAL("database_updated"))
# Wait until delay is passed
while time.time() - start_time < self.time_interval:
continue
self.main_widget.axisControl.z.start_moving(self.stack_incr,'um',relative = True)
time.sleep(2)
elif self.stack_type == self.stack_type_list[2]:
time.sleep(0.2)
for i in range(self.num_captures):
exposure = self.setup.camera.exposure
time.sleep(0.2)
image_name = self.setup.chip.file_name()
image_name += '_' + 'exposure-' + str(exposure) + '-ms'
image_name += '_' + str(i+1)
for k in range(self.num_avg):
# If stop button was pressed, exit loop
if self.stop_thread:
break
# If pause button was pressed, wait until it is pressed again
while self.pause_thread:
continue
# Record start time
start_time = time.time()
# Try a few times to capture/save
print('Capturing ( ' + image_name + ' ): ' + str(i+1))
num_attempts = 10
for j in range(num_attempts):
img,retval = self.setup.camera.get_raw_img()
curr_time = start_time - experiment_start_time
if retval:
if k == 0:
avg_image = img
else:
avg_image += img
if k == (self.num_avg-1):
avg_image = avg_image/self.num_avg
if self.crop_image:
self.setup.camera.crop_and_save_img(self.image_path+'/'+image_name, avg_image)
break
else:
self.setup.camera.save_img(self.image_path+'/'+image_name, avg_image)
break
# Store data in SQL database
# update database
entry = mologram_processing.calc_datapoint_entry(i,curr_time,z_position,exposure,img,retval)
db.add_entry(entry,self.database_path)
if self.update_plots:
self.emit(QtCore.SIGNAL("database_updated"))
while time.time() - start_time < self.time_interval:
continue
self.main_widget.axisControl.TE.start_moving(self.stack_incr,'deg',relative = True)
time.sleep(2)
self.stop_thread = False
self.emit(QtCore.SIGNAL("done_experiment"))
