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authorCharles Harris <charlesr.harris@gmail.com>2013-06-20 20:44:54 -0600
committerCharles Harris <charlesr.harris@gmail.com>2013-08-12 22:33:55 -0600
commitfcb0fef5c673ed0a5442b18bcd8c391907b4f9a7 (patch)
tree24726ff3fbb7a167a8fdf89ac5cb74792c9cc6e7 /numpy/lib
parent777b6453e166df252298a47ef4f0e867614ac94a (diff)
downloadnumpy-fcb0fef5c673ed0a5442b18bcd8c391907b4f9a7.tar.gz
MAINT: Separate nan functions into their own module.
New files lib/nanfunctions.py and lib/tests/test_nanfunctions.py are added and both the previous and new nan functions and tests are moved into them. The existing nan functions moved from lib/function_base are: nansum, nanmin, nanmax, nanargmin, nanargmax The added nan functions moved from core/numeric are: nanmean, nanvar, nanstd
Diffstat (limited to 'numpy/lib')
-rw-r--r--numpy/lib/__init__.py5
-rw-r--r--numpy/lib/function_base.py342
-rw-r--r--numpy/lib/nanfunctions.py678
-rw-r--r--numpy/lib/tests/test_function_base.py133
-rw-r--r--numpy/lib/tests/test_nanfunctions.py240
5 files changed, 935 insertions, 463 deletions
diff --git a/numpy/lib/__init__.py b/numpy/lib/__init__.py
index 12acae95b..64a8550c6 100644
--- a/numpy/lib/__init__.py
+++ b/numpy/lib/__init__.py
@@ -1,11 +1,14 @@
from __future__ import division, absolute_import, print_function
+import math
+
from .info import __doc__
from numpy.version import version as __version__
from .type_check import *
from .index_tricks import *
from .function_base import *
+from .nanfunctions import *
from .shape_base import *
from .stride_tricks import *
from .twodim_base import *
@@ -18,7 +21,6 @@ from .utils import *
from .arraysetops import *
from .npyio import *
from .financial import *
-import math
from .arrayterator import *
from .arraypad import *
@@ -36,6 +38,7 @@ __all__ += utils.__all__
__all__ += arraysetops.__all__
__all__ += npyio.__all__
__all__ += financial.__all__
+__all__ += nanfunctions.__all__
from numpy.testing import Tester
test = Tester().test
diff --git a/numpy/lib/function_base.py b/numpy/lib/function_base.py
index b3b5ef735..9336579af 100644
--- a/numpy/lib/function_base.py
+++ b/numpy/lib/function_base.py
@@ -1,15 +1,14 @@
from __future__ import division, absolute_import, print_function
__docformat__ = "restructuredtext en"
-__all__ = ['select', 'piecewise', 'trim_zeros', 'copy', 'iterable',
- 'percentile', 'diff', 'gradient', 'angle', 'unwrap', 'sort_complex',
- 'disp', 'extract', 'place', 'nansum', 'nanmax', 'nanargmax',
- 'nanargmin', 'nanmin', 'vectorize', 'asarray_chkfinite', 'average',
- 'histogram', 'histogramdd', 'bincount', 'digitize', 'cov',
- 'corrcoef', 'msort', 'median', 'sinc', 'hamming', 'hanning',
- 'bartlett', 'blackman', 'kaiser', 'trapz', 'i0', 'add_newdoc',
- 'add_docstring', 'meshgrid', 'delete', 'insert', 'append', 'interp',
- 'add_newdoc_ufunc']
+__all__ = [
+ 'select', 'piecewise', 'trim_zeros', 'copy', 'iterable', 'percentile',
+ 'diff', 'gradient', 'angle', 'unwrap', 'sort_complex', 'disp',
+ 'extract', 'place', 'vectorize', 'asarray_chkfinite', 'average',
+ 'histogram', 'histogramdd', 'bincount', 'digitize', 'cov', 'corrcoef',
+ 'msort', 'median', 'sinc', 'hamming', 'hanning', 'bartlett',
+ 'blackman', 'kaiser', 'trapz', 'i0', 'add_newdoc', 'add_docstring',
+ 'meshgrid', 'delete', 'insert', 'append', 'interp', 'add_newdoc_ufunc']
import warnings
import types
@@ -1361,331 +1360,6 @@ def place(arr, mask, vals):
"""
return _insert(arr, mask, vals)
-def _nanop(op, fill, a, axis=None):
- """
- General operation on arrays with not-a-number values.
-
- Parameters
- ----------
- op : callable
- Operation to perform.
- fill : float
- NaN values are set to fill before doing the operation.
- a : array-like
- Input array.
- axis : {int, None}, optional
- Axis along which the operation is computed.
- By default the input is flattened.
-
- Returns
- -------
- y : {ndarray, scalar}
- Processed data.
-
- """
- y = array(a, subok=True)
-
- # We only need to take care of NaN's in floating point arrays
- dt = y.dtype
- if np.issubdtype(dt, np.integer) or np.issubdtype(dt, np.bool_):
- return op(y, axis=axis)
-
- mask = isnan(a)
- # y[mask] = fill
- # We can't use fancy indexing here as it'll mess w/ MaskedArrays
- # Instead, let's fill the array directly...
- np.copyto(y, fill, where=mask)
- res = op(y, axis=axis)
- mask_all_along_axis = mask.all(axis=axis)
-
- # Along some axes, only nan's were encountered. As such, any values
- # calculated along that axis should be set to nan.
- if mask_all_along_axis.any():
- if np.isscalar(res):
- res = np.nan
- else:
- res[mask_all_along_axis] = np.nan
-
- return res
-
-def nansum(a, axis=None):
- """
- Return the sum of array elements over a given axis treating
- Not a Numbers (NaNs) as zero.
-
- Parameters
- ----------
- a : array_like
- Array containing numbers whose sum is desired. If `a` is not an
- array, a conversion is attempted.
- axis : int, optional
- Axis along which the sum is computed. The default is to compute
- the sum of the flattened array.
-
- Returns
- -------
- y : ndarray
- An array with the same shape as a, with the specified axis removed.
- If a is a 0-d array, or if axis is None, a scalar is returned with
- the same dtype as `a`.
-
- See Also
- --------
- numpy.sum : Sum across array including Not a Numbers.
- isnan : Shows which elements are Not a Number (NaN).
- isfinite: Shows which elements are not: Not a Number, positive and
- negative infinity
-
- Notes
- -----
- Numpy uses the IEEE Standard for Binary Floating-Point for Arithmetic
- (IEEE 754). This means that Not a Number is not equivalent to infinity.
- If positive or negative infinity are present the result is positive or
- negative infinity. But if both positive and negative infinity are present,
- the result is Not A Number (NaN).
-
- Arithmetic is modular when using integer types (all elements of `a` must
- be finite i.e. no elements that are NaNs, positive infinity and negative
- infinity because NaNs are floating point types), and no error is raised
- on overflow.
-
-
- Examples
- --------
- >>> np.nansum(1)
- 1
- >>> np.nansum([1])
- 1
- >>> np.nansum([1, np.nan])
- 1.0
- >>> a = np.array([[1, 1], [1, np.nan]])
- >>> np.nansum(a)
- 3.0
- >>> np.nansum(a, axis=0)
- array([ 2., 1.])
-
- When positive infinity and negative infinity are present
-
- >>> np.nansum([1, np.nan, np.inf])
- inf
- >>> np.nansum([1, np.nan, np.NINF])
- -inf
- >>> np.nansum([1, np.nan, np.inf, np.NINF])
- nan
-
- """
- return _nanop(np.sum, 0, a, axis)
-
-def nanmin(a, axis=None):
- """
- Return the minimum of an array or minimum along an axis, ignoring any NaNs.
-
- Parameters
- ----------
- a : array_like
- Array containing numbers whose minimum is desired. If `a` is not
- an array, a conversion is attempted.
- axis : int, optional
- Axis along which the minimum is computed. The default is to compute
- the minimum of the flattened array.
-
- Returns
- -------
- nanmin : ndarray
- An array with the same shape as `a`, with the specified axis removed.
- If `a` is a 0-d array, or if axis is None, an ndarray scalar is
- returned. The same dtype as `a` is returned.
-
- See Also
- --------
- nanmax :
- The maximum value of an array along a given axis, ignoring any NaNs.
- amin :
- The minimum value of an array along a given axis, propagating any NaNs.
- fmin :
- Element-wise minimum of two arrays, ignoring any NaNs.
- minimum :
- Element-wise minimum of two arrays, propagating any NaNs.
- isnan :
- Shows which elements are Not a Number (NaN).
- isfinite:
- Shows which elements are neither NaN nor infinity.
-
- amax, fmax, maximum
-
- Notes
- -----
- Numpy uses the IEEE Standard for Binary Floating-Point for Arithmetic
- (IEEE 754). This means that Not a Number is not equivalent to infinity.
- Positive infinity is treated as a very large number and negative infinity
- is treated as a very small (i.e. negative) number.
-
- If the input has a integer type the function is equivalent to np.min.
-
- Examples
- --------
- >>> a = np.array([[1, 2], [3, np.nan]])
- >>> np.nanmin(a)
- 1.0
- >>> np.nanmin(a, axis=0)
- array([ 1., 2.])
- >>> np.nanmin(a, axis=1)
- array([ 1., 3.])
-
- When positive infinity and negative infinity are present:
-
- >>> np.nanmin([1, 2, np.nan, np.inf])
- 1.0
- >>> np.nanmin([1, 2, np.nan, np.NINF])
- -inf
-
- """
- a = np.asanyarray(a)
- if axis is not None:
- return np.fmin.reduce(a, axis)
- else:
- return np.fmin.reduce(a.flat)
-
-def nanargmin(a, axis=None):
- """
- Return indices of the minimum values over an axis, ignoring NaNs.
-
- Parameters
- ----------
- a : array_like
- Input data.
- axis : int, optional
- Axis along which to operate. By default flattened input is used.
-
- Returns
- -------
- index_array : ndarray
- An array of indices or a single index value.
-
- See Also
- --------
- argmin, nanargmax
-
- Examples
- --------
- >>> a = np.array([[np.nan, 4], [2, 3]])
- >>> np.argmin(a)
- 0
- >>> np.nanargmin(a)
- 2
- >>> np.nanargmin(a, axis=0)
- array([1, 1])
- >>> np.nanargmin(a, axis=1)
- array([1, 0])
-
- """
- return _nanop(np.argmin, np.inf, a, axis)
-
-def nanmax(a, axis=None):
- """
- Return the maximum of an array or maximum along an axis, ignoring any NaNs.
-
- Parameters
- ----------
- a : array_like
- Array containing numbers whose maximum is desired. If `a` is not
- an array, a conversion is attempted.
- axis : int, optional
- Axis along which the maximum is computed. The default is to compute
- the maximum of the flattened array.
-
- Returns
- -------
- nanmax : ndarray
- An array with the same shape as `a`, with the specified axis removed.
- If `a` is a 0-d array, or if axis is None, an ndarray scalar is
- returned. The same dtype as `a` is returned.
-
- See Also
- --------
- nanmin :
- The minimum value of an array along a given axis, ignoring any NaNs.
- amax :
- The maximum value of an array along a given axis, propagating any NaNs.
- fmax :
- Element-wise maximum of two arrays, ignoring any NaNs.
- maximum :
- Element-wise maximum of two arrays, propagating any NaNs.
- isnan :
- Shows which elements are Not a Number (NaN).
- isfinite:
- Shows which elements are neither NaN nor infinity.
-
- amin, fmin, minimum
-
- Notes
- -----
- Numpy uses the IEEE Standard for Binary Floating-Point for Arithmetic
- (IEEE 754). This means that Not a Number is not equivalent to infinity.
- Positive infinity is treated as a very large number and negative infinity
- is treated as a very small (i.e. negative) number.
-
- If the input has a integer type the function is equivalent to np.max.
-
- Examples
- --------
- >>> a = np.array([[1, 2], [3, np.nan]])
- >>> np.nanmax(a)
- 3.0
- >>> np.nanmax(a, axis=0)
- array([ 3., 2.])
- >>> np.nanmax(a, axis=1)
- array([ 2., 3.])
-
- When positive infinity and negative infinity are present:
-
- >>> np.nanmax([1, 2, np.nan, np.NINF])
- 2.0
- >>> np.nanmax([1, 2, np.nan, np.inf])
- inf
-
- """
- a = np.asanyarray(a)
- if axis is not None:
- return np.fmax.reduce(a, axis)
- else:
- return np.fmax.reduce(a.flat)
-
-def nanargmax(a, axis=None):
- """
- Return indices of the maximum values over an axis, ignoring NaNs.
-
- Parameters
- ----------
- a : array_like
- Input data.
- axis : int, optional
- Axis along which to operate. By default flattened input is used.
-
- Returns
- -------
- index_array : ndarray
- An array of indices or a single index value.
-
- See Also
- --------
- argmax, nanargmin
-
- Examples
- --------
- >>> a = np.array([[np.nan, 4], [2, 3]])
- >>> np.argmax(a)
- 0
- >>> np.nanargmax(a)
- 1
- >>> np.nanargmax(a, axis=0)
- array([1, 0])
- >>> np.nanargmax(a, axis=1)
- array([1, 1])
-
- """
- return _nanop(np.argmax, -np.inf, a, axis)
-
def disp(mesg, device=None, linefeed=True):
"""
Display a message on a device.
diff --git a/numpy/lib/nanfunctions.py b/numpy/lib/nanfunctions.py
new file mode 100644
index 000000000..f0e635791
--- /dev/null
+++ b/numpy/lib/nanfunctions.py
@@ -0,0 +1,678 @@
+"""Functions that ignore nan.
+
+"""
+from __future__ import division, absolute_import, print_function
+
+import numpy as np
+
+__all__ = [
+ 'nansum', 'nanmax', 'nanmin', 'nanargmax', 'nanargmin', 'nanmean',
+ 'nanvar', 'nanstd'
+ ]
+
+
+def _nanmean(a, axis=None, dtype=None, out=None, keepdims=False):
+ # Using array() instead of asanyarray() because the former always
+ # makes a copy, which is important due to the copyto() action later
+ arr = np.array(a, subok=True)
+ mask = np.isnan(arr)
+
+ # Cast bool, unsigned int, and int to float64
+ if np.dtype is None and issubclass(arr.dtype.type, (np.integer, np.bool_)):
+ ret = np.add.reduce(arr, axis=axis, dtype='f8',
+ out=out, keepdims=keepdims)
+ else:
+ np.copyto(arr, 0.0, where=mask)
+ ret = np.add.reduce(arr, axis=axis, dtype=dtype,
+ out=out, keepdims=keepdims)
+ rcount = (~mask).sum(axis=axis)
+ if isinstance(ret, np.ndarray):
+ ret = np.true_divide(ret, rcount, out=ret, casting='unsafe',
+ subok=False)
+ else:
+ ret = ret / rcount
+ return ret
+
+
+def _nanvar(a, axis=None, dtype=None, out=None, ddof=0, keepdims=False):
+ # Using array() instead of asanyarray() because the former always
+ # makes a copy, which is important due to the copyto() action later
+ arr = np.array(a, subok=True)
+ mask = np.isnan(arr)
+
+ # First compute the mean, saving 'rcount' for reuse later
+ if dtype is None and issubclass(arr.dtype.type, (np.integer, np.bool_)):
+ arrmean = np.add.reduce(arr, axis=axis, dtype='f8', keepdims=True)
+ else:
+ np.copyto(arr, 0.0, where=mask)
+ arrmean = np.add.reduce(arr, axis=axis, dtype=dtype, keepdims=True)
+ rcount = (~mask).sum(axis=axis, keepdims=True)
+ if isinstance(arrmean, np.ndarray):
+ arrmean = np.true_divide(arrmean, rcount,
+ out=arrmean, casting='unsafe', subok=False)
+ else:
+ arrmean = arrmean / rcount
+
+ # arr - arrmean
+ x = arr - arrmean
+ np.copyto(x, 0.0, where=mask)
+
+ # (arr - arrmean) ** 2
+ if issubclass(arr.dtype.type, np.complex_):
+ x = np.multiply(x, np.conjugate(x), out=x).real
+ else:
+ x = np.multiply(x, x, out=x)
+
+ # add.reduce((arr - arrmean) ** 2, axis)
+ ret = np.add.reduce(x, axis=axis, dtype=dtype, out=out, keepdims=keepdims)
+
+ # add.reduce((arr - arrmean) ** 2, axis) / (n - ddof)
+ if not keepdims and isinstance(rcount, np.ndarray):
+ rcount = rcount.squeeze(axis=axis)
+ rcount -= ddof
+ if isinstance(ret, np.ndarray):
+ ret = np.true_divide(ret, rcount, out=ret, casting='unsafe', subok=False)
+ else:
+ ret = ret / rcount
+
+ return ret
+
+
+def _nanstd(a, axis=None, dtype=None, out=None, ddof=0, keepdims=False):
+ ret = _nanvar(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
+ keepdims=keepdims)
+
+ if isinstance(ret, np.ndarray):
+ ret = np.sqrt(ret, out=ret)
+ else:
+ ret = np.sqrt(ret)
+
+ return ret
+
+
+def _nanop(op, fill, a, axis=None):
+ """
+ General operation on arrays with not-a-number values.
+
+ Parameters
+ ----------
+ op : callable
+ Operation to perform.
+ fill : float
+ NaN values are set to fill before doing the operation.
+ a : array-like
+ Input array.
+ axis : {int, None}, optional
+ Axis along which the operation is computed.
+ By default the input is flattened.
+
+ Returns
+ -------
+ y : {ndarray, scalar}
+ Processed data.
+
+ """
+ y = np.array(a, subok=True)
+
+ # We only need to take care of NaN's in floating point arrays
+ dt = y.dtype
+ if np.issubdtype(dt, np.integer) or np.issubdtype(dt, np.bool_):
+ return op(y, axis=axis)
+
+ mask = np.isnan(a)
+ # y[mask] = fill
+ # We can't use fancy indexing here as it'll mess w/ MaskedArrays
+ # Instead, let's fill the array directly...
+ np.copyto(y, fill, where=mask)
+ res = op(y, axis=axis)
+ mask_all_along_axis = mask.all(axis=axis)
+
+ # Along some axes, only nan's were encountered. As such, any values
+ # calculated along that axis should be set to nan.
+ if mask_all_along_axis.any():
+ if np.isscalar(res):
+ res = np.nan
+ else:
+ res[mask_all_along_axis] = np.nan
+
+ return res
+
+
+def nansum(a, axis=None):
+ """
+ Return the sum of array elements over a given axis treating
+ Not a Numbers (NaNs) as zero.
+
+ Parameters
+ ----------
+ a : array_like
+ Array containing numbers whose sum is desired. If `a` is not an
+ array, a conversion is attempted.
+ axis : int, optional
+ Axis along which the sum is computed. The default is to compute
+ the sum of the flattened array.
+
+ Returns
+ -------
+ y : ndarray
+ An array with the same shape as a, with the specified axis removed.
+ If a is a 0-d array, or if axis is None, a scalar is returned with
+ the same dtype as `a`.
+
+ See Also
+ --------
+ numpy.sum : Sum across array including Not a Numbers.
+ isnan : Shows which elements are Not a Number (NaN).
+ isfinite: Shows which elements are not: Not a Number, positive and
+ negative infinity
+
+ Notes
+ -----
+ Numpy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+ (IEEE 754). This means that Not a Number is not equivalent to infinity.
+ If positive or negative infinity are present the result is positive or
+ negative infinity. But if both positive and negative infinity are present,
+ the result is Not A Number (NaN).
+
+ Arithmetic is modular when using integer types (all elements of `a` must
+ be finite i.e. no elements that are NaNs, positive infinity and negative
+ infinity because NaNs are floating point types), and no error is raised
+ on overflow.
+
+
+ Examples
+ --------
+ >>> np.nansum(1)
+ 1
+ >>> np.nansum([1])
+ 1
+ >>> np.nansum([1, np.nan])
+ 1.0
+ >>> a = np.array([[1, 1], [1, np.nan]])
+ >>> np.nansum(a)
+ 3.0
+ >>> np.nansum(a, axis=0)
+ array([ 2., 1.])
+
+ When positive infinity and negative infinity are present
+
+ >>> np.nansum([1, np.nan, np.inf])
+ inf
+ >>> np.nansum([1, np.nan, np.NINF])
+ -inf
+ >>> np.nansum([1, np.nan, np.inf, np.NINF])
+ nan
+
+ """
+ return _nanop(np.sum, 0, a, axis)
+
+
+def nanmin(a, axis=None):
+ """
+ Return the minimum of an array or minimum along an axis, ignoring any NaNs.
+
+ Parameters
+ ----------
+ a : array_like
+ Array containing numbers whose minimum is desired. If `a` is not
+ an array, a conversion is attempted.
+ axis : int, optional
+ Axis along which the minimum is computed. The default is to compute
+ the minimum of the flattened array.
+
+ Returns
+ -------
+ nanmin : ndarray
+ An array with the same shape as `a`, with the specified axis removed.
+ If `a` is a 0-d array, or if axis is None, an ndarray scalar is
+ returned. The same dtype as `a` is returned.
+
+ See Also
+ --------
+ nanmax :
+ The maximum value of an array along a given axis, ignoring any NaNs.
+ amin :
+ The minimum value of an array along a given axis, propagating any NaNs.
+ fmin :
+ Element-wise minimum of two arrays, ignoring any NaNs.
+ minimum :
+ Element-wise minimum of two arrays, propagating any NaNs.
+ isnan :
+ Shows which elements are Not a Number (NaN).
+ isfinite:
+ Shows which elements are neither NaN nor infinity.
+
+ amax, fmax, maximum
+
+ Notes
+ -----
+ Numpy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+ (IEEE 754). This means that Not a Number is not equivalent to infinity.
+ Positive infinity is treated as a very large number and negative infinity
+ is treated as a very small (i.e. negative) number.
+
+ If the input has a integer type the function is equivalent to np.min.
+
+ Examples
+ --------
+ >>> a = np.array([[1, 2], [3, np.nan]])
+ >>> np.nanmin(a)
+ 1.0
+ >>> np.nanmin(a, axis=0)
+ array([ 1., 2.])
+ >>> np.nanmin(a, axis=1)
+ array([ 1., 3.])
+
+ When positive infinity and negative infinity are present:
+
+ >>> np.nanmin([1, 2, np.nan, np.inf])
+ 1.0
+ >>> np.nanmin([1, 2, np.nan, np.NINF])
+ -inf
+
+ """
+ a = np.asanyarray(a)
+ if axis is not None:
+ return np.fmin.reduce(a, axis)
+ else:
+ return np.fmin.reduce(a.flat)
+
+
+def nanargmin(a, axis=None):
+ """
+ Return indices of the minimum values over an axis, ignoring NaNs.
+
+ Parameters
+ ----------
+ a : array_like
+ Input data.
+ axis : int, optional
+ Axis along which to operate. By default flattened input is used.
+
+ Returns
+ -------
+ index_array : ndarray
+ An array of indices or a single index value.
+
+ See Also
+ --------
+ argmin, nanargmax
+
+ Examples
+ --------
+ >>> a = np.array([[np.nan, 4], [2, 3]])
+ >>> np.argmin(a)
+ 0
+ >>> np.nanargmin(a)
+ 2
+ >>> np.nanargmin(a, axis=0)
+ array([1, 1])
+ >>> np.nanargmin(a, axis=1)
+ array([1, 0])
+
+ """
+ return _nanop(np.argmin, np.inf, a, axis)
+
+
+def nanmax(a, axis=None):
+ """
+ Return the maximum of an array or maximum along an axis, ignoring any NaNs.
+
+ Parameters
+ ----------
+ a : array_like
+ Array containing numbers whose maximum is desired. If `a` is not
+ an array, a conversion is attempted.
+ axis : int, optional
+ Axis along which the maximum is computed. The default is to compute
+ the maximum of the flattened array.
+
+ Returns
+ -------
+ nanmax : ndarray
+ An array with the same shape as `a`, with the specified axis removed.
+ If `a` is a 0-d array, or if axis is None, an ndarray scalar is
+ returned. The same dtype as `a` is returned.
+
+ See Also
+ --------
+ nanmin :
+ The minimum value of an array along a given axis, ignoring any NaNs.
+ amax :
+ The maximum value of an array along a given axis, propagating any NaNs.
+ fmax :
+ Element-wise maximum of two arrays, ignoring any NaNs.
+ maximum :
+ Element-wise maximum of two arrays, propagating any NaNs.
+ isnan :
+ Shows which elements are Not a Number (NaN).
+ isfinite:
+ Shows which elements are neither NaN nor infinity.
+
+ amin, fmin, minimum
+
+ Notes
+ -----
+ Numpy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+ (IEEE 754). This means that Not a Number is not equivalent to infinity.
+ Positive infinity is treated as a very large number and negative infinity
+ is treated as a very small (i.e. negative) number.
+
+ If the input has a integer type the function is equivalent to np.max.
+
+ Examples
+ --------
+ >>> a = np.array([[1, 2], [3, np.nan]])
+ >>> np.nanmax(a)
+ 3.0
+ >>> np.nanmax(a, axis=0)
+ array([ 3., 2.])
+ >>> np.nanmax(a, axis=1)
+ array([ 2., 3.])
+
+ When positive infinity and negative infinity are present:
+
+ >>> np.nanmax([1, 2, np.nan, np.NINF])
+ 2.0
+ >>> np.nanmax([1, 2, np.nan, np.inf])
+ inf
+
+ """
+ a = np.asanyarray(a)
+ if axis is not None:
+ return np.fmax.reduce(a, axis)
+ else:
+ return np.fmax.reduce(a.flat)
+
+
+def nanargmax(a, axis=None):
+ """
+ Return indices of the maximum values over an axis, ignoring NaNs.
+
+ Parameters
+ ----------
+ a : array_like
+ Input data.
+ axis : int, optional
+ Axis along which to operate. By default flattened input is used.
+
+ Returns
+ -------
+ index_array : ndarray
+ An array of indices or a single index value.
+
+ See Also
+ --------
+ argmax, nanargmin
+
+ Examples
+ --------
+ >>> a = np.array([[np.nan, 4], [2, 3]])
+ >>> np.argmax(a)
+ 0
+ >>> np.nanargmax(a)
+ 1
+ >>> np.nanargmax(a, axis=0)
+ array([1, 0])
+ >>> np.nanargmax(a, axis=1)
+ array([1, 1])
+
+ """
+ return _nanop(np.argmax, -np.inf, a, axis)
+
+
+def nanmean(a, axis=None, dtype=None, out=None, keepdims=False):
+ """
+ Compute the arithmetic mean along the specified axis, ignoring NaNs.
+
+ Returns the average of the array elements. The average is taken over
+ the flattened array by default, otherwise over the specified axis.
+ `float64` intermediate and return values are used for integer inputs.
+
+ Parameters
+ ----------
+ a : array_like
+ Array containing numbers whose mean is desired. If `a` is not an
+ array, a conversion is attempted.
+ axis : int, optional
+ Axis along which the means are computed. The default is to compute
+ the mean of the flattened array.
+ dtype : data-type, optional
+ Type to use in computing the mean. For integer inputs, the default
+ is `float64`; for floating point inputs, it is the same as the
+ input dtype.
+ out : ndarray, optional
+ Alternate output array in which to place the result. The default
+ is ``None``; if provided, it must have the same shape as the
+ expected output, but the type will be cast if necessary.
+ See `doc.ufuncs` for details.
+ 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`.
+
+ Returns
+ -------
+ m : ndarray, see dtype parameter above
+ If `out=None`, returns a new array containing the mean values,
+ otherwise a reference to the output array is returned.
+
+ See Also
+ --------
+ average : Weighted average
+ mean : Arithmetic mean taken while not ignoring NaNs
+ var, nanvar
+
+ Notes
+ -----
+ The arithmetic mean is the sum of the non-nan elements along the axis
+ divided by the number of non-nan elements.
+
+ Note that for floating-point input, the mean is computed using the
+ same precision the input has. Depending on the input data, this can
+ cause the results to be inaccurate, especially for `float32`.
+ Specifying a higher-precision accumulator using the `dtype` keyword
+ can alleviate this issue.
+
+ Examples
+ --------
+ >>> a = np.array([[1, np.nan], [3, 4]])
+ >>> np.nanmean(a)
+ 2.6666666666666665
+ >>> np.nanmean(a, axis=0)
+ array([ 2., 4.])
+ >>> np.nanmean(a, axis=1)
+ array([ 1., 3.5])
+
+ """
+ if not (type(a) is np.ndarray):
+ try:
+ mean = a.nanmean
+ return mean(axis=axis, dtype=dtype, out=out)
+ except AttributeError:
+ pass
+
+ return _nanmean(a, axis=axis, dtype=dtype, out=out, keepdims=keepdims)
+
+
+def nanstd(a, axis=None, dtype=None, out=None, ddof=0, keepdims=False):
+ """
+ Compute the standard deviation along the specified axis, while
+ ignoring NaNs.
+
+ Returns the standard deviation, a measure of the spread of a distribution,
+ of the non-NaN array elements. The standard deviation is computed for the
+ flattened array by default, otherwise over the specified axis.
+
+ Parameters
+ ----------
+ a : array_like
+ Calculate the standard deviation of the non-NaN values.
+ axis : int, optional
+ Axis along which the standard deviation is computed. The default is
+ to compute the standard deviation of the flattened array.
+ dtype : dtype, optional
+ Type to use in computing the standard deviation. For arrays of
+ integer type the default is float64, for arrays of float types it is
+ the same as the array type.
+ out : ndarray, optional
+ Alternative output array in which to place the result. It must have
+ the same shape as the expected output but the type (of the calculated
+ values) will be cast if necessary.
+ ddof : int, optional
+ Means Delta Degrees of Freedom. The divisor used in calculations
+ is ``N - ddof``, where ``N`` represents the number of elements.
+ By default `ddof` is zero.
+ 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`.
+
+ Returns
+ -------
+ standard_deviation : ndarray, see dtype parameter above.
+ If `out` is None, return a new array containing the standard deviation,
+ otherwise return a reference to the output array.
+
+ See Also
+ --------
+ var, mean, std
+ nanvar, nanmean
+ numpy.doc.ufuncs : Section "Output arguments"
+
+ Notes
+ -----
+ The standard deviation is the square root of the average of the squared
+ deviations from the mean, i.e., ``std = sqrt(mean(abs(x - x.mean())**2))``.
+
+ The average squared deviation is normally calculated as
+ ``x.sum() / N``, where ``N = len(x)``. If, however, `ddof` is specified,
+ the divisor ``N - ddof`` is used instead. In standard statistical
+ practice, ``ddof=1`` provides an unbiased estimator of the variance
+ of the infinite population. ``ddof=0`` provides a maximum likelihood
+ estimate of the variance for normally distributed variables. The
+ standard deviation computed in this function is the square root of
+ the estimated variance, so even with ``ddof=1``, it will not be an
+ unbiased estimate of the standard deviation per se.
+
+ Note that, for complex numbers, `std` takes the absolute
+ value before squaring, so that the result is always real and nonnegative.
+
+ For floating-point input, the *std* is computed using the same
+ precision the input has. Depending on the input data, this can cause
+ the results to be inaccurate, especially for float32 (see example below).
+ Specifying a higher-accuracy accumulator using the `dtype` keyword can
+ alleviate this issue.
+
+ Examples
+ --------
+ >>> a = np.array([[1, np.nan], [3, 4]])
+ >>> np.nanstd(a)
+ 1.247219128924647
+ >>> np.nanstd(a, axis=0)
+ array([ 1., 0.])
+ >>> np.nanstd(a, axis=1)
+ array([ 0., 0.5])
+
+ """
+
+ if not (type(a) is np.ndarray):
+ try:
+ nanstd = a.nanstd
+ return nanstd(axis=axis, dtype=dtype, out=out, ddof=ddof)
+ except AttributeError:
+ pass
+
+ return _nanstd(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
+ keepdims=keepdims)
+
+
+def nanvar(a, axis=None, dtype=None, out=None, ddof=0,
+ keepdims=False):
+ """
+ Compute the variance along the specified axis, while ignoring NaNs.
+
+ Returns the variance of the array elements, a measure of the spread of a
+ distribution. The variance is computed for the flattened array by
+ default, otherwise over the specified axis.
+
+ Parameters
+ ----------
+ a : array_like
+ Array containing numbers whose variance is desired. If `a` is not an
+ array, a conversion is attempted.
+ axis : int, optional
+ Axis along which the variance is computed. The default is to compute
+ the variance of the flattened array.
+ dtype : data-type, optional
+ Type to use in computing the variance. For arrays of integer type
+ the default is `float32`; for arrays of float types it is the same as
+ the array type.
+ out : ndarray, optional
+ Alternate output array in which to place the result. It must have
+ the same shape as the expected output, but the type is cast if
+ necessary.
+ ddof : int, optional
+ "Delta Degrees of Freedom": the divisor used in the calculation is
+ ``N - ddof``, where ``N`` represents the number of elements. By
+ default `ddof` is zero.
+ 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`.
+
+ Returns
+ -------
+ variance : ndarray, see dtype parameter above
+ If ``out=None``, returns a new array containing the variance;
+ otherwise, a reference to the output array is returned.
+
+ See Also
+ --------
+ std : Standard deviation
+ mean : Average
+ var : Variance while not ignoring NaNs
+ nanstd, nanmean
+ numpy.doc.ufuncs : Section "Output arguments"
+
+ Notes
+ -----
+ The variance is the average of the squared deviations from the mean,
+ i.e., ``var = mean(abs(x - x.mean())**2)``.
+
+ The mean is normally calculated as ``x.sum() / N``, where ``N = len(x)``.
+ If, however, `ddof` is specified, the divisor ``N - ddof`` is used
+ instead. In standard statistical practice, ``ddof=1`` provides an
+ unbiased estimator of the variance of a hypothetical infinite population.
+ ``ddof=0`` provides a maximum likelihood estimate of the variance for
+ normally distributed variables.
+
+ Note that for complex numbers, the absolute value is taken before
+ squaring, so that the result is always real and nonnegative.
+
+ For floating-point input, the variance is computed using the same
+ precision the input has. Depending on the input data, this can cause
+ the results to be inaccurate, especially for `float32` (see example
+ below). Specifying a higher-accuracy accumulator using the ``dtype``
+ keyword can alleviate this issue.
+
+ Examples
+ --------
+ >>> a = np.array([[1, np.nan], [3, 4]])
+ >>> np.var(a)
+ 1.5555555555555554
+ >>> np.nanvar(a, axis=0)
+ array([ 1., 0.])
+ >>> np.nanvar(a, axis=1)
+ array([ 0., 0.25])
+
+ """
+ if not (type(a) is np.ndarray):
+ try:
+ nanvar = a.nanvar
+ return nanvar(axis=axis, dtype=dtype, out=out, ddof=ddof)
+ except AttributeError:
+ pass
+
+ return _nanvar(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
+ keepdims=keepdims)
diff --git a/numpy/lib/tests/test_function_base.py b/numpy/lib/tests/test_function_base.py
index 814743442..cf303993b 100644
--- a/numpy/lib/tests/test_function_base.py
+++ b/numpy/lib/tests/test_function_base.py
@@ -3,10 +3,10 @@ from __future__ import division, absolute_import, print_function
import warnings
import numpy as np
from numpy.testing import (
- run_module_suite, TestCase, assert_, assert_equal,
- assert_array_equal, assert_almost_equal, assert_array_almost_equal,
- assert_raises, assert_allclose, assert_array_max_ulp, assert_warns
- )
+ run_module_suite, TestCase, assert_, assert_equal, assert_array_equal,
+ assert_almost_equal, assert_array_almost_equal, assert_raises,
+ assert_allclose, assert_array_max_ulp, assert_warns
+ )
from numpy.random import rand
from numpy.lib import *
from numpy.compat import long
@@ -1111,127 +1111,6 @@ class TestCheckFinite(TestCase):
assert_(a.dtype == np.float64)
-class TestNaNFuncts(TestCase):
- def setUp(self):
- self.A = np.array([[[ np.nan, 0.01319214, 0.01620964],
- [ 0.11704017, np.nan, 0.75157887],
- [ 0.28333658, 0.1630199 , np.nan ]],
- [[ 0.59541557, np.nan, 0.37910852],
- [ np.nan, 0.87964135, np.nan ],
- [ 0.70543747, np.nan, 0.34306596]],
- [[ 0.72687499, 0.91084584, np.nan ],
- [ 0.84386844, 0.38944762, 0.23913896],
- [ np.nan, 0.37068164, 0.33850425]]])
-
- def test_nansum(self):
- assert_almost_equal(nansum(self.A), 8.0664079100000006)
- assert_almost_equal(nansum(self.A, 0),
- np.array([[ 1.32229056, 0.92403798, 0.39531816],
- [ 0.96090861, 1.26908897, 0.99071783],
- [ 0.98877405, 0.53370154, 0.68157021]]))
- assert_almost_equal(nansum(self.A, 1),
- np.array([[ 0.40037675, 0.17621204, 0.76778851],
- [ 1.30085304, 0.87964135, 0.72217448],
- [ 1.57074343, 1.6709751 , 0.57764321]]))
- assert_almost_equal(nansum(self.A, 2),
- np.array([[ 0.02940178, 0.86861904, 0.44635648],
- [ 0.97452409, 0.87964135, 1.04850343],
- [ 1.63772083, 1.47245502, 0.70918589]]))
-
- def test_nanmin(self):
- assert_almost_equal(nanmin(self.A), 0.01319214)
- assert_almost_equal(nanmin(self.A, 0),
- np.array([[ 0.59541557, 0.01319214, 0.01620964],
- [ 0.11704017, 0.38944762, 0.23913896],
- [ 0.28333658, 0.1630199 , 0.33850425]]))
- assert_almost_equal(nanmin(self.A, 1),
- np.array([[ 0.11704017, 0.01319214, 0.01620964],
- [ 0.59541557, 0.87964135, 0.34306596],
- [ 0.72687499, 0.37068164, 0.23913896]]))
- assert_almost_equal(nanmin(self.A, 2),
- np.array([[ 0.01319214, 0.11704017, 0.1630199 ],
- [ 0.37910852, 0.87964135, 0.34306596],
- [ 0.72687499, 0.23913896, 0.33850425]]))
- assert_(np.isnan(nanmin([np.nan, np.nan])))
-
- def test_nanargmin(self):
- assert_almost_equal(nanargmin(self.A), 1)
- assert_almost_equal(nanargmin(self.A, 0),
- np.array([[1, 0, 0],
- [0, 2, 2],
- [0, 0, 2]]))
- assert_almost_equal(nanargmin(self.A, 1),
- np.array([[1, 0, 0],
- [0, 1, 2],
- [0, 2, 1]]))
- assert_almost_equal(nanargmin(self.A, 2),
- np.array([[1, 0, 1],
- [2, 1, 2],
- [0, 2, 2]]))
-
- def test_nanmax(self):
- assert_almost_equal(nanmax(self.A), 0.91084584000000002)
- assert_almost_equal(nanmax(self.A, 0),
- np.array([[ 0.72687499, 0.91084584, 0.37910852],
- [ 0.84386844, 0.87964135, 0.75157887],
- [ 0.70543747, 0.37068164, 0.34306596]]))
- assert_almost_equal(nanmax(self.A, 1),
- np.array([[ 0.28333658, 0.1630199 , 0.75157887],
- [ 0.70543747, 0.87964135, 0.37910852],
- [ 0.84386844, 0.91084584, 0.33850425]]))
- assert_almost_equal(nanmax(self.A, 2),
- np.array([[ 0.01620964, 0.75157887, 0.28333658],
- [ 0.59541557, 0.87964135, 0.70543747],
- [ 0.91084584, 0.84386844, 0.37068164]]))
- assert_(np.isnan(nanmax([np.nan, np.nan])))
-
- def test_nanmin_allnan_on_axis(self):
- assert_array_equal(np.isnan(nanmin([[np.nan] * 2] * 3, axis=1)),
- [True, True, True])
-
- def test_nanmin_masked(self):
- a = np.ma.fix_invalid([[2, 1, 3, np.nan], [5, 2, 3, np.nan]])
- ctrl_mask = a._mask.copy()
- test = np.nanmin(a, axis=1)
- assert_equal(test, [1, 2])
- assert_equal(a._mask, ctrl_mask)
- assert_equal(np.isinf(a), np.zeros((2, 4), dtype=bool))
-
-
-class TestNanFunctsIntTypes(TestCase):
-
- int_types = (
- np.int8, np.int16, np.int32, np.int64, np.uint8,
- np.uint16, np.uint32, np.uint64)
-
- def setUp(self, *args, **kwargs):
- self.A = np.array([127, 39, 93, 87, 46])
-
- def integer_arrays(self):
- for dtype in self.int_types:
- yield self.A.astype(dtype)
-
- def test_nanmin(self):
- min_value = min(self.A)
- for A in self.integer_arrays():
- assert_equal(nanmin(A), min_value)
-
- def test_nanmax(self):
- max_value = max(self.A)
- for A in self.integer_arrays():
- assert_equal(nanmax(A), max_value)
-
- def test_nanargmin(self):
- min_arg = np.argmin(self.A)
- for A in self.integer_arrays():
- assert_equal(nanargmin(A), min_arg)
-
- def test_nanargmax(self):
- max_arg = np.argmax(self.A)
- for A in self.integer_arrays():
- assert_equal(nanargmax(A), max_arg)
-
-
class TestCorrCoef(TestCase):
A = np.array([[ 0.15391142, 0.18045767, 0.14197213],
[ 0.70461506, 0.96474128, 0.27906989],
@@ -1278,7 +1157,7 @@ class TestCov(TestCase):
assert_equal(cov(np.array([]).reshape(0, 2)).shape, (0, 2))
-class Test_i0(TestCase):
+class Test_I0(TestCase):
def test_simple(self):
assert_almost_equal(i0(0.5), np.array(1.0634833707413234))
A = np.array([ 0.49842636, 0.6969809 , 0.22011976, 0.0155549])
@@ -1596,7 +1475,5 @@ class TestAdd_newdoc_ufunc(TestCase):
assert_raises(TypeError, add_newdoc_ufunc, np.add, 3)
-
-
if __name__ == "__main__":
run_module_suite()
diff --git a/numpy/lib/tests/test_nanfunctions.py b/numpy/lib/tests/test_nanfunctions.py
new file mode 100644
index 000000000..1d11862e9
--- /dev/null
+++ b/numpy/lib/tests/test_nanfunctions.py
@@ -0,0 +1,240 @@
+from __future__ import division, absolute_import, print_function
+
+import warnings
+
+import numpy as np
+from numpy.testing import (
+ run_module_suite, TestCase, assert_, assert_equal, assert_almost_equal
+ )
+from numpy.lib import (
+ nansum, nanmax, nanargmax, nanargmin, nanmin, nanmean, nanvar, nanstd
+ )
+
+class TestNaNFuncts(TestCase):
+ def setUp(self):
+ self.A = np.array([[[ np.nan, 0.01319214, 0.01620964],
+ [ 0.11704017, np.nan, 0.75157887],
+ [ 0.28333658, 0.1630199 , np.nan ]],
+ [[ 0.59541557, np.nan, 0.37910852],
+ [ np.nan, 0.87964135, np.nan ],
+ [ 0.70543747, np.nan, 0.34306596]],
+ [[ 0.72687499, 0.91084584, np.nan ],
+ [ 0.84386844, 0.38944762, 0.23913896],
+ [ np.nan, 0.37068164, 0.33850425]]])
+
+ def test_nansum(self):
+ assert_almost_equal(nansum(self.A), 8.0664079100000006)
+ assert_almost_equal(nansum(self.A, 0),
+ np.array([[ 1.32229056, 0.92403798, 0.39531816],
+ [ 0.96090861, 1.26908897, 0.99071783],
+ [ 0.98877405, 0.53370154, 0.68157021]]))
+ assert_almost_equal(nansum(self.A, 1),
+ np.array([[ 0.40037675, 0.17621204, 0.76778851],
+ [ 1.30085304, 0.87964135, 0.72217448],
+ [ 1.57074343, 1.6709751 , 0.57764321]]))
+ assert_almost_equal(nansum(self.A, 2),
+ np.array([[ 0.02940178, 0.86861904, 0.44635648],
+ [ 0.97452409, 0.87964135, 1.04850343],
+ [ 1.63772083, 1.47245502, 0.70918589]]))
+
+ def test_nanmin(self):
+ assert_almost_equal(nanmin(self.A), 0.01319214)
+ assert_almost_equal(nanmin(self.A, 0),
+ np.array([[ 0.59541557, 0.01319214, 0.01620964],
+ [ 0.11704017, 0.38944762, 0.23913896],
+ [ 0.28333658, 0.1630199 , 0.33850425]]))
+ assert_almost_equal(nanmin(self.A, 1),
+ np.array([[ 0.11704017, 0.01319214, 0.01620964],
+ [ 0.59541557, 0.87964135, 0.34306596],
+ [ 0.72687499, 0.37068164, 0.23913896]]))
+ assert_almost_equal(nanmin(self.A, 2),
+ np.array([[ 0.01319214, 0.11704017, 0.1630199 ],
+ [ 0.37910852, 0.87964135, 0.34306596],
+ [ 0.72687499, 0.23913896, 0.33850425]]))
+ assert_(np.isnan(nanmin([np.nan, np.nan])))
+
+ def test_nanargmin(self):
+ assert_almost_equal(nanargmin(self.A), 1)
+ assert_almost_equal(nanargmin(self.A, 0),
+ np.array([[1, 0, 0],
+ [0, 2, 2],
+ [0, 0, 2]]))
+ assert_almost_equal(nanargmin(self.A, 1),
+ np.array([[1, 0, 0],
+ [0, 1, 2],
+ [0, 2, 1]]))
+ assert_almost_equal(nanargmin(self.A, 2),
+ np.array([[1, 0, 1],
+ [2, 1, 2],
+ [0, 2, 2]]))
+
+ def test_nanmax(self):
+ assert_almost_equal(nanmax(self.A), 0.91084584000000002)
+ assert_almost_equal(nanmax(self.A, 0),
+ np.array([[ 0.72687499, 0.91084584, 0.37910852],
+ [ 0.84386844, 0.87964135, 0.75157887],
+ [ 0.70543747, 0.37068164, 0.34306596]]))
+ assert_almost_equal(nanmax(self.A, 1),
+ np.array([[ 0.28333658, 0.1630199 , 0.75157887],
+ [ 0.70543747, 0.87964135, 0.37910852],
+ [ 0.84386844, 0.91084584, 0.33850425]]))
+ assert_almost_equal(nanmax(self.A, 2),
+ np.array([[ 0.01620964, 0.75157887, 0.28333658],
+ [ 0.59541557, 0.87964135, 0.70543747],
+ [ 0.91084584, 0.84386844, 0.37068164]]))
+ assert_(np.isnan(nanmax([np.nan, np.nan])))
+
+ def test_nanmin_allnan_on_axis(self):
+ assert_equal(np.isnan(nanmin([[np.nan] * 2] * 3, axis=1)),
+ [True, True, True])
+
+ def test_nanmin_masked(self):
+ a = np.ma.fix_invalid([[2, 1, 3, np.nan], [5, 2, 3, np.nan]])
+ ctrl_mask = a._mask.copy()
+ test = np.nanmin(a, axis=1)
+ assert_equal(test, [1, 2])
+ assert_equal(a._mask, ctrl_mask)
+ assert_equal(np.isinf(a), np.zeros((2, 4), dtype=bool))
+
+ def test_nanmean(self):
+ A = [[1, np.nan, np.nan], [np.nan, 4, 5]]
+ assert_(nanmean(A) == (10.0 / 3))
+ assert_(all(nanmean(A,0) == np.array([1, 4, 5])))
+ assert_(all(nanmean(A,1) == np.array([1, 4.5])))
+
+ def test_nanstd(self):
+ A = [[1, np.nan, np.nan], [np.nan, 4, 5]]
+ assert_almost_equal(nanstd(A), 1.699673171197595)
+ assert_almost_equal(nanstd(A,0), np.array([0.0, 0.0, 0.0]))
+ assert_almost_equal(nanstd(A,1), np.array([0.0, 0.5]))
+
+ def test_nanvar(self):
+ A = [[1, np.nan, np.nan], [np.nan, 4, 5]]
+ assert_almost_equal(nanvar(A), 2.88888888889)
+ assert_almost_equal(nanvar(A,0), np.array([0.0, 0.0, 0.0]))
+ assert_almost_equal(nanvar(A,1), np.array([0.0, 0.25]))
+
+
+class TestNaNMean(TestCase):
+ def setUp(self):
+ self.A = np.array([1, np.nan, -1, np.nan, np.nan, 1, -1])
+ self.B = np.array([np.nan, np.nan, np.nan, np.nan])
+ self.real_mean = 0
+
+ def test_basic(self):
+ assert_almost_equal(nanmean(self.A),self.real_mean)
+
+ def test_mutation(self):
+ # Because of the "messing around" we do to replace NaNs with zeros
+ # this is meant to ensure we don't actually replace the NaNs in the
+ # actual _array.
+ a_copy = self.A.copy()
+ b_copy = self.B.copy()
+ with warnings.catch_warnings(record=True) as w:
+ warnings.filterwarnings('always', '', RuntimeWarning)
+ a_ret = nanmean(self.A)
+ assert_equal(self.A, a_copy)
+ b_ret = nanmean(self.B)
+ assert_equal(self.B, b_copy)
+
+ def test_allnans(self):
+ with warnings.catch_warnings(record=True) as w:
+ warnings.filterwarnings('always', '', RuntimeWarning)
+ assert_(np.isnan(nanmean(self.B)))
+ assert_(w[0].category is RuntimeWarning)
+
+ def test_empty(self):
+ with warnings.catch_warnings(record=True) as w:
+ warnings.filterwarnings('always', '', RuntimeWarning)
+ assert_(np.isnan(nanmean(np.array([]))))
+ assert_(w[0].category is RuntimeWarning)
+
+
+class TestNaNStdVar(TestCase):
+ def setUp(self):
+ self.A = np.array([np.nan, 1, -1, np.nan, 1, np.nan, -1])
+ self.B = np.array([np.nan, np.nan, np.nan, np.nan])
+ self.real_var = 1
+
+ def test_basic(self):
+ assert_almost_equal(nanvar(self.A),self.real_var)
+ assert_almost_equal(nanstd(self.A)**2,self.real_var)
+
+ def test_mutation(self):
+ # Because of the "messing around" we do to replace NaNs with zeros
+ # this is meant to ensure we don't actually replace the NaNs in the
+ # actual array.
+ with warnings.catch_warnings(record=True) as w:
+ warnings.filterwarnings('always', '', RuntimeWarning)
+ a_copy = self.A.copy()
+ b_copy = self.B.copy()
+ a_ret = nanvar(self.A)
+ assert_equal(self.A, a_copy)
+ b_ret = nanstd(self.B)
+ assert_equal(self.B, b_copy)
+
+ def test_ddof1(self):
+ mask = ~np.isnan(self.A)
+ assert_almost_equal(nanvar(self.A,ddof=1),
+ self.real_var*sum(mask)/float(sum(mask) - 1))
+ assert_almost_equal(nanstd(self.A,ddof=1)**2,
+ self.real_var*sum(mask)/float(sum(mask) - 1))
+
+ def test_ddof2(self):
+ mask = ~np.isnan(self.A)
+ assert_almost_equal(nanvar(self.A,ddof=2),
+ self.real_var*sum(mask)/float(sum(mask) - 2))
+ assert_almost_equal(nanstd(self.A,ddof=2)**2,
+ self.real_var*sum(mask)/float(sum(mask) - 2))
+
+ def test_allnans(self):
+ with warnings.catch_warnings(record=True) as w:
+ warnings.filterwarnings('always', '', RuntimeWarning)
+ assert_(np.isnan(nanvar(self.B)))
+ assert_(np.isnan(nanstd(self.B)))
+ assert_(w[0].category is RuntimeWarning)
+
+ def test_empty(self):
+ with warnings.catch_warnings(record=True) as w:
+ warnings.filterwarnings('always', '', RuntimeWarning)
+ assert_(np.isnan(nanvar(np.array([]))))
+ assert_(np.isnan(nanstd(np.array([]))))
+ assert_(w[0].category is RuntimeWarning)
+
+
+class TestNanFunctsIntTypes(TestCase):
+
+ int_types = (
+ np.int8, np.int16, np.int32, np.int64, np.uint8,
+ np.uint16, np.uint32, np.uint64)
+
+ def setUp(self, *args, **kwargs):
+ self.A = np.array([127, 39, 93, 87, 46])
+
+ def integer_arrays(self):
+ for dtype in self.int_types:
+ yield self.A.astype(dtype)
+
+ def test_nanmin(self):
+ min_value = min(self.A)
+ for A in self.integer_arrays():
+ assert_equal(nanmin(A), min_value)
+
+ def test_nanmax(self):
+ max_value = max(self.A)
+ for A in self.integer_arrays():
+ assert_equal(nanmax(A), max_value)
+
+ def test_nanargmin(self):
+ min_arg = np.argmin(self.A)
+ for A in self.integer_arrays():
+ assert_equal(nanargmin(A), min_arg)
+
+ def test_nanargmax(self):
+ max_arg = np.argmax(self.A)
+ for A in self.integer_arrays():
+ assert_equal(nanargmax(A), max_arg)
+
+
+if __name__ == "__main__":
+ run_module_suite()