Merge pull request #7363 from seberg/masked-silence-2

ENH: Make no unshare mask future warnings less noisy

3 files changed, 47 insertions, 21 deletions

diff --git a/doc/release/1.11.0-notes.rst b/doc/release/1.11.0-notes.rst
index c9b7a6d3e..2aa6daad1 100644
--- a/doc/release/1.11.0-notes.rst
+++ b/doc/release/1.11.0-notes.rst
@@ -41,8 +41,6 @@ Future Changes
 The following changes are scheduled for Numpy 1.12.0.
 
 * Support for Python 2.6, 3.2, and 3.3 will be dropped.
-* Slicing a ``MaskedArray`` will return views of both data **and** mask.
-  Currently the mask is returned as a copy.
 * Relaxed stride checking will become the default. See the 1.8.0 release
   notes for a more extended discussion of what this change implies.
 * The behavior of the datetime64 "not a time" (NaT) value will be changed
@@ -70,6 +68,33 @@ In a future release the following changes will be made.
   change.  That differs from the current behavior where arrays that are
   f_contiguous but not c_contiguous can be viewed as a dtype type of
   different size causing the first dimension to change.
+* Currently, taking a view of a masked array produces a confusing result.
+  For example, if we write ``masked_view = masked_original[:]``, then
+  ``masked_view``'s data array will be a view of ``masked_original``'s data
+  array, so modifications to one array's data will also affect the other:
+  ``masked_view[0] = 123; assert masked_original[0] == 123``. But currently,
+  the *mask* array is copied during assignment operations. While
+  mask is *initially* a view it is considered to be *shared*.
+  The first assignment to the masked array will thus cause an implicit
+  copy, so that changes of one array's mask will not affect the other:
+  ``masked_view[0] = np.ma.masked; assert masked_original[0] is not
+  np.ma.masked``.
+  A similar situation happens when explicitly constructing a masked
+  array using ``MaskedArray(data, mask)`` -- the returned array will have
+  a view of ``data`` and "shares" the ``mask``. In the future, these cases
+  will be normalized so that the data and mask arrays are treated the
+  same way, and modifications to either will propagate between views.
+  The mask will not be copied during assignment operations and instead
+  the original mask will be modified as well. In 1.11, numpy will issue a
+  ``MaskedArrayFutureWarning`` warning whenever user code modifies the mask
+  of a view and this may cause values to propagate to another array.
+  To silence these warnings, and make your code robust against the
+  upcoming changes, you have two options: if you want to keep the current
+  behavior, call ``masked_view.unshare_mask()`` before modifying the mask.
+  If you want to get the future behavior early, use
+  ``masked_view._sharedmask = False``. However, note that setting
+  the ``_sharedmask`` attribute will break following explicit calls to
+  ``masked_view.unshare_mask()``.
 
 
 Compatibility notes
diff --git a/numpy/ma/core.py b/numpy/ma/core.py
index 709542bc4..41e9d48b7 100644
--- a/numpy/ma/core.py
+++ b/numpy/ma/core.py
@@ -3123,7 +3123,6 @@ class MaskedArray(ndarray):
         Return the item described by i, as a masked array.
 
         """
-
         dout = self.data[indx]
         # We could directly use ndarray.__getitem__ on self.
         # But then we would have to modify __array_finalize__ to prevent the
@@ -3194,19 +3193,6 @@ class MaskedArray(ndarray):
         locations.
 
         """
-        # 2016.01.15 -- v1.11.0
-        self._oldsharedmask = getattr(self, "_oldsharedmask", False)
-        self._oldsharedmask = self._oldsharedmask or self._sharedmask
-        if (self._mask is not nomask) and self._oldsharedmask:
-            warnings.warn(
-                "Currently, slicing will try to return a view of the data, but"
-                " will return a copy of the mask. In the future, it will try"
-                " to  return both as views. This means that using"
-                " `__setitem__` will propagate values back through all masks"
-                " that are present.",
-                MaskedArrayFutureWarning
-            )
-
         if self is masked:
             raise MaskError('Cannot alter the masked element.')
         _data = self._data
@@ -3248,10 +3234,24 @@ class MaskedArray(ndarray):
                 _mask[indx] = mval
         elif not self._hardmask:
             # Unshare the mask if necessary to avoid propagation
+            # We want to remove the unshare logic from this place in the
+            # future. Note that _sharedmask has lots of false positives.
             if not self._isfield:
-                _oldsharedmask = self._oldsharedmask
+                if self._sharedmask and not (
+                        # If no one else holds a reference (we have two
+                        # references (_mask and self._mask) -- add one for
+                        # getrefcount) and the array owns its own data
+                        # copying the mask should do nothing.
+                        (sys.getrefcount(_mask) == 3) and _mask.flags.owndata):
+                    # 2016.01.15 -- v1.11.0
+                    warnings.warn(
+                       "setting an item on a masked array which has a shared "
+                       "mask will not copy the mask and also change the "
+                       "original mask array in the future.\n"
+                       "Check the NumPy 1.11 release notes for more "
+                       "information.",
+                       MaskedArrayFutureWarning, stacklevel=2)
                 self.unshare_mask()
-                self._oldsharedmask = _oldsharedmask
                 _mask = self._mask
             # Set the data, then the mask
             _data[indx] = dval
@@ -3457,7 +3457,6 @@ class MaskedArray(ndarray):
         if self._sharedmask:
             self._mask = self._mask.copy()
             self._sharedmask = False
-            self._oldsharedmask = False
         return self
 
     sharedmask = property(fget=lambda self: self._sharedmask,
diff --git a/numpy/ma/extras.py b/numpy/ma/extras.py
index 9855b4e76..6e091652e 100644
--- a/numpy/ma/extras.py
+++ b/numpy/ma/extras.py
@@ -689,6 +689,7 @@ def median(a, axis=None, out=None, overwrite_input=False):
     # insert indices of low and high median
     ind.insert(axis, h - 1)
     low = asorted[ind]
+    low._sharedmask = False
     ind[axis] = h
     high = asorted[ind]
     # duplicate high if odd number of elements so mean does nothing
@@ -1173,9 +1174,9 @@ def _covhelper(x, y=None, rowvar=True, allow_masked=True):
                 # Define some common mask
                 common_mask = np.logical_or(xmask, ymask)
                 if common_mask is not nomask:
-                    x.unshare_mask()
-                    y.unshare_mask()
                     xmask = x._mask = y._mask = ymask = common_mask
+                    x._sharedmask = False
+                    y._sharedmask = False
         x = ma.concatenate((x, y), axis)
         xnotmask = np.logical_not(np.concatenate((xmask, ymask), axis)).astype(int)
     x -= x.mean(axis=rowvar)[tup]
@@ -1326,6 +1327,7 @@ def corrcoef(x, y=None, rowvar=True, bias=np._NoValue, allow_masked=True,
         _denom = ma.sqrt(ma.multiply.outer(diag, diag))
     else:
         _denom = diagflat(diag)
+        _denom._sharedmask = False  # We know return is always a copy
         n = x.shape[1 - rowvar]
         if rowvar:
             for i in range(n - 1):