def __init__(self):
super().__init__(self)
self.options = self.main_menu_options
self.system = CESystem()
self.auto_run = AutomatedControl.AutoRun(self.system)
self.auto_run.path_information.add_callback(print)
self.view = None # type: tkinter.Tk
self.menu = None
self.ce_display = None
# Define Submenus
self.system_menu = SystemMenu(self, self)
self.config_menu = ConfigMenu(self, self)
def __init__(self, system: CESystem()):
"""
Creates and AutoRun object that groups templates and methods together and coordinates the actions on a
CE system object so that an automated run can take place.
:param system: CE system object that will be automated
"""
self.system = system # L3 CE Systems object
self.style = 'CE'
self.methods = []
self.gate = GateSpecial()
self.repetitions = 1
self.repetition_style = 'method'
self._queue = Queue()
self.is_running = threading.Event()
self.continue_event = threading.Event()
self.continue_callbacks = {}
self.simple_wait_callbacks = []
self.traced_thread = Util.TracedThread()
self.traced_thread.name = 'AutoRun'
self.data_dir = get_system_var('data_dir')[0]
self.safe_enabled = False
self.template = None
self.template: Template
self.path_information = PathTrace()
self.last_path = None
#of_x = FileIO.get_system_var('offset_x')
#of_y = FileIO.get_system_var('offset_y')
self.offset = (0, 0)
else:
extra_t = xcalc / vmax
extra_v = np.linspace(vmax, vmax, int(round(extra_t * 1000)))
v_profile = velocity.copy()
v_profile = np.concatenate((v_profile, extra_v))
if extra:
extra_a = np.zeros(int(round(extra_t * 1000)))
accel = np.concatenate((accel, extra_a, -accel))
v_profile = np.concatenate((v_profile, np.flip(velocity)))
x = np.zeros(len(v_profile))
for i, v in enumerate(v_profile):
x[i] = np.trapz(v_profile[:i])
if extra:
return x / 1000, v_profile, accel
return x / 1000
if __name__ == "__main__":
logger = logging.getLogger()
logger.setLevel(logging.INFO)
system = CESystem()
system.load_config()
system.open_controllers()
tm = AutomatedControl.Template()
xyz0 = [20, 20, 3]
xyz1 = [100, 35, 10]
path = SafeMove(system, tm, xyz0, xyz1, visual=True).move()
def __init__(self, system: CESystem()):
super().__init__(system)
self.style = 'CHIP'
:param lower_y:
:param right_x:
:param upper_y:
:return:
"""
self.dimensions = [left_x, lower_y, right_x, upper_y]
class AutoSpecial:
pass
if __name__ == "__main__":
import matplotlib.pyplot as plt
import numpy as np
import logging
import os
os.chdir(os.path.abspath('..'))
logger = logging.getLogger()
logger.setLevel(logging.INFO)
system = CESystem()
system.load_config(
config_file=r'E:\Scripts\AutomatedCE\config\TestChip.cfg')
system.open_controllers()
auto = ChipRun(system)
auto.add_method(r'E:\Scripts\AutomatedCE\config\methods-chep.txt')
# auto.set_template()
auto.repetitions = 2
# auto.start_run()
class MainMenu(mui.Menu):
main_menu_options = """
CE Main Menu:
1. System Menu
2. Config Menu
3. Start Run
4. Stop CE
5. Simulate Run
"""
def __init__(self):
super().__init__(self)
self.options = self.main_menu_options
self.system = CESystem()
self.auto_run = AutomatedControl.AutoRun(self.system)
self.auto_run.path_information.add_callback(print)
self.view = None # type: tkinter.Tk
self.menu = None
self.ce_display = None
# Define Submenus
self.system_menu = SystemMenu(self, self)
self.config_menu = ConfigMenu(self, self)
def setup(self):
# Assign Callbacks
self.auto_run.continue_callbacks[
'manual_cell'] = lambda msg: messagebox.askokcancel(
"Manual Cell Lysis and Loading", msg)
self.menu = ManualCellPopup(self.view, None, None, True, self.auto_run,
self.system)
self.auto_run.continue_callbacks[
'manual_cell'] = lambda message, step, simulation: self.menu.update_step(
message, step, simulation)
self.menu.top.withdraw()
def interpret(self, text: str):
"""
Interprets the Main menu options
:param text: string identifier for the method
:return: new menu to be loaded
:rtype: mui.Menu
"""
if text == "1":
return self.system_menu
elif text == "2":
return self.config_menu
elif text == "3":
self.ce_display = DisplayWindows.TkCEDisplay(
self.system, self.view)
self.ce_display.start_live_view()
self.auto_run.start_run()
elif text == "4":
self.system.stop_ce()
self.auto_run.stop_run()
elif text == "5":
self.auto_run.start_run(simulated=True)
return self
:param args:
:return: list of artists for animation function
"""
data = self.system.detector.get_data()
power_data = self.system.high_voltage.get_data()
ax1, ax2 = self.plot_axes[0:2]
try:
ax1.set_xlim(min(data['time_data']), max(data['time_data']))
ax1.set_ylim(min(data['rfu']) * 0.95, max(data['rfu'] * 1.05))
# ax2.set_ylim(min(power_data['current'])*0.95, max(power_data['current'])*1.05)
except ValueError:
logging.warning("No data to plot")
return self._artists
self._artists[0].set_data(data['time_data'], data['rfu'])
self._artists[1].set_data(power_data['time_data'],
power_data['current'])
return self._artists
if __name__ == "__main__":
import sys
import os
os.chdir(os.path.abspath('..'))
sys = CESystem()
sys.load_config(config_file=r'E:\Scripts\AutomatedCE\config\TestChip.cfg')
sys.open_controllers()
sys.startup_utilities()
c = sys.camera
wn = PLTMicroscopeDisplay(sys)