pyextal.jaxGeo.settings
=======================

.. py:module:: pyextal.jaxGeo.settings

.. autoapi-nested-parse::

   Every option of a refinement, in one place.

   `RefineSettings` is what `jaxGeo.refine.refine` runs and what the command line
   (`jaxGeo.cli`) fills in; the command line takes its defaults from an instance,
   so a script sets dataset defaults by building one. `resolved` checks the
   options against each other and returns a copy with every field in canonical
   form, so the Python API and the command line accept the same spellings.



Attributes
----------

.. autoapisummary::

   pyextal.jaxGeo.settings.GEOMETRY
   pyextal.jaxGeo.settings.PROBE_RANGE
   pyextal.jaxGeo.settings.SF_MASKS


Exceptions
----------

.. autoapisummary::

   pyextal.jaxGeo.settings.SetupError


Classes
-------

.. autoapisummary::

   pyextal.jaxGeo.settings.RefineSettings


Functions
---------

.. autoapisummary::

   pyextal.jaxGeo.settings._tuple
   pyextal.jaxGeo.settings._hkl


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

.. py:exception:: SetupError

   Bases: :py:obj:`ValueError`


   A dataset, file or option problem found before anything is refined.


.. py:data:: GEOMETRY
   :value: ('gl', 'rotation', 'tiltx', 'tilty')


.. py:data:: PROBE_RANGE
   :value: (0.05, 3.0)


.. py:data:: SF_MASKS

.. py:function:: _tuple(value, kind)

   A comma-separated string or a sequence, as a tuple of ``kind``.


.. py:function:: _hkl(value)

   ``'1,0,0'``, ``(1, 0, 0)`` -> ``(1, 0, 0)``.


.. py:class:: RefineSettings

   Options for `jaxGeo.refine.refine`.

   Field names match the command-line options (``geo_max_block`` is
   ``--geo-max-block``); the command line's ``--help`` describes each.


   .. py:attribute:: h5
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: dat
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: subsample
      :type:  int
      :value: 2



   .. py:attribute:: reflections
      :type:  Union[str, int, tuple]
      :value: 'review'



   .. py:attribute:: review_dir
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: symmetry
      :type:  Optional[str]
      :value: None



   .. py:attribute:: imag
      :type:  str
      :value: 'none'



   .. py:attribute:: layers
      :type:  int
      :value: 1



   .. py:attribute:: layer_fractions
      :type:  Optional[Tuple[float, ...]]
      :value: None



   .. py:attribute:: refine_layers
      :type:  Optional[Tuple[int, ...]]
      :value: None



   .. py:attribute:: diagonalise_measured
      :type:  bool
      :value: True



   .. py:attribute:: steps
      :type:  int
      :value: 800



   .. py:attribute:: warmup
      :type:  int
      :value: 5



   .. py:attribute:: lr
      :type:  float
      :value: 0.0001



   .. py:attribute:: tile
      :type:  int
      :value: 32



   .. py:attribute:: thickness_window
      :type:  float
      :value: 0.2



   .. py:attribute:: scale_window
      :type:  float
      :value: 0.05



   .. py:attribute:: background_window
      :type:  float
      :value: 0.05



   .. py:attribute:: kernel_radius
      :type:  int
      :value: 4



   .. py:attribute:: voigt
      :type:  bool
      :value: True



   .. py:attribute:: probe_sigma_start
      :type:  float
      :value: 0.5



   .. py:attribute:: probe_gamma_start
      :type:  float
      :value: 0.5



   .. py:attribute:: tilt_batch
      :type:  Optional[int]
      :value: None



   .. py:attribute:: sim_batch
      :type:  Optional[int]
      :value: None



   .. py:attribute:: sim_memory
      :type:  float
      :value: 1.5



   .. py:attribute:: memory_warn
      :type:  float
      :value: 8.0



   .. py:attribute:: figure
      :type:  Union[pathlib.Path, str, None]
      :value: 'auto'



   .. py:attribute:: history
      :type:  bool
      :value: True



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



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



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



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



   .. py:attribute:: precision
      :type:  str
      :value: 'highest'



   .. py:attribute:: geometry
      :type:  bool
      :value: True



   .. py:attribute:: geo_start
      :type:  int
      :value: 100



   .. py:attribute:: geo_every
      :type:  int
      :value: 100



   .. py:attribute:: geo_params
      :type:  Tuple[str, ...]
      :value: ('gl', 'rotation', 'tiltx', 'tilty')



   .. py:attribute:: geo_iters
      :type:  int
      :value: 8



   .. py:attribute:: geo_hessian
      :type:  str
      :value: 'auto'



   .. py:attribute:: geo_max_block
      :type:  Optional[float]
      :value: None



   .. py:attribute:: geo_tile
      :type:  Optional[int]
      :value: None



   .. py:attribute:: geo_step_gl
      :type:  float
      :value: 0.01



   .. py:attribute:: geo_step_rotation
      :type:  float
      :value: 0.2



   .. py:attribute:: geo_step_tilt
      :type:  float
      :value: 0.02



   .. py:attribute:: geo_trust
      :type:  float
      :value: 1.0



   .. py:attribute:: geo_refresh
      :type:  float
      :value: 2.0



   .. py:attribute:: geo_lambda
      :type:  float
      :value: 0.001



   .. py:attribute:: geo_tol
      :type:  float
      :value: 1e-05



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



   .. py:attribute:: oversub
      :type:  Tuple[Tuple[int, int, int], ...]
      :value: ()



   .. py:attribute:: oversub_start
      :type:  Optional[int]
      :value: None



   .. py:attribute:: oversub_leak
      :type:  bool
      :value: True



   .. py:method:: resolved()

      Checks the options and returns a canonical copy.

      :returns: ``reflections`` as 'exported'/'review'/int/tuple of
                triples, ``symmetry`` decided, ``layer_fractions`` normalised to
                sum to one, ``refine_layers`` and ``geo_params`` as tuples,
                ``oversub`` as triples and ``oversub_start`` filled in.
      :rtype: RefineSettings

      :raises SetupError: On any inconsistent or unknown option.



   .. py:property:: frozen_layers

      0-based layers whose structure factors are held (``OptConfig.frozen_layers``).


   .. py:method:: field_names()
      :classmethod: