cellmap_flow.portable
=====================

.. py:module:: cellmap_flow.portable

.. autoapi-nested-parse::

   The logic both modes run, written once.

   Python importable with the standard library, numpy, scipy, pydantic and
   Pillow alone, so that the server runs it in its process and the browser runs
   the same files in chunkmirage's Pyodide workers (web/build/portable.ts bundles
   them as text, ``Inference.python`` calls them; ``calls.py`` is what the
   browser calls, and ``volume_calls.py`` for a volume's plan and its good
   regions, ``volume.py`` and ``regions.py``). ``label_it.py`` is Label it's
   segmentation of a prediction, read by
   ``dashboard/routes/finetune/view_labels.py`` and, through
   ``label_it_calls.py``, by ``web/src/backend/routes/view-labels.ts``.
   ``activation.py`` reads a model's output activation from its network's
   graph, for the inference server (inference/runner.py) and the browser's
   served model (web/src/finetune/onnx-proto.ts, through ``calls.py``).
   ``tests/portable/test_boundary.py`` holds every module here to that
   boundary. Nothing here reads a file, a zarr or the network: the callers do,
   around it (``finetune/session/volume.py``'s ``carry_paint`` and
   ``plan_volume``,
   ``dashboard/routes/finetune/rank_routes.py``, ``web/src/backend/routes/rank.ts``).
   A finetune's training targets are ``targets.py``, which the server's
   ``finetune/target_transforms.py`` wraps and the browser calls through
   ``targets_calls.py``.
   AI-assisted annotation's plane, image, mask and labels are ``ai_annotate.py``
   (the browser calls ``ai_annotate_calls.py``), and the label decisions under
   it and the Finetune tab's box tools are ``fill.py`` (the browser's box tools
   call ``fill_calls.py``).
   A model published to Hugging Face, its card, its manifest's "published"
   block and the app's links to it, is ``publish.py``, which the server's
   publish route calls and the browser's through ``publish_calls.py``.
   A dataset path as a person pastes it, a path copied from Neuroglancer with
   its format, is ``pasted.py``, whose pattern the browser reads from the
   export (``web/build/export_data.py``) rather than through Pyodide: it is
   needed before any worker is started.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/cellmap_flow/portable/activation/index
   /autoapi/cellmap_flow/portable/ai_annotate/index
   /autoapi/cellmap_flow/portable/ai_annotate_calls/index
   /autoapi/cellmap_flow/portable/calls/index
   /autoapi/cellmap_flow/portable/carry/index
   /autoapi/cellmap_flow/portable/fill/index
   /autoapi/cellmap_flow/portable/fill_calls/index
   /autoapi/cellmap_flow/portable/label_it/index
   /autoapi/cellmap_flow/portable/label_it_calls/index
   /autoapi/cellmap_flow/portable/pasted/index
   /autoapi/cellmap_flow/portable/publish/index
   /autoapi/cellmap_flow/portable/publish_calls/index
   /autoapi/cellmap_flow/portable/rank/index
   /autoapi/cellmap_flow/portable/regions/index
   /autoapi/cellmap_flow/portable/targets/index
   /autoapi/cellmap_flow/portable/targets_calls/index
   /autoapi/cellmap_flow/portable/volume/index
   /autoapi/cellmap_flow/portable/volume_calls/index