pivot & unstack with nan in the index

doc/source/whatsnew/v0.16.0.txt

@@ -67,6 +67,7 @@ Bug Fixes
 
 
 - Bug in ``MultiIndex.has_duplicates`` when having many levels causes an indexer overflow (:issue:`9075`)
+- Bug in ``pivot`` and `unstack`` where ``nan`` values would break index alignment (:issue:`7466`)
 
 
 

pandas/core/groupby.py

@@ -6,7 +6,7 @@
 
 from pandas.compat import(
     zip, builtins, range, long, lzip,
-    OrderedDict, callable
+    OrderedDict, callable, filter, map
 )
 from pandas import compat
 
@@ -3510,6 +3510,61 @@ def get_group_index(label_list, shape):
     np.putmask(group_index, mask, -1)
     return group_index
 
+
+def get_flat_ids(labels, shape, retain_lex_rank):
+    """
+    Given a list of labels at each level, returns a flat array of int64 ids
+    corresponding to unique tuples across the labels. If `retain_lex_rank`,
+    rank of returned ids preserve lexical ranks of labels.
+
+    Parameters
+    ----------
+    labels: sequence of arrays
+        Integers identifying levels at each location
+    shape: sequence of ints same length as labels
+        Number of unique levels at each location
+    retain_lex_rank: boolean
+        If the ranks of returned ids should match lexical ranks of labels
+
+    Returns
+    -------
+    An array of type int64 where two elements are equal if their corresponding
+    labels are equal at all location.
+    """
+    def loop(labels, shape):
+        # how many levels can be done without overflow:
+        pred = lambda i: not _int64_overflow_possible(shape[:i])
+        nlev = next(filter(pred, range(len(shape), 0, -1)))
+
+        # compute flat ids for the first `nlev` levels
+        stride = np.prod(shape[1:nlev], dtype='i8')
+        out = stride * labels[0].astype('i8', subok=False, copy=False)
+
+        for i in range(1, nlev):
+            stride //= shape[i]
+            out += labels[i] * stride
+
+        if nlev == len(shape):  # all levels done!
+            return out
+
+        # compress what has been done so far in order to avoid overflow
+        # to retain lexical ranks, obs_ids should be sorted
+        comp_ids, obs_ids = _compress_group_index(out, sort=retain_lex_rank)
+
+        labels = [comp_ids] + labels[nlev:]
+        shape = [len(obs_ids)] + shape[nlev:]
+
+        return loop(labels, shape)
+
+    def maybe_lift(lab, size):  # pormote nan values
+        return (lab + 1, size + 1) if (lab == -1).any() else (lab, size)
+
+    labels = map(com._ensure_int64, labels)
+    labels, shape = map(list, zip(*map(maybe_lift, labels, shape)))
+
+    return loop(labels, shape)
+
+
 _INT64_MAX = np.iinfo(np.int64).max
 
 

pandas/core/index.py

@@ -3226,44 +3226,13 @@ def _has_complex_internals(self):
     @cache_readonly
     def is_unique(self):
         from pandas.hashtable import Int64HashTable
-
-        def _get_group_index(labels, shape):
-            from pandas.core.groupby import _int64_overflow_possible, \
-                                            _compress_group_index
-
-            # how many levels can be done without overflow
-            pred = lambda i: not _int64_overflow_possible(shape[:i])
-            nlev = next(filter(pred, range(len(shape), 0, -1)))
-
-            # compute group indicies for the first `nlev` levels
-            group_index = labels[0].astype('i8', subok=False, copy=True)
-            stride = shape[0]
-
-            for i in range(1, nlev):
-                group_index += labels[i] * stride
-                stride *= shape[i]
-
-            if nlev == len(shape):
-                return group_index
-
-            comp_ids, obs_ids = _compress_group_index(group_index, sort=False)
-
-            labels = [comp_ids] + labels[nlev:]
-            shape = [len(obs_ids)] + shape[nlev:]
-
-            return _get_group_index(labels, shape)
-
-        def _maybe_lift(lab, size):  # pormote nan values
-            return (lab + 1, size + 1) if (lab == -1).any() else (lab, size)
+        from pandas.core.groupby import get_flat_ids
 
         shape = map(len, self.levels)
-        labels = map(_ensure_int64, self.labels)
-
-        labels, shape = map(list, zip(*map(_maybe_lift, labels, shape)))
-        group_index = _get_group_index(labels, shape)
+        ids = get_flat_ids(self.labels, shape, False)
+        table = Int64HashTable(min(1 << 20, len(ids)))
 
-        table = Int64HashTable(min(1 << 20, len(group_index)))
-        return len(table.unique(group_index)) == len(self)
+        return len(table.unique(ids)) == len(self)
 
     def get_value(self, series, key):
         # somewhat broken encapsulation

pandas/core/reshape.py

@@ -82,18 +82,10 @@ def __init__(self, values, index, level=-1, value_columns=None):
 
         self.level = self.index._get_level_number(level)
 
-        levels = index.levels
-        labels = index.labels
-
-        def _make_index(lev, lab):
-            values = _make_index_array_level(lev.values, lab)
-            i = lev._simple_new(values, lev.name,
-                                freq=getattr(lev, 'freq', None),
-                                tz=getattr(lev, 'tz', None))
-            return i
-
-        self.new_index_levels = [_make_index(lev, lab)
-                                 for lev, lab in zip(levels, labels)]
+        # when index includes `nan`, need to lift levels/strides by 1
+        self.lift = 1 if -1 in self.index.labels[self.level] else 0
+
+        self.new_index_levels = list(index.levels)
         self.new_index_names = list(index.names)
 
         self.removed_name = self.new_index_names.pop(self.level)
@@ -134,10 +126,10 @@ def _make_selectors(self):
         ngroups = len(obs_ids)
 
         comp_index = _ensure_platform_int(comp_index)
-        stride = self.index.levshape[self.level]
+        stride = self.index.levshape[self.level] + self.lift
         self.full_shape = ngroups, stride
 
-        selector = self.sorted_labels[-1] + stride * comp_index
+        selector = self.sorted_labels[-1] + stride * comp_index + self.lift
         mask = np.zeros(np.prod(self.full_shape), dtype=bool)
         mask.put(selector, True)
 
@@ -166,20 +158,6 @@ def get_result(self):
                 values = com.take_nd(values, inds, axis=1)
                 columns = columns[inds]
 
-        # we might have a missing index
-        if len(index) != values.shape[0]:
-            mask = isnull(index)
-            if mask.any():
-                l = np.arange(len(index))
-                values, orig_values = (np.empty((len(index), values.shape[1])),
-                                       values)
-                values.fill(np.nan)
-                values_indexer = com._ensure_int64(l[~mask])
-                for i, j in enumerate(values_indexer):
-                    values[j] = orig_values[i]
-            else:
-                index = index.take(self.unique_groups)
-
         # may need to coerce categoricals here
         if self.is_categorical is not None:
             values = [ Categorical.from_array(values[:,i],
@@ -220,9 +198,16 @@ def get_new_values(self):
 
     def get_new_columns(self):
         if self.value_columns is None:
-            return self.removed_level
+            if self.lift == 0:
+                return self.removed_level
+
+            lev = self.removed_level
+            vals = np.insert(lev.astype('object'), 0,
+                             _get_na_value(lev.dtype.type))
+
+            return lev._shallow_copy(vals)
 
-        stride = len(self.removed_level)
+        stride = len(self.removed_level) + self.lift
         width = len(self.value_columns)
         propagator = np.repeat(np.arange(width), stride)
         if isinstance(self.value_columns, MultiIndex):
@@ -231,59 +216,34 @@ def get_new_columns(self):
 
             new_labels = [lab.take(propagator)
                           for lab in self.value_columns.labels]
-            new_labels.append(np.tile(np.arange(stride), width))
         else:
             new_levels = [self.value_columns, self.removed_level]
             new_names = [self.value_columns.name, self.removed_name]
+            new_labels = [propagator]
 
-            new_labels = []
-
-            new_labels.append(propagator)
-            new_labels.append(np.tile(np.arange(stride), width))
-
+        new_labels.append(np.tile(np.arange(stride) - self.lift, width))
         return MultiIndex(levels=new_levels, labels=new_labels,
                           names=new_names, verify_integrity=False)
 
     def get_new_index(self):
-        result_labels = []
-        for cur in self.sorted_labels[:-1]:
-            labels = cur.take(self.compressor)
-            labels = _make_index_array_level(labels, cur)
-            result_labels.append(labels)
+        result_labels = [lab.take(self.compressor)
+                         for lab in self.sorted_labels[:-1]]
 
         # construct the new index
         if len(self.new_index_levels) == 1:
-            new_index = self.new_index_levels[0]
-            new_index.name = self.new_index_names[0]
-        else:
-            new_index = MultiIndex(levels=self.new_index_levels,
-                                   labels=result_labels,
-                                   names=self.new_index_names,
-                                   verify_integrity=False)
-
-        return new_index
+            lev, lab = self.new_index_levels[0], result_labels[0]
+            if not (lab == -1).any():
+                return lev.take(lab)
 
+            vals = np.insert(lev.astype('object'), len(lev),
+                             _get_na_value(lev.dtype.type)).take(lab)
 
-def _make_index_array_level(lev, lab):
-    """ create the combined index array, preserving nans, return an array """
-    mask = lab == -1
-    if not mask.any():
-        return lev
-
-    l = np.arange(len(lab))
-    mask_labels = np.empty(len(mask[mask]), dtype=object)
-    mask_labels.fill(_get_na_value(lev.dtype.type))
-    mask_indexer = com._ensure_int64(l[mask])
-
-    labels = lev
-    labels_indexer = com._ensure_int64(l[~mask])
-
-    new_labels = np.empty(tuple([len(lab)]), dtype=object)
-    new_labels[labels_indexer] = labels
-    new_labels[mask_indexer] = mask_labels
-
-    return new_labels
+            return lev._shallow_copy(vals)
 
+        return MultiIndex(levels=self.new_index_levels,
+                          labels=result_labels,
+                          names=self.new_index_names,
+                          verify_integrity=False)
 
 def _unstack_multiple(data, clocs):
     if len(clocs) == 0:
@@ -483,29 +443,10 @@ def _unstack_frame(obj, level):
 
 
 def get_compressed_ids(labels, sizes):
-    # no overflow
-    if com._long_prod(sizes) < 2 ** 63:
-        group_index = get_group_index(labels, sizes)
-        comp_index, obs_ids = _compress_group_index(group_index)
-    else:
-        n = len(labels[0])
-        mask = np.zeros(n, dtype=bool)
-        for v in labels:
-            mask |= v < 0
-
-        while com._long_prod(sizes) >= 2 ** 63:
-            i = len(sizes)
-            while com._long_prod(sizes[:i]) >= 2 ** 63:
-                i -= 1
-
-            rem_index, rem_ids = get_compressed_ids(labels[:i],
-                                                    sizes[:i])
-            sizes = [len(rem_ids)] + sizes[i:]
-            labels = [rem_index] + labels[i:]
-
-        return get_compressed_ids(labels, sizes)
+    from pandas.core.groupby import get_flat_ids
 
-    return comp_index, obs_ids
+    ids = get_flat_ids(labels, sizes, True)
+    return _compress_group_index(ids, sort=True)
 
 
 def stack(frame, level=-1, dropna=True):

pandas/tests/test_frame.py

@@ -11,7 +11,7 @@
 import nose
 import functools
 import itertools
-from itertools import product
+from itertools import product, permutations
 from distutils.version import LooseVersion
 
 from pandas.compat import(
@@ -12334,6 +12334,53 @@ def test_unstack_non_unique_index_names(self):
         with tm.assertRaises(ValueError):
             df.T.stack('c1')
 
+    def test_unstack_nan_index(self):  # GH7466
+        cast = lambda val: '{0:1}'.format('' if val != val else val)
+        nan = np.nan
+
+        def verify(df):
+            mk_list = lambda a: list(a) if isinstance(a, tuple) else [a]
+            rows, cols = df.notnull().values.nonzero()
+            for i, j in zip(rows, cols):
+                left = sorted(df.iloc[i, j].split('.'))
+                right = mk_list(df.index[i]) + mk_list(df.columns[j])
+                right = sorted(list(map(cast, right)))
+                self.assertEqual(left, right)
+
+        df = DataFrame({'jim':['a', 'b', nan, 'd'],
+                        'joe':['w', 'x', 'y', 'z'],
+                        'jolie':['a.w', 'b.x', ' .y', 'd.z']})
+
+        left  = df.set_index(['jim', 'joe']).unstack()['jolie']
+        right = df.set_index(['joe', 'jim']).unstack()['jolie'].T
+        assert_frame_equal(left, right)
+
+        for idx in permutations(df.columns[:2]):
+            mi = df.set_index(list(idx))
+            for lev in range(2):
+                udf = mi.unstack(level=lev)
+                self.assertEqual(udf.notnull().values.sum(), len(df))
+                verify(udf['jolie'])
+
+        df = DataFrame({'1st':['d'] * 3 + [nan] * 5 + ['a'] * 2 +
+                              ['c'] * 3 + ['e'] * 2 + ['b'] * 5,
+                        '2nd':['y'] * 2 + ['w'] * 3 + [nan] * 3 +
+                              ['z'] * 4 + [nan] * 3 + ['x'] * 3 + [nan] * 2,
+                        '3rd':[67,39,53,72,57,80,31,18,11,30,59,
+                               50,62,59,76,52,14,53,60,51]})
+
+        df['4th'], df['5th'] = \
+                df.apply(lambda r: '.'.join(map(cast, r)), axis=1), \
+                df.apply(lambda r: '.'.join(map(cast, r.iloc[::-1])), axis=1)
+
+        for idx in permutations(['1st', '2nd', '3rd']):
+            mi = df.set_index(list(idx))
+            for lev in range(3):
+                udf = mi.unstack(level=lev)
+                self.assertEqual(udf.notnull().values.sum(), 2 * len(df))
+                for col in ['4th', '5th']:
+                    verify(udf[col])
+
     def test_stack_datetime_column_multiIndex(self):
         # GH 8039
         t = datetime(2014, 1, 1)