neu_vol.ops.roi

Extract / crop / pad a region of interest into a new multiscale volume.

A thin wrapper over convert(), adding the crop-and-pad contract: start may be negative and stop may exceed the source extent, and the margin is filled with pad_value rather than trimmed. Metadata, including the source’s offset, comes from the source as in convert, so the ROI lands in the source’s frame.

Attributes

logger

Functions

extract_roi(src, dst, start, stop[, voxel_size, ...]) → dict

Extract src[start:stop] (spatial) into a new volume at dst.

Module Contents

neu_vol.ops.roi.extract_roi(src: str | dict, dst: str, start: Sequence[int], stop: Sequence[int], voxel_size: Sequence[float] | None = None, *, src_format: str | None = None, pad_value: float = 0, units: str | None = None, axes: Sequence[str] | None = None, offset: Sequence[float] | None = None, has_channels: bool | None = None, profile: str = 'local', chunk: Sequence[int] | None = None, shard: Sequence[int] | None = None, dtype: str | None = None, kind: str = 'image', encoding: str | None = None, compressed_segmentation_block_size: Sequence[int] = (8, 8, 8), multiscale: bool = False, factors: Sequence[Sequence[int]] | None = None, max_levels: int = 8, min_dim: int = 128, name: str = 'image', client: Any | None = None, npartitions: int | None = None, delete_existing: bool = False, resume: bool = False, verify: bool = False, progress_path: str | None = None, validate: bool = True) → dict

Extract src[start:stop] (spatial) into a new volume at dst.

start may be negative and stop may exceed the source extent; the out-of-bounds margin is filled with pad_value (crop and pad in one). To trim to the volume instead — the right default when copying real data — call convert(..., crop_start=, crop_stop=), which clips.

voxel_size/units/axes/offset are read from the source when it carries them and only need passing for a source that does not (bare arrays, HDF5, image stacks) or to override what it says.

neu_vol.ops.roi.logger