cellmap_flow.finetune.session.fill

Labelling a whole box of an annotation volume at once.

The Finetune tab’s “Seed” and “All background” buttons label the box on screen in one click: from the model’s own prediction, for the user to clean up with the brush, or all background (1), for a region of false positives. Either way only unannotated voxels (0) are filled. A stroke the user painted is a decision about that voxel; a seed is a guess. “Split objects” relabels the box’s foreground by connected component (relabel_objects), so a background wall painted through a merged object gives it two ids again.

The objects a seed writes come from post.segment, the segmenter that fits the model (seed_labels takes its labels). Split Objects is 6-connected by default (face neighbours, scipy’s default): a one-voxel wall the brush paints cuts an object under it, where under 26-connectivity the voxels across a diagonal wall would still touch.

The write goes to MinIO, as cc3d_relabel’s does, not to the volume on disk: MinIO holds strokes the periodic sync has not pulled yet, which is what “only fill 0s” must see, and it is what neuroglancer reads. The caller then pulls the changed chunks to disk with sync.sync_volume, so disk and MinIO agree and the periodic sync has nothing to revert.

Attributes

logger

Functions

box_voxels(volume, offset_nm, shape_nm, volume_shape)	(lo, hi): the annotation voxels whose centres lie in a box, clipped to the volume.
seed_labels(objects, existing[, count_up])	Labels for a box from a segmentation: an id per object inside, 1 outside.
relabel_objects(existing[, count_up, connectivity, ...])	The box's foreground (labels 2 and up) relabelled by connected component.
open_served_labels(state, volume_id)	The volume's annotation/s0 as MinIO serves it, open for writing.
fill_unpainted(state, volume_id, lo, hi, labels_for[, ...])	Write labels_for(existing) into the box [lo, hi) where the volume holds 0.
rewrite_foreground(state, volume_id, lo, hi, relabel)	Write relabel(existing)'s labels over the box's foreground voxels.
restore_box(state, volume_id, lo, hi, before, after)	Put the box back to before where it still holds after: an undo.

Module Contents

cellmap_flow.finetune.session.fill.logger

cellmap_flow.finetune.session.fill.box_voxels(volume, offset_nm, shape_nm, volume_shape)

(lo, hi): the annotation voxels whose centres lie in a box, clipped to the volume.

offset_nm and shape_nm are the box’s lower corner and size in world nm, as a good region records them; volume is the volume’s record, for its grid. None when no voxel of the volume is in the box.

cellmap_flow.finetune.session.fill.seed_labels(objects, existing, count_up=False)

Labels for a box from a segmentation: an id per object inside, 1 outside.

objects is a post.segment segmenter’s output over the box (0 background, objects 1..n), existing what the box holds now. Each object gets an id of its own (_fresh_ids; count_up for an instance target), so neighbouring objects are told apart, and a merge the model made shows as one colour to split; but an object the user has already painted part of takes the id painted there most, or the unpainted rest of it would be taught as a different object from its painted part. A binary or distance target reads every id as foreground, so the ids cost it nothing.

cellmap_flow.finetune.session.fill.relabel_objects(existing, count_up=False, connectivity=1, per_slice=False)

The box’s foreground (labels 2 and up) relabelled by connected component.

Each component takes the id most of its voxels hold, so a stroke that joins two objects merges them into the id of the bigger. An id left on several components, an object a background wall cut in two, stays on the largest and the others get fresh ids (_fresh_ids). Background (1) and unpainted (0) voxels are left alone. Returns (labels, counts): counts has objects, split (components given a fresh id) and merged (components that held more than one id).

A cut has to go through every slice the object spans: the brush paints one slice, and an object cut in one slice is still one object above and below it. split is 0 then, which the page says. With per_slice each z slice’s pieces are components on their own, so a wall in one slice splits that slice, and every slice of an object gets its own id. connectivity: as for post.segment.connected_components.

cellmap_flow.finetune.session.fill.open_served_labels(state, volume_id)

The volume’s annotation/s0 as MinIO serves it, open for writing.

The bucket key is <volume_id>.zarr, as for the sync.

cellmap_flow.finetune.session.fill.fill_unpainted(state, volume_id, lo, hi, labels_for, local_zarr_path=None, undo=None)

Write labels_for(existing) into the box [lo, hi) where the volume holds 0.

labels_for gets the box as MinIO holds it and returns labels of the same shape (0 for “leave as it is”). Returns (n_foreground, n_background): how many voxels were filled with each. Nothing is written when nothing would change. undo, a list, gets (lo, hi, before, after) appended when something was written (restore_box).

cellmap_flow.finetune.session.fill.rewrite_foreground(state, volume_id, lo, hi, relabel, local_zarr_path=None, undo=None)

Write relabel(existing)’s labels over the box’s foreground voxels.

relabel gets the box as MinIO holds it and returns (labels, counts) (relabel_objects); only foreground voxels (2 and up) whose label changed are written, so a stroke painted meanwhile elsewhere in the box is kept. Returns (n_changed, counts). undo: as for fill_unpainted.

cellmap_flow.finetune.session.fill.restore_box(state, volume_id, lo, hi, before, after)

Put the box back to before where it still holds after: an undo.

Only voxels the action changed and nobody has touched since go back, so a stroke painted in the box after the action is kept. Returns how many voxels were restored.