Project axis

CHANGELOG.md

@@ -2,6 +2,19 @@
 
 ## Unreleased
 
+### Fixed
+
+- Rectangular affines now have the correct input and output dimensions
+
+### Added
+
+- ProjectAxis transformation for adding and dropping axes
+
+### Changed
+
+- Expose all transforms under `.transforms`, even if they are optional
+- BREAKING: Rename `GeometryAdapter` to `ShapelyAdapter`
+
 ## 0.5.0 - 2026-06-17
 
 ### Added

README.md

@@ -44,24 +44,23 @@ All transforms are accessed under the `transformnd.transforms` subpackage.
 | `MapAxis` | | Rearrange axes of the input coordinates |
 | `Affine` | | Multiply augmented coordinates by an affine transformation matrix. Can represent all of the above transformations. Can be composed with matrix multiplication `aff2 @ aff1`. |
 | `ByDimension` | | Apply different transformations to subsets of the input coordinates' dimensions |
-| `moving_least_squares.MovingLeastSquares` | `movingleastsquares` | Landmark-based transformation. |
-| `thin_plate_splines.ThinPlateSplines` | `thinplatesplines` | Landmark-based transformation. |
-| `vector_field.Coordinates` | `vectorfield` for in-memory, `vectorfield-dask` for chunked | Look up output coordinates in a vector field indexed by the input coordinates |
-| `vector_field.Displacements` | `vectorfield`, `vectorfield-dask` for chunked | Look up translations in a vector field indexed by the input coordinates, and add them to input coordinates |
+| `MovingLeastSquares` | `movingleastsquares` | Landmark-based transformation. |
+| `ThinPlateSplines` | `thinplatesplines` | Landmark-based transformation. |
+| `Coordinates` | `vectorfield` for in-memory, `vectorfield-dask` for chunked | Look up output coordinates in a vector field indexed by the input coordinates |
+| `Displacements` | `vectorfield`, `vectorfield-dask` for chunked | Look up translations in a vector field indexed by the input coordinates, and add them to input coordinates |
 
 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`)
+- Geometries from `shapely` (`transformnd.adapters.shapely.ShapelyAdapter`)
 - Objects composed of transformable attributes (`transformnd.adapters.AttrAdapter`).
 
 ## Additional transforms and adapters

justfile

@@ -47,5 +47,8 @@ bump level:
     git commit -m "Bump to v$(uv version --short)"
     git tag -a "v$(uv version --short)" -m "$(changelog entry latest)"
 
+pre-commit:
+    uv run --group dev prek run --all-files
+
 repl:
     uv run --all-groups --all-extras --with ipython ipython

src/transformnd/adapters/__init__.py

@@ -12,7 +12,6 @@
 
 See `.pandas.DataFrameAdapter` for an example of creating an adapter
 for an external type.
-
 """
 
 from .base import (
@@ -23,6 +22,9 @@
     ReshapeAdapter,
     SimpleAdapter,
 )
+from .pandas import PandasAdapter
+from .polars import PolarsAdapter
+from .shapely import ShapelyAdapter
 
 __all__ = [
     "BaseAdapter",
@@ -31,4 +33,7 @@
     "FnAdapter",
     "AttrAdapter",
     "ReshapeAdapter",
+    "PandasAdapter",
+    "PolarsAdapter",
+    "ShapelyAdapter",
 ]

src/transformnd/adapters/pandas.py

@@ -1,15 +1,18 @@
 """Adapt pandas DataFrames for transformation."""
 
 from collections.abc import Hashable
+from typing import TYPE_CHECKING
 
-import pandas as pd
 import numpy as np
 
 from ..base import Transform
 from .base import BaseAdapter
 
+if TYPE_CHECKING:
+    import pandas as pd
 
-class PandasAdapter(BaseAdapter[pd.DataFrame, np.ndarray]):
+
+class PandasAdapter(BaseAdapter["pd.DataFrame", np.ndarray]):
     def __init__(self, columns: list[Hashable]):
         """Adapt transformation for coordinates stored in a pandas DataFrame.
 
@@ -21,8 +24,8 @@ def __init__(self, columns: list[Hashable]):
         self.columns = columns
 
     def apply(
-        self, transform: Transform, df: pd.DataFrame, in_place: bool = False
-    ) -> pd.DataFrame:
+        self, transform: Transform, df: "pd.DataFrame", in_place: bool = False
+    ) -> "pd.DataFrame":
         """Transform the dataframe, optionally in-place.
 
         Parameters

src/transformnd/adapters/polars.py

@@ -1,13 +1,16 @@
 """Adapt polars DataFrames for transformation."""
 
-import polars as pl
+from typing import TYPE_CHECKING
 import numpy as np
 
 from ..base import Transform
 from .base import BaseAdapter
 
+if TYPE_CHECKING:
+    import polars as pl
 
-class PolarsAdapter(BaseAdapter[pl.DataFrame, np.ndarray]):
+
+class PolarsAdapter(BaseAdapter["pl.DataFrame", np.ndarray]):
     def __init__(self, columns: list[str]):
         """Adapt transformation for coordinates stored in a polars DataFrame.
 
@@ -19,8 +22,8 @@ def __init__(self, columns: list[str]):
         self.columns = columns
 
     def apply(
-        self, transform: Transform, df: pl.DataFrame, in_place: bool = False
-    ) -> pl.DataFrame:
+        self, transform: Transform, df: "pl.DataFrame", in_place: bool = False
+    ) -> "pl.DataFrame":
         """Transform the dataframe, optionally in-place.
 
         Parameters

src/transformnd/adapters/shapely.py

@@ -1,21 +1,24 @@
 import logging
+from typing import TYPE_CHECKING
 
 import numpy as np
-import shapely
-from shapely.geometry.base import BaseGeometry
-from shapely.coords import CoordinateSequence
 
 from ..base import Transform, ArrayT
 from .base import BaseAdapter
 
+if TYPE_CHECKING:
+    from shapely.geometry.base import BaseGeometry
+    from shapely.coords import CoordinateSequence
+
+
 logger = logging.getLogger(__name__)
 
 
-def as_numpy(coords: CoordinateSequence) -> np.ndarray:
+def as_numpy(coords: "CoordinateSequence") -> np.ndarray:
     return np.asarray(coords)
 
 
-class GeometryAdapter(BaseAdapter[BaseGeometry, ArrayT]):
+class ShapelyAdapter(BaseAdapter["BaseGeometry", ArrayT]):
     """Transform shapely geometries.
 
     As well as the generic `apply()`,
@@ -27,7 +30,7 @@ class GeometryAdapter(BaseAdapter[BaseGeometry, ArrayT]):
     N.B. shapely geometries' coordinates are in `XY(Z)` order
     """
 
-    def apply[T: BaseGeometry](
+    def apply[T: "BaseGeometry"](
         self,
         transform: Transform,
         obj: T,
@@ -51,6 +54,7 @@ def apply[T: BaseGeometry](
         T
             An object of the same type as the input.
         """
+        import shapely
 
         def fn(coords: np.ndarray) -> np.ndarray:
             c = coords.copy()

src/transformnd/transforms/__init__.py

@@ -5,15 +5,27 @@
 from .simple import Identity, Scale, Translate
 from .map_axis import MapAxis
 from .bijection import Bijection
-from .by_dimension import ByDimension
+from .project_axis import ProjectAxis, Insert, Remove
+from .by_dimension import ByDimension, SubTransform
+from .vector_field import Coordinates, Displacements
+from .moving_least_squares import MovingLeastSquares
+from .thinplate import ThinPlateSplines
 
 __all__ = [
     "Affine",
     "Identity",
+    "ProjectAxis",
+    "Insert",
+    "Remove",
     "Reflect",
     "Scale",
     "Translate",
     "MapAxis",
     "Bijection",
     "ByDimension",
+    "SubTransform",
+    "Coordinates",
+    "Displacements",
+    "MovingLeastSquares",
+    "ThinPlateSplines",
 ]

src/transformnd/transforms/affine.py

@@ -42,7 +42,7 @@ def __init__(
         ----------
         matrix
             Affine transformation matrix,
-            i.e. a 2D array-like with shape `(Di + 1, Do + 1)`,
+            i.e. a 2D array-like with shape `(Do + 1, Di + 1)`,
             where the bottom row is all 0s except in the rightmost column, which is 1.
         spaces
             Optional source and target spaces
@@ -64,7 +64,7 @@ def __init__(
                 f"Transformation matrix is not affine (expected bottom row {expected}, got {bottom_row})."
             )
 
-        super().__init__(NDims(m.shape[0] - 1, m.shape[1] - 1), spaces=spaces)
+        super().__init__(NDims(m.shape[1] - 1, m.shape[0] - 1), spaces=spaces)
 
         self.matrix: np.ndarray = m
 

src/transformnd/transforms/by_dimension.py

@@ -8,14 +8,35 @@
 
 
 class SubTransform[ArrayT]:
-    """Transformation to apply to subsets of the input dimensions and which output dimensions they calculate."""
+    """Component of the `ByDimension` transformation.
+
+    Transformation to apply to subsets of the input dimensions and which output dimensions they calculate.
+    """
 
     def __init__(
         self,
         transform: Transform[ArrayT],
         input_axes: list[int],
         output_axes: list[int] | None = None,
     ):
+        """
+        Parameters
+        ----------
+        transform
+            Transformation to apply to the subset of axes.
+        input_axes
+            Which axes to apply the transformation to, in order.
+            The length must match the input dimensionality of `transform`.
+        output_axes
+            Which axes to apply the transformation to, in order.
+            The length must match the input dimensionality of `transform`.
+            If None, re-use the input axes.
+
+        Raises
+        ------
+        ValueError
+            `transform`'s dimensionality does not match the input/output axes.
+        """
 
         self.input_axes = input_axes
         if output_axes is None:

src/transformnd/transforms/moving_least_squares.py

@@ -7,7 +7,6 @@
 from array_api_compat import array_namespace
 import numpy as np
 from typing import Self
-from molesq.transform import Transformer as _Transformer
 
 from ..base import Transform
 from ..types import NDims, Spaces
@@ -18,6 +17,8 @@ class MovingLeastSquares(Transform[np.ndarray]):
     """Moving least squares transformation.
 
     Deform based on a matched pairs of source and target control points; see <https://dl.acm.org/doi/10.1145/1141911.1141920>
+
+    REQUIRES: `movingleastsquares` extra.
     """
 
     def __init__(
@@ -39,9 +40,11 @@ def __init__(
         spaces
             Optional source and target spaces
         """
+        from molesq.transform import Transformer
+
         s = as_floats(source_control_points)
         t = as_floats(target_control_points)
-        self._transformer = _Transformer(s, t)
+        self._transformer = Transformer(s, t)
         super().__init__(
             NDims(
                 s.shape[1],