:py:mod:`science_jubilee.tools.Sonicator`
=========================================

.. py:module:: science_jubilee.tools.Sonicator


Module Contents
---------------

Classes
~~~~~~~

.. autoapisummary::

   science_jubilee.tools.Sonicator.Sonicator




Attributes
~~~~~~~~~~

.. autoapisummary::

   science_jubilee.tools.Sonicator.logger


.. py:data:: logger

   

.. py:class:: Sonicator(index, name, mode: str, port: str = None)


   Bases: :py:obj:`science_jubilee.tools.Tool.Tool`

   A class representation for a Qsonica Sonicator tool.

   .. py:method:: _raspberrypi_hat()

      Initialize the pins used on the Raspberry Pi Hat.


   .. py:method:: _raspberrypi_pico(port: str)

      Initialize serial interface with Raspberry Pi Pico microcontroller.

      :param port: port to connect to the Pico microcontroller, this is computer dependent.
      :type port: str


   .. py:method:: _set_sonication_power(power: float)

      Set the power of the sonicator to a value between 0.4 and 1.0.

      :param power: power level to set the sonicator to. Must be between 0.4 and 1.0.
      :type power: float


   .. py:method:: _sonication_on()

      Turn on the sonicator.


   .. py:method:: _sonication_off()

      Turn off the sonicator.


   .. py:method:: _sonicate(exposure_time: float = 1.0, power: float = 0.4, pulse_duty_cycle: float = 0.5, pulse_interval: float = 1.0, verbose: bool = False)

      Enable the sonicator at the power level for the exposure time.

      :param exposure_time: total time to sonicate for, defaults to 1.0
      :type exposure_time: float, optional
      :param power: power level to sonicate at, defaults to 0.4
      :type power: float, optional
      :param pulse_duty_cycle: duty cycle of the sonicator pulse, defaults to 0.5
      :type pulse_duty_cycle: float, optional
      :param pulse_interval: interval between pulses, defaults to 1.0
      :type pulse_interval: float, optional
      :param verbose: whether or not to print out the time elapsed, defaults to False
      :type verbose: bool, optional


   .. py:method:: sonicate_well(location: Union[science_jubilee.labware.Labware.Well, Tuple, science_jubilee.labware.Labware.Location], plunge_depth: float, sonication_time: float, power: float = 0.4, pulse_duty_cycle: float = 0.5, pulse_interval: float = 1.0, verbose: bool = False, autoclean: bool = False, *args)

      Sonicate one well at a specified depth for a given time.

      :param location: location of the well to sonicate
      :type location: Union[Well, Tuple, Location]
      :param plunge_depth: depth (in mm) to plunge from the top of the plate.
      :type plunge_depth: float
      :param sonication_time: time (in sec) to sonicate for
      :type sonication_time: float
      :param power: sonicator power level ranging from 0.4 (default, min) through 1.0 (max).
      :type power: float
      :param pulse_duty_cycle: duty cycle of the sonicator pulse, defaults to 0.5
      :type pulse_duty_cycle: float, optional
      :param pulse_interval: interval between pulses, defaults to 1.0
      :type pulse_interval: float, optional
      :param verbose: whether or not to print out the time elapsed, defaults to False
      :type verbose: bool, optional
      :param autoclean: whether or not to perform the cleaning protocol after sonication, defaults to False
      :type autoclean: bool, optional
      :param args: if location is of type Tuple, the depth of the well needs to be specified
      :type args: tuple
      :raises ValueError: if the plunge depth is too deep

       Note: sonicator does not turn on below power level of 0.4.


   .. py:method:: set_cleaning_protocol(wells: List[science_jubilee.labware.Labware.Well], power: List[float], time: List[float], plunge_depth: float = None)

      Set the cleaning protocol for the sonicator.

      :param wells: list of wells to clean
      :type wells: List[Well]
      :param power: power level to clean at
      :type power: List[float]
      :param time: time to clean for
      :type time: List[float]
      :param plunge_depth: depth of the sonicator into the well, defaults to None
      :type plunge_depth: float, optional


   .. py:method:: perform_cleanining_protocol(plunge_depth: float = None)

      Perform the cleaning protocol on the sonicator.

      :param plunge_depth: depth to plunge the sonicator into the well, defaults to None
      :type plunge_depth: float, optional