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Commit 7bd5d64

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tacaswelltacaswell
authored
Merge pull request #9477 from anntzer/clip-log-further
API: In LogTransform, clip after log, not before.
2 parents 73da078 + e3b777f commit 7bd5d64
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‎doc/api/api_changes.rst

Copy file name to clipboardExpand all lines: doc/api/api_changes.rst
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Original file line numberDiff line numberDiff line change
@@ -10,9 +10,24 @@ out what caused the breakage and how to fix it by updating your code.
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For new features that were added to Matplotlib, please see
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:ref:`whats-new`.
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API Changes in 2.1.1
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====================
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Default behavior of log scales reverted to clip <= 0 values
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-----------------------------------------------------------
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The change it 2.1.0 to mask in logscale by default had more disruptive
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changes than anticipated and has been reverted, however the clipping is now
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done in a way that fixes the issues that motivated changing the default behavior
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to ``'mask'``.
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As a side effect of this change, error bars which go negative now work as expected
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on log scales.
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API Changes in 2.1.0
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====================
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Default behavior of log scales changed to mask <= 0 values
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----------------------------------------------------------
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‎lib/matplotlib/axes/_axes.py

Copy file name to clipboardExpand all lines: lib/matplotlib/axes/_axes.py
-7Lines changed: 0 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1555,11 +1555,9 @@ def loglog(self, *args, **kwargs):
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dx = {'basex': kwargs.pop('basex', 10),
15571557
'subsx': kwargs.pop('subsx', None),
1558-
'nonposx': kwargs.pop('nonposx', 'mask'),
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}
15601559
dy = {'basey': kwargs.pop('basey', 10),
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'subsy': kwargs.pop('subsy', None),
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'nonposy': kwargs.pop('nonposy', 'mask'),
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}
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15651563
self.set_xscale('log', **dx)
@@ -2850,11 +2848,6 @@ def errorbar(self, x, y, yerr=None, xerr=None,
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Valid kwargs for the marker properties are
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%(Line2D)s
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Notes
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-----
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Error bars with negative values will not be shown when plotted on a
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logarithmic axis.
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"""
28592852
kwargs = cbook.normalize_kwargs(kwargs, _alias_map)
28602853
# anything that comes in as 'None', drop so the default thing

‎lib/matplotlib/axes/_base.py

Copy file name to clipboardExpand all lines: lib/matplotlib/axes/_base.py
-10Lines changed: 0 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -2971,11 +2971,6 @@ def set_xscale(self, value, **kwargs):
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matplotlib.scale.LogisticTransform : logit transform
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"""
2974-
# If the scale is being set to log, mask nonposx to prevent headaches
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# around zero
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if value.lower() == 'log' and 'nonposx' not in kwargs:
2977-
kwargs['nonposx'] = 'mask'
2978-
29792974
g = self.get_shared_x_axes()
29802975
for ax in g.get_siblings(self):
29812976
ax.xaxis._set_scale(value, **kwargs)
@@ -3293,11 +3288,6 @@ def set_yscale(self, value, **kwargs):
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32943289
matplotlib.scale.LogisticTransform : logit transform
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"""
3296-
# If the scale is being set to log, mask nonposy to prevent headaches
3297-
# around zero
3298-
if value.lower() == 'log' and 'nonposy' not in kwargs:
3299-
kwargs['nonposy'] = 'mask'
3300-
33013291
g = self.get_shared_y_axes()
33023292
for ax in g.get_siblings(self):
33033293
ax.yaxis._set_scale(value, **kwargs)

‎lib/matplotlib/scale.py

Copy file name to clipboardExpand all lines: lib/matplotlib/scale.py
+31-17Lines changed: 31 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -92,15 +92,24 @@ class LogTransformBase(Transform):
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def __init__(self, nonpos):
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Transform.__init__(self)
95-
if nonpos == 'mask':
96-
self._fill_value = np.nan
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else:
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self._fill_value = 1e-300
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self._clip = {"clip": True, "mask": False}[nonpos]
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10097
def transform_non_affine(self, a):
101-
with np.errstate(invalid="ignore"):
102-
a = np.where(a <= 0, self._fill_value, a)
103-
return np.divide(np.log(a, out=a), np.log(self.base), out=a)
98+
with np.errstate(divide="ignore", invalid="ignore"):
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out = np.log(a)
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out /= np.log(self.base)
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if self._clip:
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# SVG spec says that conforming viewers must support values up
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# to 3.4e38 (C float); however experiments suggest that Inkscape
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# (which uses cairo for rendering) runs into cairo's 24-bit limit
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# (which is apparently shared by Agg).
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# Ghostscript (used for pdf rendering appears to overflow even
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# earlier, with the max value around 2 ** 15 for the tests to pass.
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# On the other hand, in practice, we want to clip beyond
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# np.log10(np.nextafter(0, 1)) ~ -323
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# so 1000 seems safe.
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out[a <= 0] = -1000
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return out
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106115
class InvertedLogTransformBase(Transform):
@@ -220,11 +229,17 @@ def __init__(self, axis, **kwargs):
220229
if axis.axis_name == 'x':
221230
base = kwargs.pop('basex', 10.0)
222231
subs = kwargs.pop('subsx', None)
223-
nonpos = kwargs.pop('nonposx', 'mask')
232+
nonpos = kwargs.pop('nonposx', 'clip')
224233
else:
225234
base = kwargs.pop('basey', 10.0)
226235
subs = kwargs.pop('subsy', None)
227-
nonpos = kwargs.pop('nonposy', 'mask')
236+
nonpos = kwargs.pop('nonposy', 'clip')
237+
238+
if len(kwargs):
239+
raise ValueError(("provided too many kwargs, can only pass "
240+
"{'basex', 'subsx', nonposx'} or "
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"{'basey', 'subsy', nonposy'}. You passed ") +
242+
"{!r}".format(kwargs))
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229244
if nonpos not in ['mask', 'clip']:
230245
raise ValueError("nonposx, nonposy kwarg must be 'mask' or 'clip'")
@@ -432,18 +447,17 @@ class LogitTransform(Transform):
432447

433448
def __init__(self, nonpos):
434449
Transform.__init__(self)
435-
if nonpos == 'mask':
436-
self._fill_value = np.nan
437-
else:
438-
self._fill_value = 1e-300
439450
self._nonpos = nonpos
451+
self._clip = {"clip": True, "mask": False}[nonpos]
440452

441453
def transform_non_affine(self, a):
442454
"""logit transform (base 10), masked or clipped"""
443-
with np.errstate(invalid="ignore"):
444-
a = np.select(
445-
[a <= 0, a >= 1], [self._fill_value, 1 - self._fill_value], a)
446-
return np.log10(a / (1 - a))
455+
with np.errstate(divide="ignore", invalid="ignore"):
456+
out = np.log10(a / (1 - a))
457+
if self._clip: # See LogTransform for choice of clip value.
458+
out[a <= 0] = -1000
459+
out[1 <= a] = 1000
460+
return out
447461

448462
def inverted(self):
449463
return LogisticTransform(self._nonpos)

‎lib/matplotlib/tests/baseline_images/test_axes/log_scales.png

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‎lib/matplotlib/tests/baseline_images/test_axes/log_scales.svg

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+2-1Lines changed: 2 additions & 1 deletion
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‎lib/matplotlib/tests/baseline_images/test_path/semi_log_with_zero.png

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-4.45 KB
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‎lib/matplotlib/tests/baseline_images/test_scale/logscale_mask.png

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-2.6 KB
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‎lib/matplotlib/tests/baseline_images/test_scale/logscale_nonpos_values.png

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16.6 KB
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‎lib/matplotlib/tests/test_path.py

Copy file name to clipboardExpand all lines: lib/matplotlib/tests/test_path.py
+4-2Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -87,13 +87,15 @@ def test_path_clipping():
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xy, facecolor='none', edgecolor='red', closed=True))
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8989

90-
@image_comparison(baseline_images=['semi_log_with_zero'], extensions=['png'])
90+
@image_comparison(baseline_images=['semi_log_with_zero'], extensions=['png'],
91+
style='mpl20')
9192
def test_log_transform_with_zero():
9293
x = np.arange(-10, 10)
9394
y = (1.0 - 1.0/(x**2+1))**20
9495

9596
fig, ax = plt.subplots()
96-
ax.semilogy(x, y, "-o", lw=15)
97+
ax.semilogy(x, y, "-o", lw=15, markeredgecolor='k')
98+
ax.set_ylim(1e-7, 1)
9799
ax.grid(True)
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99101

‎lib/matplotlib/tests/test_scale.py

Copy file name to clipboardExpand all lines: lib/matplotlib/tests/test_scale.py
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Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@
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import matplotlib.pyplot as plt
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import numpy as np
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import io
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import pytest
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89

910
@image_comparison(baseline_images=['log_scales'], remove_text=True)
@@ -65,3 +66,36 @@ def test_logscale_mask():
6566
ax.plot(np.exp(-xs**2))
6667
fig.canvas.draw()
6768
ax.set(yscale="log")
69+
70+
71+
def test_extra_kwargs_raise():
72+
fig, ax = plt.subplots()
73+
with pytest.raises(ValueError):
74+
ax.set_yscale('log', nonpos='mask')
75+
76+
77+
@image_comparison(baseline_images=['logscale_nonpos_values'], remove_text=True,
78+
extensions=['png'], style='mpl20')
79+
def test_logscale_nonpos_values():
80+
np.random.seed(19680801)
81+
xs = np.random.normal(size=int(1e3))
82+
fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2)
83+
ax1.hist(xs, range=(-5, 5), bins=10)
84+
ax1.set_yscale('log')
85+
ax2.hist(xs, range=(-5, 5), bins=10)
86+
ax2.set_yscale('log', nonposy='mask')
87+
88+
xdata = np.arange(0, 10, 0.01)
89+
ydata = np.exp(-xdata)
90+
edata = 0.2*(10-xdata)*np.cos(5*xdata)*np.exp(-xdata)
91+
92+
ax3.fill_between(xdata, ydata - edata, ydata + edata)
93+
ax3.set_yscale('log')
94+
95+
x = np.logspace(-1, 1)
96+
y = x ** 3
97+
yerr = x**2
98+
ax4.errorbar(x, y, yerr=yerr)
99+
100+
ax4.set_yscale('log')
101+
ax4.set_xscale('log')

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