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__init__.py
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__init__.py
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import sys
from PyQt5.QtWidgets import QApplication, QWidget, QLabel, QVBoxLayout, QHBoxLayout, QSlider, QPushButton, QLineEdit, QCheckBox, QFrame, QGridLayout
from PyQt5.QtGui import QPixmap, QImage, QIntValidator
from PyQt5.QtCore import Qt, QTimer
import MCM300 as mc
import threading
import serial
import time
from optotune_lens import Lens
from pycromanager import Acquisition, multi_d_acquisition_events, Core
default_um_btn_move = 10
class MicroscopeControlGUI(QWidget):
def __init__(self):
super().__init__()
#Init the stage
self.controller_mcm = mc.Controller(which_port='COM4',
stages=('ZFM2020', 'ZFM2020', 'ZFM2020'),
reverse=(False, False, False),
verbose=True,
very_verbose=False)
#set all the counters for the stage in 0
for channel in range(3):
self.controller_mcm._set_encoder_counts_to_zero(channel)
# Init the optotune lens
self.lens = Lens('COM5', debug=False)
print(self.lens.firmware_type)
print(self.lens.firmware_version)
print(self.lens.get_firmware_branch())
print('Lens serial number:', self.lens.lens_serial)
print('Lens temperature:', self.lens.get_temperature())
self.lens.to_current_mode()
# Check if umanager is open
try:
self.core = Core()
print(self.core)
print("micromanager connection established succesfully!")
except:
print("Did you open uManager with the proper configuration?")
return -1
# Init arduino serial communication
self.arduino = serial.Serial(port="COM6", baudrate=115200, timeout=1)
self.initUI()
def initUI(self):
self.setWindowTitle('LSM Control')
self.label_joystick = QLabel('10 um steps for sample stage')
# Create buttons for X, Y, Z control
self.create_control_buttons()
# Sliders for velocity and position
x_layout, self.x_slider, self.x_text = self.create_slider_with_text('X Position (um)', -10000, 10000, 0, self.move_stage, channel=0)
y_layout, self.y_slider, self.y_text = self.create_slider_with_text('Y Position (um)', -10000, 10000, 0, self.move_stage, channel=1)
z_layout, self.z_slider, self.z_text = self.create_slider_with_text('Z Position (um)', -10000, 10000, 0, self.move_stage, channel=2)
# Slider for current value
current_layout, self.current_slider, self.current_text = self.create_slider_with_text('Current', -300, 300, 0, self.change_optotune_current)
# Sliders for motor frequency and amplitude
acceleration_layout, self.acceleration_slider, self.acceleration_text = self.create_slider_with_text('Acceleration', 1000, 15000, 5000, self.send_acc_serial_command)
amplitude_layout, self.amplitude_slider, self.amplitude_text = self.create_slider_with_text('Amplitude', 20, 100, 100, self.send_width_serial_command)
# Button for stop and start stepper motor operation
self.stop_stepper_motor_btn = QPushButton("Stop stepper motor")
self.stop_stepper_motor_btn.clicked.connect(lambda: self.send_command_arduino("h?"))
self.start_stepper_motor_btn = QPushButton("Start stepper motor")
self.start_stepper_motor_btn.clicked.connect(lambda: self.send_command_arduino("s?"))
# Create a layout for the previous buttons
light_house_layout = QGridLayout()
light_house_layout.addWidget(self.stop_stepper_motor_btn, 0, 0)
light_house_layout.addWidget(self.start_stepper_motor_btn, 0, 1)
# Z max and min position and z step
self.z_max_label = QLabel('Z-Max')
self.z_max_btn = QPushButton('Set Z-Max')
self.z_max_btn.clicked.connect(lambda: self.set_z_position('max'))
self.z_min_label = QLabel('Z-Min')
self.z_min_btn = QPushButton('Set Z-Min')
self.z_min_btn.clicked.connect(lambda: self.set_z_position('min'))
self.z_step_label = QLabel('Z-Step')
self.z_step_text = QLineEdit('10')
self.z_step_text.setValidator(QIntValidator(1, 500))
self.z_step_text.setFixedWidth(50)
self.z_step_text.setAlignment(Qt.AlignCenter)
# Button for start acquisition
self.start_acquisition_btn = QPushButton("Start Acquisition")
self.start_acquisition_btn.clicked.connect(self.start_acquisition)
# Stop acquisition
self.stop_acquisition_btn = QPushButton("Stop Acquisition")
self.stop_acquisition_btn.clicked.connect(self.stop_acquisition)
# Main layout setup
main_layout = QVBoxLayout()
# Joystick and Z control layout
joystick_z_layout = QHBoxLayout()
joystick_z_layout.addLayout(self.joystick_layout)
main_layout.addWidget(self.label_joystick)
main_layout.addLayout(joystick_z_layout)
# Add other components below the joystick and Z controls
main_layout.addLayout(x_layout)
main_layout.addLayout(y_layout)
main_layout.addLayout(z_layout)
main_layout.addLayout(current_layout)
main_layout.addLayout(acceleration_layout)
main_layout.addLayout(amplitude_layout)
main_layout.addLayout(light_house_layout)
# Z position buttons and step layout
z_pos_layout = QHBoxLayout()
z_pos_layout.addWidget(self.z_max_label)
z_pos_layout.addWidget(self.z_max_btn)
z_pos_layout.addWidget(self.z_min_label)
z_pos_layout.addWidget(self.z_min_btn)
z_pos_layout.addWidget(self.z_step_label)
z_pos_layout.addWidget(self.z_step_text)
main_layout.addLayout(z_pos_layout)
main_layout.addWidget(self.start_acquisition_btn)
main_layout.addWidget(self.stop_acquisition_btn)
self.setLayout(main_layout)
self.show()
def closeEvent(self, event):
# This method is called when the window is closed
self.send_command_arduino("h?") # to stop the stepper motor
self.arduino.close()
self.controller_mcm.close()
event.accept()
def create_slider_with_text(self, label, min_val, max_val, default_val, callback, channel=None):
slider = QSlider(Qt.Horizontal)
slider.setMinimum(min_val)
slider.setMaximum(max_val)
slider.setValue(default_val)
slider.setTickPosition(QSlider.TicksBelow)
text_box = QLineEdit(str(default_val))
text_box.setFixedWidth(40)
text_box.setAlignment(Qt.AlignCenter)
hbox = QHBoxLayout()
hbox.addWidget(QLabel(label))
hbox.addWidget(slider)
hbox.addWidget(text_box)
# Update textbox and slider values if one of them changed
slider.valueChanged.connect(lambda value, text_box=text_box: self.update_text_box_from_slider(value, text_box))
text_box.textChanged.connect(lambda text, slider=slider, min_val=min_val, max_val=max_val: self.update_slider_from_text_box(text, slider, min_val, max_val))
# Move the stage only when the slider is released or after pressing enter in the textbox (more safe)
if channel is not None:
slider.sliderReleased.connect(lambda: callback(channel, slider.value()))
text_box.editingFinished.connect(lambda: callback(channel, slider.value()))
else:
# General callback function
slider.sliderReleased.connect(lambda: callback(slider.value()))
text_box.editingFinished.connect(lambda: callback(slider.value()))
return hbox, slider, text_box
def change_optotune_current(self,value):
thread = threading.Thread(target=self.lens.set_current, args=([value]))
thread.start()
def send_acc_serial_command(self,value):
command = "a?"+str(value)
self.arduino.write(bytes(command, 'utf-8'))
time.sleep(0.5)
def send_width_serial_command(self,value):
command = "w?"+str(value)
self.arduino.write(bytes(command, 'utf-8'))
time.sleep(0.5)
def update_text_box_from_slider(self, value, text_box):
text_box.setText(str(value))
def update_slider_from_text_box(self, text, slider, min_val, max_val):
try:
value = int(text)
if value < min_val:
value = min_val
elif value > max_val:
value = max_val
slider.setValue(value)
except ValueError:
pass
# Update slider and text values from the joystick btns
def update_ui_elements(self, channel, value):
if channel == 0:
new_value = value + int(self.x_text.text())
self.x_text.setText(str(new_value))
self.x_slider.setValue(new_value)
elif channel == 1:
new_value = value + int(self.y_text.text())
self.y_text.setText(str(new_value))
self.y_slider.setValue(new_value)
elif channel == 2:
new_value = value + int(self.z_text.text())
self.z_text.setText(str(new_value))
self.z_slider.setValue(new_value)
def create_control_buttons(self):
self.joystick_layout = QGridLayout()
# X and Y control buttons
up_button = QPushButton('X↑')
up_button.clicked.connect(lambda: self.move_stage_2(0, 1))
down_button = QPushButton('X↓')
down_button.clicked.connect(lambda: self.move_stage_2(0, -1))
left_button = QPushButton('←Y')
left_button.clicked.connect(lambda: self.move_stage_2(1, -1))
right_button = QPushButton('Y→')
right_button.clicked.connect(lambda: self.move_stage_2(1, 1))
# Arrange the joystick buttons
self.joystick_layout.addWidget(up_button, 0, 1)
self.joystick_layout.addWidget(left_button, 1, 0)
self.joystick_layout.addWidget(right_button, 1, 2)
self.joystick_layout.addWidget(down_button, 2, 1)
# Z control buttons
z_up_button = QPushButton('Z↑')
z_up_button.clicked.connect(lambda: self.move_stage_2(2, 1))
z_down_button = QPushButton('Z↓')
z_down_button.clicked.connect(lambda: self.move_stage_2(2, -1))
# Arrange the Z buttons
self.joystick_layout.addWidget(z_up_button,0,3)
self.joystick_layout.addWidget(z_down_button,2,3)
def move_stage(self, channel, value):
thread = threading.Thread(target=self.controller_mcm.move_um, args=(channel, value, False))
thread.start()
def move_stage_2(self, channel, direction):
move_value = default_um_btn_move * direction
thread = threading.Thread(target=self.controller_mcm.move_um, args=(channel, default_um_btn_move*direction, True))
thread.start()
self.update_ui_elements(channel, move_value)
def send_command_arduino(self,command):
self.arduino.write(bytes(command, 'utf-8'))
time.sleep(0.5)
def set_z_position(self, position_type):
current_z_position = self.z_slider.value()
if position_type == 'max':
self.z_max_label.setText(f'Z-Max: {current_z_position}')
elif position_type == 'min':
self.z_min_label.setText(f'Z-Min: {current_z_position}')
def start_acquisition(self):
try:
z_min = int(self.z_min_label.text().split(": ")[1])
z_max = int(self.z_max_label.text().split(": ")[1])
z_step = int(self.z_step_text.text())
except ValueError:
print("Invalid Z values or Z step")
return
self.acquisition_running = True # Set the running flag to True
self.send_command_arduino("s?") # Start stepper motor
def move_z():
for z in range(z_min, z_max+z_step, z_step):
if not self.acquisition_running:
break
self.move_stage(2, z)
if not z == z_min:
self.update_ui_elements(2, z_step) # do not add a delta the first time
time.sleep(1) # Wait for 1 second
self.send_command_arduino("h?") # Stop stepper motor
self.acquisition_thread = threading.Thread(target=move_z)
self.acquisition_thread.start()
def stop_acquisition(self):
self.acquisition_running = False
self.send_command_arduino("h?") # Stop stepper motor
if __name__ == '__main__':
app = QApplication(sys.argv)
window = MicroscopeControlGUI()
sys.exit(app.exec_())