def run(self):
experiment_length = self.experiment_length
exposures = self.old_database_content[:,self.db_column_names.index('exposure')]
time = self.old_database_content[:,self.db_column_names.index('time')]
try:
z_position = self.old_database_content[:,self.db_column_names.index('zPoss')]
except Exception:
z_position = np.ones((experiment_length,1))
columns = []
for i in self.column_names:
columns.append(i)
self.num_columns = len(columns)
con = sqlite3.connect(self.database_path + '/mologram_data.db')
cur = con.cursor()
cur.execute('DROP TABLE mologram_data')
con.commit()
con.close()
con = sqlite3.connect(self.database_path + '/mologram_data.db')
cur = con.cursor()
cur.execute("CREATE TABLE mologram_data(" + ','.join(columns) + ")")
con.commit()
con.close()
#self.database.create_sql_database(self.column_names,self.experiment_folder_path + '/database')
# Go through all available images and re-process them
for index in range(experiment_length):
# Send signal to update progress bar in main thread
self.emit(QtCore.SIGNAL("update_progress_bar(int,int)"),index,experiment_length)
# keys in SQL database start at 1
key = index + 1
# If abort signal was received, stop processing
if self.abort_processing:
break
# Get next image path
image_path,image_name = self.image_path(key,exposures)
# If image exists, read data and process it
if os.path.isfile(image_path):
im = Image.open(self.experiment_folder_path + '/images/' + image_name)
im = np.array(im.getdata()).reshape(im.size[0], im.size[1])
im = im.astype('uint16')
entry = mologram_processing.calc_datapoint_entry(key,time[index],z_position[index,0],exposures[index],im,1)
elif os.path.isfile(image_path + '.tiff'):
im = Image.open(self.experiment_folder_path + '/images/' + image_name + '.tiff')
im = np.array(im.getdata()).reshape(im.size[1], im.size[0])
im = im.astype('uint16')
entry = mologram_processing.calc_datapoint_entry(key,time[index],z_position[index,0],exposures[index],im,1)
else:
print('Unable to find image file: ' + self.experiment_folder_path + '/images/' + image_name)
mologram_intensity = -1
con = sqlite3.connect(self.database_path + '/mologram_data.db')
cur = con.cursor()
cur.execute('INSERT INTO mologram_data VALUES (' + entry + ')')
con.commit()
con.close()
#print(image_name + ': ' + str(mologram_intensity))
# Send signal to update progress bar in main thread
self.emit(QtCore.SIGNAL("update_progress_bar(int,int)"),key,experiment_length)
# fetch all rows from database
# if not new_column_name in self.db_column_names():
# executed = False
# while executed == False:
# try:
# cur.execute('ALTER TABLE mologram_data ADD COLUMN ' + new_column_name + ' real')
# con.commit()
# executed = True
# except Exception as inst:
# print(inst)
# for i in range(len(new_column)):
# key = i+1
# val = new_column[key]
# cmd = "UPDATE mologram_data SET " + new_column_name + "=" + str(val) + " where key=" + str(key)
# print(cmd)
# cur.execute(cmd)
# con.commit()
# Close connection with SQL databse
# con.close()
# let GUI know that movement is finished
self.emit(QtCore.SIGNAL("done_processing"))
def updateImage(self,mask = False,Stack = False):
# acquire image from camera, this should not be the case, you get images multiple times
# like this
if Stack:
# get the last image that was saved in the folder images
print("Stack")
# experiment_folder_path = self.main_widget.get_experiment_folder_path()
# image_path = experiment_folder_path + '/images/'
# file_names = []
# index = []
# for file in os.listdir(image_path):
# index.append(int(file.split('_')[-1]))
# file_names.append(file)
# print(file_names)
# print(np.argmax(np.asarray(index)))
# max_index = np.argmax(np.asarray(index))
# im = Image.open(experiment_folder_path + '/images/' + file_names[max_index])
# im = np.array(im.getdata()).reshape(im.size[0], im.size[1])
# self.img = im.astype('uint16')
# retval = 1
else:
if mask == False:
self.img,retval = self.main_widget.setup.camera.get_raw_img()
else:
img,retval = self.main_widget.setup.camera.get_raw_img()
self.img = processing.processed_image(img)
self.img *= 1024
retval = None
# if there was an error, display a text box
if retval == -1:
msg = QtGui.QMessageBox()
msg.setWindowTitle("Camera Error")
msg.setIcon(QtGui.QMessageBox.Critical)
msg.setStandardButtons(QtGui.QMessageBox.Ok)
msg.setText("Cannot fetch image from camera")
msg.setInformativeText("You must restart the program to fix the issue, your current position will be saved")
msg.exec_()
else:
self.settings.set_Magnification(int(str(self.microscopy_mag.currentText())))
self.im.set_data(self.img)
self.scale_bar()
#self.molo_circle()
molo_intensity,Airy_disk_radius, bkg_mean,bkg_std = mologram_processing.calc_IntAiryDisk(self.img)
self.molo_intensity.setText(str(molo_intensity))
self.bg_int.setText(str(bkg_mean) + ',' + str(bkg_std))
self.sum_int.setText(str(np.sum(self.img)/(2560*1920)))
self.max_pixel.setText(str(np.max(self.img)))
print(self.settings.magnification)
# draw a circle, where you detect the mologram
# update the image
self.canvas.draw()
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"))
