def move_robot(event, x, y, flags, param):
global deck_ref_points, img_points
if event == cv2.EVENT_LBUTTONUP:
rx = transform(x, 0)
ry = transform(y,1)
print("Robot: {}, {}".format(rx, ry))
robot.move_head(x=rx, y=ry)
def btest(n, photoary): petri1 = [89, 125] petri2 = [181, 125] petri3 = [272, 125] petri = [petri1, petri2, petri3] for i in range(n): count = 0 pipette.pick_up_tip(tiprack.wells(i)) for num in range(336): x = 0 y = 0 while y < 640: while x < 480: color = photoary[i][y,x] print(color) x+= 20 if color == 255 : pipette.aspirate(100, water[i]) robot.move_head(x=(petri[i][0] + (x/10)), y= (petri[i][1] +(y/10)), z=100) robot.move_head(x=(petri[i][0] + (x/10)), y= (petri[i][1] +(y/10)), z=-40) pipette.aspirate(100) pipette.dispense(200, pcr[i].wells(count).bottom()) count += 1 if count == 96: return y+= 20 count += 1
def mouse_callback(event):
status_str.set("clicked at " + str(event.x) + " " + str(event.y))
pos = c.coords(marker)
# cant use move_marker bc mouse y coords are not flipped like the robot coords are
x1 = pos[0]
y1 = pos[1]
x2 = event.x
y2 = event.y
dx = x2 - x1
dy = y2 - y1
print("x1:",x1,"y1:",y1,"x2:",x2,"y2:",y2,"dx:",dx,"dy:",dy)
x = x2
y = Y_MAX - y2
z = get_coords().z
print("MPUSE x:", x,"y:",y,"z",z)
if in_bounds(x,y,z):
c.move(marker, dx, dy)
robot.move_head(x=x, y=y, z=z)
print("moving robot to: x= ",x," y= ",y, " z= ",z, sep='')
pos_str.set("x: " + str(x) + "\ny: " + str(y) + "\nz: " + str(z))
print(status_str.get())
def test_move_head(virtual_smoothie_env):
robot.reset()
robot.move_head(x=100, y=0)
assert isclose(
pose_tracker.absolute(
robot.poses,
robot.gantry)[:2],
(100, 0, 0)[:2]
).all()
def samplepick(x1, y1, z1): robot.move_head(x=x1, y=y1, z=100) robot.move_head(x=x1, y=y1, z=z1) #wiggle robot.move_head(x=x1+.5, y=y1+.5, z=z1) robot.move_head(x=x1-1, y=y1-1, z=z1) pipette.aspirate(100) robot.move_head(x=x1, y=y1, z=10)
def move_to(x, y, z):
try:
old_x = get_coords().x
old_y = get_coords().y
move_marker(old_x, old_y, x, y)
robot.move_head(x=x, y=y, z=z)
print("moving robot to: x= ",x," y= ",y, " z= ",z, sep='')
pos_str.set("x: " + str(x) + "\ny: " + str(y) + "\nz: " + str(z))
except RuntimeWarning:
print("about to crash pls move in the opposite direction")
except RuntimeError:
print("rip")
def aspirate_from_current_position():
axis = request.json.get("axis")
try:
# this action mimics 1.2 app experience
# but should be re-thought to take advantage of API features
instrument = robot._instruments[axis.upper()]
robot.move_head(z=20, mode='relative')
instrument.motor.move(instrument.positions['blow_out'])
instrument.motor.move(instrument.positions['bottom'])
robot.move_head(z=-20, mode='relative')
instrument.motor.move(instrument.positions['top'])
except Exception as e:
emit_notifications([str(e)], 'danger')
return flask.jsonify({'status': 'error', 'data': str(e)})
return flask.jsonify({'status': 'success', 'data': ''})
def aspirate_from_current_position():
axis = request.json.get("axis")
try:
_, _, robot_max_z = robot._driver.get_dimensions()
current_z = robot._driver.get_position()['current']['z']
jog_up_distance = min(robot_max_z - current_z, 20)
robot.move_head(z=jog_up_distance, mode='relative')
instrument = robot._instruments[axis.upper()]
instrument.motor.move(instrument.positions['blow_out'])
instrument.motor.move(instrument.positions['bottom'])
robot.move_head(z=-jog_up_distance, mode='relative')
instrument.motor.move(instrument.positions['top'])
except Exception as e:
emit_notifications([str(e)], 'danger')
return flask.jsonify({'status': 'error', 'data': str(e)})
return flask.jsonify({'status': 'success', 'data': ''})
def measure(pipette, scale): # dispense onto scale pipette.blow_out(scale.wells(0)) time.sleep(2) # get scale coords use deltas tpo get screen coords = get_coords() new_x = coords[0] + 10 new_y = coords[1] - 90 new_z = coords[2] - 5 robot.move_head(x=new_x, y=new_y, z=new_z) # take a picture of the scale cap = cv2.VideoCapture(2) ret, frame = cap.read() # feed pic into code val = read_scale(frame) # return results return val
def pipscale(pipette, scale, tiprack, trough, trash):
# calibrates pipette
calibrate_plunger(pipette)
# pick up tip
pipette.pick_up_tip(tiprack[0])
last_reading = 0
readings = []
for j in range(3):
pipette.aspirate(200, trough.wells(0))
pipette.blow_out(scale.wells(0))
time.sleep(2)
# get scale coords use deltas tpo get screen
coords = get_coords()
# pipette.move_to(scale_screen)
new_x = coords[0] + 10
new_y = coords[1] - 90
new_z = coords[2] - 5
robot.move_head(x=new_x, y=new_y, z=new_z)
scale_reading = read_scale(debug='on')
while scale_reading == -1:
scale_reading = read_scale(debug='on')
amount = to_vol_measurement(scale_reading)
tared = amount - last_reading
print(amount, tared)
readings.append(tared)
last_reading = amount
total = 0
for val in readings:
total += val
ave = float(total / len(readings))
print("average out of 3:", ave)
pipette.max_volume = ave
print(pipette.max_volume)
pipette.update_calibrations()
def move_to_slot():
robot = Robot.get_instance()
status = 'success'
result = ''
try:
slot = request.json.get("slot")
slot = robot._deck[slot]
slot_x, slot_y, _ = slot.from_center(x=-1,
y=0,
z=0,
reference=robot._deck)
_, _, robot_max_z = robot._driver.get_dimensions()
robot.move_head(z=robot_max_z)
robot.move_head(x=slot_x, y=slot_y)
except Exception as e:
result = str(e)
status = 'error'
emit_notifications([result], 'danger')
return flask.jsonify({'status': status, 'data': result})
def jog():
robot = Robot.get_instance()
coords = request.json
status = 'success'
result = ''
try:
if coords.get("a") or coords.get("b"):
result = robot._driver.move_plunger(mode="relative", **coords)
else:
result = robot.move_head(mode="relative", **coords)
except Exception as e:
result = str(e)
status = 'error'
emit_notifications([result], 'danger')
return flask.jsonify({'status': status, 'data': result})
def move_to_container():
robot = Robot.get_instance()
slot = request.json.get("slot")
name = request.json.get("label")
axis = request.json.get("axis")
try:
instrument = robot._instruments[axis.upper()]
container = robot._deck[slot].get_child_by_name(name)
well_x, well_y, well_z = tuple(
instrument.calibrator.convert(container[0],
container[0].bottom()[1]))
_, _, robot_max_z = robot._driver.get_dimensions()
# move to max Z to avoid collisions while calibrating
robot.move_head(z=robot_max_z)
robot.move_head(x=well_x, y=well_y)
robot.move_head(z=well_z)
except Exception as e:
emit_notifications([str(e)], 'danger')
return flask.jsonify({'status': 'error', 'data': str(e)})
return flask.jsonify({'status': 'success', 'data': ''})
def goto1(): robot.move_head(x=89, y=125, z=100)
def goto3(): robot.move_head(x=272, y=125, z=100)
def goto2(): robot.move_head(x=181, y=125, z=100)
def goto2():
robot.move_head(x=175, y=108, z=100)
def goto1():
robot.move_head(x=83, y=108, z=100)
def goto3():
robot.move_head(x=269, y=108, z=100)
def main(stdscr):
currentlyCalibrating=placeableNames[0]
currentPipette=pipetteNames[0]
movementAmount=1
position=list(robot._driver.get_head_position()["current"])
position[0]=0
def chooseWhatToCalibrate():
nonlocal currentlyCalibrating
stdscr.clear()
stdscr.addstr("What should we calibrate?\n")
for i,value in enumerate(placeableNames):
stdscr.addstr(str(i+1)+" - " + value+"\n")
curses.echo() # Enable echoing of characters
s = stdscr.getstr(15,0, 15)
stdscr.addstr(s)
currentlyCalibrating=placeableNames[int(s)-1]
curses.noecho()
def chooseWhatPipetteToCalibrate():
nonlocal currentPipette
stdscr.clear()
stdscr.addstr("What pipette should we calibrate?\n")
for i,value in enumerate(pipetteNames):
stdscr.addstr(str(i+1)+" - " + value+"\n")
curses.echo() # Enable echoing of characters
s = stdscr.getstr(10,0, 15)
stdscr.addstr(s)
currentPipette=pipetteNames[int(s)-1]
curses.noecho()
# This raises ZeroDivisionError when i == 10.
def calibratePlunger():
plungerPos=0
plungerTarget="top"
plungerInc=1
while 1:
stdscr.clear()
stdscr.addstr("PLASMOTRON CALIBRATION MODE - PLUNGER MODE\n\n")
stdscr.addstr("Keyboard shortcuts:\n\n")
stdscr.addstr("T - start calibrating the 'top' position\n")
stdscr.addstr("B - start calibrating the 'bottom' position\n")
stdscr.addstr("O - start calibrating the 'blowout' position\n")
stdscr.addstr("E - start calibrating the 'eject' position\n\n")
stdscr.addstr("Numbers 1-8 - choose how far to move\n")
stdscr.addstr("Arrow keys - move plunger up/down\n")
stdscr.addstr("S - save this position\n")
stdscr.addstr("M - move to this position\n")
stdscr.addstr("\n\n")
stdscr.addstr("V - switch back to container mode\n\n")
stdscr.addstr("Currently calibrating plunger position: ")
stdscr.addstr( str(plungerTarget)+"\n",curses.A_STANDOUT)
stdscr.addstr("with pipette: ")
stdscr.addstr(str(currentPipette)+"\n",curses.A_STANDOUT)
stdscr.addstr("Movement increment: ")
stdscr.addstr(str(plungerInc)+" mm\n",curses.A_STANDOUT)
stdscr.addstr("Current position - X: ")
stdscr.addstr(str(plungerPos),curses.A_STANDOUT)
key=stdscr.getkey()
curses.flushinp()
if key=="t":
plungerTarget="top"
if key=="b":
plungerTarget="bottom"
if key=="o":
plungerTarget="blow_out"
if key=="e":
plungerTarget="drop_tip"
if key=="s":
equipment[currentPipette].calibrate(plungerTarget)
stdscr.clear()
stdscr.addstr("plunger position saved")
stdscr.refresh()
time.sleep(1)
if key=="m":
equipment[currentPipette].motor.move(equipment[currentPipette]._get_plunger_position(plungerTarget))
plungerPos=equipment[currentPipette]._get_plunger_position(plungerTarget)
if key=="h":
equipment[currentPipette].home()
plungerPos=0
if key=="v":
return()
try:
if int(key) in movementamounts:
plungerInc= movementamounts[int(key)]
except ValueError:
pass
if key == "KEY_UP":
plungerPos=plungerPos-plungerInc
if key == "KEY_DOWN":
plungerPos=plungerPos+plungerInc
#stdscr.addstr("Key"+key)
equipment[currentPipette].motor.move(plungerPos)
stdscr.refresh()
while 1:
stdscr.clear()
stdscr.addstr("PLASMOTRON CALIBRATION MODE\n\n")
stdscr.addstr("Keyboard shortcuts:\n")
stdscr.addstr("Control+C - exit\n")
stdscr.addstr("P - choose what pipette to calibrate with\n")
stdscr.addstr("C - choose what container to calibrate\n")
stdscr.addstr("S - save this position\n")
stdscr.addstr("H - home\n")
stdscr.addstr("M - move to the currently saved position\n\n")
stdscr.addstr("Numbers 1-8 - choose how far to move\n")
stdscr.addstr("Arrow keys - move forwards/back/left/right\n")
stdscr.addstr("Control + arrow keys or a and z keys - move up/down\n\n")
stdscr.addstr("V - switch to calibrate this pipettes plunger/volume\n\n")
stdscr.addstr("Currently pipette: ")
stdscr.addstr(str(currentPipette)+"\n",curses.A_STANDOUT)
stdscr.addstr("going to: ")
stdscr.addstr(str(currentlyCalibrating)+"\n",curses.A_STANDOUT)
stdscr.addstr("Movement increment: ")
stdscr.addstr( str(movementAmount)+" mm\n",curses.A_STANDOUT)
stdscr.addstr("Current position - ")
stdscr.addstr("X:"+ str(position[0])+",Y:"+ str(position[1])+",Z:"+ str(position[2]),curses.A_STANDOUT)
key=stdscr.getkey()
curses.flushinp()
if key=="c":
chooseWhatToCalibrate()
if key=="v":
calibratePlunger()
if key=="p":
chooseWhatPipetteToCalibrate()
if key=="s":
well = equipment[currentlyCalibrating][0]
pos = well.from_center(x=0, y=0, z=-1, reference=equipment[currentlyCalibrating])
location = (equipment[currentlyCalibrating], pos)
equipment[currentPipette].calibrate_position(location)
stdscr.clear()
stdscr.addstr("position saved")
stdscr.refresh()
time.sleep(1)
if key=="m":
well = equipment[currentlyCalibrating][0]
pos = well.from_center(x=0, y=0, z=-1, reference=equipment[currentlyCalibrating])
location = (equipment[currentlyCalibrating], pos)
equipment[currentPipette].move_to(location)
position=list(robot._driver.get_head_position()["current"])
if key=="h":
robot.home()
position=list(robot._driver.get_head_position()["current"])
try:
if int(key) in movementamounts:
movementAmount= movementamounts[int(key)]
except ValueError:
pass
if key == "kUP5" or key =="a":
position[2]=position[2]+movementAmount
if key == "kDN5" or key =="z":
position[2]=position[2]-movementAmount
if key == "KEY_LEFT":
position[0]=position[0]-movementAmount
if key == "KEY_RIGHT":
position[0]=position[0]+movementAmount
if key == "KEY_UP":
position[1]=position[1]+movementAmount
if key == "KEY_DOWN":
position[1]=position[1]-movementAmount
#stdscr.addstr("Key"+key)
robot.move_head(x=position[0],y=position[1],z=position[2])
stdscr.refresh()
p200.pick_up_tip(tiprack[0])
# p200.pick_up_tip(water[0])
# p200.pick_up_tip(scale[0])
# p200.pick_up_tip(scale_screen[0])
last_reading = 0
readings = []
print('beginning image collection')
for j in range(100):
for i in range(150, 200, 5):
p200.aspirate(i, water.wells(0))
p200.blow_out(scale.wells(0))
time.sleep(2)
p200.move_to(scale_screen)
take_pic(2, 0, img_dir)
# random xyz variations
print('adding random xyz variations')
coords = get_coords()
for j in range(3):
take_pic(2, 0, img_dir)
# coords = get_coords()
new_x = coords[0] + random.uniform(-30, 30)
new_y = coords[1] + random.uniform(-30, 30)
new_z = coords[2] + random.uniform(-30, 30)
robot.move_head(x=new_x, y=new_y, z=coords[2])
take_pic(2, 0, img_dir)
robot.disconnect()
