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

.. py:module:: science_jubilee.tools.Spectrometer


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

Classes
~~~~~~~

.. autoapisummary::

   science_jubilee.tools.Spectrometer.SpectroscopyTool
   science_jubilee.tools.Spectrometer.MeasurementManager




.. py:class:: SpectroscopyTool(index, name)


   Bases: :py:obj:`science_jubilee.tools.Tool.Tool`, :py:obj:`oceandirect.OceanDirectAPI.OceanDirectAPI`

   A class representation for an Ocean Optics Spectrometer, Light source, and Probe

   For that we wil be unfortunately using their own SDK package, which is NOT
   open-source.

   .. py:property:: _api_version

      The version of the Ocean Insight SDK

   .. py:property:: _usb_device


   .. py:property:: _device_id

      The ID of the spectrometer

   .. py:property:: _model

      The spectrometer model

   .. py:property:: _serial_number

      The spectrometer serial number

   .. py:property:: _integration_time


   .. py:property:: wavelengths

      Return list containing the wavelengths of the spectrometer.

      :return: A list of wavelengths
      :rtype: list

   .. py:method:: _open_device()

      Connects to the spectrometer device


   .. py:method:: integration_time(t: float, units: str = 'ms')

      Sets the integration time for the spectrometer.

      :param t: integration time
      :type t: float
      :param units: units of integration time, defaults to 'ms'
      :type units: str, optional


   .. py:method:: scans_to_average(n: int)

      Set the number of scans to average together to compose a single spectrum.

      :param n: number of scans to average
      :type n:int



   .. py:method:: boxcar_width(w: int = None)

      Unit used to smooth the spectrum.

      The boxcar width is the number of adjacent pixels that are averaged together to smooth the spectrum.
      Pixel average = 2* boxcar_width + 1

      :param w: boxcar width
      :type w: int


   .. py:method:: lamp_shutter(open=True)

      Opens or closes light source shutter, if feature is available on light source.)

      :param open: True opens the shutter/False closes it, defaults to False
      :type state: bool, optional


   .. py:method:: _take_spectrum(open=True)

      Collect a spectrum with the specified experimental parameters


   .. py:method:: dark_spectrum(int_time: float, scan_num: int, boxcar_w: int = None, save: bool = False, path: str = None, filename: str = None)

      Collect a dark spectrum with the specified experimental parameters.

      A dark spectrum is collected when no light is incident on the detector.
      This shuold later be used to correct the actual spectrum for dark counts (i.e. thermal noise).
      Note: these shuold be the same as the ones used for the actual spectrum.

      :param int_time: integration time


   .. py:method:: _collect_raw_spectrum(int_time: float, scan_num: int, boxcar_w: int, int_time_units: str = 'ms')

      Collect a spectrum with the specified experimental parameters

      :param int_time: integration time
      :type int_time: float
      :param scan_num: number of scans to average
      :type scan_num: int
      :param boxcar_w: boxcar width for smoothing the spectrum, defaults to None
      :type boxcar_w: int, optional
      :param int_time_units: units of integration time, defaults to 'ms'
      :type int_time_units: str, optional
      :return: spectrum
      :rtype: numpy array


   .. py:method:: collect_spectrum(location: Union[science_jubilee.labware.Labware.Well, Tuple, science_jubilee.labware.Labware.Location], int_time, scan_num, boxcar_w, int_time_units='ms', save: bool = False, filename: str = None, path: str = None)

      Collect spectrum at the specified location on the labware


   .. py:method:: save_to_file(data, dark: bool = False, path: str = None, filename: str = None)

      Save the spectrum to a file


   .. py:method:: read_from_file(filepath, scale=True, reference_spectrum=None)


   .. py:method:: scale_intensity(data: list, reference_spectrum: list)
      :staticmethod:



.. py:class:: MeasurementManager(metadata, raw_data)


   A class to manage the measurements taken by the SpectroscopyTool

   .. py:method:: pretty_print()


   .. py:method:: generate_file(filename, path)


   .. py:method:: read_file()