Refactor affine transformations and add deprecation utils

kwave/utils/deprecation.py

@@ -0,0 +1,35 @@
+"""Utilities for handling deprecation warnings in k-Wave."""
+
+import functools
+import warnings
+from typing import Callable, TypeVar, Any
+
+F = TypeVar("F", bound=Callable[..., Any])
+
+
+def deprecated(message: str, target_version: str = "2.0.0") -> Callable[[F], F]:
+    """Decorator to mark functions as deprecated.
+
+    Args:
+        message: Message explaining what to use instead
+        target_version: Version in which the function will be removed
+
+    Example:
+        @deprecated("Use new_function() instead", "2.0.0")
+        def old_function():
+            pass
+    """
+
+    def decorator(func: F) -> F:
+        @functools.wraps(func)
+        def wrapper(*args: Any, **kwargs: Any) -> Any:
+            warnings.warn(
+                f"{func.__name__} is deprecated and will be removed in version {target_version}. {message}",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            return func(*args, **kwargs)
+
+        return wrapper
+
+    return decorator

kwave/utils/kwave_array.py

@@ -13,7 +13,7 @@
 from kwave.utils.conversion import tol_star
 from kwave.utils.interp import get_delta_bli
 from kwave.utils.mapgen import trim_cart_points, make_cart_rect, make_cart_arc, make_cart_bowl, make_cart_disc, make_cart_spherical_segment
-from kwave.utils.math import sinc, get_affine_matrix
+from kwave.utils.math import sinc, make_affine
 from kwave.utils.matlab import matlab_assign, matlab_mask, matlab_find
 
 
@@ -680,8 +680,13 @@ def combine_sensor_data(self, kgrid, sensor_data):
         return combined_sensor_data
 
     def set_array_position(self, translation, rotation):
-        # get affine matrix and store
-        self.array_transformation = get_affine_matrix(translation, rotation)
+        """Set the array position using translation and rotation.
+
+        Args:
+            translation: Vector of translation values [dx, dy] or [dx, dy, dz]
+            rotation: Single angle (in degrees) for 2D or [x_angle, y_angle, z_angle] for 3D
+        """
+        self.array_transformation = make_affine(translation, rotation)
 
     def set_affine_transform(self, affine_transform):
         # check array has elements

kwave/utils/mapgen.py

@@ -10,16 +10,18 @@
 from beartype import beartype as typechecker
 from beartype.typing import Union, List, Tuple, cast, Optional
 from jaxtyping import Float, Complex, Int, Real, Integer
+from scipy.spatial.transform import Rotation
 
 from .conversion import db2neper, neper2db
 from .data import scale_SI
-from .math import cosd, sind, Rz, Ry, Rx, compute_linear_transform
+from .math import cosd, sind
 from .matlab import matlab_assign, matlab_find, ind2sub, sub2ind
 from .matrix import max_nd
 from .tictoc import TicToc
 from ..data import Vector
 
 import kwave.utils.typing as kt
+from kwave.utils.math import compute_linear_transform, compute_rotation_between_vectors
 
 # GLOBALS
 # define literals (ref: http://www.wolframalpha.com/input/?i=golden+angle)
@@ -2625,8 +2627,8 @@ def make_cart_rect(
             # No rotation
             R = np.eye(3)
         else:
-            # Using intrinsic rotations chain from right to left (z-y'-z'' rotations)
-            R = np.dot(Rz(theta[2]), np.dot(Ry(theta[1]), Rx(theta[0])))
+            # Using intrinsic rotations chain from right to left (xyz rotations)
+            R = Rotation.from_euler("xyz", theta, degrees=True).as_matrix()
 
     # Combine scaling and rotation matrices
     A = np.dot(R, S)