def delay(self, seconds):
def _do():
self.plunger.wait(seconds)
description = "Delaying {} seconds".format(seconds)
self.robot.add_command(Command(do=_do, description=description))
return self
def aspirate(self, volume=None, location=None, rate=1.0):
def _do_aspirate():
nonlocal volume
nonlocal location
if not isinstance(volume, (int, float, complex)):
if volume and not location:
location = volume
volume = self.max_volume - self.current_volume
if self.current_volume + volume > self.max_volume:
raise RuntimeWarning(
'Pipette cannot hold volume {}'
.format(self.current_volume + volume)
)
self.position_for_aspirate(location)
self.current_volume += volume
distance, _ = self.plunge_distance(self.current_volume)
destination = self.positions['bottom'] - distance
speed = self.speeds['aspirate'] * rate
self.plunger.speed(speed)
self.plunger.move(destination)
description = "Aspirating {0}uL at {1}".format(
volume,
(humanize_location(location) if location else '<In Place>')
)
self.robot.add_command(
Command(do=_do_aspirate, description=description))
return self
def dispense(self, volume=None, location=None, rate=1.0):
def _do():
nonlocal location
nonlocal volume
if not isinstance(volume, (int, float, complex)):
if volume and not location:
location = volume
volume = self.current_volume
if self.current_volume - volume < 0:
volume = self.current_volume
if location:
self.move_to(location, now=True)
if volume:
self.current_volume -= volume
distance, _ = self.plunge_distance(self.current_volume)
destination = self.positions['bottom'] - distance
speed = self.speeds['dispense'] * rate
self.plunger.speed(speed)
self.plunger.move(destination)
description = "Dispensing {0}uL at {1}".format(
volume,
(humanize_location(location) if location else '<In Place>')
)
self.robot.add_command(Command(do=_do, description=description))
return self
def move_to(self, location, instrument=None, create_path=True, now=False):
placeable, coordinates = containers.unpack_location(location)
if instrument:
coordinates = instrument.calibrator.convert(
placeable,
coordinates)
else:
coordinates += placeable.coordinates(placeable.get_deck())
tallest_z = self._deck.max_dimensions(self._deck)[2][1][2]
tallest_z += 10
def _do():
if create_path:
self._driver.move_head(z=tallest_z)
self._driver.move_head(x=coordinates[0], y=coordinates[1])
self._driver.move_head(z=coordinates[2])
else:
self._driver.move_head(
x=coordinates[0],
y=coordinates[1],
z=coordinates[2]
)
if now:
_do()
else:
self.add_command(Command(do=_do))
def delay(self, seconds):
def _do():
self.mosfet.wait(seconds)
description = "Delaying Magbead for {} seconds".format(seconds)
self.robot.add_command(Command(do=_do, description=description))
return self
def disengage(self):
def _do():
self.mosfet.disengage()
description = "Engaging Magbead at mosfet #{}".format(self.mosfet)
self.robot.add_command(Command(do=_do, description=description))
return self
def test_command(self):
expected = None
def _do():
nonlocal expected
expected = 'test'
description = 'test'
command = Command(do=_do, description=description)
command()
self.assertEquals(expected, command.description)
def blow_out(self, location=None):
def _do():
nonlocal location
if location:
self.move_to(location, now=True)
self.plunger.move(self.positions['blow_out'])
self.current_volume = 0
description = "Blow_out at {}".format(
humanize_location(location) if location else '<In Place>'
)
self.robot.add_command(Command(do=_do, description=description))
return self
def drop_tip(self, location=None):
def _do():
nonlocal location
if location:
self.go_to_bottom(location, now=True)
self.plunger.move(self.positions['drop_tip'])
self.plunger.home()
self.current_volume = 0
description = "Drop_tip at {}".format(
(humanize_location(location) if location else '<In Place>'))
self.robot.add_command(Command(do=_do, description=description))
return self
def home(self, *args, **kwargs):
def _do():
if self._driver.calm_down():
if args:
return self._driver.home(*args)
else:
self._driver.home('z')
return self._driver.home('x', 'y', 'b', 'a')
else:
return False
if kwargs.get('now'):
return _do()
else:
description = "Homing Robot"
self.add_command(Command(do=_do, description=description))
def mix(self, volume=None, location=None, repetitions=3):
def _do():
# plunger movements are handled w/ aspirate/dispense
# using Command for printing description
pass
description = "Mixing {0} times with a volume of {1}ul".format(
repetitions, str(self.current_volume))
self.robot.add_command(Command(do=_do, description=description))
self.aspirate(location=location, volume=volume)
for i in range(repetitions - 1):
self.dispense(volume)
self.aspirate(volume)
self.dispense(volume)
return self
def test_macro(self):
expected = []
macro = Macro('macro_test')
for i in range(3):
def _do():
nonlocal expected
expected.append('test')
command = Command(do=_do)
macro.add(command)
macro.do()
self.assertEquals(expected, ['test', 'test', 'test'])
def touch_tip(self, location=None):
def _do():
nonlocal location
if location:
self.move_to(location, now=True)
else:
location = self.placeables[-1]
self.go_to(
(location, location.from_center(x=1, y=0, z=1)), now=True)
self.go_to(
(location, location.from_center(x=-1, y=0, z=1)), now=True)
self.go_to(
(location, location.from_center(x=0, y=1, z=1)), now=True)
self.go_to(
(location, location.from_center(x=0, y=-1, z=1)), now=True)
description = 'Touching tip'
self.robot.add_command(Command(do=_do, description=description))
return self
def pick_up_tip(self, location=None):
def _do():
nonlocal location
if location:
self.go_to_bottom(location, now=True)
# TODO: actual plunge depth for picking up a tip
# varies based on the tip
# right now it's accounted for via plunge depth
# TODO: Need to talk about containers z positioning
tip_plunge = 6
# Dip into tip and pull it up
for _ in range(3):
self.robot.move_head(z=-tip_plunge, mode='relative')
self.robot.move_head(z=tip_plunge, mode='relative')
self.robot.home('z')
description = "Picking up tip from {0}".format(
(humanize_location(location) if location else '<In Place>')
)
self.robot.add_command(Command(do=_do, description=description))
return self
def commandable():
self.add_command(Command(do=callback))