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Fixed issues with errorbar limits #2452

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Merged
merged 8 commits into from
Apr 4, 2014
Merged

Fixed issues with errorbar limits #2452

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b76263c
Fixed issues with errorbar limits
larrybradley Sep 23, 2013
2be7e7f
Condensed setting values in lines_kw and plot_kw in the errorbar func…
larrybradley Oct 1, 2013
f5c787f
added errorbar limit test
larrybradley Feb 14, 2014
8039d12
added comments; fixed typo
larrybradley Feb 25, 2014
263b070
removed extra space; pep8
larrybradley Feb 25, 2014
1b06302
fixes direction of arrowhead plot symbol for inverted x or y axes
larrybradley Mar 18, 2014
af6a89b
updated api_changes and whats_new
larrybradley Mar 18, 2014
7cc983d
removed rebase marker in test_axes
larrybradley Mar 26, 2014
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4 changes: 4 additions & 0 deletions doc/api/api_changes.rst
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Expand Up @@ -47,6 +47,10 @@ original location:
- mstream -> `from matplotlib import stream as mstream`
- mtable -> `from matplotlib import table as mtable`

* The :func:`~matplotlib.pyplot.errorbar` method has been changed such that
the upper and lower limits (*lolims*, *uplims*, *xlolims*, *xuplims*) now
point in the correct direction.

* The Sphinx extensions `ipython_directive` and
`ipython_console_highlighting` have been moved to the IPython
project itself. While they remain in matplotlib for this release,
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5 changes: 5 additions & 0 deletions doc/users/whats_new.rst
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Expand Up @@ -139,6 +139,11 @@ specify wedgeprops = {'linewidth':3} to specify the width of the borders of
the wedges in the pie. For more properties that the user can specify, look at
the docs for the wedge and text objects.

Fixed the direction of errorbar upper/lower limits
``````````````````````````````````````````````````
Larry Bradley fixed the :func:`~matplotlib.pyplot.errorbar` method such
that the upper and lower limits (*lolims*, *uplims*, *xlolims*,
*xuplims*) now point in the correct direction.

Date handling
-------------
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53 changes: 53 additions & 0 deletions examples/statistics/errorbar_limits.py
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@@ -0,0 +1,53 @@
"""
Demo of the errorbar function, including upper and lower limits
"""
import numpy as np
import matplotlib.pyplot as plt

# example data
x = np.arange(0.5, 5.5, 0.5)
y = np.exp(-x)
xerr = 0.1
yerr = 0.2
ls = 'dotted'

fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)

# standard error bars
plt.errorbar(x, y, xerr=xerr, yerr=yerr, ls=ls, color='blue')

# including upper limits
uplims = np.zeros(x.shape)
uplims[[1, 5, 9]] = True
plt.errorbar(x, y+0.5, xerr=xerr, yerr=yerr, uplims=uplims, ls=ls,
color='green')

# including lower limits
lolims = np.zeros(x.shape)
lolims[[2, 4, 8]] = True
plt.errorbar(x, y+1.0, xerr=xerr, yerr=yerr, lolims=lolims, ls=ls,
color='red')

# including upper and lower limits
plt.errorbar(x, y+1.5, marker='o', ms=8, xerr=xerr, yerr=yerr,
lolims=lolims, uplims=uplims, ls=ls, color='magenta')

# including xlower and xupper limits
xerr = 0.2
yerr = np.zeros(x.shape) + 0.2
yerr[[3, 6]] = 0.3
xlolims = lolims
xuplims = uplims
lolims = np.zeros(x.shape)
uplims = np.zeros(x.shape)
lolims[[6]] = True
uplims[[3]] = True
plt.errorbar(x, y+2.1, marker='o', ms=8, xerr=xerr, yerr=yerr,
xlolims=xlolims, xuplims=xuplims, uplims=uplims, lolims=lolims,
ls='none', mec='blue', capsize=0, color='cyan')

ax.set_xlim((0, 5.5))
ax.set_title('Errorbar upper and lower limits')
plt.show()

193 changes: 103 additions & 90 deletions lib/matplotlib/axes/_axes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2602,7 +2602,9 @@ def errorbar(self, x, y, yerr=None, xerr=None,
These arguments can be used to indicate that a value gives
only upper/lower limits. In that case a caret symbol is
used to indicate this. lims-arguments may be of the same
type as *xerr* and *yerr*.
type as *xerr* and *yerr*. To use limits with inverted
axes, :meth:`set_xlim` or :meth:`set_ylim` must be called
before :meth:`errorbar`.

*errorevery*: positive integer
subsamples the errorbars. e.g., if everyerror=5, errorbars for
Expand Down Expand Up @@ -2682,16 +2684,12 @@ def errorbar(self, x, y, yerr=None, xerr=None,
if elinewidth:
lines_kw['linewidth'] = elinewidth
else:
if 'linewidth' in kwargs:
lines_kw['linewidth'] = kwargs['linewidth']
if 'lw' in kwargs:
lines_kw['lw'] = kwargs['lw']
if 'transform' in kwargs:
lines_kw['transform'] = kwargs['transform']
if 'alpha' in kwargs:
lines_kw['alpha'] = kwargs['alpha']
if 'zorder' in kwargs:
lines_kw['zorder'] = kwargs['zorder']
for key in ('linewidth', 'lw'):
if key in kwargs:
lines_kw[key] = kwargs[key]
for key in ('transform', 'alpha', 'zorder'):
if key in kwargs:
lines_kw[key] = kwargs[key]

# arrays fine here, they are booleans and hence not units
if not iterable(lolims):
Expand Down Expand Up @@ -2727,29 +2725,21 @@ def xywhere(xs, ys, mask):
ys = [thisy for thisy, b in zip(ys, mask) if b]
return xs, ys

plot_kw = {'label': '_nolegend_'}
if capsize > 0:
plot_kw = {
'ms': 2 * capsize,
'label': '_nolegend_'}
if capthick is not None:
# 'mew' has higher priority, I believe,
# if both 'mew' and 'markeredgewidth' exists.
# So, save capthick to markeredgewidth so that
# explicitly setting mew or markeredgewidth will
# over-write capthick.
plot_kw['markeredgewidth'] = capthick
# For backwards-compat, allow explicit setting of
# 'mew' or 'markeredgewidth' to over-ride capthick.
if 'markeredgewidth' in kwargs:
plot_kw['markeredgewidth'] = kwargs['markeredgewidth']
if 'mew' in kwargs:
plot_kw['mew'] = kwargs['mew']
if 'transform' in kwargs:
plot_kw['transform'] = kwargs['transform']
if 'alpha' in kwargs:
plot_kw['alpha'] = kwargs['alpha']
if 'zorder' in kwargs:
plot_kw['zorder'] = kwargs['zorder']
plot_kw['ms'] = 2. * capsize
if capthick is not None:
# 'mew' has higher priority, I believe,
# if both 'mew' and 'markeredgewidth' exists.
# So, save capthick to markeredgewidth so that
# explicitly setting mew or markeredgewidth will
# over-write capthick.
plot_kw['markeredgewidth'] = capthick
# For backwards-compat, allow explicit setting of
# 'mew' or 'markeredgewidth' to over-ride capthick.
for key in ('markeredgewidth', 'mew', 'transform', 'alpha', 'zorder'):
if key in kwargs:
plot_kw[key] = kwargs[key]

if xerr is not None:
if (iterable(xerr) and len(xerr) == 2 and
Expand All @@ -2766,38 +2756,48 @@ def xywhere(xs, ys, mask):
right = [thisx + thiserr for (thisx, thiserr)
in cbook.safezip(x, xerr)]

yo, _ = xywhere(y, right, everymask)
lo, ro = xywhere(left, right, everymask)
barcols.append(self.hlines(yo, lo, ro, **lines_kw))
if capsize > 0:
if xlolims.any():
# can't use numpy logical indexing since left and
# y are lists
leftlo, ylo = xywhere(left, y, xlolims & everymask)

caplines.extend(
self.plot(leftlo, ylo, ls='None',
marker=mlines.CARETLEFT, **plot_kw))
xlolims = ~xlolims
leftlo, ylo = xywhere(left, y, xlolims & everymask)
caplines.extend(self.plot(leftlo, ylo, 'k|', **plot_kw))
# select points without upper/lower limits in x and
# draw normal errorbars for these points
noxlims = ~(xlolims | xuplims)
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This line deserves a comment

if noxlims.any():
yo, _ = xywhere(y, right, noxlims & everymask)
lo, ro = xywhere(left, right, noxlims & everymask)
barcols.append(self.hlines(yo, lo, ro, **lines_kw))
if capsize > 0:
caplines.extend(self.plot(lo, yo, 'k|', **plot_kw))
caplines.extend(self.plot(ro, yo, 'k|', **plot_kw))

if xlolims.any():
yo, _ = xywhere(y, right, xlolims & everymask)
lo, ro = xywhere(x, right, xlolims & everymask)
barcols.append(self.hlines(yo, lo, ro, **lines_kw))
rightup, yup = xywhere(right, y, xlolims & everymask)
if self.xaxis_inverted():
marker = mlines.CARETLEFT
else:

leftlo, ylo = xywhere(left, y, everymask)
caplines.extend(self.plot(leftlo, ylo, 'k|', **plot_kw))

if xuplims.any():

rightup, yup = xywhere(right, y, xuplims & everymask)
caplines.extend(
self.plot(rightup, yup, ls='None',
marker=mlines.CARETRIGHT, **plot_kw))
xuplims = ~xuplims
rightup, yup = xywhere(right, y, xuplims & everymask)
caplines.extend(self.plot(rightup, yup, 'k|', **plot_kw))
marker = mlines.CARETRIGHT
caplines.extend(
self.plot(rightup, yup, ls='None', marker=marker,
**plot_kw))
if capsize > 0:
xlo, ylo = xywhere(x, y, xlolims & everymask)
caplines.extend(self.plot(xlo, ylo, 'k|', **plot_kw))

if xuplims.any():
yo, _ = xywhere(y, right, xuplims & everymask)
lo, ro = xywhere(left, x, xuplims & everymask)
barcols.append(self.hlines(yo, lo, ro, **lines_kw))
leftlo, ylo = xywhere(left, y, xuplims & everymask)
if self.xaxis_inverted():
marker = mlines.CARETRIGHT
else:
rightup, yup = xywhere(right, y, everymask)
caplines.extend(self.plot(rightup, yup, 'k|', **plot_kw))
marker = mlines.CARETLEFT
caplines.extend(
self.plot(leftlo, ylo, ls='None', marker=marker,
**plot_kw))
if capsize > 0:
xup, yup = xywhere(x, y, xuplims & everymask)
caplines.extend(self.plot(xup, yup, 'k|', **plot_kw))

if yerr is not None:
if (iterable(yerr) and len(yerr) == 2 and
Expand All @@ -2814,35 +2814,48 @@ def xywhere(xs, ys, mask):
upper = [thisy + thiserr for (thisy, thiserr)
in cbook.safezip(y, yerr)]

xo, _ = xywhere(x, lower, everymask)
lo, uo = xywhere(lower, upper, everymask)
barcols.append(self.vlines(xo, lo, uo, **lines_kw))
if capsize > 0:

if lolims.any():
xlo, lowerlo = xywhere(x, lower, lolims & everymask)
caplines.extend(
self.plot(xlo, lowerlo, ls='None',
marker=mlines.CARETDOWN, **plot_kw))
lolims = ~lolims
xlo, lowerlo = xywhere(x, lower, lolims & everymask)
caplines.extend(self.plot(xlo, lowerlo, 'k_', **plot_kw))
# select points without upper/lower limits in y and
# draw normal errorbars for these points
noylims = ~(lolims | uplims)
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for consistency, this line should also get a similar comment

if noylims.any():
xo, _ = xywhere(x, lower, noylims & everymask)
lo, uo = xywhere(lower, upper, noylims & everymask)
barcols.append(self.vlines(xo, lo, uo, **lines_kw))
if capsize > 0:
caplines.extend(self.plot(xo, lo, 'k_', **plot_kw))
caplines.extend(self.plot(xo, uo, 'k_', **plot_kw))

if lolims.any():
xo, _ = xywhere(x, lower, lolims & everymask)
lo, uo = xywhere(y, upper, lolims & everymask)
barcols.append(self.vlines(xo, lo, uo, **lines_kw))
xup, upperup = xywhere(x, upper, lolims & everymask)
if self.yaxis_inverted():
marker = mlines.CARETDOWN
else:
xlo, lowerlo = xywhere(x, lower, everymask)
caplines.extend(self.plot(xlo, lowerlo, 'k_', **plot_kw))

if uplims.any():
xup, upperup = xywhere(x, upper, uplims & everymask)

caplines.extend(
self.plot(xup, upperup, ls='None',
marker=mlines.CARETUP, **plot_kw))
uplims = ~uplims
xup, upperup = xywhere(x, upper, uplims & everymask)
caplines.extend(self.plot(xup, upperup, 'k_', **plot_kw))
marker = mlines.CARETUP
caplines.extend(
self.plot(xup, upperup, ls='None', marker=marker,
**plot_kw))
if capsize > 0:
xlo, ylo = xywhere(x, y, lolims & everymask)
caplines.extend(self.plot(xlo, ylo, 'k_', **plot_kw))

if uplims.any():
xo, _ = xywhere(x, lower, uplims & everymask)
lo, uo = xywhere(lower, y, uplims & everymask)
barcols.append(self.vlines(xo, lo, uo, **lines_kw))
xlo, lowerlo = xywhere(x, lower, uplims & everymask)
if self.yaxis_inverted():
marker = mlines.CARETUP
else:
xup, upperup = xywhere(x, upper, everymask)
caplines.extend(self.plot(xup, upperup, 'k_', **plot_kw))
marker = mlines.CARETDOWN
caplines.extend(
self.plot(xlo, lowerlo, ls='None', marker=marker,
**plot_kw))
if capsize > 0:
xup, yup = xywhere(x, y, uplims & everymask)
caplines.extend(self.plot(xup, yup, 'k_', **plot_kw))

if not barsabove and fmt is not None:
l0, = self.plot(x, y, fmt, **kwargs)
Expand Down
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