"""
Histogram-related functions
"""
from __future__ import division, absolute_import, print_function
import operator
import warnings
import numpy as np
from numpy.compat.py3k import basestring
__all__ = ['histogram', 'histogramdd', 'histogram_bin_edges']
# range is a keyword argument to many functions, so save the builtin so they can
# use it.
_range = range
def _hist_bin_sqrt(x):
"""
Square root histogram bin estimator.
Bin width is inversely proportional to the data size. Used by many
programs for its simplicity.
Parameters
----------
x : array_like
Input data that is to be histogrammed, trimmed to range. May not
be empty.
Returns
-------
h : An estimate of the optimal bin width for the given data.
"""
return x.ptp() / np.sqrt(x.size)
def _hist_bin_sturges(x):
"""
Sturges histogram bin estimator.
A very simplistic estimator based on the assumption of normality of
the data. This estimator has poor performance for non-normal data,
which becomes especially obvious for large data sets. The estimate
depends only on size of the data.
Parameters
----------
x : array_like
Input data that is to be histogrammed, trimmed to range. May not
be empty.
Returns
-------
h : An estimate of the optimal bin width for the given data.
"""
return x.ptp() / (np.log2(x.size) + 1.0)
def _hist_bin_rice(x):
"""
Rice histogram bin estimator.
Another simple estimator with no normality assumption. It has better
performance for large data than Sturges, but tends to overestimate
the number of bins. The number of bins is proportional to the cube
root of data size (asymptotically optimal). The estimate depends
only on size of the data.
Parameters
----------
x : array_like
Input data that is to be histogrammed, trimmed to range. May not
be empty.
Returns
-------
h : An estimate of the optimal bin width for the given data.
"""
return x.ptp() / (2.0 * x.size ** (1.0 / 3))
def _hist_bin_scott(x):
"""
Scott histogram bin estimator.
The binwidth is proportional to the standard deviation of the data
and inversely proportional to the cube root of data size
(asymptotically optimal).
Parameters
----------
x : array_like
Input data that is to be histogrammed, trimmed to range. May not
be empty.
Returns
-------
h : An estimate of the optimal bin width for the given data.
"""
return (24.0 * np.pi**0.5 / x.size)**(1.0 / 3.0) * np.std(x)
def _hist_bin_doane(x):
"""
Doane's histogram bin estimator.
Improved version of Sturges' formula which works better for
non-normal data. See
stats.stackexchange.com/questions/55134/doanes-formula-for-histogram-binning
Parameters
----------
x : array_like
Input data that is to be histogrammed, trimmed to range. May not
be empty.
Returns
-------
h : An estimate of the optimal bin width for the given data.
"""
if x.size > 2:
sg1 = np.sqrt(6.0 * (x.size - 2) / ((x.size + 1.0) * (x.size + 3)))
sigma = np.std(x)
if sigma > 0.0:
# These three operations add up to
# g1 = np.mean(((x - np.mean(x)) / sigma)**3)
# but use only one temp array instead of three
temp = x - np.mean(x)
np.true_divide(temp, sigma, temp)
np.power(temp, 3, temp)
g1 = np.mean(temp)
return x.ptp() / (1.0 + np.log2(x.size) +
np.log2(1.0 + np.absolute(g1) / sg1))
return 0.0
def _hist_bin_fd(x):
"""
The Freedman-Diaconis histogram bin estimator.
The Freedman-Diaconis rule uses interquartile range (IQR) to
estimate binwidth. It is considered a variation of the Scott rule
with more robustness as the IQR is less affected by outliers than
the standard deviation. However, the IQR depends on fewer points
than the standard deviation, so it is less accurate, especially for
long tailed distributions.
If the IQR is 0, this function returns 1 for the number of bins.
Binwidth is inversely proportional to the cube root of data size
(asymptotically optimal).
Parameters
----------
x : array_like
Input data that is to be histogrammed, trimmed to range. May not
be empty.
Returns
-------
h : An estimate of the optimal bin width for the given data.
"""
iqr = np.subtract(*np.percentile(x, [75, 25]))
return 2.0 * iqr * x.size ** (-1.0 / 3.0)
def _hist_bin_auto(x):
"""
Histogram bin estimator that uses the minimum width of the
Freedman-Diaconis and Sturges estimators if the FD bandwidth is non zero
and the Sturges estimator if the FD bandwidth is 0.
The FD estimator is usually the most robust method, but its width
estimate tends to be too large for small `x` and bad for data with limited
variance. The Sturges estimator is quite good for small (<1000) datasets
and is the default in the R language. This method gives good off the shelf
behaviour.
.. versionchanged:: 1.15.0
If there is limited variance the IQR can be 0, which results in the
FD bin width being 0 too. This is not a valid bin width, so
``np.histogram_bin_edges`` chooses 1 bin instead, which may not be optimal.
If the IQR is 0, it's unlikely any variance based estimators will be of
use, so we revert to the sturges estimator, which only uses the size of the
dataset in its calculation.
Parameters
----------
x : array_like
Input data that is to be histogrammed, trimmed to range. May not
be empty.
Returns
-------
h : An estimate of the optimal bin width for the given data.
See Also
--------
_hist_bin_fd, _hist_bin_sturges
"""
fd_bw = _hist_bin_fd(x)
sturges_bw = _hist_bin_sturges(x)
if fd_bw:
return min(fd_bw, sturges_bw)
else:
# limited variance, so we return a len dependent bw estimator
return sturges_bw
# Private dict initialized at module load time
_hist_bin_selectors = {'auto': _hist_bin_auto,
'doane': _hist_bin_doane,
'fd': _hist_bin_fd,
'rice': _hist_bin_rice,
'scott': _hist_bin_scott,
'sqrt': _hist_bin_sqrt,
'sturges': _hist_bin_sturges}
def _ravel_and_check_weights(a, weights):
""" Check a and weights have matching shapes, and ravel both """
a = np.asarray(a)
# Ensure that the array is a "subtractable" dtype
if a.dtype == np.bool_:
warnings.warn("Converting input from {} to {} for compatibility."
.format(a.dtype, np.uint8),
RuntimeWarning, stacklevel=2)
a = a.astype(np.uint8)
if weights is not None:
weights = np.asarray(weights)
if weights.shape != a.shape:
raise ValueError(
'weights should have the same shape as a.')
weights = weights.ravel()
a = a.ravel()
return a, weights
def _get_outer_edges(a, range):
"""
Determine the outer bin edges to use, from either the data or the range
argument
"""
if range is not None:
first_edge, last_edge = range
if first_edge > last_edge:
raise ValueError(
'max must be larger than min in range parameter.')
if not (np.isfinite(first_edge) and np.isfinite(last_edge)):
raise ValueError(
"supplied range of [{}, {}] is not finite".format(first_edge, last_edge))
elif a.size == 0:
# handle empty arrays. Can't determine range, so use 0-1.
first_edge, last_edge = 0, 1
else:
first_edge, last_edge = a.min(), a.max()
if not (np.isfinite(first_edge) and np.isfinite(last_edge)):
raise ValueError(
"autodetected range of [{}, {}] is not finite".format(first_edge, last_edge))
# expand empty range to avoid divide by zero
if first_edge == last_edge:
first_edge = first_edge - 0.5
last_edge = last_edge + 0.5
return first_edge, last_edge
def _unsigned_subtract(a, b):
"""
Subtract two values where a >= b, and produce an unsigned result
This is needed when finding the difference between the upper and lower
bound of an int16 histogram
"""
# coerce to a single type
signed_to_unsigned = {
np.byte: np.ubyte,
np.short: np.ushort,
np.intc: np.uintc,
np.int_: np.uint,
np.longlong: np.ulonglong
}
dt = np.result_type(a, b)
try:
dt = signed_to_unsigned[dt.type]
except KeyError:
return np.subtract(a, b, dtype=dt)
else:
# we know the inputs are integers, and we are deliberately casting
# signed to unsigned
return np.subtract(a, b, casting='unsafe', dtype=dt)
def _get_bin_edges(a, bins, range, weights):
"""
Computes the bins used internally by `histogram`.
Parameters
==========
a : ndarray
Ravelled data array
bins, range
Forwarded arguments from `histogram`.
weights : ndarray, optional
Ravelled weights array, or None
Returns
=======
bin_edges : ndarray
Array of bin edges
uniform_bins : (Number, Number, int):
The upper bound, lowerbound, and number of bins, used in the optimized
implementation of `histogram` that works on uniform bins.
"""
# parse the overloaded bins argument
n_equal_bins = None
bin_edges = None
if isinstance(bins, basestring):
bin_name = bins
# if `bins` is a string for an automatic method,
# this will replace it with the number of bins calculated
if bin_name not in _hist_bin_selectors:
raise ValueError(
"{!r} is not a valid estimator for `bins`".format(bin_name))
if weights is not None:
raise TypeError("Automated estimation of the number of "
"bins is not supported for weighted data")
first_edge, last_edge = _get_outer_edges(a, range)
# truncate the range if needed
if range is not None:
keep = (a >= first_edge)
keep &= (a <= last_edge)
if not np.logical_and.reduce(keep):
a = a[keep]
if a.size == 0:
n_equal_bins = 1
else:
# Do not call selectors on empty arrays
width = _hist_bin_selectors[bin_name](a)
if width:
n_equal_bins = int(np.ceil(_unsigned_subtract(last_edge, first_edge) / width))
else:
# Width can be zero for some estimators, e.g. FD when
# the IQR of the data is zero.
n_equal_bins = 1
elif np.ndim(bins) == 0:
try:
n_equal_bins = operator.index(bins)
except TypeError:
raise TypeError(
'`bins` must be an integer, a string, or an array')
if n_equal_bins < 1:
raise ValueError('`bins` must be positive, when an integer')
first_edge, last_edge = _get_outer_edges(a, range)
elif np.ndim(bins) == 1:
bin_edges = np.asarray(bins)
if np.any(bin_edges[:-1] > bin_edges[1:]):
raise ValueError(
'`bins` must increase monotonically, when an array')
else:
raise ValueError('`bins` must be 1d, when an array')
if n_equal_bins is not None:
# gh-10322 means that type resolution rules are dependent on array
# shapes. To avoid this causing problems, we pick a type now and stick
# with it throughout.
bin_type = np.result_type(first_edge, last_edge, a)
if np.issubdtype(bin_type, np.integer):
bin_type = np.result_type(bin_type, float)
# bin edges must be computed
bin_edges = np.linspace(
first_edge, last_edge, n_equal_bins + 1,
endpoint=True, dtype=bin_type)
return bin_edges, (first_edge, last_edge, n_equal_bins)
else:
return bin_edges, None
def _search_sorted_inclusive(a, v):
"""
Like `searchsorted`, but where the last item in `v` is placed on the right.
In the context of a histogram, this makes the last bin edge inclusive
"""
return np.concatenate((
a.searchsorted(v[:-1], 'left'),
a.searchsorted(v[-1:], 'right')
))
def histogram_bin_edges(a, bins=10, range=None, weights=None):
r"""
Function to calculate only the edges of the bins used by the `histogram` function.
Parameters
----------
a : array_like
Input data. The histogram is computed over the flattened array.
bins : int or sequence of scalars or str, optional
If `bins` is an int, it defines the number of equal-width
bins in the given range (10, by default). If `bins` is a
sequence, it defines the bin edges, including the rightmost
edge, allowing for non-uniform bin widths.
If `bins` is a string from the list below, `histogram_bin_edges` will use
the method chosen to calculate the optimal bin width and
consequently the number of bins (see `Notes` for more detail on
the estimators) from the data that falls within the requested
range. While the bin width will be optimal for the actual data
in the range, the number of bins will be computed to fill the
entire range, including the empty portions. For visualisation,
using the 'auto' option is suggested. Weighted data is not
supported for automated bin size selection.
'auto'
Maximum of the 'sturges' and 'fd' estimators. Provides good
all around performance.
'fd' (Freedman Diaconis Estimator)
Robust (resilient to outliers) estimator that takes into
account data variability and data size.
'doane'
An improved version of Sturges' estimator that works better
with non-normal datasets.
'scott'
Less robust estimator that that takes into account data
variability and data size.
'rice'
Estimator does not take variability into account, only data
size. Commonly overestimates number of bins required.
'sturges'
R's default method, only accounts for data size. Only
optimal for gaussian data and underestimates number of bins
for large non-gaussian datasets.
'sqrt'
Square root (of data size) estimator, used by Excel and
other programs for its speed and simplicity.
range : (float, float), optional
The lower and upper range of the bins. If not provided, range
is simply ``(a.min(), a.max())``. Values outside the range are
ignored. The first element of the range must be less than or
equal to the second. `range` affects the automatic bin
computation as well. While bin width is computed to be optimal
based on the actual data within `range`, the bin count will fill
the entire range including portions containing no data.
weights : array_like, optional
An array of weights, of the same shape as `a`. Each value in
`a` only contributes its associated weight towards the bin count
(instead of 1). This is currently not used by any of the bin estimators,
but may be in the future.
Returns
-------
bin_edges : array of dtype float
The edges to pass into `histogram`
See Also
--------
histogram
Notes
-----
The methods to estimate the optimal number of bins are well founded
in literature, and are inspired by the choices R provides for
histogram visualisation. Note that having the number of bins
proportional to :math:`n^{1/3}` is asymptotically optimal, which is
why it appears in most estimators. These are simply plug-in methods
that give good starting points for number of bins. In the equations
below, :math:`h` is the binwidth and :math:`n_h` is the number of
bins. All estimators that compute bin counts are recast to bin width
using the `ptp` of the data. The final bin count is obtained from
``np.round(np.ceil(range / h))``.
'Auto' (maximum of the 'Sturges' and 'FD' estimators)
A compromise to get a good value. For small datasets the Sturges
value will usually be chosen, while larger datasets will usually
default to FD. Avoids the overly conservative behaviour of FD
and Sturges for small and large datasets respectively.
Switchover point is usually :math:`a.size \approx 1000`.
'FD' (Freedman Diaconis Estimator)
.. math:: h = 2 \frac{IQR}{n^{1/3}}
The binwidth is proportional to the interquartile range (IQR)
and inversely proportional to cube root of a.size. Can be too
conservative for small datasets, but is quite good for large
datasets. The IQR is very robust to outliers.
'Scott'
.. math:: h = \sigma \sqrt[3]{\frac{24 * \sqrt{\pi}}{n}}
The binwidth is proportional to the standard deviation of the
data and inversely proportional to cube root of ``x.size``. Can
be too conservative for small datasets, but is quite good for
large datasets. The standard deviation is not very robust to
outliers. Values are very similar to the Freedman-Diaconis
estimator in the absence of outliers.
'Rice'
.. math:: n_h = 2n^{1/3}
The number of bins is only proportional to cube root of
``a.size``. It tends to overestimate the number of bins and it
does not take into account data variability.
'Sturges'
.. math:: n_h = \log _{2}n+1
The number of bins is the base 2 log of ``a.size``. This
estimator assumes normality of data and is too conservative for
larger, non-normal datasets. This is the default method in R's
``hist`` method.
'Doane'
.. math:: n_h = 1 + \log_{2}(n) +
\log_{2}(1 + \frac{|g_1|}{\sigma_{g_1}})
g_1 = mean[(\frac{x - \mu}{\sigma})^3]
\sigma_{g_1} = \sqrt{\frac{6(n - 2)}{(n + 1)(n + 3)}}
An improved version of Sturges' formula that produces better
estimates for non-normal datasets. This estimator attempts to
account for the skew of the data.
'Sqrt'
.. math:: n_h = \sqrt n
The simplest and fastest estimator. Only takes into account the
data size.
Examples
--------
>>> arr = np.array([0, 0, 0, 1, 2, 3, 3, 4, 5])
>>> np.histogram_bin_edges(arr, bins='auto', range=(0, 1))
array([0. , 0.25, 0.5 , 0.75, 1. ])
>>> np.histogram_bin_edges(arr, bins=2)
array([0. , 2.5, 5. ])
For consistency with histogram, an array of pre-computed bins is
passed through unmodified:
>>> np.histogram_bin_edges(arr, [1, 2])
array([1, 2])
This function allows one set of bins to be computed, and reused across
multiple histograms:
>>> shared_bins = np.histogram_bin_edges(arr, bins='auto')
>>> shared_bins
array([0., 1., 2., 3., 4., 5.])
>>> group_id = np.array([0, 1, 1, 0, 1, 1, 0, 1, 1])
>>> hist_0, _ = np.histogram(arr[group_id == 0], bins=shared_bins)
>>> hist_1, _ = np.histogram(arr[group_id == 1], bins=shared_bins)
>>> hist_0; hist_1
array([1, 1, 0, 1, 0])
array([2, 0, 1, 1, 2])
Which gives more easily comparable results than using separate bins for
each histogram:
>>> hist_0, bins_0 = np.histogram(arr[group_id == 0], bins='auto')
>>> hist_1, bins_1 = np.histogram(arr[group_id == 1], bins='auto')
>>> hist_0; hist1
array([1, 1, 1])
array([2, 1, 1, 2])
>>> bins_0; bins_1
array([0., 1., 2., 3.])
array([0. , 1.25, 2.5 , 3.75, 5. ])
"""
a, weights = _ravel_and_check_weights(a, weights)
bin_edges, _ = _get_bin_edges(a, bins, range, weights)
return bin_edges
def histogram(a, bins=10, range=None, normed=None, weights=None,
density=None):
r"""
Compute the histogram of a set of data.
Parameters
----------
a : array_like
Input data. The histogram is computed over the flattened array.
bins : int or sequence of scalars or str, optional
If `bins` is an int, it defines the number of equal-width
bins in the given range (10, by default). If `bins` is a
sequence, it defines the bin edges, including the rightmost
edge, allowing for non-uniform bin widths.
.. versionadded:: 1.11.0
If `bins` is a string, it defines the method used to calculate the
optimal bin width, as defined by `histogram_bin_edges`.
range : (float, float), optional
The lower and upper range of the bins. If not provided, range
is simply ``(a.min(), a.max())``. Values outside the range are
ignored. The first element of the range must be less than or
equal to the second. `range` affects the automatic bin
computation as well. While bin width is computed to be optimal
based on the actual data within `range`, the bin count will fill
the entire range including portions containing no data.
normed : bool, optional
.. deprecated:: 1.6.0
This is equivalent to the `density` argument, but produces incorrect
results for unequal bin widths. It should not be used.
.. versionchanged:: 1.15.0
DeprecationWarnings are actually emitted.
weights : array_like, optional
An array of weights, of the same shape as `a`. Each value in
`a` only contributes its associated weight towards the bin count
(instead of 1). If `density` is True, the weights are
normalized, so that the integral of the density over the range
remains 1.
density : bool, optional
If ``False``, the result will contain the number of samples in
each bin. If ``True``, the result is the value of the
probability *density* function at the bin, normalized such that
the *integral* over the range is 1. Note that the sum of the
histogram values will not be equal to 1 unless bins of unity
width are chosen; it is not a probability *mass* function.
Overrides the ``normed`` keyword if given.
Returns
-------
hist : array
The values of the histogram. See `density` and `weights` for a
description of the possible semantics.
bin_edges : array of dtype float
Return the bin edges ``(length(hist)+1)``.
See Also
--------
histogramdd, bincount, searchsorted, digitize, histogram_bin_edges
Notes
-----
All but the last (righthand-most) bin is half-open. In other words,
if `bins` is::
[1, 2, 3, 4]
then the first bin is ``[1, 2)`` (including 1, but excluding 2) and
the second ``[2, 3)``. The last bin, however, is ``[3, 4]``, which
*includes* 4.
Examples
--------
>>> np.histogram([1, 2, 1], bins=[0, 1, 2, 3])
(array([0, 2, 1]), array([0, 1, 2, 3]))
>>> np.histogram(np.arange(4), bins=np.arange(5), density=True)
(array([ 0.25, 0.25, 0.25, 0.25]), array([0, 1, 2, 3, 4]))
>>> np.histogram([[1, 2, 1], [1, 0, 1]], bins=[0,1,2,3])
(array([1, 4, 1]), array([0, 1, 2, 3]))
>>> a = np.arange(5)
>>> hist, bin_edges = np.histogram(a, density=True)
>>> hist
array([ 0.5, 0. , 0.5, 0. , 0. , 0.5, 0. , 0.5, 0. , 0.5])
>>> hist.sum()
2.4999999999999996
>>> np.sum(hist * np.diff(bin_edges))
1.0
.. versionadded:: 1.11.0
Automated Bin Selection Methods example, using 2 peak random data
with 2000 points:
>>> import matplotlib.pyplot as plt
>>> rng = np.random.RandomState(10) # deterministic random data
>>> a = np.hstack((rng.normal(size=1000),
... rng.normal(loc=5, scale=2, size=1000)))
>>> plt.hist(a, bins='auto') # arguments are passed to np.histogram
>>> plt.title("Histogram with 'auto' bins")
>>> plt.show()
"""
a, weights = _ravel_and_check_weights(a, weights)
bin_edges, uniform_bins = _get_bin_edges(a, bins, range, weights)
# Histogram is an integer or a float array depending on the weights.
if weights is None:
ntype = np.dtype(np.intp)
else:
ntype = weights.dtype
# We set a block size, as this allows us to iterate over chunks when
# computing histograms, to minimize memory usage.
BLOCK = 65536
# The fast path uses bincount, but that only works for certain types
# of weight
simple_weights = (
weights is None or
np.can_cast(weights.dtype, np.double) or
np.can_cast(weights.dtype, complex)
)
if uniform_bins is not None and simple_weights:
# Fast algorithm for equal bins
# We now convert values of a to bin indices, under the assumption of
# equal bin widths (which is valid here).
first_edge, last_edge, n_equal_bins = uniform_bins
# Initialize empty histogram
n = np.zeros(n_equal_bins, ntype)
# Pre-compute histogram scaling factor
norm = n_equal_bins / _unsigned_subtract(last_edge, first_edge)
# We iterate over blocks here for two reasons: the first is that for
# large arrays, it is actually faster (for example for a 10^8 array it
# is 2x as fast) and it results in a memory footprint 3x lower in the
# limit of large arrays.
for i in _range(0, len(a), BLOCK):
tmp_a = a[i:i+BLOCK]
if weights is None:
tmp_w = None
else:
tmp_w = weights[i:i + BLOCK]
# Only include values in the right range
keep = (tmp_a >= first_edge)
keep &= (tmp_a <= last_edge)
if not np.logical_and.reduce(keep):
tmp_a = tmp_a[keep]
if tmp_w is not None:
tmp_w = tmp_w[keep]
# This cast ensures no type promotions occur below, which gh-10322
# make unpredictable. Getting it wrong leads to precision errors
# like gh-8123.
tmp_a = tmp_a.astype(bin_edges.dtype, copy=False)
# Compute the bin indices, and for values that lie exactly on
# last_edge we need to subtract one
f_indices = _unsigned_subtract(tmp_a, first_edge) * norm
indices = f_indices.astype(np.intp)
indices[indices == n_equal_bins] -= 1
# The index computation is not guaranteed to give exactly
# consistent results within ~1 ULP of the bin edges.
decrement = tmp_a < bin_edges[indices]
indices[decrement] -= 1
# The last bin includes the right edge. The other bins do not.
increment = ((tmp_a >= bin_edges[indices + 1])
& (indices != n_equal_bins - 1))
indices[increment] += 1
# We now compute the histogram using bincount
if ntype.kind == 'c':
n.real += np.bincount(indices, weights=tmp_w.real,
minlength=n_equal_bins)
n.imag += np.bincount(indices, weights=tmp_w.imag,
minlength=n_equal_bins)
else:
n += np.bincount(indices, weights=tmp_w,
minlength=n_equal_bins).astype(ntype)
else:
# Compute via cumulative histogram
cum_n = np.zeros(bin_edges.shape, ntype)
if weights is None:
for i in _range(0, len(a), BLOCK):
sa = np.sort(a[i:i+BLOCK])
cum_n += _search_sorted_inclusive(sa, bin_edges)
else:
zero = np.zeros(1, dtype=ntype)
for i in _range(0, len(a), BLOCK):
tmp_a = a[i:i+BLOCK]
tmp_w = weights[i:i+BLOCK]
sorting_index = np.argsort(tmp_a)
sa = tmp_a[sorting_index]
sw = tmp_w[sorting_index]
cw = np.concatenate((zero, sw.cumsum()))
bin_index = _search_sorted_inclusive(sa, bin_edges)
cum_n += cw[bin_index]
n = np.diff(cum_n)
# density overrides the normed keyword
if density is not None:
if normed is not None:
# 2018-06-13, numpy 1.15.0 (this was not noisily deprecated in 1.6)
warnings.warn(
"The normed argument is ignored when density is provided. "
"In future passing both will result in an error.",
DeprecationWarning, stacklevel=2)
normed = None
if density:
db = np.array(np.diff(bin_edges), float)
return n/db/n.sum(), bin_edges
elif normed:
# 2018-06-13, numpy 1.15.0 (this was not noisily deprecated in 1.6)
warnings.warn(
"Passing `normed=True` on non-uniform bins has always been "
"broken, and computes neither the probability density "
"function nor the probability mass function. "
"The result is only correct if the bins are uniform, when "
"density=True will produce the same result anyway. "
"The argument will be removed in a future version of "
"numpy.",
np.VisibleDeprecationWarning, stacklevel=2)
# this normalization is incorrect, but
db = np.array(np.diff(bin_edges), float)
return n/(n*db).sum(), bin_edges
else:
if normed is not None:
# 2018-06-13, numpy 1.15.0 (this was not noisily deprecated in 1.6)
warnings.warn(
"Passing normed=False is deprecated, and has no effect. "
"Consider passing the density argument instead.",
DeprecationWarning, stacklevel=2)
return n, bin_edges
def histogramdd(sample, bins=10, range=None, normed=None, weights=None,
density=None):
"""
Compute the multidimensional histogram of some data.
Parameters
----------
sample : (N, D) array, or (D, N) array_like
The data to be histogrammed.
Note the unusual interpretation of sample when an array_like:
* When an array, each row is a coordinate in a D-dimensional space -
such as ``histogramgramdd(np.array([p1, p2, p3]))``.
* When an array_like, each element is the list of values for single
coordinate - such as ``histogramgramdd((X, Y, Z))``.
The first form should be preferred.
bins : sequence or int, optional
The bin specification:
* A sequence of arrays describing the bin edges along each dimension.
* The number of bins for each dimension (nx, ny, ... =bins)
* The number of bins for all dimensions (nx=ny=...=bins).
range : sequence, optional
A sequence of length D, each an optional (lower, upper) tuple giving
the outer bin edges to be used if the edges are not given explicitly in
`bins`.
An entry of None in the sequence results in the minimum and maximum
values being used for the corresponding dimension.
The default, None, is equivalent to passing a tuple of D None values.
density : bool, optional
If False, the default, returns the number of samples in each bin.
If True, returns the probability *density* function at the bin,
``bin_count / sample_count / bin_volume``.
normed : bool, optional
An alias for the density argument that behaves identically. To avoid
confusion with the broken normed argument to `histogram`, `density`
should be preferred.
weights : (N,) array_like, optional
An array of values `w_i` weighing each sample `(x_i, y_i, z_i, ...)`.
Weights are normalized to 1 if normed is True. If normed is False,
the values of the returned histogram are equal to the sum of the
weights belonging to the samples falling into each bin.
Returns
-------
H : ndarray
The multidimensional histogram of sample x. See normed and weights
for the different possible semantics.
edges : list
A list of D arrays describing the bin edges for each dimension.
See Also
--------
histogram: 1-D histogram
histogram2d: 2-D histogram
Examples
--------
>>> r = np.random.randn(100,3)
>>> H, edges = np.histogramdd(r, bins = (5, 8, 4))
>>> H.shape, edges[0].size, edges[1].size, edges[2].size
((5, 8, 4), 6, 9, 5)
"""
try:
# Sample is an ND-array.
N, D = sample.shape
except (AttributeError, ValueError):
# Sample is a sequence of 1D arrays.
sample = np.atleast_2d(sample).T
N, D = sample.shape
nbin = np.empty(D, int)
edges = D*[None]
dedges = D*[None]
if weights is not None:
weights = np.asarray(weights)
try:
M = len(bins)
if M != D:
raise ValueError(
'The dimension of bins must be equal to the dimension of the '
' sample x.')
except TypeError:
# bins is an integer
bins = D*[bins]
# normalize the range argument
if range is None:
range = (None,) * D
elif len(range) != D:
raise ValueError('range argument must have one entry per dimension')
# Create edge arrays
for i in _range(D):
if np.ndim(bins[i]) == 0:
if bins[i] < 1:
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)
elif np.ndim(bins[i]) == 1:
edges[i] = np.asarray(bins[i])
if np.any(edges[i][:-1] > edges[i][1:]):
raise ValueError(
'`bins[{}]` must be monotonically increasing, when an array'
.format(i))
else:
raise ValueError(
'`bins[{}]` must be a scalar or 1d array'.format(i))
nbin[i] = len(edges[i]) + 1 # includes an outlier on each end
dedges[i] = np.diff(edges[i])
# Compute the bin number each sample falls into.
Ncount = tuple(
# avoid np.digitize to work around gh-11022
np.searchsorted(edges[i], sample[:, i], side='right')
for i in _range(D)
)
# Using digitize, values that fall on an edge are put in the right bin.
# 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):
# 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.
xy = np.ravel_multi_index(Ncount, nbin)
# Compute the number of repetitions in xy and assign it to the
# flattened histmat.
hist = np.bincount(xy, weights, minlength=nbin.prod())
# Shape into a proper matrix
hist = hist.reshape(nbin)
# This preserves the (bad) behavior observed in gh-7845, for now.
hist = hist.astype(float, casting='safe')
# Remove outliers (indices 0 and -1 for each dimension).
core = D*(slice(1, -1),)
hist = hist[core]
# handle the aliasing normed argument
if normed is None:
if density is None:
density = False
elif density is None:
# an explicit normed argument was passed, alias it to the new name
density = normed
else:
raise TypeError("Cannot specify both 'normed' and 'density'")
if density:
# calculate the probability density function
s = hist.sum()
for i in _range(D):
shape = np.ones(D, int)
shape[i] = nbin[i] - 2
hist = hist / dedges[i].reshape(shape)
hist /= s
if (hist.shape != nbin - 2).any():
raise RuntimeError(
"Internal Shape Error")
return hist, edges
