Move encode_array to utils module from sgkit-plink (#55)

Author: tomwhite

sgkit/tests/test_utils.py

@@ -1,7 +1,10 @@
+from typing import Any, List
+
 import numpy as np
 import pytest
 
-from sgkit.utils import check_array_like
+from sgkit.typing import ArrayLike
+from sgkit.utils import check_array_like, encode_array
 
 
 def test_check_array_like():
@@ -18,3 +21,27 @@ def test_check_array_like():
         check_array_like(a, ndim=2)
     with pytest.raises(ValueError):
         check_array_like(a, ndim={2, 3})
+
+
+def test_encode_array():
+    def check(x: ArrayLike, values: ArrayLike, names: List[Any]) -> None:
+        v, n = encode_array(x)
+        np.testing.assert_equal(v, values)
+        np.testing.assert_equal(n, names)
+
+    check([], [], [])
+    check(["a"], [0], ["a"])
+    check(["a", "b"], [0, 1], ["a", "b"])
+    check(["b", "a"], [0, 1], ["b", "a"])
+    check(["a", "b", "b"], [0, 1, 1], ["a", "b"])
+    check(["b", "b", "a"], [0, 0, 1], ["b", "a"])
+    check(["b", "b", "a", "a"], [0, 0, 1, 1], ["b", "a"])
+    check(["c", "a", "a", "b"], [0, 1, 1, 2], ["c", "a", "b"])
+    check(["b", "b", "c", "c", "c", "a", "a"], [0, 0, 1, 1, 1, 2, 2], ["b", "c", "a"])
+    check(["b", "c", "b", "c", "a"], [0, 1, 0, 1, 2], ["b", "c", "a"])
+    check([2, 2, 1, 3, 1, 5, 5, 1], [0, 0, 1, 2, 1, 3, 3, 1], [2.0, 1.0, 3.0, 5.0])
+    check(
+        [2.0, 2.0, 1.0, 3.0, 1.0, 5.0, 5.0, 1.0],
+        [0, 0, 1, 2, 1, 3, 3, 1],
+        [2.0, 1.0, 3.0, 5.0],
+    )

sgkit/utils.py

@@ -1,8 +1,8 @@
-from typing import Any, Set, Union
+from typing import Any, List, Set, Tuple, Union
 
 import numpy as np
 
-from .typing import DType
+from .typing import ArrayLike, DType
 
 
 def check_array_like(
@@ -31,3 +31,36 @@ def check_array_like(
                 raise ValueError
         elif ndim != a.ndim:
             raise ValueError
+
+
+def encode_array(x: ArrayLike) -> Tuple[ArrayLike, List[Any]]:
+    """Encode array values as integers indexing unique values
+
+    The codes created for each unique element in the array correspond
+    to order of appearance, not the natural sort order for the array
+    dtype.
+
+    Examples
+    --------
+
+    >>> encode_array(['c', 'a', 'a', 'b'])
+    (array([0, 1, 1, 2]), array(['c', 'a', 'b'], dtype='<U1'))
+
+    Parameters
+    ----------
+    x : (M,) array-like
+        Array of elements to encode of any type
+
+    Returns
+    -------
+    indexes : (M,) ndarray
+        Encoded values as integer indices
+    values : ndarray
+        Unique values in original array in order of appearance
+    """
+    # argsort not implemented in dask: https://github.com/dask/dask/issues/4368
+    names, index, inverse = np.unique(x, return_index=True, return_inverse=True)
+    index = np.argsort(index)
+    rank = np.empty_like(index)
+    rank[index] = np.arange(len(index))
+    return rank[inverse], names[index]