Source code for autoprotocol.liquid_handle.mix

"""Mix LiquidHandleMethod

Base LiquidHandleMethod used by Protocol.mix to generate a series of
movements within individual wells.

    :copyright: 2021 by The Autoprotocol Development Team, see AUTHORS
        for more details.
    :license: BSD, see LICENSE for more details
"""
from ..instruction import LiquidHandle
from ..unit import Unit
from ..util import parse_unit
from .transfer import LiquidHandleMethod


# pylint: disable=protected-access
[docs]class Mix(LiquidHandleMethod): """LiquidHandleMethod for generating transfers within wells LiquidHandleMethod for moving volume within a single well. Attributes ---------- _liquid : LiquidClass used to determine calibration, flowrates, and sensing thresholds Notes ----- The primary entry points that for this class are: - _mix_transports : generates transports within a single location See Also -------- LiquidHandleMethod : base LiquidHandleMethod with reused functionality Protocol.mix : the standard interface for interacting with Mix """ def __init__(self, tip_type=None, blowout=True, repetitions=None, position_z=None): """ Parameters ---------- tip_type : str, optional tip_type to be used for the LiquidHandlingMethod blowout : bool or dict, optional whether to execute a blowout step or the parameters for one. this generates two operations, an initial air aspiration before entering any wells, and a corresponding final air dispense after the last operation that involves liquid See Also LiquidHandle.builders.blowout repetitions : int the number of times the mix should be repeated position_z : dict the position that the tip should move to prior to mixing, if the position references the `liquid_surface` then mix movements will track the surface with the defined offset. See Also LiquidHandle.builders.position_z """ super(Mix, self).__init__(tip_type=tip_type, blowout=blowout) # parameters for required behavior self.repetitions = repetitions self.position_z = position_z # LiquidHandle parameters that are generated and modified at runtime self._liquid = None def _has_calibration(self): liquids = [self._liquid] return any(_ and _._has_calibration() for _ in liquids) def _calculate_overage_volume(self, volume): calibration_overage = ( self._estimate_calibrated_volume(volume, self._liquid, self.tip_type) - volume ) return calibration_overage
[docs] def default_blowout(self, volume): return LiquidHandle.builders.blowout( volume=Unit("5:ul"), initial_z=self.default_well_top_position_z(), flowrate=None, )
def _mix_transports(self, volume): """Generates mix transports Generates and returns all of the transports that should happen within the well of a mix operation. Calls a series of _transport_`y` helper methods that each query the `y` parameter and default_`y` method to decide on a set of behavior and use that to define transports that are appended to the _transports list. Parameters ---------- volume : Unit Notes ----- This method defines what lower level transport-generating methods are called and in what order. It can be overwritten when adding an entirely new set of transport-generating behavior. Return ------ list transports corresponding to the mix operation """ self._transports = [] volume = parse_unit(volume, "ul") # No transports if no volume specified if volume == Unit("0:ul"): return [] self._transport_pre_buffer(volume) self._transport_mix(volume) self._transport_blowout(volume) return self._transports def _transport_mix(self, volume): """Mixes the volume Parameters ---------- volume : Unit Raises ------ TypeError if mix repetitions is not an int See Also -------- repetitions : holds any user defined repetition parameters default_repetitions : specifies default repetition parameters position_z : holds any user defined position_z parameters default_position_z : specifies default position_z parameters _mix : lower level helper that generates the mix transports """ repetitions = self.repetitions or self.default_repetitions(volume) position_z = self.position_z or self.default_position_z(volume) if not isinstance(repetitions, int): raise TypeError(f"Mix repetitions {repetitions} was not an int.") position_z = LiquidHandle.builders.position_z(**position_z) self._mix( volume=volume, repetitions=repetitions, initial_z=position_z, asp_flowrate=self._liquid._get_aspirate_flowrate(volume, self.tip_type), dsp_flowrate=self._liquid._get_dispense_flowrate(volume, self.tip_type), delay_time=self._liquid.delay_time, liquid_class=self._liquid.name, ) # pylint: disable=unused-argument
[docs] def default_repetitions(self, volume): """Default mix repetitions Parameters ---------- volume: Unit Returns ------- int number of mix repetitions See Also -------- repetitions : holds any user defined repetition parameters _transport_mix : generates the actual mix transports """ return 10
# pylint: disable=unused-argument
[docs] def default_position_z(self, volume): """Default position_z Parameters ---------- volume : Unit Returns ------- dict mix position_z See Also -------- position_z : holds any user defined position_z parameters _transport_mix : generates the actual mix transports """ if self._is_single_channel(): position_z = self.default_lld_position_z(self._liquid) else: position_z = self.default_well_bottom_position_z() return position_z