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Commitbebc51a

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Merge pull request#16541 from tacaswell/auto-backport-of-pr-16404-on-v3.2.x
Merge pull request#16404 from jklymak/fix-add-base-symlognorm
2 parentsd15be69 +86c7e6c commitbebc51a

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6 files changed

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-26
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6 files changed

+77
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‎doc/api/prev_api_changes/api_changes_3.2.0/behavior.rst

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -307,3 +307,15 @@ mplot3d auto-registration
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longer necessary to import mplot3d to create 3d axes with ::
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ax = fig.add_subplot(111, projection="3d")
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`.SymLogNorm` now has a *base* parameter
312+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Previously, `.SymLogNorm` had no *base* keyword argument and the base was
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hard-coded to ``base=np.e``. This was inconsistent with the default
316+
behavior of `.SymLogScale` (which defaults to ``base=10``) and the use
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of the word "decade" in the documentation.
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In preparation for changing the default base to 10, calling
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`.SymLogNorm` without the new *base* kwarg emits a deprecation
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warning.

‎examples/userdemo/colormap_normalizations.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@
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pcm=ax[0].pcolormesh(X,Y,Z1,
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norm=colors.SymLogNorm(linthresh=0.03,linscale=0.03,
72-
vmin=-1.0,vmax=1.0),
72+
vmin=-1.0,vmax=1.0,base=10),
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cmap='RdBu_r')
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fig.colorbar(pcm,ax=ax[0],extend='both')
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‎examples/userdemo/colormap_normalizations_symlognorm.py

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Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@
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pcm=ax[0].pcolormesh(X,Y,Z,
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norm=colors.SymLogNorm(linthresh=0.03,linscale=0.03,
32-
vmin=-1.0,vmax=1.0),
32+
vmin=-1.0,vmax=1.0,base=10),
3333
cmap='RdBu_r')
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fig.colorbar(pcm,ax=ax[0],extend='both')
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‎lib/matplotlib/colors.py

Lines changed: 41 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1209,25 +1209,47 @@ class SymLogNorm(Normalize):
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*linthresh* allows the user to specify the size of this range
12101210
(-*linthresh*, *linthresh*).
12111211
"""
1212-
def__init__(self,linthresh,linscale=1.0,
1213-
vmin=None,vmax=None,clip=False):
1212+
def__init__(self,linthresh,linscale=1.0,vmin=None,vmax=None,
1213+
clip=False,*,base=None):
12141214
"""
1215-
*linthresh*:
1216-
The range within which the plot is linear (to
1217-
avoid having the plot go to infinity around zero).
1218-
1219-
*linscale*:
1220-
This allows the linear range (-*linthresh* to *linthresh*)
1221-
to be stretched relative to the logarithmic range. Its
1222-
value is the number of decades to use for each half of the
1223-
linear range. For example, when *linscale* == 1.0 (the
1224-
default), the space used for the positive and negative
1225-
halves of the linear range will be equal to one decade in
1226-
the logarithmic range. Defaults to 1.
1215+
Parameters
1216+
----------
1217+
linthresh : float
1218+
The range within which the plot is linear (to avoid having the plot
1219+
go to infinity around zero).
1220+
linscale : float, default: 1
1221+
This allows the linear range (-*linthresh* to *linthresh*)
1222+
to be stretched relative to the logarithmic range. Its
1223+
value is the number of powers of *base* to use for each
1224+
half of the linear range.
1225+
1226+
For example, when *linscale* == 1.0 (the default) and
1227+
``base=10``, then space used for the positive and negative
1228+
halves of the linear range will be equal to a decade in
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the logarithmic.
1230+
1231+
base : float, default: None
1232+
If not given, defaults to ``np.e`` (consistent with prior
1233+
behavior) and warns.
1234+
1235+
In v3.3 the default value will change to 10 to be consistent with
1236+
`.SymLogNorm`.
1237+
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To suppress the warning pass *base* as a keyword argument.
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12271240
"""
12281241
Normalize.__init__(self,vmin,vmax,clip)
1242+
ifbaseisNone:
1243+
self._base=np.e
1244+
cbook.warn_deprecated("3.3",message="default base may change "
1245+
"from np.e to 10. To suppress this warning specify the base "
1246+
"keyword argument.")
1247+
else:
1248+
self._base=base
1249+
self._log_base=np.log(self._base)
1250+
12291251
self.linthresh=float(linthresh)
1230-
self._linscale_adj= (linscale/ (1.0-np.e**-1))
1252+
self._linscale_adj= (linscale/ (1.0-self._base**-1))
12311253
ifvminisnotNoneandvmaxisnotNone:
12321254
self._transform_vmin_vmax()
12331255

@@ -1262,7 +1284,8 @@ def _transform(self, a):
12621284
withnp.errstate(invalid="ignore"):
12631285
masked=np.abs(a)>self.linthresh
12641286
sign=np.sign(a[masked])
1265-
log= (self._linscale_adj+np.log(np.abs(a[masked])/self.linthresh))
1287+
log= (self._linscale_adj+
1288+
np.log(np.abs(a[masked])/self.linthresh)/self._log_base)
12661289
log*=sign*self.linthresh
12671290
a[masked]=log
12681291
a[~masked]*=self._linscale_adj
@@ -1272,7 +1295,8 @@ def _inv_transform(self, a):
12721295
"""Inverse inplace Transformation."""
12731296
masked=np.abs(a)> (self.linthresh*self._linscale_adj)
12741297
sign=np.sign(a[masked])
1275-
exp=np.exp(sign*a[masked]/self.linthresh-self._linscale_adj)
1298+
exp=np.power(self._base,
1299+
sign*a[masked]/self.linthresh-self._linscale_adj)
12761300
exp*=sign*self.linthresh
12771301
a[masked]=exp
12781302
a[~masked]/=self._linscale_adj

‎lib/matplotlib/tests/test_colors.py

Lines changed: 21 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -388,7 +388,7 @@ def test_SymLogNorm():
388388
"""
389389
Test SymLogNorm behavior
390390
"""
391-
norm=mcolors.SymLogNorm(3,vmax=5,linscale=1.2)
391+
norm=mcolors.SymLogNorm(3,vmax=5,linscale=1.2,base=np.e)
392392
vals=np.array([-30,-1,2,6],dtype=float)
393393
normed_vals=norm(vals)
394394
expected= [0.,0.53980074,0.826991,1.02758204]
@@ -398,16 +398,30 @@ def test_SymLogNorm():
398398
_mask_tester(norm,vals)
399399

400400
# Ensure that specifying vmin returns the same result as above
401-
norm=mcolors.SymLogNorm(3,vmin=-30,vmax=5,linscale=1.2)
401+
norm=mcolors.SymLogNorm(3,vmin=-30,vmax=5,linscale=1.2,base=np.e)
402402
normed_vals=norm(vals)
403403
assert_array_almost_equal(normed_vals,expected)
404404

405+
# test something more easily checked.
406+
norm=mcolors.SymLogNorm(1,vmin=-np.e**3,vmax=np.e**3,base=np.e)
407+
nn=norm([-np.e**3,-np.e**2,-np.e**1,-1,
408+
0,1,np.e**1,np.e**2,np.e**3])
409+
xx=np.array([0.,0.109123,0.218246,0.32737,0.5,0.67263,
410+
0.781754,0.890877,1.])
411+
assert_array_almost_equal(nn,xx)
412+
norm=mcolors.SymLogNorm(1,vmin=-10**3,vmax=10**3,base=10)
413+
nn=norm([-10**3,-10**2,-10**1,-1,
414+
0,1,10**1,10**2,10**3])
415+
xx=np.array([0.,0.121622,0.243243,0.364865,0.5,0.635135,
416+
0.756757,0.878378,1.])
417+
assert_array_almost_equal(nn,xx)
418+
405419

406420
deftest_SymLogNorm_colorbar():
407421
"""
408422
Test un-called SymLogNorm in a colorbar.
409423
"""
410-
norm=mcolors.SymLogNorm(0.1,vmin=-1,vmax=1,linscale=1)
424+
norm=mcolors.SymLogNorm(0.1,vmin=-1,vmax=1,linscale=1,base=np.e)
411425
fig=plt.figure()
412426
mcolorbar.ColorbarBase(fig.add_subplot(111),norm=norm)
413427
plt.close(fig)
@@ -418,7 +432,7 @@ def test_SymLogNorm_single_zero():
418432
Test SymLogNorm to ensure it is not adding sub-ticks to zero label
419433
"""
420434
fig=plt.figure()
421-
norm=mcolors.SymLogNorm(1e-5,vmin=-1,vmax=1)
435+
norm=mcolors.SymLogNorm(1e-5,vmin=-1,vmax=1,base=np.e)
422436
cbar=mcolorbar.ColorbarBase(fig.add_subplot(111),norm=norm)
423437
ticks=cbar.get_ticks()
424438
assertsum(ticks==0)==1
@@ -895,9 +909,10 @@ def __add__(self, other):
895909
mydata=data.view(MyArray)
896910

897911
fornormin [mcolors.Normalize(),mcolors.LogNorm(),
898-
mcolors.SymLogNorm(3,vmax=5,linscale=1),
912+
mcolors.SymLogNorm(3,vmax=5,linscale=1,base=np.e),
899913
mcolors.Normalize(vmin=mydata.min(),vmax=mydata.max()),
900-
mcolors.SymLogNorm(3,vmin=mydata.min(),vmax=mydata.max()),
914+
mcolors.SymLogNorm(3,vmin=mydata.min(),vmax=mydata.max(),
915+
base=np.e),
901916
mcolors.PowerNorm(1)]:
902917
assert_array_equal(norm(mydata),norm(data))
903918
fig,ax=plt.subplots()

‎tutorials/colors/colormapnorms.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -98,7 +98,7 @@
9898

9999
pcm=ax[0].pcolormesh(X,Y,Z,
100100
norm=colors.SymLogNorm(linthresh=0.03,linscale=0.03,
101-
vmin=-1.0,vmax=1.0),
101+
vmin=-1.0,vmax=1.0,base=10),
102102
cmap='RdBu_r')
103103
fig.colorbar(pcm,ax=ax[0],extend='both')
104104

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