Merge pull request numpy#3908 from juliantaylor/median-percentile

add extended axis and keepdims support to percentile and median

Author: charris

numpy/lib/function_base.py

@@ -13,6 +13,7 @@
 import warnings
 import sys
 import collections
+import operator
 
 import numpy as np
 import numpy.core.numeric as _nx
@@ -2694,7 +2695,67 @@ def msort(a):
     return b
 
 
-def median(a, axis=None, out=None, overwrite_input=False):
+def _ureduce(a, func, **kwargs):
+    """
+    Internal Function.
+    Call `func` with `a` as first argument swapping the axes to use extended
+    axis on functions that don't support it natively.
+
+    Returns result and a.shape with axis dims set to 1.
+
+    Parameters
+    ----------
+    a : array_like
+        Input array or object that can be converted to an array.
+    func : callable
+        Reduction function Kapable of receiving an axis argument.
+        It is is called with `a` as first argument followed by `kwargs`.
+     kwargs : keyword arguments
+        additional keyword arguments to pass to `func`.
+
+    Returns
+    -------
+    result : tuple
+        Result of func(a, **kwargs) and a.shape with axis dims set to 1
+        which can be used to reshape the result to the same shape a ufunc with
+        keepdims=True would produce.
+
+    """
+    a = np.asanyarray(a)
+    axis = kwargs.get('axis', None)
+    if axis is not None:
+        keepdim = list(a.shape)
+        nd = a.ndim
+        try:
+            axis = operator.index(axis)
+            if axis >= nd or axis < -nd:
+                raise IndexError("axis %d out of bounds (%d)" % (axis, a.ndim))
+            keepdim[axis] = 1
+        except TypeError:
+            sax = set()
+            for x in axis:
+                if x >= nd or x < -nd:
+                    raise IndexError("axis %d out of bounds (%d)" % (x, nd))
+                if x in sax:
+                    raise ValueError("duplicate value in axis")
+                sax.add(x % nd)
+                keepdim[x] = 1
+            keep = sax.symmetric_difference(frozenset(range(nd)))
+            nkeep = len(keep)
+            # swap axis that should not be reduced to front
+            for i, s in enumerate(sorted(keep)):
+                a = a.swapaxes(i, s)
+            # merge reduced axis
+            a = a.reshape(a.shape[:nkeep] + (-1,))
+            kwargs['axis'] = -1
+    else:
+        keepdim = [1] * a.ndim
+
+    r = func(a, **kwargs)
+    return r, keepdim
+
+
+def median(a, axis=None, out=None, overwrite_input=False, keepdims=False):
     """
     Compute the median along the specified axis.
 
@@ -2704,9 +2765,10 @@ def median(a, axis=None, out=None, overwrite_input=False):
     ----------
     a : array_like
         Input array or object that can be converted to an array.
-    axis : int, optional
+    axis : int or sequence of int, optional
         Axis along which the medians are computed. The default (axis=None)
         is to compute the median along a flattened version of the array.
+        A sequence of axes is supported since version 1.9.0.
     out : ndarray, optional
         Alternative output array in which to place the result. It must have
         the same shape and buffer length as the expected output, but the
@@ -2719,6 +2781,13 @@ def median(a, axis=None, out=None, overwrite_input=False):
        will probably be fully or partially sorted. Default is False. Note
        that, if `overwrite_input` is True and the input is not already an
        ndarray, an error will be raised.
+    keepdims : bool, optional
+        If this is set to True, the axes which are reduced are left
+        in the result as dimensions with size one. With this option,
+        the result will broadcast correctly against the original `arr`.
+
+        .. versionadded:: 1.9.0
+
 
     Returns
     -------
@@ -2768,6 +2837,16 @@ def median(a, axis=None, out=None, overwrite_input=False):
     >>> assert not np.all(a==b)
 
     """
+    r, k = _ureduce(a, func=_median, axis=axis, out=out,
+                    overwrite_input=overwrite_input)
+    if keepdims:
+        return r.reshape(k)
+    else:
+        return r
+
+def _median(a, axis=None, out=None, overwrite_input=False):
+    # can't be reasonably be implemented in terms of percentile as we have to
+    # call mean to not break astropy
     a = np.asanyarray(a)
     if axis is not None and axis >= a.ndim:
         raise IndexError(
@@ -2817,7 +2896,7 @@ def median(a, axis=None, out=None, overwrite_input=False):
 
 
 def percentile(a, q, axis=None, out=None,
-               overwrite_input=False, interpolation='linear'):
+               overwrite_input=False, interpolation='linear', keepdims=False):
     """
     Compute the qth percentile of the data along the specified axis.
 
@@ -2829,9 +2908,10 @@ def percentile(a, q, axis=None, out=None,
         Input array or object that can be converted to an array.
     q : float in range of [0,100] (or sequence of floats)
         Percentile to compute which must be between 0 and 100 inclusive.
-    axis : int, optional
+    axis : int or sequence of int, optional
         Axis along which the percentiles are computed. The default (None)
         is to compute the percentiles along a flattened version of the array.
+        A sequence of axes is supported since version 1.9.0.
     out : ndarray, optional
         Alternative output array in which to place the result. It must
         have the same shape and buffer length as the expected output,
@@ -2857,6 +2937,12 @@ def percentile(a, q, axis=None, out=None,
             * midpoint: (`i` + `j`) / 2.
 
         .. versionadded:: 1.9.0
+    keepdims : bool, optional
+        If this is set to True, the axes which are reduced are left
+        in the result as dimensions with size one. With this option,
+        the result will broadcast correctly against the original `arr`.
+
+        .. versionadded:: 1.9.0
 
     Returns
     -------
@@ -2913,19 +2999,40 @@ def percentile(a, q, axis=None, out=None,
     array([ 3.5])
 
     """
+    q = asarray(q, dtype=np.float64)
+    r, k = _ureduce(a, func=_percentile, q=q, axis=axis, out=out,
+                    overwrite_input=overwrite_input,
+                    interpolation=interpolation)
+    if keepdims:
+        if q.ndim == 0:
+            return r.reshape(k)
+        else:
+            return r.reshape([len(q)] + k)
+    else:
+        return r
+
+
+def _percentile(a, q, axis=None, out=None,
+                overwrite_input=False, interpolation='linear', keepdims=False):
     a = asarray(a)
-    q = asarray(q)
     if q.ndim == 0:
         # Do not allow 0-d arrays because following code fails for scalar
         zerod = True
         q = q[None]
     else:
         zerod = False
 
-    q = q / 100.0
-    if (q < 0).any() or (q > 1).any():
-        raise ValueError(
-            "Percentiles must be in the range [0,100]")
+    # avoid expensive reductions, relevant for arrays with < O(1000) elements
+    if q.size < 10:
+        for i in range(q.size):
+            if q[i] < 0. or q[i] > 100.:
+                raise ValueError("Percentiles must be in the range [0,100]")
+            q[i] /= 100.
+    else:
+        # faster than any()
+        if np.count_nonzero(q < 0.) or np.count_nonzero(q > 100.):
+            raise ValueError("Percentiles must be in the range [0,100]")
+        q /= 100.
 
     # prepare a for partioning
     if overwrite_input:

numpy/lib/tests/test_function_base.py

@@ -1688,6 +1688,8 @@ def test_exception(self):
                       interpolation='foobar')
         assert_raises(ValueError, np.percentile, [1], 101)
         assert_raises(ValueError, np.percentile, [1], -1)
+        assert_raises(ValueError, np.percentile, [1], list(range(50)) + [101])
+        assert_raises(ValueError, np.percentile, [1], list(range(50)) + [-0.1])
 
     def test_percentile_list(self):
         assert_equal(np.percentile([1, 2, 3], 0), 1)
@@ -1779,26 +1781,85 @@ def test_percentile_overwrite(self):
         b = np.percentile([2, 3, 4, 1], [50], overwrite_input=True)
         assert_equal(b, np.array([2.5]))
 
+    def test_extended_axis(self):
+        o = np.random.normal(size=(71, 23))
+        x = np.dstack([o] * 10)
+        assert_equal(np.percentile(x, 30, axis=(0, 1)), np.percentile(o, 30))
+        x = np.rollaxis(x, -1, 0)
+        assert_equal(np.percentile(x, 30, axis=(-2, -1)), np.percentile(o, 30))
+        x = x.swapaxes(0, 1).copy()
+        assert_equal(np.percentile(x, 30, axis=(0, -1)), np.percentile(o, 30))
+        x = x.swapaxes(0, 1).copy()
+
+        assert_equal(np.percentile(x, [25, 60], axis=(0, 1, 2)),
+                     np.percentile(x, [25, 60], axis=None))
+        assert_equal(np.percentile(x, [25, 60], axis=(0,)),
+                     np.percentile(x, [25, 60], axis=0))
+
+        d = np.arange(3 * 5 * 7 * 11).reshape(3, 5, 7, 11)
+        np.random.shuffle(d)
+        assert_equal(np.percentile(d, 25,  axis=(0, 1, 2))[0],
+                     np.percentile(d[:, :, :, 0].flatten(), 25))
+        assert_equal(np.percentile(d, [10, 90], axis=(0, 1, 3))[:, 1],
+                     np.percentile(d[:, :, 1, :].flatten(), [10, 90]))
+        assert_equal(np.percentile(d, 25, axis=(3, 1, -4))[2],
+                     np.percentile(d[:, :, 2, :].flatten(), 25))
+        assert_equal(np.percentile(d, 25, axis=(3, 1, 2))[2],
+                     np.percentile(d[2, :, :, :].flatten(), 25))
+        assert_equal(np.percentile(d, 25, axis=(3, 2))[2, 1],
+                     np.percentile(d[2, 1, :, :].flatten(), 25))
+        assert_equal(np.percentile(d, 25, axis=(1, -2))[2, 1],
+                     np.percentile(d[2, :, :, 1].flatten(), 25))
+        assert_equal(np.percentile(d, 25, axis=(1, 3))[2, 2],
+                     np.percentile(d[2, :, 2, :].flatten(), 25))
+
+    def test_extended_axis_invalid(self):
+        d = np.ones((3, 5, 7, 11))
+        assert_raises(IndexError, np.percentile, d, axis=-5, q=25)
+        assert_raises(IndexError, np.percentile, d, axis=(0, -5), q=25)
+        assert_raises(IndexError, np.percentile, d, axis=4, q=25)
+        assert_raises(IndexError, np.percentile, d, axis=(0, 4), q=25)
+        assert_raises(ValueError, np.percentile, d, axis=(1, 1), q=25)
+
+    def test_keepdims(self):
+        d = np.ones((3, 5, 7, 11))
+        assert_equal(np.percentile(d, 7, axis=None, keepdims=True).shape,
+                     (1, 1, 1, 1))
+        assert_equal(np.percentile(d, 7, axis=(0, 1), keepdims=True).shape,
+                     (1, 1, 7, 11))
+        assert_equal(np.percentile(d, 7, axis=(0, 3), keepdims=True).shape,
+                     (1, 5, 7, 1))
+        assert_equal(np.percentile(d, 7, axis=(1,), keepdims=True).shape,
+                     (3, 1, 7, 11))
+        assert_equal(np.percentile(d, 7, (0, 1, 2, 3), keepdims=True).shape,
+                     (1, 1, 1, 1))
+        assert_equal(np.percentile(d, 7, axis=(0, 1, 3), keepdims=True).shape,
+                     (1, 1, 7, 1))
+
+        assert_equal(np.percentile(d, [1, 7], axis=(0, 1, 3),
+                                   keepdims=True).shape, (2, 1, 1, 7, 1))
+        assert_equal(np.percentile(d, [1, 7], axis=(0, 3),
+                                   keepdims=True).shape, (2, 1, 5, 7, 1))
 
 
 class TestMedian(TestCase):
     def test_basic(self):
         a0 = np.array(1)
         a1 = np.arange(2)
         a2 = np.arange(6).reshape(2, 3)
-        assert_allclose(np.median(a0), 1)
+        assert_equal(np.median(a0), 1)
         assert_allclose(np.median(a1), 0.5)
         assert_allclose(np.median(a2), 2.5)
         assert_allclose(np.median(a2, axis=0), [1.5,  2.5,  3.5])
-        assert_allclose(np.median(a2, axis=1), [1, 4])
+        assert_equal(np.median(a2, axis=1), [1, 4])
         assert_allclose(np.median(a2, axis=None), 2.5)
 
         a = np.array([0.0444502, 0.0463301, 0.141249, 0.0606775])
         assert_almost_equal((a[1] + a[3]) / 2., np.median(a))
         a = np.array([0.0463301, 0.0444502, 0.141249])
-        assert_almost_equal(a[0], np.median(a))
+        assert_equal(a[0], np.median(a))
         a = np.array([0.0444502, 0.141249, 0.0463301])
-        assert_almost_equal(a[-1], np.median(a))
+        assert_equal(a[-1], np.median(a))
 
     def test_axis_keyword(self):
         a3 = np.array([[2, 3],
@@ -1872,6 +1933,60 @@ def mean(self, axis=None, dtype=None, out=None):
         a = MySubClass([1,2,3])
         assert_equal(np.median(a), -7)
 
+    def test_extended_axis(self):
+        o = np.random.normal(size=(71, 23))
+        x = np.dstack([o] * 10)
+        assert_equal(np.median(x, axis=(0, 1)), np.median(o))
+        x = np.rollaxis(x, -1, 0)
+        assert_equal(np.median(x, axis=(-2, -1)), np.median(o))
+        x = x.swapaxes(0, 1).copy()
+        assert_equal(np.median(x, axis=(0, -1)), np.median(o))
+
+        assert_equal(np.median(x, axis=(0, 1, 2)), np.median(x, axis=None))
+        assert_equal(np.median(x, axis=(0, )), np.median(x, axis=0))
+        assert_equal(np.median(x, axis=(-1, )), np.median(x, axis=-1))
+
+        d = np.arange(3 * 5 * 7 * 11).reshape(3, 5, 7, 11)
+        np.random.shuffle(d)
+        assert_equal(np.median(d, axis=(0, 1, 2))[0],
+                     np.median(d[:, :, :, 0].flatten()))
+        assert_equal(np.median(d, axis=(0, 1, 3))[1],
+                     np.median(d[:, :, 1, :].flatten()))
+        assert_equal(np.median(d, axis=(3, 1, -4))[2],
+                     np.median(d[:, :, 2, :].flatten()))
+        assert_equal(np.median(d, axis=(3, 1, 2))[2],
+                     np.median(d[2, :, :, :].flatten()))
+        assert_equal(np.median(d, axis=(3, 2))[2, 1],
+                     np.median(d[2, 1, :, :].flatten()))
+        assert_equal(np.median(d, axis=(1, -2))[2, 1],
+                     np.median(d[2, :, :, 1].flatten()))
+        assert_equal(np.median(d, axis=(1, 3))[2, 2],
+                     np.median(d[2, :, 2, :].flatten()))
+
+    def test_extended_axis_invalid(self):
+        d = np.ones((3, 5, 7, 11))
+        assert_raises(IndexError, np.median, d, axis=-5)
+        assert_raises(IndexError, np.median, d, axis=(0, -5))
+        assert_raises(IndexError, np.median, d, axis=4)
+        assert_raises(IndexError, np.median, d, axis=(0, 4))
+        assert_raises(ValueError, np.median, d, axis=(1, 1))
+
+    def test_keepdims(self):
+        d = np.ones((3, 5, 7, 11))
+        assert_equal(np.median(d, axis=None, keepdims=True).shape,
+                     (1, 1, 1, 1))
+        assert_equal(np.median(d, axis=(0, 1), keepdims=True).shape,
+                     (1, 1, 7, 11))
+        assert_equal(np.median(d, axis=(0, 3), keepdims=True).shape,
+                     (1, 5, 7, 1))
+        assert_equal(np.median(d, axis=(1,), keepdims=True).shape,
+                     (3, 1, 7, 11))
+        assert_equal(np.median(d, axis=(0, 1, 2, 3), keepdims=True).shape,
+                     (1, 1, 1, 1))
+        assert_equal(np.median(d, axis=(0, 1, 3), keepdims=True).shape,
+                     (1, 1, 7, 1))
+
+
 
 class TestAdd_newdoc_ufunc(TestCase):