transformnd 0.3.0

ND coordinate transformations

transformnd

A library providing an API for coordinate transformations, as well as some common transforms. The goal is to allow downstream applications which require such transformations (e.g. image registration) to be generic over anything inheriting from transformnd.Transform.

The base classes and utilities are very lightweight with few dependencies, for use as an API; additional transforms and features use extras.

Heavily inspired by/ cribbed directly from Philipp Schlegel's work in navis; co-developed with xform as a red team prototype.

N coordinates in D dimensions are given as a numpy array of shape (N, D).

Transform subclasses which are restricted to certain dimensionalities can specify this in their ndim class variable. Instances of Transform subclasses can further restrict their ndim. Use self._validate_coords(coords) in the apply method to ensure the coordinates are of valid type and dimensions.

Additionally, transformnd provides an interface for transforming types other than NxD numpy arrays, and implements these adapters for a few common types.

See the tutorial here. It is a marimo notebook. Open it with uv run --group tutorial marimo edit examples/tutorial.py.

Implemented transforms

• Identity (transformnd.transforms.Identity)
• Translation (transformnd.transforms.Translate)
• Scale (transformnd.transforms.Scale)
• Reflection (transformnd.transforms.Reflect)
• Affine (transformnd.transforms.Affine)
  • Can be composed efficiently with @ operator; the right hand operand is effectively applied first
• MapAxis (transformnd.transforms.MapAxis): permute coordinate axes
• ByDimension (transformnd.transforms.ByDimension): apply transformations to subsets of coordinate axes
• Moving Least Squares, affine (transformnd.transforms.moving_least_squares.MovingLeastSquares)
  • uses movingleastsquares extra
• Thin Plate Splines (transformnd.transforms.thinplate.ThinPlateSplines)
  • uses thinplatesplines extra

Arbitrary transforms can be composed into a TransformSequence with transform1 | transform2. A graph of transforms between defined spaces can be traversed using the TransformGraph.

Implemented adapters

• Numpy arrays of shape (..., D, ...) (transformnd.adapters.ReshapeAdapter)
• meshio.Mesh (transformnd.adapters.meshio.MeshAdapter)
• pandas.DataFrame (transformnd.adapters.pandas.PandasAdapter)
  • Takes a subset of columns as a coordinate array
• polars.DataFrame (transformnd.adapters.polars.PolarsAdapter)
  • Similar to the pandas adapter
  • Currently, only scalar columns are supported (e.g. not a single struct column with fields x, y, z)
• Geometries from shapely (transformnd.adapters.shapely.GeometryAdapter)
• Objects composed of transformable attributes (transformnd.adapters.AttrAdapter).

Additional transforms and adapters

Contributions of additional transforms and adapters are welcome! Even if they're only thin wrappers around an external library, the downstream ecosystem benefits from a consistent API.

Such external transformation libraries should be specified as "extras" (pyproject.toml:project.optional-dependencies), and be contained in a submodule so that they are not immediately imported with transformnd.

Alternatively, consider adopting transformnd's base classes in your own library, and have your transformation instantly compatible for downstream users.

Methods which MUST be implemented:

• __init__: should validate parameters and must call the super() constructor
• apply: should call _validate_coords method early to check that the given coordinates are the correct shape

Methods which SHOULD be implemented if applicable:

• to_device: if any of the transformation's parameters need to be placed on a specific device (e.g. affine matrices on the GPU)
• is_identity: if you can cheaply check whether your transformation is an identity transformation. The base class implementation returns False.
• to_affine: if your transformation can be represented as an affine matrix. The base class implementation returns None.
• invert: if your transformation can be inverted (default None if not)
  • This automatically implements __invert__ (the ~my_transform operator), which returns NotImplemented (probably raising NotImplementedError) if invert would return None.

Contributing

• Use uv for environment and dependency management.
  • uv sync to set up the environment.
• Use prek for running pre-commit hooks.
  • prek install-hooks && prek run --all-files to get started.
• Use just for common development tasks (format, lint, test, generate docs, run benchmarks).
  • just to list commands.
• Docs are generated with pdoc (use just doc) and hosted on ReadTheDocs
• just bump bumps the version, commits, and tags (but does not push); depends on schpet/changelog

Thanks

Thanks to contributors

• Francesca Drummer
• Lorenzo Cerrone
• Maks Hess
• Silvia Maria Macrì