def move_to(self, location, instrument=None, strategy='arc', **kwargs):
"""
Move an instrument to a coordinate, container or a coordinate within
a container.
Parameters
----------
location : one of the following:
1. :class:`Placeable` (i.e. Container, Deck, Slot, Well) — will
move to the origin of a container.
2. :class:`Vector` move to the given coordinate in Deck coordinate
system.
3. (:class:`Placeable`, :class:`Vector`) move to a given coordinate
within object's coordinate system.
instrument :
Instrument to move relative to. If ``None``, move relative to the
center of a gantry.
strategy : {'arc', 'direct'}
``arc`` : move to the point using arc trajectory
avoiding obstacles.
``direct`` : move to the point in a straight line.
Examples
--------
>>> from opentrons import Robot
>>> robot.reset() # doctest: +ELLIPSIS
<opentrons.robot.robot.Robot object at ...>
>>> robot.connect('Virtual Smoothie')
>>> robot.home()
>>> plate = robot.add_container('96-flat', 'A1', 'plate')
>>> robot.move_to(plate[0])
>>> robot.move_to(plate[0].top())
"""
placeable, coordinates = containers.unpack_location(location)
if instrument:
coordinates = instrument.calibrator.convert(placeable, coordinates)
else:
coordinates += placeable.coordinates(placeable.get_deck())
if strategy == 'arc':
arc_coords = self._create_arc(coordinates, placeable, instrument)
for coord in arc_coords:
self._driver.move_head(**coord)
elif strategy == 'direct':
self._driver.move_head(x=coordinates[0],
y=coordinates[1],
z=coordinates[2])
else:
raise RuntimeError('Unknown move strategy: {}'.format(strategy))
def _associate_placeable(self, location):
"""
Saves a reference to a placeable
"""
if not location:
return
placeable, _ = unpack_location(location)
self.previous_placeable = placeable
if not self.placeables or (placeable != self.placeables[-1]):
self.placeables.append(placeable)
def _associate_placeable(self, location):
"""
Saves a reference to a placeable
"""
if not location:
return
placeable, _ = containers.unpack_location(location)
self.previous_placeable = placeable
if not self.placeables or (placeable != self.placeables[-1]):
self.placeables.append(placeable)
def _dispense_during_transfer(self, vol, loc, **kwargs):
"""
Performs a :any:`dispense` when running a :any:`transfer`, and
optionally a :any:`mix`, :any:`touch_tip`, and/or
:any:`blow_out` afterwards.
"""
mix_after = kwargs.get('mix_after', (0, 0))
rate = kwargs.get('rate', 1)
air_gap = kwargs.get('air_gap', 0)
well, _ = unpack_location(loc)
if air_gap:
self.dispense(air_gap, well.top(5), rate=rate)
self.dispense(vol, loc, rate=rate)
self._mix_during_transfer(mix_after, well, **kwargs)
def _aspirate_during_transfer(self, vol, loc, **kwargs):
"""
Performs an :any:`aspirate` when running a :any:`transfer`, and
optionally a :any:`touch_tip` afterwards.
"""
rate = kwargs.get('rate', 1)
mix_before = kwargs.get('mix', kwargs.get('mix_before', (0, 0)))
air_gap = kwargs.get('air_gap', 0)
touch_tip = kwargs.get('touch_tip', False)
well, _ = unpack_location(loc)
if self.current_volume == 0:
self._mix_during_transfer(mix_before, well, **kwargs)
self.aspirate(vol, loc, rate=rate)
if air_gap:
self.air_gap(air_gap)
if touch_tip or touch_tip is 0:
self.touch_tip(touch_tip)
def _position_for_aspirate(self, location=None):
"""
Position this :any:`Pipette` for an aspiration,
given it's current state
"""
# first go to the destination
if location:
placeable, _ = unpack_location(location)
self.move_to(placeable.top(), strategy='arc')
# setup the plunger above the liquid
if self.current_volume == 0:
self.motor.move(self._get_plunger_position('bottom'))
# then go inside the location
if location:
if isinstance(location, Placeable):
location = location.bottom(min(location.z_size(), 1))
self.move_to(location, strategy='direct')
def _position_for_aspirate(self, location=None, plunger_empty=False):
"""
Position this :any:`Pipette` for an aspiration,
given it's current state
"""
# first go to the destination
if location:
placeable, _ = containers.unpack_location(location)
self.move_to(placeable.top(), strategy='arc', enqueue=False)
# setup the plunger above the liquid
if plunger_empty:
self.motor.move(self._get_plunger_position('bottom'))
# then go inside the location
if location:
if isinstance(location, Placeable):
location = location.bottom(1)
self.move_to(location, strategy='direct', enqueue=False)
def _position_for_aspirate(self, location=None, plunger_empty=False):
"""
Position this :any:`Pipette` for an aspiration,
given it's current state
"""
# first go to the destination
if location:
placeable, _ = containers.unpack_location(location)
self.move_to(placeable.top(), strategy='arc', enqueue=False)
# setup the plunger above the liquid
if plunger_empty:
self.motor.move(self._get_plunger_position('bottom'))
# then go inside the location
if location:
if isinstance(location, Placeable):
location = location.bottom(1)
self.move_to(location, strategy='direct', enqueue=False)
def _setup():
nonlocal location
if not location:
if self.has_tip_rack():
# TODO: raise warning/exception if looped back to first tip
location = next(self.tip_rack_iter)
else:
self.robot.add_warning(
'pick_up_tip called with no reference to a tip')
self.current_tip_home_well = None
if location:
placeable, _ = containers.unpack_location(location)
self.current_tip_home_well = placeable
if isinstance(location, Placeable):
location = location.bottom()
self._associate_placeable(location)
self.current_volume = 0
def _setup():
nonlocal location
if not location:
if self.has_tip_rack():
# TODO: raise warning/exception if looped back to first tip
location = next(self.tip_rack_iter)
else:
self.robot.add_warning(
'pick_up_tip called with no reference to a tip')
self.current_tip_home_well = None
if location:
placeable, _ = containers.unpack_location(location)
self.current_tip_home_well = placeable
if isinstance(location, Placeable):
location = location.bottom()
self._associate_placeable(location)
self.current_volume = 0
def pick_up_tip(self, location=None, presses=3):
"""
Pick up a tip for the Pipette to run liquid-handling commands with
Notes
-----
A tip can be manually set by passing a `location`. If no location
is passed, the Pipette will pick up the next available tip in
it's `tip_racks` list (see :any:`Pipette`)
Parameters
----------
location : :any:`Placeable` or tuple(:any:`Placeable`, :any:`Vector`)
The :any:`Placeable` (:any:`Well`) to perform the pick_up_tip.
Can also be a tuple with first item :any:`Placeable`,
second item relative :any:`Vector`
Returns
-------
This instance of :class:`Pipette`.
Examples
--------
..
>>> robot.reset() # doctest: +ELLIPSIS
<opentrons.robot.robot.Robot object at ...>
>>> tiprack = containers.load('tiprack-200ul', 'A1')
>>> p200 = instruments.Pipette(axis='a', tip_racks=[tiprack])
>>> p200.pick_up_tip(tiprack[0]) # doctest: +ELLIPSIS
<opentrons.instruments.pipette.Pipette object at ...>
>>> p200.return_tip() # doctest: +ELLIPSIS
<opentrons.instruments.pipette.Pipette object at ...>
>>> # `pick_up_tip` will automatically go to tiprack[1]
>>> p200.pick_up_tip() # doctest: +ELLIPSIS
<opentrons.instruments.pipette.Pipette object at ...>
>>> p200.return_tip() # doctest: +ELLIPSIS
<opentrons.instruments.pipette.Pipette object at ...>
"""
if not location:
location = self.get_next_tip()
self.current_tip(None)
if location:
placeable, _ = unpack_location(location)
self.current_tip(placeable)
if isinstance(location, Placeable):
location = location.bottom()
_description = "Picking up tip {0}".format(
('from ' +
humanize_location(location) if location else '')) # NOQA
self.robot.add_command(_description)
presses = (1 if not helpers.is_number(presses) else presses)
self.motor.move(self._get_plunger_position('bottom'))
self.current_volume = 0
if location:
self.move_to(location, strategy='arc')
tip_plunge = 6
for i in range(int(presses) - 1):
self.robot.move_head(z=tip_plunge, mode='relative')
self.robot.move_head(z=-tip_plunge, mode='relative')
return self
def move_to(self, location, instrument=None, strategy="arc", **kwargs):
"""
Move an instrument to a coordinate, container or a coordinate within
a container.
Parameters
----------
location : one of the following:
1. :class:`Placeable` (i.e. Container, Deck, Slot, Well) — will
move to the origin of a container.
2. :class:`Vector` move to the given coordinate in Deck coordinate
system.
3. (:class:`Placeable`, :class:`Vector`) move to a given coordinate
within object's coordinate system.
instrument :
Instrument to move relative to. If ``None``, move relative to the
center of a gantry.
strategy : {'arc', 'direct'}
``arc`` : move to the point using arc trajectory
avoiding obstacles.
``direct`` : move to the point in a straight line.
Examples
--------
>>> from opentrons import Robot
>>> robot.reset() # doctest: +ELLIPSIS
<opentrons.robot.robot.Robot object at ...>
>>> robot.connect('Virtual Smoothie')
True
>>> robot.home()
True
>>> plate = robot.add_container('96-flat', 'A1', 'plate')
>>> robot.move_to(plate[0])
>>> robot.move_to(plate[0].top())
"""
enqueue = kwargs.get("enqueue", False)
# Adding this for backwards compatibility with old move_to(now=False)
# convention.
if "now" in kwargs:
enqueue = not kwargs.get("now")
placeable, coordinates = containers.unpack_location(location)
if instrument:
coordinates = instrument.calibrator.convert(placeable, coordinates)
else:
coordinates += placeable.coordinates(placeable.get_deck())
def _do():
if strategy == "arc":
arc_coords = self._create_arc(coordinates, placeable)
for coord in arc_coords:
self._driver.move_head(**coord)
elif strategy == "direct":
self._driver.move_head(x=coordinates[0], y=coordinates[1], z=coordinates[2])
else:
raise RuntimeError("Unknown move strategy: {}".format(strategy))
if enqueue:
self.add_command(Command(do=_do))
else:
_do()
def move_to(self, location, instrument, strategy='arc', **kwargs):
"""
Move an instrument to a coordinate, container or a coordinate within
a container.
Parameters
----------
location : one of the following:
1. :class:`Placeable` (i.e. Container, Deck, Slot, Well) — will
move to the origin of a container.
2. :class:`Vector` move to the given coordinate in Deck coordinate
system.
3. (:class:`Placeable`, :class:`Vector`) move to a given coordinate
within object's coordinate system.
instrument :
Instrument to move relative to. If ``None``, move relative to the
center of a gantry.
strategy : {'arc', 'direct'}
``arc`` : move to the point using arc trajectory
avoiding obstacles.
``direct`` : move to the point in a straight line.
"""
placeable, coordinates = containers.unpack_location(location)
# because the top position is what is tracked,
# this checks if coordinates doesn't equal top
offset = subtract(coordinates, placeable.top()[1])
if 'trough' in repr(placeable):
# Move the pipette so that a multi-channel pipette is centered in
# the trough well to prevent crashing into the side, which would
# happen if you send the "A1" tip to the center of the well. See
# `robot.calibrate_container_with_instrument` for corresponding
# offset and comment.
offset = offset + (0, Y_OFFSET_MULTI, 0)
if isinstance(placeable, containers.WellSeries):
placeable = placeable[0]
target = add(pose_tracker.absolute(self.poses, placeable),
offset.coordinates)
if self._previous_instrument:
if self._previous_instrument != instrument:
self._previous_instrument.retract()
# because we're switching pipettes, this ensures a large (safe)
# Z arc height will be used for the new pipette
self._prev_container = None
self._previous_instrument = instrument
if strategy == 'arc':
arc_coords = self._create_arc(instrument, target, placeable)
for coord in arc_coords:
self.poses = instrument._move(self.poses, **coord)
elif strategy == 'direct':
position = {'x': target[0], 'y': target[1], 'z': target[2]}
self.poses = instrument._move(self.poses, **position)
else:
raise RuntimeError('Unknown move strategy: {}'.format(strategy))
