Merge pull request #4760 from juliantaylor/masked-median

ENH: rewrite ma.median to improve poor performance for multiple dimensions

1 files changed, 19 insertions, 1 deletions

diff --git a/numpy/lib/nanfunctions.py b/numpy/lib/nanfunctions.py
index 478e7cf7e..7120760b5 100644
--- a/numpy/lib/nanfunctions.py
+++ b/numpy/lib/nanfunctions.py
@@ -635,7 +635,7 @@ def _nanmedian(a, axis=None, out=None, overwrite_input=False):
     See nanmedian for parameter usage
 
     """
-    if axis is None:
+    if axis is None or a.ndim == 1:
         part = a.ravel()
         if out is None:
             return _nanmedian1d(part, overwrite_input)
@@ -643,11 +643,29 @@ def _nanmedian(a, axis=None, out=None, overwrite_input=False):
             out[...] = _nanmedian1d(part, overwrite_input)
             return out
     else:
+        # for small medians use sort + indexing which is still faster than
+        # apply_along_axis
+        if a.shape[axis] < 400:
+            return _nanmedian_small(a, axis, out, overwrite_input)
         result = np.apply_along_axis(_nanmedian1d, axis, a, overwrite_input)
         if out is not None:
             out[...] = result
         return result
 
+def _nanmedian_small(a, axis=None, out=None, overwrite_input=False):
+    """
+    sort + indexing median, faster for small medians along multiple dimensions
+    due to the high overhead of apply_along_axis
+    see nanmedian for parameter usage
+    """
+    a = np.ma.masked_array(a, np.isnan(a))
+    m = np.ma.median(a, axis=axis, overwrite_input=overwrite_input)
+    for i in range(np.count_nonzero(m.mask.ravel())):
+        warnings.warn("All-NaN slice encountered", RuntimeWarning)
+    if out is not None:
+        out[...] = m.filled(np.nan)
+        return out
+    return m.filled(np.nan)
 
 def nanmedian(a, axis=None, out=None, overwrite_input=False, keepdims=False):
     """