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SemiManualCollection.py
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SemiManualCollection.py
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"""
Created on Mon May 13 17:46:12 2024
@author: hemesath
"""
import os
import json
from pipython import GCSDevice
from pipython.pitools import waitonwalk
from leicame import LeicaMicrotomeController
import serial
import time
from time import sleep
from Wafer_sim import square
from debug_joystick import move_joystick
import time
from pipython import GCSDevice
from pipython.pitools import waitonwalk
from time import sleep
import pygame
from cap import ncdt6500_get_data, ncdt6500_decode
import ne1000
class SemiManualCollection:
def __init__(self):
self.AXES = ['1', '2', '3', '4']
self.internal_water_level_control = True
self.manual_water_refill = False
self.auto_loop = False
self.interrupt = True
if self.internal_water_level_control:
self.TCP_ADDRESS = '169.254.168.150'
self.PORT = 'COM5'
self.ADDRESS = 1
self.DIA = 38
self.dev = ne1000.Ne1000Serial(self.PORT)
self.volume = ne1000.Ne1000Volume(2, 'ml')
self.rate = ne1000.Ne1000Rate(10, 'MM')
self.pump = ne1000.Ne1000(self.dev, self.ADDRESS)
self.pump.diameter_mm(self.DIA)
self.pump.volume(self.volume)
self.pump.rate(self.rate)
self.pump.direction_infuse()
pygame.init()
pygame.joystick.init()
self.joystick = pygame.joystick.Joystick(0)
self.joystick.init()
pygame.event.get()
# Create an instance of the controller
self.mycon = LeicaMicrotomeController()
# Get Part ID
print("Getting Part ID...")
part_id = self.mycon.get_part_id()
print("Setting cutting thickness to 500 nm...")
self.td = 500
self.set_cutting_thickness()
print("Setting cutting speed to 0.8mm/s...")
self.sd = 800
#Set stage positions
if os.path.isfile('stage_posS.json'):
with open('stage_posS.json', 'r') as f:
self.stage_posS = json.load(f)
else:
self.stage_posS['start_pos'] = [132, 91, 120, 140]
self.stage_posS['pickup_pos_xy'] = [132, 91]
self.stage_posS['pickup_pos_z'] = 122
self.stage_posS['dropoff_pos_xy'] = [70, 91]
self.stage_posS['dropoff_pos_z'] = 120
self.main_menu()
def main_menu(self):
print('\n\n######################\n\nMain Menu\n\n######################\n\n')
print('1) Start collection with Robot\n')
print('2) Change cutting thickness\n')
print('3) Change cutting speed\n')
print('4) Change wafer position\n')
c = input('\nChoose an option:\n')
if c == '1':
self.robot_collection()
elif c == '2':
try:
td = input('\nEnter cutting thickness in nm:\n')
self.td = int(td)
self.set_cutting_thickness()
except ValueError:
print('An error occurred: Cutting thickness could not be changed')
input()
self.main_menu()
elif c == '3':
try:
sd = input('\nEnter cutting cutting speed in um/s:\n')
self.sd = int(sd)
self.set_cutting_speed()
except ValueError:
print('An error occurred: Cutting speed could not be changed')
input()
self.main_menu()
elif c == '4':
try:
sp = input('\nEnter position of wafer stage in mm:\n')
#self.stage_pos[3] = int(sp)
except ValueError:
print('An error occurred: Wafer position could not be changed')
input()
self.main_menu()
def set_cutting_thickness(self):
th = hex(self.td).split('x')[-1]
th1 = '0000' + th
self.mycon.set_feedrate(th1[-4:])
thickness = self.mycon.get_feedrate() # Get current thickness
print(f"Current cutting thickness: {int(thickness[7:11], 16)}nm")
def set_cutting_speed(self):
sh = hex(self.sd).split('x')[-1]
sh1 = '0000' + sh
self.mycon.set_cutting_speed(sh1[-4:])
speed = self.mycon.get_cutting_speed() # Get current speed
print(f"Current cutting speed: {int(speed[7:11], 16)}um/s")
def robot_collection(self):
with GCSDevice() as pidevice:
if self.internal_water_level_control:
if not self.manual_water_refill:
self.calibrate_cap_sensor()
pidevice.ConnectUSB(serialnum="120060503")
print('connected: {:s}'.format(pidevice.qIDN().strip()))
pidevice.VEL(1, 20)
pidevice.VEL(2, 20)
pidevice.VEL(3, 20)
pidevice.VEL(4, 20)
pidevice.MOV(1, self.stage_posS['start_pos'][0])
pidevice.MOV(2, self.stage_posS['start_pos'][1])
pidevice.MOV(3, self.stage_posS['start_pos'][2])
pidevice.MOV(4, self.stage_posS['start_pos'][3])
while True:
##### Cut the slice
print("Turn motor on...")
motor_on = self.mycon.cutting_motor_on()
motor_status = self.mycon.cutting_motor_status()
if motor_status[7:9] == b'01':
print("it's on")
elif motor_status[7:9] == b'00':
print("it's off")
break
elif motor_status[7:9] == b'E0':
print("invalid callabration")
break
else:
print("invalid response")
break
cut_finished = False
was_in_cutting_window = False
while not cut_finished:
current_state = self.mycon.get_handwheel_position()[7:9]
# print(time.time())
print(current_state)
if current_state == b"03":
was_in_cutting_window = True
elif current_state == b"00" and was_in_cutting_window:
cut_finished = True
print("cut finished")
break
# continue
# time.sleep(0.1)
print("Turn motor off...")
motor_off = self.mycon.cutting_motor_off()
motor_status = self.mycon.cutting_motor_status()
if motor_status[7:9] == b'01':
print("it's on")
break
elif motor_status[7:9] == b'00':
print("it's off")
elif motor_status[7:9] == b'E0':
print("invalid callabration")
break
else:
print("invalid response")
break
if self.internal_water_level_control:
if not self.manual_water_refill:
self.water_level_control()
# Adjust pickup point
if self.auto_loop:
self.check_events()
if self.interrupt:
self.stage_posS['pickup_pos_xy'][0], self.stage_posS['pickup_pos_xy'][1], temp_pos_z, end_collection = move_joystick(
pidevice, self.joystick, self.pump)
self.interrupt = False
else:
self.stage_posS['pickup_pos_xy'][0], self.stage_posS['pickup_pos_xy'][1], temp_pos_z, end_collection = move_joystick(pidevice, self.joystick, self.pump)
if end_collection:
print('remove the wafer')
_, _, _, _ = move_joystick(pidevice, self.joystick, self.pump)
pygame.joystick.quit()
pidevice.CloseConnection()
self.save_stage_pos()
self.mycon.close()
print("Connection closed.")
break
if temp_pos_z > 0:
self.stage_posS['pickup_pos_z'] = temp_pos_z
# Pick section up (lowing the tip)
pidevice.MOV(3, self.stage_posS['pickup_pos_z'])
sleep(1)
# detach section from knife
pidevice.MOV(1, pidevice.qPOS()["1"] - 5)
sleep(1)
# Move section to wafer boat
pidevice.MOV(1, self.stage_posS['dropoff_pos_xy'][0])
pidevice.MOV(2, self.stage_posS['dropoff_pos_xy'][1])
sleep(10)
# Move section to wafer with joystick
if self.auto_loop:
self.check_events()
if self.interrupt:
_, _, _, end_collection = move_joystick(pidevice, self.joystick, self.pump, positions=self.stage_posS)
self.interrupt = False
else:
_, _, _, end_collection = move_joystick(pidevice, self.joystick, self.pump, positions=self.stage_posS)
if end_collection:
print('remove the wafer')
_, _, _, _ = move_joystick(pidevice, self.joystick, self.pump)
pygame.joystick.quit()
pidevice.CloseConnection()
self.save_stage_pos()
self.mycon.close()
print("Connection closed.")
break
# Lift tip
pidevice.MOV(3, self.stage_posS['dropoff_pos_z'])
sleep(1)
# Move arm back to pickup point
pidevice.MOV(1, self.stage_posS['pickup_pos_xy'][0])
pidevice.MOV(2, self.stage_posS['pickup_pos_xy'][1])
sleep(10)
def calibrate_cap_sensor(self):
cap_reading = input('Please adjust the water level and the Z position of the cap sensor.\nThen enter the output of the cap sensor (in percent) to calibrate the reading:\n')
x = int(cap_reading)
y = x * 0.1
self.ue = y + 0.5
self.ut = y - 0.5
print(self.ue)
print(self.ut)
def water_level_control(self):
for channel, raw_data in enumerate(ncdt6500_get_data()):
print(f"channel #{channel}: {ncdt6500_decode(raw_data):.4g} V")
waterlevel = ncdt6500_decode(raw_data)
if waterlevel < self.ut - 0.5:
raise ValueError('Large change in cap sensor reading detected. Please check the cap sensor for water drops.')
if waterlevel > self.ue:
self.pump.run()
time.sleep(15)
# if waterlevel < ut:
# pump = ne1000.Ne1000(dev, ADDRESS)
# pump.diameter_mm(DIA)
# pump.volume(volume)
# pump.rate(rate)
# pump.direction_withdraw()
# pump.run()
# time.sleep(10)
elif waterlevel <= self.ue:
#continue
time.sleep(0.1)
def save_stage_pos(self):
self.stage_posS['start_pos'][0] = self.stage_posS['pickup_pos_xy'][0]
self.stage_posS['start_pos'][1] = self.stage_posS['pickup_pos_xy'][1]
stage_posF = {'start_pos': self.stage_posS['start_pos'],
'pickup_pos_xy': self.stage_posS['pickup_pos_xy'],
'pickup_pos_z': self.stage_posS['pickup_pos_z'],
'dropoff_pos_xy': self.stage_posS['dropoff_pos_xy'],
'dropoff_pos_z': self.stage_posS['dropoff_pos_z']}
with open('stage_posS.json', 'w') as f:
json.dump(stage_posF, f)
def check_events(self):
events = pygame.event.get()
for e in events:
if e.type == 1539:
if e.dict['button'] == 0:
self.interrupt = True
elif e.dict['button'] == 15:
if self.manual_water_refill:
self.pump.run()
sleep(15)
if __name__ == '__main__':
collect = SemiManualCollection()