clophfit.prtecan.models
=======================

.. py:module:: clophfit.prtecan.models

.. autoapi-nested-parse::

   Prtecan/prtecan.py.



Classes
-------

.. autoapisummary::

   clophfit.prtecan.models.Labelblock
   clophfit.prtecan.models.Tecanfile
   clophfit.prtecan.models.LabelblocksGroup
   clophfit.prtecan.models.TecanfilesGroup
   clophfit.prtecan.models.PlateScheme


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

.. py:class:: Labelblock

   Parse a label block.

   :param lines:

   :raises ValueError: When data do not correspond to a complete 96-well plate.
   :raises TypeError: When normalization parameters are not numerical.

   .. rubric:: Notes

   Logs a warning when it replaces "OVER" with ``np.nan`` for saturated values.


   .. py:attribute:: lines
      :type:  dataclasses.InitVar[list[list[str | int | float]]]

      Lines to create this Labelblock.


   .. py:attribute:: filename
      :type:  str
      :value: ''


      Path of the corresponding Tecan file.


   .. py:attribute:: metadata
      :type:  dict[str, clophfit.prtecan.parsers.Metadata]

      Metadata specific for this Labelblock.


   .. py:attribute:: data
      :type:  dict[str, float]

      Plate data values as {'well_name', value}.


   .. py:attribute:: data_nrm
      :type:  dict[str, float]

      Plate data values normalized as {'well_name', value}.


   .. py:method:: almost_equal(other)

      Check if two Labelblocks are almost equal (same excitation and emission).



.. py:class:: Tecanfile

   Parse a Tecan .xls file.

   :param path: Path to `.xls` file.
   :type path: Path

   :raises FileNotFoundError: When path does not exist.
   :raises ValueError: When no Labelblock is found or file format is invalid.


   .. py:attribute:: metadata
      :type:  dict[str, clophfit.prtecan.parsers.Metadata]

      General metadata for Tecanfile, like `Date` and `Shaking Duration`.


   .. py:attribute:: labelblocks
      :type:  dict[int, Labelblock]

      All labelblocks contained in this file.


.. py:class:: LabelblocksGroup

   Group labelblocks with compatible metadata.

   :param labelblocks: Labelblocks to be grouped.
   :type labelblocks: list[Labelblock]
   :param allequal:

   :raises Exception: When labelblocks are neither equal nor almost equal.


   .. py:attribute:: allequal
      :type:  bool
      :value: False


      True if labelblocks already tested equal.


   .. py:attribute:: metadata
      :type:  dict[str, clophfit.prtecan.parsers.Metadata]

      Metadata shared by all labelblocks.


   .. py:property:: data
      :type: dict[str, list[float]]


      Grouped data if labelblocks are equal, otherwise empty.


   .. py:property:: data_nrm
      :type: dict[str, list[float]]


      Normalized data by number of flashes, integration time and gain.


.. py:class:: TecanfilesGroup

   Group of Tecanfiles containing at least one common Labelblock.

   :param tecanfiles: List of Tecanfiles.
   :type tecanfiles: list[Tecanfile]

   :raises ValueError: When no common Labelblock is found across all Tecanfiles.

   .. rubric:: Notes

   Logs a warning if the Tecanfiles do not contain the same number of
   Labelblocks that can be merged in the same order. In such cases,
   fewer LabelblocksGroup may be created.


   .. py:attribute:: labelblocksgroups
      :type:  dict[int, LabelblocksGroup]

      Each group contains its own data like a titration.


   .. py:attribute:: metadata
      :type:  dict[str, clophfit.prtecan.parsers.Metadata]

      Metadata shared by all tecanfiles.


.. py:class:: PlateScheme

   Define buffer, discard, ctrl and unk wells, and ctrl names.

   :param file: File path to the scheme file [<well Id, sample name>].
   :type file: Path


   .. py:property:: nofit_keys
      :type: set[str]


      Buffer and discarded wells.


   .. py:property:: buffer
      :type: list[str]


      List of buffer wells.


   .. py:property:: discard
      :type: list[str]


      List of discard wells.


   .. py:property:: ctrl
      :type: list[str]


      List of CTR wells.


   .. py:property:: names
      :type: dict[str, set[str]]


      A dictionary mapping sample names to their associated list of wells.