cellmap_flow.portable.regions

Good regions on numbers alone: the region a mark makes, its size, which stored entries are regions, and where a region anchors the model on a volume’s grid, so that the server and the browser make, draw and place a region the same way. dashboard/routes/finetune/good_regions.py says what good regions are for; its routes and the server’s trainer (finetune/data/sampler.py) call these in their process, and the browser’s routes and trainer (web/src/backend/routes/good-regions.ts, web/src/finetune/run.ts) call them through volume_calls.py.

A region is {"id", "label", "offset_nm", "shape_nm"}: a box in world nm, z, y, x, its lower corner and its size, as good_regions.json keeps it.

Attributes

DEFAULT_REGION_SIZE_NM

Functions

`default_size_nm`([output_size, output_voxel_size]) → list	One model output patch of a volume, in nm (see DEFAULT_REGION_SIZE_NM):
`region_size_nm`(size_nm[, output_size, output_voxel_size]) → list	The size a mark asks for, in nm, z, y, x.
`new_region`(centre_nm, size_nm, count[, label, region_id]) → dict	The region a mark makes: a box of `size_nm` centred on `centre_nm`,
`region_box_nm`(region) → Optional[tuple]	`(offset_nm, shape_nm)` of a stored region, as float arrays, or None
`region_centre_voxels`(region, corner_nm, voxel_nm, ...) → tuple	Where a region's centre lies on a volume's grid: `(where, centre)`.
`anchor_boxes`(regions, corner_nm, voxel_nm, ...) → dict	The box of the volume's voxels each region anchors, and which were skipped.

Module Contents

cellmap_flow.portable.regions.DEFAULT_REGION_SIZE_NM = 896.0

cellmap_flow.portable.regions.default_size_nm(output_size=None, output_voxel_size=None) → list: One model output patch of a volume, in nm (see DEFAULT_REGION_SIZE_NM): output_size voxels of output_voxel_size nm, or 896 nm a side when either is missing or not numbers.

cellmap_flow.portable.regions.region_size_nm(size_nm, output_size=None, output_voxel_size=None) → list

The size a mark asks for, in nm, z, y, x.

No size (None, 0, an empty list) is one output patch of the volume (default_size_nm of output_size and output_voxel_size); one number, alone or in a list, is the same along every axis; else three numbers. ValueError (“size_nm must be positive”) for anything else: a size that is not a number, not finite or not positive, or of another length.

cellmap_flow.portable.regions.new_region(centre_nm, size_nm, count: int, label=None, region_id: str | None = None) → dict: The region a mark makes: a box of size_nm centred on centre_nm, labelled label (a non-empty string), or good-<count + 1> after count regions; its id eight hex digits unless region_id is given.

cellmap_flow.portable.regions.region_box_nm(region) → tuple | None: (offset_nm, shape_nm) of a stored region, as float arrays, or None when the entry is not a region: a mapping whose offset_nm and shape_nm are three finite numbers each, its shape positive. Its id and label are not needed to place it.

cellmap_flow.portable.regions.region_centre_voxels(region, corner_nm, voxel_nm, shape_voxels) → tuple

Where a region’s centre lies on a volume’s grid: (where, centre).

corner_nm is the volume’s voxel-0 lower corner (volume_corner_nm), voxel_nm its output voxel size and shape_voxels its shape. The centre is in voxels from the corner (voxel v spans [v, v + 1)). where is “malformed” (not a region, region_box_nm; the centre is None), “outside” (a region marked on another volume, which would anchor the model to padding) or “inside”.

cellmap_flow.portable.regions.anchor_boxes(regions, corner_nm, voxel_nm, shape_voxels, block) → dict

The box of the volume’s voxels each region anchors, and which were skipped.

The box is the rehearsal patch the server’s trainer cuts for the region: one output block whose start is the region’s centre snapped so that the block is whole voxels (PatchReader.snap: floor(c - block/2 + 1/2)), clipped to the volume. Answers {"boxes": [{"region", "lo", "hi"}], "malformed": [...], "outside": [...]}, each region by its index in regions and each box [lo, hi) in voxels, z, y, x.