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-rw-r--r--numpy/lib/_iotools.py4
-rw-r--r--numpy/lib/arraypad.py154
-rw-r--r--numpy/lib/arraysetops.py65
-rw-r--r--numpy/lib/format.py6
-rw-r--r--numpy/lib/histograms.py32
-rw-r--r--numpy/lib/index_tricks.py2
-rw-r--r--numpy/lib/npyio.py65
-rw-r--r--numpy/lib/polynomial.py5
-rw-r--r--numpy/lib/recfunctions.py13
-rw-r--r--numpy/lib/scimath.py2
-rw-r--r--numpy/lib/shape_base.py227
-rw-r--r--numpy/lib/tests/test__iotools.py5
-rw-r--r--numpy/lib/tests/test_arraysetops.py43
-rw-r--r--numpy/lib/tests/test_function_base.py21
-rw-r--r--numpy/lib/tests/test_histograms.py41
-rw-r--r--numpy/lib/tests/test_index_tricks.py42
-rw-r--r--numpy/lib/tests/test_nanfunctions.py105
-rw-r--r--numpy/lib/tests/test_shape_base.py114
-rw-r--r--numpy/lib/twodim_base.py2
19 files changed, 661 insertions, 287 deletions
diff --git a/numpy/lib/_iotools.py b/numpy/lib/_iotools.py
index 27143e5c6..b604b8c52 100644
--- a/numpy/lib/_iotools.py
+++ b/numpy/lib/_iotools.py
@@ -205,7 +205,11 @@ class LineSplitter(object):
#
def __init__(self, delimiter=None, comments='#', autostrip=True, encoding=None):
+ delimiter = _decode_line(delimiter)
+ comments = _decode_line(comments)
+
self.comments = comments
+
# Delimiter is a character
if (delimiter is None) or isinstance(delimiter, basestring):
delimiter = delimiter or None
diff --git a/numpy/lib/arraypad.py b/numpy/lib/arraypad.py
index 600301c56..e9ca9de4d 100644
--- a/numpy/lib/arraypad.py
+++ b/numpy/lib/arraypad.py
@@ -74,6 +74,35 @@ def _round_ifneeded(arr, dtype):
arr.round(out=arr)
+def _slice_at_axis(shape, sl, axis):
+ """
+ Construct a slice tuple the length of shape, with sl at the specified axis
+ """
+ slice_tup = (slice(None),)
+ return slice_tup * axis + (sl,) + slice_tup * (len(shape) - axis - 1)
+
+
+def _slice_first(shape, n, axis):
+ """ Construct a slice tuple to take the first n elements along axis """
+ return _slice_at_axis(shape, slice(0, n), axis=axis)
+
+
+def _slice_last(shape, n, axis):
+ """ Construct a slice tuple to take the last n elements along axis """
+ dim = shape[axis] # doing this explicitly makes n=0 work
+ return _slice_at_axis(shape, slice(dim - n, dim), axis=axis)
+
+
+def _do_prepend(arr, pad_chunk, axis):
+ return np.concatenate(
+ (pad_chunk.astype(arr.dtype, copy=False), arr), axis=axis)
+
+
+def _do_append(arr, pad_chunk, axis):
+ return np.concatenate(
+ (arr, pad_chunk.astype(arr.dtype, copy=False)), axis=axis)
+
+
def _prepend_const(arr, pad_amt, val, axis=-1):
"""
Prepend constant `val` along `axis` of `arr`.
@@ -100,8 +129,7 @@ def _prepend_const(arr, pad_amt, val, axis=-1):
return arr
padshape = tuple(x if i != axis else pad_amt
for (i, x) in enumerate(arr.shape))
- return np.concatenate((np.full(padshape, val, dtype=arr.dtype), arr),
- axis=axis)
+ return _do_prepend(arr, np.full(padshape, val, dtype=arr.dtype), axis)
def _append_const(arr, pad_amt, val, axis=-1):
@@ -130,8 +158,8 @@ def _append_const(arr, pad_amt, val, axis=-1):
return arr
padshape = tuple(x if i != axis else pad_amt
for (i, x) in enumerate(arr.shape))
- return np.concatenate((arr, np.full(padshape, val, dtype=arr.dtype)),
- axis=axis)
+ return _do_append(arr, np.full(padshape, val, dtype=arr.dtype), axis)
+
def _prepend_edge(arr, pad_amt, axis=-1):
@@ -156,11 +184,9 @@ def _prepend_edge(arr, pad_amt, axis=-1):
if pad_amt == 0:
return arr
- edge_slice = tuple(slice(None) if i != axis else slice(0, 1)
- for (i, x) in enumerate(arr.shape))
+ edge_slice = _slice_first(arr.shape, 1, axis=axis)
edge_arr = arr[edge_slice]
- return np.concatenate((edge_arr.repeat(pad_amt, axis=axis), arr),
- axis=axis)
+ return _do_prepend(arr, edge_arr.repeat(pad_amt, axis=axis), axis)
def _append_edge(arr, pad_amt, axis=-1):
@@ -186,11 +212,9 @@ def _append_edge(arr, pad_amt, axis=-1):
if pad_amt == 0:
return arr
- edge_slice = tuple(slice(None) if i != axis else slice(x - 1, x)
- for (i, x) in enumerate(arr.shape))
+ edge_slice = _slice_last(arr.shape, 1, axis=axis)
edge_arr = arr[edge_slice]
- return np.concatenate((arr, edge_arr.repeat(pad_amt, axis=axis)),
- axis=axis)
+ return _do_append(arr, edge_arr.repeat(pad_amt, axis=axis), axis)
def _prepend_ramp(arr, pad_amt, end, axis=-1):
@@ -228,8 +252,7 @@ def _prepend_ramp(arr, pad_amt, end, axis=-1):
reverse=True).astype(np.float64)
# Appropriate slicing to extract n-dimensional edge along `axis`
- edge_slice = tuple(slice(None) if i != axis else slice(0, 1)
- for (i, x) in enumerate(arr.shape))
+ edge_slice = _slice_first(arr.shape, 1, axis=axis)
# Extract edge, and extend along `axis`
edge_pad = arr[edge_slice].repeat(pad_amt, axis)
@@ -241,7 +264,7 @@ def _prepend_ramp(arr, pad_amt, end, axis=-1):
_round_ifneeded(ramp_arr, arr.dtype)
# Ramp values will most likely be float, cast them to the same type as arr
- return np.concatenate((ramp_arr.astype(arr.dtype), arr), axis=axis)
+ return _do_prepend(arr, ramp_arr, axis)
def _append_ramp(arr, pad_amt, end, axis=-1):
@@ -279,8 +302,7 @@ def _append_ramp(arr, pad_amt, end, axis=-1):
reverse=False).astype(np.float64)
# Slice a chunk from the edge to calculate stats on
- edge_slice = tuple(slice(None) if i != axis else slice(x - 1, x)
- for (i, x) in enumerate(arr.shape))
+ edge_slice = _slice_last(arr.shape, 1, axis=axis)
# Extract edge, and extend along `axis`
edge_pad = arr[edge_slice].repeat(pad_amt, axis)
@@ -292,7 +314,7 @@ def _append_ramp(arr, pad_amt, end, axis=-1):
_round_ifneeded(ramp_arr, arr.dtype)
# Ramp values will most likely be float, cast them to the same type as arr
- return np.concatenate((arr, ramp_arr.astype(arr.dtype)), axis=axis)
+ return _do_append(arr, ramp_arr, axis)
def _prepend_max(arr, pad_amt, num, axis=-1):
@@ -332,15 +354,13 @@ def _prepend_max(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- max_slice = tuple(slice(None) if i != axis else slice(num)
- for (i, x) in enumerate(arr.shape))
+ max_slice = _slice_first(arr.shape, num, axis=axis)
# Extract slice, calculate max
max_chunk = arr[max_slice].max(axis=axis, keepdims=True)
# Concatenate `arr` with `max_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate((max_chunk.repeat(pad_amt, axis=axis), arr),
- axis=axis)
+ return _do_prepend(arr, max_chunk.repeat(pad_amt, axis=axis), axis)
def _append_max(arr, pad_amt, num, axis=-1):
@@ -379,11 +399,8 @@ def _append_max(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- end = arr.shape[axis] - 1
if num is not None:
- max_slice = tuple(
- slice(None) if i != axis else slice(end, end - num, -1)
- for (i, x) in enumerate(arr.shape))
+ max_slice = _slice_last(arr.shape, num, axis=axis)
else:
max_slice = tuple(slice(None) for x in arr.shape)
@@ -391,8 +408,7 @@ def _append_max(arr, pad_amt, num, axis=-1):
max_chunk = arr[max_slice].max(axis=axis, keepdims=True)
# Concatenate `arr` with `max_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate((arr, max_chunk.repeat(pad_amt, axis=axis)),
- axis=axis)
+ return _do_append(arr, max_chunk.repeat(pad_amt, axis=axis), axis)
def _prepend_mean(arr, pad_amt, num, axis=-1):
@@ -431,16 +447,14 @@ def _prepend_mean(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- mean_slice = tuple(slice(None) if i != axis else slice(num)
- for (i, x) in enumerate(arr.shape))
+ mean_slice = _slice_first(arr.shape, num, axis=axis)
# Extract slice, calculate mean
mean_chunk = arr[mean_slice].mean(axis, keepdims=True)
_round_ifneeded(mean_chunk, arr.dtype)
# Concatenate `arr` with `mean_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate((mean_chunk.repeat(pad_amt, axis).astype(arr.dtype),
- arr), axis=axis)
+ return _do_prepend(arr, mean_chunk.repeat(pad_amt, axis), axis=axis)
def _append_mean(arr, pad_amt, num, axis=-1):
@@ -479,11 +493,8 @@ def _append_mean(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- end = arr.shape[axis] - 1
if num is not None:
- mean_slice = tuple(
- slice(None) if i != axis else slice(end, end - num, -1)
- for (i, x) in enumerate(arr.shape))
+ mean_slice = _slice_last(arr.shape, num, axis=axis)
else:
mean_slice = tuple(slice(None) for x in arr.shape)
@@ -492,8 +503,7 @@ def _append_mean(arr, pad_amt, num, axis=-1):
_round_ifneeded(mean_chunk, arr.dtype)
# Concatenate `arr` with `mean_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate(
- (arr, mean_chunk.repeat(pad_amt, axis).astype(arr.dtype)), axis=axis)
+ return _do_append(arr, mean_chunk.repeat(pad_amt, axis), axis=axis)
def _prepend_med(arr, pad_amt, num, axis=-1):
@@ -532,16 +542,14 @@ def _prepend_med(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- med_slice = tuple(slice(None) if i != axis else slice(num)
- for (i, x) in enumerate(arr.shape))
+ med_slice = _slice_first(arr.shape, num, axis=axis)
# Extract slice, calculate median
med_chunk = np.median(arr[med_slice], axis=axis, keepdims=True)
_round_ifneeded(med_chunk, arr.dtype)
# Concatenate `arr` with `med_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate(
- (med_chunk.repeat(pad_amt, axis).astype(arr.dtype), arr), axis=axis)
+ return _do_prepend(arr, med_chunk.repeat(pad_amt, axis), axis=axis)
def _append_med(arr, pad_amt, num, axis=-1):
@@ -580,11 +588,8 @@ def _append_med(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- end = arr.shape[axis] - 1
if num is not None:
- med_slice = tuple(
- slice(None) if i != axis else slice(end, end - num, -1)
- for (i, x) in enumerate(arr.shape))
+ med_slice = _slice_last(arr.shape, num, axis=axis)
else:
med_slice = tuple(slice(None) for x in arr.shape)
@@ -593,8 +598,7 @@ def _append_med(arr, pad_amt, num, axis=-1):
_round_ifneeded(med_chunk, arr.dtype)
# Concatenate `arr` with `med_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate(
- (arr, med_chunk.repeat(pad_amt, axis).astype(arr.dtype)), axis=axis)
+ return _do_append(arr, med_chunk.repeat(pad_amt, axis), axis=axis)
def _prepend_min(arr, pad_amt, num, axis=-1):
@@ -634,15 +638,13 @@ def _prepend_min(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- min_slice = tuple(slice(None) if i != axis else slice(num)
- for (i, x) in enumerate(arr.shape))
+ min_slice = _slice_first(arr.shape, num, axis=axis)
# Extract slice, calculate min
min_chunk = arr[min_slice].min(axis=axis, keepdims=True)
# Concatenate `arr` with `min_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate((min_chunk.repeat(pad_amt, axis=axis), arr),
- axis=axis)
+ return _do_prepend(arr, min_chunk.repeat(pad_amt, axis), axis=axis)
def _append_min(arr, pad_amt, num, axis=-1):
@@ -681,11 +683,8 @@ def _append_min(arr, pad_amt, num, axis=-1):
num = None
# Slice a chunk from the edge to calculate stats on
- end = arr.shape[axis] - 1
if num is not None:
- min_slice = tuple(
- slice(None) if i != axis else slice(end, end - num, -1)
- for (i, x) in enumerate(arr.shape))
+ min_slice = _slice_last(arr.shape, num, axis=axis)
else:
min_slice = tuple(slice(None) for x in arr.shape)
@@ -693,8 +692,7 @@ def _append_min(arr, pad_amt, num, axis=-1):
min_chunk = arr[min_slice].min(axis=axis, keepdims=True)
# Concatenate `arr` with `min_chunk`, extended along `axis` by `pad_amt`
- return np.concatenate((arr, min_chunk.repeat(pad_amt, axis=axis)),
- axis=axis)
+ return _do_append(arr, min_chunk.repeat(pad_amt, axis), axis=axis)
def _pad_ref(arr, pad_amt, method, axis=-1):
@@ -737,15 +735,13 @@ def _pad_ref(arr, pad_amt, method, axis=-1):
# Prepended region
# Slice off a reverse indexed chunk from near edge to pad `arr` before
- ref_slice = tuple(slice(None) if i != axis else slice(pad_amt[0], 0, -1)
- for (i, x) in enumerate(arr.shape))
+ ref_slice = _slice_at_axis(arr.shape, slice(pad_amt[0], 0, -1), axis=axis)
ref_chunk1 = arr[ref_slice]
# Memory/computationally more expensive, only do this if `method='odd'`
if 'odd' in method and pad_amt[0] > 0:
- edge_slice1 = tuple(slice(None) if i != axis else slice(0, 1)
- for (i, x) in enumerate(arr.shape))
+ edge_slice1 = _slice_first(arr.shape, 1, axis=axis)
edge_chunk = arr[edge_slice1]
ref_chunk1 = 2 * edge_chunk - ref_chunk1
del edge_chunk
@@ -756,15 +752,12 @@ def _pad_ref(arr, pad_amt, method, axis=-1):
# Slice off a reverse indexed chunk from far edge to pad `arr` after
start = arr.shape[axis] - pad_amt[1] - 1
end = arr.shape[axis] - 1
- ref_slice = tuple(slice(None) if i != axis else slice(start, end)
- for (i, x) in enumerate(arr.shape))
- rev_idx = tuple(slice(None) if i != axis else slice(None, None, -1)
- for (i, x) in enumerate(arr.shape))
+ ref_slice = _slice_at_axis(arr.shape, slice(start, end), axis=axis)
+ rev_idx = _slice_at_axis(arr.shape, slice(None, None, -1), axis=axis)
ref_chunk2 = arr[ref_slice][rev_idx]
if 'odd' in method:
- edge_slice2 = tuple(slice(None) if i != axis else slice(x - 1, x)
- for (i, x) in enumerate(arr.shape))
+ edge_slice2 = _slice_last(arr.shape, 1, axis=axis)
edge_chunk = arr[edge_slice2]
ref_chunk2 = 2 * edge_chunk - ref_chunk2
del edge_chunk
@@ -813,16 +806,13 @@ def _pad_sym(arr, pad_amt, method, axis=-1):
# Prepended region
# Slice off a reverse indexed chunk from near edge to pad `arr` before
- sym_slice = tuple(slice(None) if i != axis else slice(0, pad_amt[0])
- for (i, x) in enumerate(arr.shape))
- rev_idx = tuple(slice(None) if i != axis else slice(None, None, -1)
- for (i, x) in enumerate(arr.shape))
+ sym_slice = _slice_first(arr.shape, pad_amt[0], axis=axis)
+ rev_idx = _slice_at_axis(arr.shape, slice(None, None, -1), axis=axis)
sym_chunk1 = arr[sym_slice][rev_idx]
# Memory/computationally more expensive, only do this if `method='odd'`
if 'odd' in method and pad_amt[0] > 0:
- edge_slice1 = tuple(slice(None) if i != axis else slice(0, 1)
- for (i, x) in enumerate(arr.shape))
+ edge_slice1 = _slice_first(arr.shape, 1, axis=axis)
edge_chunk = arr[edge_slice1]
sym_chunk1 = 2 * edge_chunk - sym_chunk1
del edge_chunk
@@ -831,15 +821,11 @@ def _pad_sym(arr, pad_amt, method, axis=-1):
# Appended region
# Slice off a reverse indexed chunk from far edge to pad `arr` after
- start = arr.shape[axis] - pad_amt[1]
- end = arr.shape[axis]
- sym_slice = tuple(slice(None) if i != axis else slice(start, end)
- for (i, x) in enumerate(arr.shape))
+ sym_slice = _slice_last(arr.shape, pad_amt[1], axis=axis)
sym_chunk2 = arr[sym_slice][rev_idx]
if 'odd' in method:
- edge_slice2 = tuple(slice(None) if i != axis else slice(x - 1, x)
- for (i, x) in enumerate(arr.shape))
+ edge_slice2 = _slice_last(arr.shape, 1, axis=axis)
edge_chunk = arr[edge_slice2]
sym_chunk2 = 2 * edge_chunk - sym_chunk2
del edge_chunk
@@ -885,18 +871,14 @@ def _pad_wrap(arr, pad_amt, axis=-1):
# Prepended region
# Slice off a reverse indexed chunk from near edge to pad `arr` before
- start = arr.shape[axis] - pad_amt[0]
- end = arr.shape[axis]
- wrap_slice = tuple(slice(None) if i != axis else slice(start, end)
- for (i, x) in enumerate(arr.shape))
+ wrap_slice = _slice_last(arr.shape, pad_amt[0], axis=axis)
wrap_chunk1 = arr[wrap_slice]
##########################################################################
# Appended region
# Slice off a reverse indexed chunk from far edge to pad `arr` after
- wrap_slice = tuple(slice(None) if i != axis else slice(0, pad_amt[1])
- for (i, x) in enumerate(arr.shape))
+ wrap_slice = _slice_first(arr.shape, pad_amt[1], axis=axis)
wrap_chunk2 = arr[wrap_slice]
# Concatenate `arr` with both chunks, extending along `axis`
diff --git a/numpy/lib/arraysetops.py b/numpy/lib/arraysetops.py
index e8eda297f..4d3f35183 100644
--- a/numpy/lib/arraysetops.py
+++ b/numpy/lib/arraysetops.py
@@ -298,7 +298,7 @@ def _unique1d(ar, return_index=False, return_inverse=False,
return ret
-def intersect1d(ar1, ar2, assume_unique=False):
+def intersect1d(ar1, ar2, assume_unique=False, return_indices=False):
"""
Find the intersection of two arrays.
@@ -307,15 +307,28 @@ def intersect1d(ar1, ar2, assume_unique=False):
Parameters
----------
ar1, ar2 : array_like
- Input arrays.
+ Input arrays. Will be flattened if not already 1D.
assume_unique : bool
If True, the input arrays are both assumed to be unique, which
can speed up the calculation. Default is False.
-
+ return_indices : bool
+ If True, the indices which correspond to the intersection of the
+ two arrays are returned. The first instance of a value is used
+ if there are multiple. Default is False.
+
+ .. versionadded:: 1.15.0
+
Returns
-------
intersect1d : ndarray
Sorted 1D array of common and unique elements.
+ comm1 : ndarray
+ The indices of the first occurrences of the common values in `ar1`.
+ Only provided if `return_indices` is True.
+ comm2 : ndarray
+ The indices of the first occurrences of the common values in `ar2`.
+ Only provided if `return_indices` is True.
+
See Also
--------
@@ -332,14 +345,49 @@ def intersect1d(ar1, ar2, assume_unique=False):
>>> from functools import reduce
>>> reduce(np.intersect1d, ([1, 3, 4, 3], [3, 1, 2, 1], [6, 3, 4, 2]))
array([3])
+
+ To return the indices of the values common to the input arrays
+ along with the intersected values:
+ >>> x = np.array([1, 1, 2, 3, 4])
+ >>> y = np.array([2, 1, 4, 6])
+ >>> xy, x_ind, y_ind = np.intersect1d(x, y, return_indices=True)
+ >>> x_ind, y_ind
+ (array([0, 2, 4]), array([1, 0, 2]))
+ >>> xy, x[x_ind], y[y_ind]
+ (array([1, 2, 4]), array([1, 2, 4]), array([1, 2, 4]))
+
"""
if not assume_unique:
- # Might be faster than unique( intersect1d( ar1, ar2 ) )?
- ar1 = unique(ar1)
- ar2 = unique(ar2)
+ if return_indices:
+ ar1, ind1 = unique(ar1, return_index=True)
+ ar2, ind2 = unique(ar2, return_index=True)
+ else:
+ ar1 = unique(ar1)
+ ar2 = unique(ar2)
+ else:
+ ar1 = ar1.ravel()
+ ar2 = ar2.ravel()
+
aux = np.concatenate((ar1, ar2))
- aux.sort()
- return aux[:-1][aux[1:] == aux[:-1]]
+ if return_indices:
+ aux_sort_indices = np.argsort(aux, kind='mergesort')
+ aux = aux[aux_sort_indices]
+ else:
+ aux.sort()
+
+ mask = aux[1:] == aux[:-1]
+ int1d = aux[:-1][mask]
+
+ if return_indices:
+ ar1_indices = aux_sort_indices[:-1][mask]
+ ar2_indices = aux_sort_indices[1:][mask] - ar1.size
+ if not assume_unique:
+ ar1_indices = ind1[ar1_indices]
+ ar2_indices = ind2[ar2_indices]
+
+ return int1d, ar1_indices, ar2_indices
+ else:
+ return int1d
def setxor1d(ar1, ar2, assume_unique=False):
"""
@@ -660,3 +708,4 @@ def setdiff1d(ar1, ar2, assume_unique=False):
ar1 = unique(ar1)
ar2 = unique(ar2)
return ar1[in1d(ar1, ar2, assume_unique=True, invert=True)]
+
diff --git a/numpy/lib/format.py b/numpy/lib/format.py
index afa154cc5..23eac7e7d 100644
--- a/numpy/lib/format.py
+++ b/numpy/lib/format.py
@@ -1,6 +1,8 @@
"""
-Binary Serialization
-====================
+Binary serialization
+
+NPY format
+==========
A simple format for saving numpy arrays to disk with the full
information about them.
diff --git a/numpy/lib/histograms.py b/numpy/lib/histograms.py
index 90e19769e..2922b3a86 100644
--- a/numpy/lib/histograms.py
+++ b/numpy/lib/histograms.py
@@ -877,12 +877,6 @@ def histogramdd(sample, bins=10, range=None, normed=False, weights=None):
# bins is an integer
bins = D*[bins]
- # avoid rounding issues for comparisons when dealing with inexact types
- if np.issubdtype(sample.dtype, np.inexact):
- edge_dt = sample.dtype
- else:
- edge_dt = float
-
# normalize the range argument
if range is None:
range = (None,) * D
@@ -896,13 +890,12 @@ def histogramdd(sample, bins=10, range=None, normed=False, weights=None):
raise ValueError(
'`bins[{}]` must be positive, when an integer'.format(i))
smin, smax = _get_outer_edges(sample[:,i], range[i])
- edges[i] = np.linspace(smin, smax, bins[i] + 1, dtype=edge_dt)
+ edges[i] = np.linspace(smin, smax, bins[i] + 1)
elif np.ndim(bins[i]) == 1:
- edges[i] = np.asarray(bins[i], edge_dt)
- # not just monotonic, due to the use of mindiff below
- if np.any(edges[i][:-1] >= edges[i][1:]):
+ edges[i] = np.asarray(bins[i])
+ if np.any(edges[i][:-1] > edges[i][1:]):
raise ValueError(
- '`bins[{}]` must be strictly increasing, when an array'
+ '`bins[{}]` must be monotonically increasing, when an array'
.format(i))
else:
raise ValueError(
@@ -913,7 +906,8 @@ def histogramdd(sample, bins=10, range=None, normed=False, weights=None):
# Compute the bin number each sample falls into.
Ncount = tuple(
- np.digitize(sample[:, i], edges[i])
+ # avoid np.digitize to work around gh-11022
+ np.searchsorted(edges[i], sample[:, i], side='right')
for i in _range(D)
)
@@ -921,16 +915,10 @@ def histogramdd(sample, bins=10, range=None, normed=False, weights=None):
# For the rightmost bin, we want values equal to the right edge to be
# counted in the last bin, and not as an outlier.
for i in _range(D):
- # Rounding precision
- mindiff = dedges[i].min()
- if not np.isinf(mindiff):
- decimal = int(-np.log10(mindiff)) + 6
- # Find which points are on the rightmost edge.
- not_smaller_than_edge = (sample[:, i] >= edges[i][-1])
- on_edge = (np.around(sample[:, i], decimal) ==
- np.around(edges[i][-1], decimal))
- # Shift these points one bin to the left.
- Ncount[i][on_edge & not_smaller_than_edge] -= 1
+ # Find which points are on the rightmost edge.
+ on_edge = (sample[:, i] == edges[i][-1])
+ # Shift these points one bin to the left.
+ Ncount[i][on_edge] -= 1
# Compute the sample indices in the flattened histogram matrix.
# This raises an error if the array is too large.
diff --git a/numpy/lib/index_tricks.py b/numpy/lib/index_tricks.py
index 43fdc5627..d2139338e 100644
--- a/numpy/lib/index_tricks.py
+++ b/numpy/lib/index_tricks.py
@@ -201,7 +201,7 @@ class nd_grid(object):
slobj = [_nx.newaxis]*len(size)
for k in range(len(size)):
slobj[k] = slice(None, None)
- nn[k] = nn[k][slobj]
+ nn[k] = nn[k][tuple(slobj)]
slobj[k] = _nx.newaxis
return nn
except (IndexError, TypeError):
diff --git a/numpy/lib/npyio.py b/numpy/lib/npyio.py
index 5d3c1e525..390927601 100644
--- a/numpy/lib/npyio.py
+++ b/numpy/lib/npyio.py
@@ -26,9 +26,11 @@ from numpy.compat import (
if sys.version_info[0] >= 3:
import pickle
+ from collections.abc import Mapping
else:
import cPickle as pickle
from future_builtins import map
+ from collections import Mapping
def loads(*args, **kwargs):
@@ -92,7 +94,7 @@ class BagObj(object):
This also enables tab-completion in an interpreter or IPython.
"""
- return object.__getattribute__(self, '_obj').keys()
+ return list(object.__getattribute__(self, '_obj').keys())
def zipfile_factory(file, *args, **kwargs):
@@ -110,7 +112,7 @@ def zipfile_factory(file, *args, **kwargs):
return zipfile.ZipFile(file, *args, **kwargs)
-class NpzFile(object):
+class NpzFile(Mapping):
"""
NpzFile(fid)
@@ -216,6 +218,13 @@ class NpzFile(object):
def __del__(self):
self.close()
+ # Implement the Mapping ABC
+ def __iter__(self):
+ return iter(self.files)
+
+ def __len__(self):
+ return len(self.files)
+
def __getitem__(self, key):
# FIXME: This seems like it will copy strings around
# more than is strictly necessary. The zipfile
@@ -225,11 +234,11 @@ class NpzFile(object):
# It would be better if the zipfile could read
# (or at least uncompress) the data
# directly into the array memory.
- member = 0
+ member = False
if key in self._files:
- member = 1
+ member = True
elif key in self.files:
- member = 1
+ member = True
key += '.npy'
if member:
bytes = self.zip.open(key)
@@ -245,31 +254,27 @@ class NpzFile(object):
else:
raise KeyError("%s is not a file in the archive" % key)
- def __iter__(self):
- return iter(self.files)
- def items(self):
- """
- Return a list of tuples, with each tuple (filename, array in file).
+ if sys.version_info.major == 3:
+ # deprecate the python 2 dict apis that we supported by accident in
+ # python 3. We forgot to implement itervalues() at all in earlier
+ # versions of numpy, so no need to deprecated it here.
- """
- return [(f, self[f]) for f in self.files]
-
- def iteritems(self):
- """Generator that returns tuples (filename, array in file)."""
- for f in self.files:
- yield (f, self[f])
-
- def keys(self):
- """Return files in the archive with a ``.npy`` extension."""
- return self.files
-
- def iterkeys(self):
- """Return an iterator over the files in the archive."""
- return self.__iter__()
+ def iteritems(self):
+ # Numpy 1.15, 2018-02-20
+ warnings.warn(
+ "NpzFile.iteritems is deprecated in python 3, to match the "
+ "removal of dict.itertems. Use .items() instead.",
+ DeprecationWarning, stacklevel=2)
+ return self.items()
- def __contains__(self, key):
- return self.files.__contains__(key)
+ def iterkeys(self):
+ # Numpy 1.15, 2018-02-20
+ warnings.warn(
+ "NpzFile.iterkeys is deprecated in python 3, to match the "
+ "removal of dict.iterkeys. Use .keys() instead.",
+ DeprecationWarning, stacklevel=2)
+ return self.keys()
def load(file, mmap_mode=None, allow_pickle=True, fix_imports=True,
@@ -475,7 +480,7 @@ def save(file, arr, allow_pickle=True, fix_imports=True):
Notes
-----
- For a description of the ``.npy`` format, see :py:mod:`numpy.lib.format`
+ For a description of the ``.npy`` format, see :py:mod:`numpy.lib.format`.
Examples
--------
@@ -559,7 +564,7 @@ def savez(file, *args, **kwds):
The ``.npz`` file format is a zipped archive of files named after the
variables they contain. The archive is not compressed and each file
in the archive contains one variable in ``.npy`` format. For a
- description of the ``.npy`` format, see :py:mod:`numpy.lib.format`
+ description of the ``.npy`` format, see :py:mod:`numpy.lib.format`.
When opening the saved ``.npz`` file with `load` a `NpzFile` object is
returned. This is a dictionary-like object which can be queried for
@@ -639,7 +644,7 @@ def savez_compressed(file, *args, **kwds):
variables they contain. The archive is compressed with
``zipfile.ZIP_DEFLATED`` and each file in the archive contains one variable
in ``.npy`` format. For a description of the ``.npy`` format, see
- :py:mod:`numpy.lib.format`
+ :py:mod:`numpy.lib.format`.
When opening the saved ``.npz`` file with `load` a `NpzFile` object is
diff --git a/numpy/lib/polynomial.py b/numpy/lib/polynomial.py
index 41b5e2f64..078608bbb 100644
--- a/numpy/lib/polynomial.py
+++ b/numpy/lib/polynomial.py
@@ -113,11 +113,6 @@ def poly(seq_of_zeros):
>>> np.poly(P)
array([ 1. , 0. , 0.16666667])
- Or a square matrix object:
-
- >>> np.poly(np.matrix(P))
- array([ 1. , 0. , 0.16666667])
-
Note how in all cases the leading coefficient is always 1.
"""
diff --git a/numpy/lib/recfunctions.py b/numpy/lib/recfunctions.py
index e9ba38f46..c455bd93f 100644
--- a/numpy/lib/recfunctions.py
+++ b/numpy/lib/recfunctions.py
@@ -397,12 +397,13 @@ def merge_arrays(seqarrays, fill_value=-1, flatten=False,
Notes
-----
* Without a mask, the missing value will be filled with something,
- * depending on what its corresponding type:
- -1 for integers
- -1.0 for floating point numbers
- '-' for characters
- '-1' for strings
- True for boolean values
+ depending on what its corresponding type:
+
+ * ``-1`` for integers
+ * ``-1.0`` for floating point numbers
+ * ``'-'`` for characters
+ * ``'-1'`` for strings
+ * ``True`` for boolean values
* XXX: I just obtained these values empirically
"""
# Only one item in the input sequence ?
diff --git a/numpy/lib/scimath.py b/numpy/lib/scimath.py
index e07caf805..f1838fee6 100644
--- a/numpy/lib/scimath.py
+++ b/numpy/lib/scimath.py
@@ -555,7 +555,7 @@ def arctanh(x):
--------
>>> np.set_printoptions(precision=4)
- >>> np.emath.arctanh(np.matrix(np.eye(2)))
+ >>> np.emath.arctanh(np.eye(2))
array([[ Inf, 0.],
[ 0., Inf]])
>>> np.emath.arctanh([1j])
diff --git a/numpy/lib/shape_base.py b/numpy/lib/shape_base.py
index 41ef28ef3..65104115a 100644
--- a/numpy/lib/shape_base.py
+++ b/numpy/lib/shape_base.py
@@ -16,10 +16,235 @@ from numpy.matrixlib.defmatrix import matrix # this raises all the right alarm
__all__ = [
'column_stack', 'row_stack', 'dstack', 'array_split', 'split',
'hsplit', 'vsplit', 'dsplit', 'apply_over_axes', 'expand_dims',
- 'apply_along_axis', 'kron', 'tile', 'get_array_wrap'
+ 'apply_along_axis', 'kron', 'tile', 'get_array_wrap', 'take_along_axis',
+ 'put_along_axis'
]
+def _make_along_axis_idx(arr_shape, indices, axis):
+ # compute dimensions to iterate over
+ if not _nx.issubdtype(indices.dtype, _nx.integer):
+ raise IndexError('`indices` must be an integer array')
+ if len(arr_shape) != indices.ndim:
+ raise ValueError(
+ "`indices` and `arr` must have the same number of dimensions")
+ shape_ones = (1,) * indices.ndim
+ dest_dims = list(range(axis)) + [None] + list(range(axis+1, indices.ndim))
+
+ # build a fancy index, consisting of orthogonal aranges, with the
+ # requested index inserted at the right location
+ fancy_index = []
+ for dim, n in zip(dest_dims, arr_shape):
+ if dim is None:
+ fancy_index.append(indices)
+ else:
+ ind_shape = shape_ones[:dim] + (-1,) + shape_ones[dim+1:]
+ fancy_index.append(_nx.arange(n).reshape(ind_shape))
+
+ return tuple(fancy_index)
+
+
+def take_along_axis(arr, indices, axis):
+ """
+ Take values from the input array by matching 1d index and data slices.
+
+ This iterates over matching 1d slices oriented along the specified axis in
+ the index and data arrays, and uses the former to look up values in the
+ latter. These slices can be different lengths.
+
+ Functions returning an index along an axis, like `argsort` and
+ `argpartition`, produce suitable indices for this function.
+
+ .. versionadded:: 1.15.0
+
+ Parameters
+ ----------
+ arr: ndarray (Ni..., M, Nk...)
+ Source array
+ indices: ndarray (Ni..., J, Nk...)
+ Indices to take along each 1d slice of `arr`. This must match the
+ dimension of arr, but dimensions Ni and Nj only need to broadcast
+ against `arr`.
+ axis: int
+ The axis to take 1d slices along. If axis is None, the input array is
+ treated as if it had first been flattened to 1d, for consistency with
+ `sort` and `argsort`.
+
+ Returns
+ -------
+ out: ndarray (Ni..., J, Nk...)
+ The indexed result.
+
+ Notes
+ -----
+ This is equivalent to (but faster than) the following use of `ndindex` and
+ `s_`, which sets each of ``ii`` and ``kk`` to a tuple of indices::
+
+ Ni, M, Nk = a.shape[:axis], a.shape[axis], a.shape[axis+1:]
+ J = indices.shape[axis] # Need not equal M
+ out = np.empty(Nk + (J,) + Nk)
+
+ for ii in ndindex(Ni):
+ for kk in ndindex(Nk):
+ a_1d = a [ii + s_[:,] + kk]
+ indices_1d = indices[ii + s_[:,] + kk]
+ out_1d = out [ii + s_[:,] + kk]
+ for j in range(J):
+ out_1d[j] = a_1d[indices_1d[j]]
+
+ Equivalently, eliminating the inner loop, the last two lines would be::
+
+ out_1d[:] = a_1d[indices_1d]
+
+ See Also
+ --------
+ take : Take along an axis, using the same indices for every 1d slice
+ put_along_axis :
+ Put values into the destination array by matching 1d index and data slices
+
+ Examples
+ --------
+
+ For this sample array
+
+ >>> a = np.array([[10, 30, 20], [60, 40, 50]])
+
+ We can sort either by using sort directly, or argsort and this function
+
+ >>> np.sort(a, axis=1)
+ array([[10, 20, 30],
+ [40, 50, 60]])
+ >>> ai = np.argsort(a, axis=1); ai
+ array([[0, 2, 1],
+ [1, 2, 0]], dtype=int64)
+ >>> np.take_along_axis(a, ai, axis=1)
+ array([[10, 20, 30],
+ [40, 50, 60]])
+
+ The same works for max and min, if you expand the dimensions:
+
+ >>> np.expand_dims(np.max(a, axis=1), axis=1)
+ array([[30],
+ [60]])
+ >>> ai = np.expand_dims(np.argmax(a, axis=1), axis=1)
+ >>> ai
+ array([[1],
+ [0], dtype=int64)
+ >>> np.take_along_axis(a, ai, axis=1)
+ array([[30],
+ [60]])
+
+ If we want to get the max and min at the same time, we can stack the
+ indices first
+
+ >>> ai_min = np.expand_dims(np.argmin(a, axis=1), axis=1)
+ >>> ai_max = np.expand_dims(np.argmax(a, axis=1), axis=1)
+ >>> ai = np.concatenate([ai_min, ai_max], axis=axis)
+ >> ai
+ array([[0, 1],
+ [1, 0]], dtype=int64)
+ >>> np.take_along_axis(a, ai, axis=1)
+ array([[10, 30],
+ [40, 60]])
+ """
+ # normalize inputs
+ if axis is None:
+ arr = arr.flat
+ arr_shape = (len(arr),) # flatiter has no .shape
+ axis = 0
+ else:
+ axis = normalize_axis_index(axis, arr.ndim)
+ arr_shape = arr.shape
+
+ # use the fancy index
+ return arr[_make_along_axis_idx(arr_shape, indices, axis)]
+
+
+def put_along_axis(arr, indices, values, axis):
+ """
+ Put values into the destination array by matching 1d index and data slices.
+
+ This iterates over matching 1d slices oriented along the specified axis in
+ the index and data arrays, and uses the former to place values into the
+ latter. These slices can be different lengths.
+
+ Functions returning an index along an axis, like `argsort` and
+ `argpartition`, produce suitable indices for this function.
+
+ .. versionadded:: 1.15.0
+
+ Parameters
+ ----------
+ arr: ndarray (Ni..., M, Nk...)
+ Destination array.
+ indices: ndarray (Ni..., J, Nk...)
+ Indices to change along each 1d slice of `arr`. This must match the
+ dimension of arr, but dimensions in Ni and Nj may be 1 to broadcast
+ against `arr`.
+ values: array_like (Ni..., J, Nk...)
+ values to insert at those indices. Its shape and dimension are
+ broadcast to match that of `indices`.
+ axis: int
+ The axis to take 1d slices along. If axis is None, the destination
+ array is treated as if a flattened 1d view had been created of it.
+
+ Notes
+ -----
+ This is equivalent to (but faster than) the following use of `ndindex` and
+ `s_`, which sets each of ``ii`` and ``kk`` to a tuple of indices::
+
+ Ni, M, Nk = a.shape[:axis], a.shape[axis], a.shape[axis+1:]
+ J = indices.shape[axis] # Need not equal M
+
+ for ii in ndindex(Ni):
+ for kk in ndindex(Nk):
+ a_1d = a [ii + s_[:,] + kk]
+ indices_1d = indices[ii + s_[:,] + kk]
+ values_1d = values [ii + s_[:,] + kk]
+ for j in range(J):
+ a_1d[indices_1d[j]] = values_1d[j]
+
+ Equivalently, eliminating the inner loop, the last two lines would be::
+
+ a_1d[indices_1d] = values_1d
+
+ See Also
+ --------
+ take_along_axis :
+ Take values from the input array by matching 1d index and data slices
+
+ Examples
+ --------
+
+ For this sample array
+
+ >>> a = np.array([[10, 30, 20], [60, 40, 50]])
+
+ We can replace the maximum values with:
+
+ >>> ai = np.expand_dims(np.argmax(a, axis=1), axis=1)
+ >>> ai
+ array([[1],
+ [0]], dtype=int64)
+ >>> np.put_along_axis(a, ai, 99, axis=1)
+ >>> a
+ array([[10, 99, 20],
+ [99, 40, 50]])
+
+ """
+ # normalize inputs
+ if axis is None:
+ arr = arr.flat
+ axis = 0
+ arr_shape = (len(arr),) # flatiter has no .shape
+ else:
+ axis = normalize_axis_index(axis, arr.ndim)
+ arr_shape = arr.shape
+
+ # use the fancy index
+ arr[_make_along_axis_idx(arr_shape, indices, axis)] = values
+
+
def apply_along_axis(func1d, axis, arr, *args, **kwargs):
"""
Apply a function to 1-D slices along the given axis.
diff --git a/numpy/lib/tests/test__iotools.py b/numpy/lib/tests/test__iotools.py
index 5f6c29a4d..b4888f1bd 100644
--- a/numpy/lib/tests/test__iotools.py
+++ b/numpy/lib/tests/test__iotools.py
@@ -53,6 +53,11 @@ class TestLineSplitter(object):
test = LineSplitter(',')(strg)
assert_equal(test, ['1', '2', '3', '4', '', '5'])
+ # gh-11028 bytes comment/delimiters should get encoded
+ strg = b" 1,2,3,4,,5 % test"
+ test = LineSplitter(delimiter=b',', comments=b'%')(strg)
+ assert_equal(test, ['1', '2', '3', '4', '', '5'])
+
def test_constant_fixed_width(self):
"Test LineSplitter w/ fixed-width fields"
strg = " 1 2 3 4 5 # test"
diff --git a/numpy/lib/tests/test_arraysetops.py b/numpy/lib/tests/test_arraysetops.py
index 76c36c53e..dace5ade8 100644
--- a/numpy/lib/tests/test_arraysetops.py
+++ b/numpy/lib/tests/test_arraysetops.py
@@ -32,7 +32,46 @@ class TestSetOps(object):
assert_array_equal(c, ed)
assert_array_equal([], intersect1d([], []))
-
+
+ def test_intersect1d_indices(self):
+ # unique inputs
+ a = np.array([1, 2, 3, 4])
+ b = np.array([2, 1, 4, 6])
+ c, i1, i2 = intersect1d(a, b, assume_unique=True, return_indices=True)
+ ee = np.array([1, 2, 4])
+ assert_array_equal(c, ee)
+ assert_array_equal(a[i1], ee)
+ assert_array_equal(b[i2], ee)
+
+ # non-unique inputs
+ a = np.array([1, 2, 2, 3, 4, 3, 2])
+ b = np.array([1, 8, 4, 2, 2, 3, 2, 3])
+ c, i1, i2 = intersect1d(a, b, return_indices=True)
+ ef = np.array([1, 2, 3, 4])
+ assert_array_equal(c, ef)
+ assert_array_equal(a[i1], ef)
+ assert_array_equal(b[i2], ef)
+
+ # non1d, unique inputs
+ a = np.array([[2, 4, 5, 6], [7, 8, 1, 15]])
+ b = np.array([[3, 2, 7, 6], [10, 12, 8, 9]])
+ c, i1, i2 = intersect1d(a, b, assume_unique=True, return_indices=True)
+ ui1 = np.unravel_index(i1, a.shape)
+ ui2 = np.unravel_index(i2, b.shape)
+ ea = np.array([2, 6, 7, 8])
+ assert_array_equal(ea, a[ui1])
+ assert_array_equal(ea, b[ui2])
+
+ # non1d, not assumed to be uniqueinputs
+ a = np.array([[2, 4, 5, 6, 6], [4, 7, 8, 7, 2]])
+ b = np.array([[3, 2, 7, 7], [10, 12, 8, 7]])
+ c, i1, i2 = intersect1d(a, b, return_indices=True)
+ ui1 = np.unravel_index(i1, a.shape)
+ ui2 = np.unravel_index(i2, b.shape)
+ ea = np.array([2, 7, 8])
+ assert_array_equal(ea, a[ui1])
+ assert_array_equal(ea, b[ui2])
+
def test_setxor1d(self):
a = np.array([5, 7, 1, 2])
b = np.array([2, 4, 3, 1, 5])
@@ -74,8 +113,6 @@ class TestSetOps(object):
assert_array_equal([1,7,8], ediff1d(two_elem, to_end=[7,8]))
assert_array_equal([7,1], ediff1d(two_elem, to_begin=7))
assert_array_equal([5,6,1], ediff1d(two_elem, to_begin=[5,6]))
- assert(isinstance(ediff1d(np.matrix(1)), np.matrix))
- assert(isinstance(ediff1d(np.matrix(1), to_begin=1), np.matrix))
def test_isin(self):
# the tests for in1d cover most of isin's behavior
diff --git a/numpy/lib/tests/test_function_base.py b/numpy/lib/tests/test_function_base.py
index 5dc96775b..4103a9eb3 100644
--- a/numpy/lib/tests/test_function_base.py
+++ b/numpy/lib/tests/test_function_base.py
@@ -287,9 +287,6 @@ class TestAverage(object):
assert_almost_equal(y5.mean(0), average(y5, 0))
assert_almost_equal(y5.mean(1), average(y5, 1))
- y6 = np.matrix(rand(5, 5))
- assert_array_equal(y6.mean(0), average(y6, 0))
-
def test_weights(self):
y = np.arange(10)
w = np.arange(10)
@@ -357,14 +354,6 @@ class TestAverage(object):
assert_equal(type(np.average(a)), subclass)
assert_equal(type(np.average(a, weights=w)), subclass)
- # also test matrices
- a = np.matrix([[1,2],[3,4]])
- w = np.matrix([[1,2],[3,4]])
-
- r = np.average(a, axis=0, weights=w)
- assert_equal(type(r), np.matrix)
- assert_equal(r, [[2.5, 10.0/3]])
-
def test_upcasting(self):
types = [('i4', 'i4', 'f8'), ('i4', 'f4', 'f8'), ('f4', 'i4', 'f8'),
('f4', 'f4', 'f4'), ('f4', 'f8', 'f8')]
@@ -1623,16 +1612,6 @@ class TestTrapz(object):
xm = np.ma.array(x, mask=mask)
assert_almost_equal(trapz(y, xm), r)
- def test_matrix(self):
- # Test to make sure matrices give the same answer as ndarrays
- x = np.linspace(0, 5)
- y = x * x
- r = trapz(y, x)
- mx = np.matrix(x)
- my = np.matrix(y)
- mr = trapz(my, mx)
- assert_almost_equal(mr, r)
-
class TestSinc(object):
diff --git a/numpy/lib/tests/test_histograms.py b/numpy/lib/tests/test_histograms.py
index 597b5b376..e16ae12c2 100644
--- a/numpy/lib/tests/test_histograms.py
+++ b/numpy/lib/tests/test_histograms.py
@@ -613,8 +613,6 @@ class TestHistogramdd(object):
assert_raises(ValueError, np.histogramdd, x, bins=[-1, 2, 4, 5])
assert_raises(ValueError, np.histogramdd, x, bins=[1, 0.99, 1, 1])
assert_raises(
- ValueError, np.histogramdd, x, bins=[1, 1, 1, [1, 2, 2, 3]])
- assert_raises(
ValueError, np.histogramdd, x, bins=[1, 1, 1, [1, 2, 3, -3]])
assert_(np.histogramdd(x, bins=[1, 1, 1, [1, 2, 3, 4]]))
@@ -646,7 +644,7 @@ class TestHistogramdd(object):
bins = [[0., 0.5, 1.0]]
hist, _ = histogramdd(x, bins=bins)
assert_(hist[0] == 0.0)
- assert_(hist[1] == 1.)
+ assert_(hist[1] == 0.0)
x = [1.0001]
bins = [[0., 0.5, 1.0]]
hist, _ = histogramdd(x, bins=bins)
@@ -660,3 +658,40 @@ class TestHistogramdd(object):
range=[[0.0, 1.0], [0.25, 0.75], [0.25, np.inf]])
assert_raises(ValueError, histogramdd, vals,
range=[[0.0, 1.0], [np.nan, 0.75], [0.25, 0.5]])
+
+ def test_equal_edges(self):
+ """ Test that adjacent entries in an edge array can be equal """
+ x = np.array([0, 1, 2])
+ y = np.array([0, 1, 2])
+ x_edges = np.array([0, 2, 2])
+ y_edges = 1
+ hist, edges = histogramdd((x, y), bins=(x_edges, y_edges))
+
+ hist_expected = np.array([
+ [2.],
+ [1.], # x == 2 falls in the final bin
+ ])
+ assert_equal(hist, hist_expected)
+
+ def test_edge_dtype(self):
+ """ Test that if an edge array is input, its type is preserved """
+ x = np.array([0, 10, 20])
+ y = x / 10
+ x_edges = np.array([0, 5, 15, 20])
+ y_edges = x_edges / 10
+ hist, edges = histogramdd((x, y), bins=(x_edges, y_edges))
+
+ assert_equal(edges[0].dtype, x_edges.dtype)
+ assert_equal(edges[1].dtype, y_edges.dtype)
+
+ def test_large_integers(self):
+ big = 2**60 # Too large to represent with a full precision float
+
+ x = np.array([0], np.int64)
+ x_edges = np.array([-1, +1], np.int64)
+ y = big + x
+ y_edges = big + x_edges
+
+ hist, edges = histogramdd((x, y), bins=(x_edges, y_edges))
+
+ assert_equal(hist[0, 0], 1)
diff --git a/numpy/lib/tests/test_index_tricks.py b/numpy/lib/tests/test_index_tricks.py
index f934e952a..315251daa 100644
--- a/numpy/lib/tests/test_index_tricks.py
+++ b/numpy/lib/tests/test_index_tricks.py
@@ -6,7 +6,7 @@ from numpy.testing import (
assert_array_almost_equal, assert_raises, assert_raises_regex
)
from numpy.lib.index_tricks import (
- mgrid, ndenumerate, fill_diagonal, diag_indices, diag_indices_from,
+ mgrid, ogrid, ndenumerate, fill_diagonal, diag_indices, diag_indices_from,
index_exp, ndindex, r_, s_, ix_
)
@@ -156,6 +156,15 @@ class TestGrid(object):
assert_array_almost_equal(d[1, :, 1] - d[1, :, 0],
0.2*np.ones(20, 'd'), 11)
+ def test_sparse(self):
+ grid_full = mgrid[-1:1:10j, -2:2:10j]
+ grid_sparse = ogrid[-1:1:10j, -2:2:10j]
+
+ # sparse grids can be made dense by broadcasting
+ grid_broadcast = np.broadcast_arrays(*grid_sparse)
+ for f, b in zip(grid_full, grid_broadcast):
+ assert_equal(f, b)
+
class TestConcatenator(object):
def test_1d(self):
@@ -184,37 +193,6 @@ class TestConcatenator(object):
assert_array_equal(d[:5, :], b)
assert_array_equal(d[5:, :], c)
- def test_matrix(self):
- a = [1, 2]
- b = [3, 4]
-
- ab_r = np.r_['r', a, b]
- ab_c = np.r_['c', a, b]
-
- assert_equal(type(ab_r), np.matrix)
- assert_equal(type(ab_c), np.matrix)
-
- assert_equal(np.array(ab_r), [[1,2,3,4]])
- assert_equal(np.array(ab_c), [[1],[2],[3],[4]])
-
- assert_raises(ValueError, lambda: np.r_['rc', a, b])
-
- def test_matrix_scalar(self):
- r = np.r_['r', [1, 2], 3]
- assert_equal(type(r), np.matrix)
- assert_equal(np.array(r), [[1,2,3]])
-
- def test_matrix_builder(self):
- a = np.array([1])
- b = np.array([2])
- c = np.array([3])
- d = np.array([4])
- actual = np.r_['a, b; c, d']
- expected = np.bmat([[a, b], [c, d]])
-
- assert_equal(actual, expected)
- assert_equal(type(actual), type(expected))
-
def test_0d(self):
assert_equal(r_[0, np.array(1), 2], [0, 1, 2])
assert_equal(r_[[0, 1, 2], np.array(3)], [0, 1, 2, 3])
diff --git a/numpy/lib/tests/test_nanfunctions.py b/numpy/lib/tests/test_nanfunctions.py
index 42e221506..504372faf 100644
--- a/numpy/lib/tests/test_nanfunctions.py
+++ b/numpy/lib/tests/test_nanfunctions.py
@@ -113,42 +113,46 @@ class TestNanFunctions_MinMax(object):
for f in self.nanfuncs:
assert_(f(0.) == 0.)
- def test_matrices(self):
+ def test_subclass(self):
+ class MyNDArray(np.ndarray):
+ pass
+
# Check that it works and that type and
# shape are preserved
- mat = np.matrix(np.eye(3))
+ mine = np.eye(3).view(MyNDArray)
for f in self.nanfuncs:
- res = f(mat, axis=0)
- assert_(isinstance(res, np.matrix))
- assert_(res.shape == (1, 3))
- res = f(mat, axis=1)
- assert_(isinstance(res, np.matrix))
- assert_(res.shape == (3, 1))
- res = f(mat)
- assert_(np.isscalar(res))
+ res = f(mine, axis=0)
+ assert_(isinstance(res, MyNDArray))
+ assert_(res.shape == (3,))
+ res = f(mine, axis=1)
+ assert_(isinstance(res, MyNDArray))
+ assert_(res.shape == (3,))
+ res = f(mine)
+ assert_(res.shape == ())
+
# check that rows of nan are dealt with for subclasses (#4628)
- mat[1] = np.nan
+ mine[1] = np.nan
for f in self.nanfuncs:
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
- res = f(mat, axis=0)
- assert_(isinstance(res, np.matrix))
+ res = f(mine, axis=0)
+ assert_(isinstance(res, MyNDArray))
assert_(not np.any(np.isnan(res)))
assert_(len(w) == 0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
- res = f(mat, axis=1)
- assert_(isinstance(res, np.matrix))
- assert_(np.isnan(res[1, 0]) and not np.isnan(res[0, 0])
- and not np.isnan(res[2, 0]))
+ res = f(mine, axis=1)
+ assert_(isinstance(res, MyNDArray))
+ assert_(np.isnan(res[1]) and not np.isnan(res[0])
+ and not np.isnan(res[2]))
assert_(len(w) == 1, 'no warning raised')
assert_(issubclass(w[0].category, RuntimeWarning))
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
- res = f(mat)
- assert_(np.isscalar(res))
+ res = f(mine)
+ assert_(res.shape == ())
assert_(res != np.nan)
assert_(len(w) == 0)
@@ -209,19 +213,22 @@ class TestNanFunctions_ArgminArgmax(object):
for f in self.nanfuncs:
assert_(f(0.) == 0.)
- def test_matrices(self):
+ def test_subclass(self):
+ class MyNDArray(np.ndarray):
+ pass
+
# Check that it works and that type and
# shape are preserved
- mat = np.matrix(np.eye(3))
+ mine = np.eye(3).view(MyNDArray)
for f in self.nanfuncs:
- res = f(mat, axis=0)
- assert_(isinstance(res, np.matrix))
- assert_(res.shape == (1, 3))
- res = f(mat, axis=1)
- assert_(isinstance(res, np.matrix))
- assert_(res.shape == (3, 1))
- res = f(mat)
- assert_(np.isscalar(res))
+ res = f(mine, axis=0)
+ assert_(isinstance(res, MyNDArray))
+ assert_(res.shape == (3,))
+ res = f(mine, axis=1)
+ assert_(isinstance(res, MyNDArray))
+ assert_(res.shape == (3,))
+ res = f(mine)
+ assert_(res.shape == ())
class TestNanFunctions_IntTypes(object):
@@ -381,19 +388,27 @@ class SharedNanFunctionsTestsMixin(object):
for f in self.nanfuncs:
assert_(f(0.) == 0.)
- def test_matrices(self):
+ def test_subclass(self):
+ class MyNDArray(np.ndarray):
+ pass
+
# Check that it works and that type and
# shape are preserved
- mat = np.matrix(np.eye(3))
+ array = np.eye(3)
+ mine = array.view(MyNDArray)
for f in self.nanfuncs:
- res = f(mat, axis=0)
- assert_(isinstance(res, np.matrix))
- assert_(res.shape == (1, 3))
- res = f(mat, axis=1)
- assert_(isinstance(res, np.matrix))
- assert_(res.shape == (3, 1))
- res = f(mat)
- assert_(np.isscalar(res))
+ expected_shape = f(array, axis=0).shape
+ res = f(mine, axis=0)
+ assert_(isinstance(res, MyNDArray))
+ assert_(res.shape == expected_shape)
+ expected_shape = f(array, axis=1).shape
+ res = f(mine, axis=1)
+ assert_(isinstance(res, MyNDArray))
+ assert_(res.shape == expected_shape)
+ expected_shape = f(array).shape
+ res = f(mine)
+ assert_(isinstance(res, MyNDArray))
+ assert_(res.shape == expected_shape)
class TestNanFunctions_SumProd(SharedNanFunctionsTestsMixin):
@@ -481,18 +496,6 @@ class TestNanFunctions_CumSumProd(SharedNanFunctionsTestsMixin):
res = f(d, axis=axis)
assert_equal(res.shape, (3, 5, 7, 11))
- def test_matrices(self):
- # Check that it works and that type and
- # shape are preserved
- mat = np.matrix(np.eye(3))
- for f in self.nanfuncs:
- for axis in np.arange(2):
- res = f(mat, axis=axis)
- assert_(isinstance(res, np.matrix))
- assert_(res.shape == (3, 3))
- res = f(mat)
- assert_(res.shape == (1, 3*3))
-
def test_result_values(self):
for axis in (-2, -1, 0, 1, None):
tgt = np.cumprod(_ndat_ones, axis=axis)
diff --git a/numpy/lib/tests/test_shape_base.py b/numpy/lib/tests/test_shape_base.py
index 0e86fbb19..c95894f94 100644
--- a/numpy/lib/tests/test_shape_base.py
+++ b/numpy/lib/tests/test_shape_base.py
@@ -2,16 +2,106 @@ from __future__ import division, absolute_import, print_function
import numpy as np
import warnings
+import functools
from numpy.lib.shape_base import (
apply_along_axis, apply_over_axes, array_split, split, hsplit, dsplit,
- vsplit, dstack, column_stack, kron, tile, expand_dims,
+ vsplit, dstack, column_stack, kron, tile, expand_dims, take_along_axis,
+ put_along_axis
)
from numpy.testing import (
assert_, assert_equal, assert_array_equal, assert_raises, assert_warns
)
+def _add_keepdims(func):
+ """ hack in keepdims behavior into a function taking an axis """
+ @functools.wraps(func)
+ def wrapped(a, axis, **kwargs):
+ res = func(a, axis=axis, **kwargs)
+ if axis is None:
+ axis = 0 # res is now a scalar, so we can insert this anywhere
+ return np.expand_dims(res, axis=axis)
+ return wrapped
+
+
+class TestTakeAlongAxis(object):
+ def test_argequivalent(self):
+ """ Test it translates from arg<func> to <func> """
+ from numpy.random import rand
+ a = rand(3, 4, 5)
+
+ funcs = [
+ (np.sort, np.argsort, dict()),
+ (_add_keepdims(np.min), _add_keepdims(np.argmin), dict()),
+ (_add_keepdims(np.max), _add_keepdims(np.argmax), dict()),
+ (np.partition, np.argpartition, dict(kth=2)),
+ ]
+
+ for func, argfunc, kwargs in funcs:
+ for axis in list(range(a.ndim)) + [None]:
+ a_func = func(a, axis=axis, **kwargs)
+ ai_func = argfunc(a, axis=axis, **kwargs)
+ assert_equal(a_func, take_along_axis(a, ai_func, axis=axis))
+
+ def test_invalid(self):
+ """ Test it errors when indices has too few dimensions """
+ a = np.ones((10, 10))
+ ai = np.ones((10, 2), dtype=np.intp)
+
+ # sanity check
+ take_along_axis(a, ai, axis=1)
+
+ # not enough indices
+ assert_raises(ValueError, take_along_axis, a, np.array(1), axis=1)
+ # bool arrays not allowed
+ assert_raises(IndexError, take_along_axis, a, ai.astype(bool), axis=1)
+ # float arrays not allowed
+ assert_raises(IndexError, take_along_axis, a, ai.astype(float), axis=1)
+ # invalid axis
+ assert_raises(np.AxisError, take_along_axis, a, ai, axis=10)
+
+ def test_empty(self):
+ """ Test everything is ok with empty results, even with inserted dims """
+ a = np.ones((3, 4, 5))
+ ai = np.ones((3, 0, 5), dtype=np.intp)
+
+ actual = take_along_axis(a, ai, axis=1)
+ assert_equal(actual.shape, ai.shape)
+
+ def test_broadcast(self):
+ """ Test that non-indexing dimensions are broadcast in both directions """
+ a = np.ones((3, 4, 1))
+ ai = np.ones((1, 2, 5), dtype=np.intp)
+ actual = take_along_axis(a, ai, axis=1)
+ assert_equal(actual.shape, (3, 2, 5))
+
+
+class TestPutAlongAxis(object):
+ def test_replace_max(self):
+ a_base = np.array([[10, 30, 20], [60, 40, 50]])
+
+ for axis in list(range(a_base.ndim)) + [None]:
+ # we mutate this in the loop
+ a = a_base.copy()
+
+ # replace the max with a small value
+ i_max = _add_keepdims(np.argmax)(a, axis=axis)
+ put_along_axis(a, i_max, -99, axis=axis)
+
+ # find the new minimum, which should max
+ i_min = _add_keepdims(np.argmin)(a, axis=axis)
+
+ assert_equal(i_min, i_max)
+
+ def test_broadcast(self):
+ """ Test that non-indexing dimensions are broadcast in both directions """
+ a = np.ones((3, 4, 1))
+ ai = np.arange(10, dtype=np.intp).reshape((1, 2, 5)) % 4
+ put_along_axis(a, ai, 20, axis=1)
+ assert_equal(take_along_axis(a, ai, axis=1), 20)
+
+
class TestApplyAlongAxis(object):
def test_simple(self):
a = np.ones((20, 10), 'd')
@@ -29,19 +119,21 @@ class TestApplyAlongAxis(object):
[[27, 30, 33], [36, 39, 42], [45, 48, 51]])
def test_preserve_subclass(self):
- # this test is particularly malicious because matrix
- # refuses to become 1d
def double(row):
return row * 2
- m = np.matrix([[0, 1], [2, 3]])
- expected = np.matrix([[0, 2], [4, 6]])
+
+ class MyNDArray(np.ndarray):
+ pass
+
+ m = np.array([[0, 1], [2, 3]]).view(MyNDArray)
+ expected = np.array([[0, 2], [4, 6]]).view(MyNDArray)
result = apply_along_axis(double, 0, m)
- assert_(isinstance(result, np.matrix))
+ assert_(isinstance(result, MyNDArray))
assert_array_equal(result, expected)
result = apply_along_axis(double, 1, m)
- assert_(isinstance(result, np.matrix))
+ assert_(isinstance(result, MyNDArray))
assert_array_equal(result, expected)
def test_subclass(self):
@@ -492,16 +584,10 @@ class TestSqueeze(object):
class TestKron(object):
def test_return_type(self):
- a = np.ones([2, 2])
- m = np.asmatrix(a)
- assert_equal(type(kron(a, a)), np.ndarray)
- assert_equal(type(kron(m, m)), np.matrix)
- assert_equal(type(kron(a, m)), np.matrix)
- assert_equal(type(kron(m, a)), np.matrix)
-
class myarray(np.ndarray):
__array_priority__ = 0.0
+ a = np.ones([2, 2])
ma = myarray(a.shape, a.dtype, a.data)
assert_equal(type(kron(a, a)), np.ndarray)
assert_equal(type(kron(ma, ma)), myarray)
diff --git a/numpy/lib/twodim_base.py b/numpy/lib/twodim_base.py
index 402c18850..cca316e9a 100644
--- a/numpy/lib/twodim_base.py
+++ b/numpy/lib/twodim_base.py
@@ -650,7 +650,7 @@ def histogram2d(x, y, bins=10, range=None, normed=False, weights=None):
N = 1
if N != 1 and N != 2:
- xedges = yedges = asarray(bins, float)
+ xedges = yedges = asarray(bins)
bins = [xedges, yedges]
hist, edges = histogramdd([x, y], bins, range, normed, weights)
return hist, edges[0], edges[1]
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