cellmap_flow.ai_annotate.pipeline
=================================

.. py:module:: cellmap_flow.ai_annotate.pipeline

.. autoapi-nested-parse::

   From a planned plane to labels: read the raw, ask the model, label the box.

   ``read_plane`` reads the plane ``geometry.plan_plane`` planned, on the image
   grid it planned and laid out as on screen; ``build_request`` makes it the
   request a backend sends; ``mask_to_write_shape`` cuts the mask the backend
   returns into its connected objects and puts them onto the write box's
   voxels, and ``labels_for_box`` (``accept_labels`` for Accept) turns those
   into the labels ``fill.paint_box`` writes: one id per object, background
   elsewhere, as a seed from a model's prediction is labelled.

   The maths is ``cellmap_flow.portable.ai_annotate``'s, which the browser runs
   too (its resampling is Pillow's, in both modes); what is the server's alone
   is reading the raw, through worldarray (``cellmap_flow.io.raw``).



Functions
---------

.. autoapisummary::

   cellmap_flow.ai_annotate.pipeline.raw_extent_nm
   cellmap_flow.ai_annotate.pipeline.read_plane
   cellmap_flow.ai_annotate.pipeline.build_request


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

.. py:function:: raw_extent_nm(volume: dict)

   ``(lo, hi)``, world nm z, y, x: where the volume's raw data is, read at
   its input voxel size (``plan_plane``'s ``data_box_nm``).


.. py:function:: read_plane(volume: dict, plan: cellmap_flow.ai_annotate.geometry.PlanePlan) -> numpy.ndarray

   The raw plane ``plan`` reads, as a 2D array of ``plan.image_shape``,
   laid out as on screen (``portable.ai_annotate.plane_image``).

   Read as stored (no input normalization: the image is scaled to 8 bits
   for the model on its own) at the plan's input voxel size, from the level
   of the volume's raw dataset for it, resampled when the volume was made
   with Resample on, as its trainer reads it. Outside the raw the read is
   padded with 0. The raw's dtype is kept unless the plane had to be
   resized to the image's grid, when it is float32.


.. py:function:: build_request(plane: numpy.ndarray, plan: cellmap_flow.ai_annotate.geometry.PlanePlan, profile, prompt_override=None)

   The ``SegmentRequest`` for ``plane``: its RGB image, the prompt and the colour.

   The prompt states ``plan.resolution_nm``, the pixel size of the image
   actually sent. ``prompt_override`` replaces the catalog's description
   (``prompts.build_recolor_prompt``).