def initUI(self):
# Define buttons
self.calibrate = QtGui.QPushButton('Calibrate')
self.set_position = QtGui.QPushButton('Set Position')
self.setSurfaceHeight = QtGui.QPushButton('Set Surface Height')
self.setMoloHeight = QtGui.QPushButton('Set Mologram Height')
self.goToSurfaceHeight = QtGui.QPushButton('Go To Surface Height')
self.goToMoloHeight = QtGui.QPushButton('Go To Mologram Height')
self.mologram_pos = MologramSelector()
# connect buttons
self.calibrate.clicked.connect(self.onCalibrateClicked)
self.set_position.clicked.connect(self.onSetPositionClicked)
self.setSurfaceHeight.clicked.connect(self.onSetSurfaceHeightClicked)
self.setMoloHeight.clicked.connect(self.onSetMologramHeightClicked)
self.goToSurfaceHeight.clicked.connect(self.onGoToSurfaceHeightClicked)
self.goToMoloHeight.clicked.connect(self.onGoToMologramHeightClicked)
# Layout
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addLayout(self.mologram_pos)
hbox.addWidget(self.set_position)
vbox.addWidget(self.calibrate)
vbox.addLayout(hbox)
vbox.addWidget(self.setSurfaceHeight)
vbox.addWidget(self.setMoloHeight)
vbox.addWidget(self.goToSurfaceHeight)
vbox.addWidget(self.goToMoloHeight)
self.calibrate.resize(self.calibrate.sizeHint())
self.set_position.resize(self.set_position.sizeHint())
self.setSurfaceHeight.resize(self.setSurfaceHeight.sizeHint())
self.setMoloHeight.resize(self.setMoloHeight.sizeHint())
self.goToSurfaceHeight.resize(self.goToSurfaceHeight.sizeHint())
self.goToMoloHeight.resize(self.goToMoloHeight.sizeHint())
def initUI(self):
# algorithm names
self.algo_names = []
self.algo_names.append('sum over background plus 3 sigma')
# different types of stacks
self.stack_type_list = []
self.stack_type_list.append('time')
self.stack_type_list.append('z-position (um)')
self.stack_type_list.append('TE-position (deg)')
self.stack_type_list.append('exposure')
self.mologram_sides = ['left','right']
self.time_unit_list = ['s','min']
# declare widgets
# labels for the form
self.editFolder_lbl = QtGui.QLabel('Experiment Folder')
self.mologram_lbl = QtGui.QLabel('Move to Mologram')
self.time_int_lbl = QtGui.QLabel('Time Interval')
self.num_caps_lbl = QtGui.QLabel('Number of Captures')
self.algorithm_lbl = QtGui.QLabel('Intensity Algorithm')
self.stack_type_lbl = QtGui.QLabel('Stack Type')
self.stack_incr_lbl = QtGui.QLabel('Stack Increment (down)')
self.start_lbl = QtGui.QLabel('')
self.stop_lbl = QtGui.QLabel('')
self.pause_lbl = QtGui.QLabel('')
self.move_to_lbl = QtGui.QLabel('Enable Move to Mologram')
self.cap_laser_lbl = QtGui.QLabel('Record Laser Intensity')
self.ref_molo_lbl = QtGui.QLabel('Reference Mologram')
self.num_avg_lbl = QtGui.QLabel('Number of Avg per capture')
self.crop_image_lbl = QtGui.QLabel('')
self.update_plots_lbl = QtGui.QLabel('Update Plots')
self.adjust_exposure_lbl= QtGui.QLabel('Adjust Exposure when saturated')
# line edits and selectors
self.editFolder = QtGui.QLineEdit()
self.mologram_pos = MologramSelector()
self.time_int_sbox = QtGui.QDoubleSpinBox(value = 3)
self.stack_incr_sbox = QtGui.QDoubleSpinBox()
self.number_caps = QtGui.QSpinBox(value = 1)
self.time_units = QtGui.QComboBox()
self.algorithms = QtGui.QComboBox()
self.stack_type = QtGui.QComboBox()
self.stack_unit = QtGui.QComboBox()
self.mologram_side = QtGui.QComboBox()
self.num_avg = QtGui.QSpinBox(value = 1)
self.crop_image = QtGui.QCheckBox('Crop image to 60 x 60 um')
self.update_plots = QtGui.QCheckBox('')
self.adjust_exposure = QtGui.QCheckBox('')
for name in self.mologram_sides:
self.mologram_side.addItem(name)
for name in self.algo_names:
self.algorithms.addItem(name)
for name in self.stack_type_list:
self.stack_type.addItem(name)
for name in self.time_unit_list:
self.time_units.addItem(name)
self.set_stack_unit()
self.number_caps.setRange(0,100000)
# Create and connect buttons
self.start = QtGui.QPushButton('Start Experiment')
self.start.clicked.connect(self.start_f)
self.start.resize(self.start.sizeHint())
self.browse = QtGui.QPushButton('browse')
self.browse.clicked.connect(self.browse_f)
self.browse.resize(self.browse.sizeHint())
self.stop = QtGui.QPushButton('Stop Experiment')
self.pause = QtGui.QPushButton('Pause/Continue Experiment')
self.stack_type.activated[str].connect(self.set_stack_unit)
self.move_to_mologram_btn = QtGui.QCheckBox('Enable')
self.move_to_mologram_btn.clicked.connect(self.toggle_move_to_mologram)
self.reference_mologram = QtGui.QCheckBox('Enable')
self.reference_mologram.clicked.connect(self.toggle_reference_mologram)
self.record_laser_btn = QtGui.QCheckBox('')
#self.record_laser_btn.clicked.connect(self.toggle_capture_laser)
# layout
hbox_folder = QtGui.QHBoxLayout()
hbox_time = QtGui.QHBoxLayout()
hbox_stack = QtGui.QHBoxLayout()
hbox_mologram = QtGui.QHBoxLayout()
hbox_ref = QtGui.QHBoxLayout()
hbox_folder.addWidget(self.editFolder)
hbox_folder.addWidget(self.browse)
hbox_time.addWidget(self.time_int_sbox)
hbox_time.addWidget(self.time_units)
hbox_stack.addWidget(self.stack_incr_sbox)
hbox_stack.addWidget(self.stack_unit)
hbox_ref.addWidget(self.reference_mologram)
hbox_ref.addWidget(self.mologram_side)
hbox_mologram.addWidget(self.move_to_mologram_btn)
hbox_mologram.addLayout(self.mologram_pos)
fbox = QtGui.QFormLayout()
fbox.addRow(self.editFolder_lbl, hbox_folder)
fbox.addRow(self.mologram_lbl, hbox_mologram)
fbox.addRow(self.crop_image_lbl,self.crop_image)
fbox.addRow(self.stack_type_lbl, self.stack_type)
fbox.addRow(self.time_int_lbl, hbox_time)
fbox.addRow(self.stack_incr_lbl, hbox_stack)
fbox.addRow(self.num_caps_lbl, self.number_caps)
fbox.addRow(self.num_avg_lbl,self.num_avg)
fbox.addRow(self.ref_molo_lbl, hbox_ref)
fbox.addRow(self.algorithm_lbl, self.algorithms)
fbox.addRow(self.cap_laser_lbl, self.record_laser_btn)
fbox.addRow(self.update_plots_lbl,self.update_plots)
fbox.addRow(self.adjust_exposure_lbl,self.adjust_exposure)
fbox.addRow(self.start_lbl, self.start)
fbox.addRow(self.stop_lbl, self.stop)
fbox.addRow(self.pause_lbl, self.pause)
hbox = QtGui.QHBoxLayout()
hbox.addLayout(fbox)
self.setLayout(hbox)
class Stack(QtGui.QWidget):
def __init__(self,main_widget):
super(Stack,self).__init__()
self.counter = 0
self.database_path = ''
self.num_captures = 0
self.time_interval = 0
self.main_widget = main_widget
self.initUI()
self.crop_image.setChecked(True)
self.update_plots.setChecked(True)
self.adjust_exposure.setChecked(True)
self.toggle_move_to_mologram()
self.toggle_reference_mologram()
def initUI(self):
# algorithm names
self.algo_names = []
self.algo_names.append('sum over background plus 3 sigma')
# different types of stacks
self.stack_type_list = []
self.stack_type_list.append('time')
self.stack_type_list.append('z-position (um)')
self.stack_type_list.append('TE-position (deg)')
self.stack_type_list.append('exposure')
self.mologram_sides = ['left','right']
self.time_unit_list = ['s','min']
# declare widgets
# labels for the form
self.editFolder_lbl = QtGui.QLabel('Experiment Folder')
self.mologram_lbl = QtGui.QLabel('Move to Mologram')
self.time_int_lbl = QtGui.QLabel('Time Interval')
self.num_caps_lbl = QtGui.QLabel('Number of Captures')
self.algorithm_lbl = QtGui.QLabel('Intensity Algorithm')
self.stack_type_lbl = QtGui.QLabel('Stack Type')
self.stack_incr_lbl = QtGui.QLabel('Stack Increment (down)')
self.start_lbl = QtGui.QLabel('')
self.stop_lbl = QtGui.QLabel('')
self.pause_lbl = QtGui.QLabel('')
self.move_to_lbl = QtGui.QLabel('Enable Move to Mologram')
self.cap_laser_lbl = QtGui.QLabel('Record Laser Intensity')
self.ref_molo_lbl = QtGui.QLabel('Reference Mologram')
self.num_avg_lbl = QtGui.QLabel('Number of Avg per capture')
self.crop_image_lbl = QtGui.QLabel('')
self.update_plots_lbl = QtGui.QLabel('Update Plots')
self.adjust_exposure_lbl= QtGui.QLabel('Adjust Exposure when saturated')
# line edits and selectors
self.editFolder = QtGui.QLineEdit()
self.mologram_pos = MologramSelector()
self.time_int_sbox = QtGui.QDoubleSpinBox(value = 3)
self.stack_incr_sbox = QtGui.QDoubleSpinBox()
self.number_caps = QtGui.QSpinBox(value = 1)
self.time_units = QtGui.QComboBox()
self.algorithms = QtGui.QComboBox()
self.stack_type = QtGui.QComboBox()
self.stack_unit = QtGui.QComboBox()
self.mologram_side = QtGui.QComboBox()
self.num_avg = QtGui.QSpinBox(value = 1)
self.crop_image = QtGui.QCheckBox('Crop image to 60 x 60 um')
self.update_plots = QtGui.QCheckBox('')
self.adjust_exposure = QtGui.QCheckBox('')
for name in self.mologram_sides:
self.mologram_side.addItem(name)
for name in self.algo_names:
self.algorithms.addItem(name)
for name in self.stack_type_list:
self.stack_type.addItem(name)
for name in self.time_unit_list:
self.time_units.addItem(name)
self.set_stack_unit()
self.number_caps.setRange(0,100000)
# Create and connect buttons
self.start = QtGui.QPushButton('Start Experiment')
self.start.clicked.connect(self.start_f)
self.start.resize(self.start.sizeHint())
self.browse = QtGui.QPushButton('browse')
self.browse.clicked.connect(self.browse_f)
self.browse.resize(self.browse.sizeHint())
self.stop = QtGui.QPushButton('Stop Experiment')
self.pause = QtGui.QPushButton('Pause/Continue Experiment')
self.stack_type.activated[str].connect(self.set_stack_unit)
self.move_to_mologram_btn = QtGui.QCheckBox('Enable')
self.move_to_mologram_btn.clicked.connect(self.toggle_move_to_mologram)
self.reference_mologram = QtGui.QCheckBox('Enable')
self.reference_mologram.clicked.connect(self.toggle_reference_mologram)
self.record_laser_btn = QtGui.QCheckBox('')
#self.record_laser_btn.clicked.connect(self.toggle_capture_laser)
# layout
hbox_folder = QtGui.QHBoxLayout()
hbox_time = QtGui.QHBoxLayout()
hbox_stack = QtGui.QHBoxLayout()
hbox_mologram = QtGui.QHBoxLayout()
hbox_ref = QtGui.QHBoxLayout()
hbox_folder.addWidget(self.editFolder)
hbox_folder.addWidget(self.browse)
hbox_time.addWidget(self.time_int_sbox)
hbox_time.addWidget(self.time_units)
hbox_stack.addWidget(self.stack_incr_sbox)
hbox_stack.addWidget(self.stack_unit)
hbox_ref.addWidget(self.reference_mologram)
hbox_ref.addWidget(self.mologram_side)
hbox_mologram.addWidget(self.move_to_mologram_btn)
hbox_mologram.addLayout(self.mologram_pos)
fbox = QtGui.QFormLayout()
fbox.addRow(self.editFolder_lbl, hbox_folder)
fbox.addRow(self.mologram_lbl, hbox_mologram)
fbox.addRow(self.crop_image_lbl,self.crop_image)
fbox.addRow(self.stack_type_lbl, self.stack_type)
fbox.addRow(self.time_int_lbl, hbox_time)
fbox.addRow(self.stack_incr_lbl, hbox_stack)
fbox.addRow(self.num_caps_lbl, self.number_caps)
fbox.addRow(self.num_avg_lbl,self.num_avg)
fbox.addRow(self.ref_molo_lbl, hbox_ref)
fbox.addRow(self.algorithm_lbl, self.algorithms)
fbox.addRow(self.cap_laser_lbl, self.record_laser_btn)
fbox.addRow(self.update_plots_lbl,self.update_plots)
fbox.addRow(self.adjust_exposure_lbl,self.adjust_exposure)
fbox.addRow(self.start_lbl, self.start)
fbox.addRow(self.stop_lbl, self.stop)
fbox.addRow(self.pause_lbl, self.pause)
hbox = QtGui.QHBoxLayout()
hbox.addLayout(fbox)
self.setLayout(hbox)
def set_stack_unit(self,str = None):
""" Depending on the current stack type, set the right units for the stack units
QComboBox. Also disables and enables other widgets in the stack selector box."""
curr_stack_type = self.stack_type.currentText()
self.stack_unit.setEnabled(True)
self.stack_incr_sbox.setEnabled(True)
self.stack_unit.clear()
if curr_stack_type == self.stack_type_list[1]:
self.num_avg.setEnabled(True)
else:
self.num_avg.setEnabled(False)
if curr_stack_type == self.stack_type_list[0]:
self.stack_unit.setEnabled(False)
self.stack_incr_sbox.setEnabled(False)
return
elif curr_stack_type == self.stack_type_list[1]:
units_list = ['um']
elif curr_stack_type == self.stack_type_list[2]:
units_list = ['deg']
elif curr_stack_type == self.stack_type_list[3]:
units_list = ['ms']
for unit in units_list:
self.stack_unit.addItem(unit)
def fetch_mologram_data(self,database_path = None):
""" Fetch all the rows in the SQL database for the given path and return all of the data as a numpy array """
# Check if datapase path was passed
if database_path == None:
database_path = self.database_path
if database_path == '':
return None
# Connect to database
con = sqlite3.connect(database_path + '/mologram_data.db')
cur = con.cursor()
# fetch all rows from database
rows = []
for row in cur.execute('SELECT * FROM mologram_data ORDER BY key'):
rows.append(row)
# Close connection with SQL databse
con.close()
# extract data
rows = np.array(rows)
print(rows.shape)
print(type(rows))
time = rows[:,1]
intensity = rows[:,7]
return time,intensity
def confirm_user_input(self,experiment_folder_path,num_captures):
# Test for incorrect user input
if experiment_folder_path == '':
msg = QtGui.QMessageBox()
msg.setWindowTitle("Folder name")
msg.setIcon(QtGui.QMessageBox.Warning)
msg.setStandardButtons(QtGui.QMessageBox.Ok)
msg.setText("Please select a valid experiment folder")
msg.exec_()
return -1
if num_captures == 0:
msg = QtGui.QMessageBox()
msg.setWindowTitle("Experiment Length")
msg.setIcon(QtGui.QMessageBox.Warning)
msg.setStandardButtons(QtGui.QMessageBox.Ok)
msg.setText("Please a valib experiment length")
msg.exec_()
return -1
# Clear existing data in selected directory and create necessary directories
if os.listdir(experiment_folder_path) != []:
msg = QtGui.QMessageBox()
msg.setWindowTitle("Question")
msg.setIcon(QtGui.QMessageBox.Warning)
msg.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
msg.setText("Are you sure you want to delete the existing data?")
retval = msg.exec_()
if retval == QtGui.QMessageBox.No:
return -1
# Clear previous results
os.system('sudo rm -rf ' + experiment_folder_path + '/*')
return 0
""" Fetch all parameters for experiment from GUI and launch the experiment in a seperate thread """
def start_f(self):
# Determine where to store results
experiment_folder_path = self.editFolder.text()
image_path = experiment_folder_path + '/images'
self.database_path = experiment_folder_path + '/database'
# Confirm user input and delete experiment information if it is already there.
if self.confirm_user_input(experiment_folder_path,self.number_caps.value()) == -1:
return
self.main_widget.set_experiment_folder_path(experiment_folder_path)
# Create directories if non-existent
directories = [experiment_folder_path,image_path,self.database_path]
for directory in directories:
if not os.path.exists(directory):
os.makedirs(directory)
# Thread for recording the Experiment
self.experiment = Experiment(self.main_widget,self.database_path)
self.connect(
self.experiment,
QtCore.SIGNAL("database_updated"),
self.main_widget.updateAllStack
)
self.connect(
self.experiment,
QtCore.SIGNAL("done_experiment"),
self.done_experiment
)
self.stop.clicked.connect(self.experiment.stop)
self.pause.clicked.connect(self.experiment.pause)
try:
self.main_widget.plotTab.set_current_plot('time_stack')
except Exception:
pass
# Adjust time_interval depending on time unit
if self.time_units.currentText() == 'ms':
time_interval /= 1000
elif self.time_units.currentText() == 'min':
time_interval *= 60
elif self.time_units.currentText() == 's':
pass
# If user wished so, move to mologram automatically
if self.move_to_mologram_btn.isChecked():
position = self.mologram_pos.position()
print('Moving to mologram ' + position)
self.main_widget.setup.chip.move_to(position)
# Create file with experiment parameters for easier analysis later on
self.create_info_file()
# Start experiment
self.experiment.record_data(
image_path = image_path,
database_path = self.database_path,
num_captures = self.number_caps.value(),
num_avg = self.num_avg.value(),
time_interval = self.time_int_sbox.value(),
stack_type = self.stack_type.currentText(),
stack_incr = self.stack_incr_sbox.value(),
stack_type_list = self.stack_type_list,
current_algo = self.algorithms.currentText(),
algo_names = self.algo_names,
record_laser = self.record_laser_btn.isChecked(),
reference_mologram = self.reference_mologram.isChecked(),
mologram_side = self.mologram_side.currentText(),
crop_image = self.crop_image.isChecked(),
update_plots = self.update_plots.isChecked(),
adjust_exposure = self.adjust_exposure.isChecked())
""" Create file with experiment parameters for easier analysis later on """
def create_info_file(self):
info = dict({})
# Add all parameters to a dictionary
info['Experiment Folder'] = self.database_path
info['Number of Captures'] = self.number_caps.value()
info['Time Interval'] = self.time_int_sbox.value()
info['Number of Averages'] = self.num_avg.value()
info['Stack Type'] = self.stack_type.currentText()
info['Stack Increment'] = self.stack_incr_sbox.value()
info['Recorded Algorithms'] = self.algorithms.currentText()
info['Record Laser'] = self.record_laser_btn.isChecked()
info['Mologram Name'] = self.main_widget.setup.chip.file_name()
info['Reference Mologram'] = self.reference_mologram.isChecked()
info['Mologram Side'] = self.mologram_side.currentText()
# Store dictionary as JSON data in an info file
file = open(self.editFolder.text() + '/experiment.info','w')
json.dump(info,file)
file.close()
""" Once experiment is done or if it stopped unexpectedly, show appropriate message box and update GUI """
def done_experiment(self):
# Indicate experiment is complete
msg = QtGui.QMessageBox()
msg.setWindowTitle("Experiment")
msg.setIcon(QtGui.QMessageBox.Information)
msg.setStandardButtons(QtGui.QMessageBox.Ok)
msg.setText("Experiment is complete")
msg.exec_()
# Update all displays
self.main_widget.updateAll()
def browse_f(self):
folder = QtGui.QFileDialog.getExistingDirectory(self, 'Open file', '/home')
self.editFolder.setText(folder)
def toggle_move_to_mologram(self):
self.mologram_pos.setEnabled(self.move_to_mologram_btn.isChecked())
def toggle_reference_mologram(self):
self.mologram_side.setEnabled(self.reference_mologram.isChecked())
class CalibrationTab(QtGui.QWidget):
def __init__(self,main_widget):
super(CalibrationTab,self).__init__()
self.main_widget = main_widget
self.heights = self.read_heights()
self.initUI()
def initUI(self):
# Define buttons
self.calibrate = QtGui.QPushButton('Calibrate')
self.set_position = QtGui.QPushButton('Set Position')
self.setSurfaceHeight = QtGui.QPushButton('Set Surface Height')
self.setMoloHeight = QtGui.QPushButton('Set Mologram Height')
self.goToSurfaceHeight = QtGui.QPushButton('Go To Surface Height')
self.goToMoloHeight = QtGui.QPushButton('Go To Mologram Height')
self.mologram_pos = MologramSelector()
# connect buttons
self.calibrate.clicked.connect(self.onCalibrateClicked)
self.set_position.clicked.connect(self.onSetPositionClicked)
self.setSurfaceHeight.clicked.connect(self.onSetSurfaceHeightClicked)
self.setMoloHeight.clicked.connect(self.onSetMologramHeightClicked)
self.goToSurfaceHeight.clicked.connect(self.onGoToSurfaceHeightClicked)
self.goToMoloHeight.clicked.connect(self.onGoToMologramHeightClicked)
# Layout
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addLayout(self.mologram_pos)
hbox.addWidget(self.set_position)
vbox.addWidget(self.calibrate)
vbox.addLayout(hbox)
vbox.addWidget(self.setSurfaceHeight)
vbox.addWidget(self.setMoloHeight)
vbox.addWidget(self.goToSurfaceHeight)
vbox.addWidget(self.goToMoloHeight)
self.calibrate.resize(self.calibrate.sizeHint())
self.set_position.resize(self.set_position.sizeHint())
self.setSurfaceHeight.resize(self.setSurfaceHeight.sizeHint())
self.setMoloHeight.resize(self.setMoloHeight.sizeHint())
self.goToSurfaceHeight.resize(self.goToSurfaceHeight.sizeHint())
self.goToMoloHeight.resize(self.goToMoloHeight.sizeHint())
def onCalibrateClicked(self):
self.main_widget.calib()
def onSetPositionClicked(self):
pos = self.mologram_pos.position()
x,y = self.main_widget.setup.chip.cartesian_position(pos)
self.main_widget.setup.motors.x.set_position(x,'mm')
self.main_widget.setup.motors.y.set_position(y,'mm')
# update position and images
self.main_widget.updateAll()
def write_heights(self,heights):
file = open('heights.txt','w')
json.dump(heights,file)
file.close()
def read_heights(self):
file = open('heights.txt','r')
heights = json.load(file)
file.close()
return heights
def onSetSurfaceHeightClicked(self):
self.heights["surface_height"] = self.main_widget.setup.motors.z.pos('mm')
self.write_heights(self.heights)
def onGoToSurfaceHeightClicked(self):
self.main_widget.axisControl.z.start_moving(
distance = self.heights["surface_height"],
unit = 'mm',
relative = False
)
def onSetMologramHeightClicked(self):
self.heights["mologram_height"] = self.main_widget.setup.motors.z.pos('mm')
self.write_heights(self.heights)
def onGoToMologramHeightClicked(self):
self.main_widget.axisControl.z.start_moving(
distance = self.heights["mologram_height"],
unit = 'mm',
relative = False
)
