cellmap_flow.finetune.session.manifest
======================================

.. py:module:: cellmap_flow.finetune.session.manifest

.. autoapi-nested-parse::

   The files a session is trained from, besides the volume itself.

   ``_virtual_sources.json`` in ``corrections/`` points the trainer at the
   annotation volume and carries the patch geometry and normalization;
   ``good_regions.json``, one level up, lists the regions the user marked as
   already right. ``has_painted_annotations`` says whether a volume holds
   scribbles as well as imported crops.



Attributes
----------

.. autoapisummary::

   cellmap_flow.finetune.session.manifest.logger
   cellmap_flow.finetune.session.manifest.VIRTUAL_MANIFEST_FILENAME
   cellmap_flow.finetune.session.manifest.GOOD_REGIONS_FILENAME


Functions
---------

.. autoapisummary::

   cellmap_flow.finetune.session.manifest.write_manifest
   cellmap_flow.finetune.session.manifest.read_manifest
   cellmap_flow.finetune.session.manifest.good_regions_path
   cellmap_flow.finetune.session.manifest.load_good_regions
   cellmap_flow.finetune.session.manifest.save_good_regions
   cellmap_flow.finetune.session.manifest.load_good_regions_for
   cellmap_flow.finetune.session.manifest.voxels_inside_any_bbox
   cellmap_flow.finetune.session.manifest.has_painted_annotations


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

.. py:data:: logger

.. py:data:: VIRTUAL_MANIFEST_FILENAME
   :value: '_virtual_sources.json'


.. py:data:: GOOD_REGIONS_FILENAME
   :value: 'good_regions.json'


.. py:function:: write_manifest(corrections_dir: str, manifest: dict) -> str

   Persist a manifest sentinel that ``create_dataloader`` looks for.


.. py:function:: read_manifest(corrections_dir: str) -> Optional[dict]

   Return the manifest if present, else ``None``.


.. py:function:: good_regions_path(corrections_dir: Optional[str]) -> Optional[str]

   Where the good regions of the session owning ``corrections_dir`` live:
   beside it, in the session directory. None without a corrections dir.


.. py:function:: load_good_regions(path: Optional[str]) -> list

   The regions stored at ``path``; [] when there are none or they can't be read.


.. py:function:: save_good_regions(path: str, regions: list) -> bool

   Replace the regions at ``path`` atomically; False if it could not be written.


.. py:function:: load_good_regions_for(corrections_dir: Optional[str]) -> list

   Read the session's good regions, if any were marked.

   Deliberately read here rather than snapshotted into the manifest: the
   manifest is written when crops are imported, and regions get marked
   afterwards, for as long as the user keeps browsing. Reading at training
   time means the run uses every region marked up to the moment it started.


.. py:function:: voxels_inside_any_bbox(voxels: numpy.ndarray, bbox_offsets: numpy.ndarray, bbox_ends: numpy.ndarray) -> numpy.ndarray

   Return a boolean mask: ``True`` where ``voxels[i]`` lies inside any
   ``[bbox_offsets[j], bbox_ends[j])`` half-open box.

   voxels: (N, 3) int. bbox_offsets, bbox_ends: (M, 3) int. Vectorized
   over both: builds an (N, M) inside-test matrix and reduces along M.
   For typical M ~ 1-10 the temporary stays small.


.. py:function:: has_painted_annotations(volume_zarr_path: str) -> bool

   Whether the volume holds annotations outside its imported crops.

   Those are painted: scribbles, sparse by construction, with unannotated
   voxels all around them. Chunks entirely inside a crop are not read.