navis.transforms.h5reg.H5transform

class navis.transforms.h5reg.H5transform(f, direction='forward', level=-1, cache=False, full_ingest=False)

Hdf5 transform of 3D spatial data.

See here for specifications of the format.

Parameters:

• f (str) – Path to Hdf5 transformation.

• direction ("forward" | "inverse") – Direction of transformation.

• level (int, optional) – For Hdf5 files with deformation fields at multiple resolutions: what level of detail to use. Negative values go backwards from the highest available resolution (-1 = highest, -2 = second highest, etc). Ignored if only a single deformation field present.

• cache (bool) – If True, we will cache the deformation field for subsequent future transforms. This will speed up future calculations in the future but comes at a memory cost.

• full_ingest (bool) – If True, will read and cache the full deformation field at initialization. This additional upfront cost can pay off if you are about to make many transforms across the volume.

Init class.

__init__(f, direction='forward', level=-1, cache=False, full_ingest=False)

Init class.

Methods

__init__(f[, direction, level, cache, ...])	Init class.
append(other)	Append another transform to this one.
check_if_possible([on_error])	Test if running the transform is possible.
copy()	Return copy.
from_file(filepath, **kwargs)	Generate H5transform from file.
full_ingest()	Fully ingest the deformation field.
precache(bbox[, padding])	Cache deformation field for given bounding box.
xform(points[, affine_fallback, force_deform])	Xform data.

Attributes

level
use_cache	Whether to cache the deformation field.