cellmap_flow.ai_annotate.organelles
===================================

.. py:module:: cellmap_flow.ai_annotate.organelles

.. autoapi-nested-parse::

   What the model is told about each structure it can be asked to paint.

   A catalog of organelles: the colour to ask the model to paint each one, and a
   description of how it looks in EM to ground the request in what the
   structure actually looks like. Adapted from ask-to-mask's ORGANELLES catalog,
   keeping only the fields this feature uses. A label name the catalog does not
   know still works (``resolve_organelle_profile``), just without a description.

   The colours are distinct within the catalog but need not be unique across it
   (cells and mitochondria are both red): one request asks for one structure.



Attributes
----------

.. autoapisummary::

   cellmap_flow.ai_annotate.organelles.ORGANELLES


Classes
-------

.. autoapisummary::

   cellmap_flow.ai_annotate.organelles.OrganelleProfile


Functions
---------

.. autoapisummary::

   cellmap_flow.ai_annotate.organelles.find_organelle_profile
   cellmap_flow.ai_annotate.organelles.resolve_organelle_profile


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

.. py:class:: OrganelleProfile

   One structure: catalog key, plural name as used in the prompt, the
   colour asked for (as words for the prompt, and as RGB to find it in the
   reply), and its EM appearance.


   .. py:attribute:: key
      :type:  str


   .. py:attribute:: name
      :type:  str


   .. py:attribute:: color_name
      :type:  str


   .. py:attribute:: rgb
      :type:  tuple[int, int, int]


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



.. py:data:: ORGANELLES
   :type:  dict[str, OrganelleProfile]

.. py:function:: find_organelle_profile(label_name: str) -> OrganelleProfile | None

   The catalog profile a free-text label name means, or None.

   Matches a key, a name or a known alias, ignoring case, surrounding
   whitespace, and ``-``/``_`` versus spaces. None lets the caller fall back
   to a generic profile.


.. py:function:: resolve_organelle_profile(label_name: str) -> OrganelleProfile

   The catalog profile for ``label_name``, or a generic one built from it.

   A label the catalog does not know still works: the prompt names it as
   typed and asks for bright red, just without an EM-appearance description.