:mod:`neuron_morphology.snap_polygons._from_lims`
=================================================

.. py:module:: neuron_morphology.snap_polygons._from_lims

.. autoapi-nested-parse::

   This module contains utilities for running snap_polygons directly from the
   Allen Institute's internal Laboratory Information Management System.

   Example Usage
   -------------
   python -m neuron_morphology.snap_polygons
       --host <lims host> 
       --port <lims port> 
       --user <username> 
       --password <password> 
       --database <lims db> 
       --focal_plane_image_series_id 522408212 # for instance
       --image_output_root /some_directory

   ..
       !! processed by numpydoc !!



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

Classes
~~~~~~~

.. autoapisummary::

   neuron_morphology.snap_polygons._from_lims.PostgresInputConfigSchema
   neuron_morphology.snap_polygons._from_lims.FromLimsSchema
   neuron_morphology.snap_polygons._from_lims.FromLimsSource



Functions
~~~~~~~~~

.. autoapisummary::

   neuron_morphology.snap_polygons._from_lims.query_for_layer_polygons
   neuron_morphology.snap_polygons._from_lims.query_for_cortical_surfaces
   neuron_morphology.snap_polygons._from_lims.query_for_images
   neuron_morphology.snap_polygons._from_lims.query_for_image_dims
   neuron_morphology.snap_polygons._from_lims.get_inputs_from_lims


.. data:: QueryEngineType
   

   

.. function:: query_for_layer_polygons(query_engine: QueryEngineType, focal_plane_image_series_id: int, validate_polys: bool = True, treatment: str = 'Biocytin') -> List[Dict[str, Union[NicePathType, str]]]

   Get all layer polygons for this image series


   :Parameters:

       **query_engine** : executes a query, passed in as a string. Must not require
           any additional database information.

       **focal_plane_image_series_id** : used to determine which polygons to fetch
           ..

       **validate_polys** : if True, fail when
           - a label is associated with multiple distinct valid geometries
           - a label is associated with one or more geometries, but none are valid

       **treatment: The layer polygons are associated with Biocytin and DAPI**
           treatments. We only need one.

   :Returns:

       A collection of labelled polygons.
           ..













   ..
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.. function:: query_for_cortical_surfaces(query_engine: QueryEngineType, focal_plane_image_series_id: int) -> Tuple[Dict[str, Union[NicePathType, str]], Dict[str, Union[NicePathType, str]]]

   Return the pia and white matter surface drawings for this image series
















   ..
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.. function:: query_for_images(query_engine: QueryEngineType, focal_plane_image_series_id: int, output_dir: str) -> List[Dict[str, str]]

   Return Biocytin and DAPI images associated with a focal plane image 
   series
















   ..
       !! processed by numpydoc !!


.. function:: query_for_image_dims(query_engine: QueryEngineType, focal_plane_image_series_id: int) -> Tuple[float, float]

   Find the dimensions of the Biocytin image associated with a focal plane
   image series
















   ..
       !! processed by numpydoc !!


.. function:: get_inputs_from_lims(host: str, port: int, database: str, user: str, password: str, imser_id: int, image_output_root: Optional[str])

   Utility for building module inputs from a direct LIMS query
















   ..
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.. py:class:: PostgresInputConfigSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

   Bases: :class:`marshmallow.Schema`

   The parameters required to query a postgres database.
















   ..
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   .. attribute:: host
      

      

   .. attribute:: database
      

      

   .. attribute:: user
      

      

   .. attribute:: password
      

      

   .. attribute:: port
      

      


.. py:class:: FromLimsSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

   Bases: :class:`neuron_morphology.snap_polygons._from_lims.PostgresInputConfigSchema`

   The parameters required to query LIMS for a set of cortical layer 
   polygons and cortical surface boundaries. 
















   ..
       !! processed by numpydoc !!

   .. attribute:: focal_plane_image_series_id
      

      

   .. attribute:: image_output_root
      

      


.. py:class:: FromLimsSource

   Bases: :class:`argschema.sources.ArgSource`

   An alternate argschema source which gets its inputs from lims directly
















   ..
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   .. attribute:: ConfigSchema
      

      

   .. method:: get_dict(self)