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Merge pull request #16404 from jklymak/fix-add-base-symlognorm
FIX: add base kwarg to symlognor
2 parents 8451629 + fe5fdf8 commit 3a8e75e

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-18
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6 files changed

+58
-18
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‎doc/api/next_api_changes/behaviour.rst

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Original file line numberDiff line numberDiff line change
@@ -85,3 +85,11 @@ Previously, rcParams entries whose values were color-like accepted "spurious"
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extra letters or characters in the "middle" of the string, e.g. ``"(0, 1a, '0.5')"``
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would be interpreted as ``(0, 1, 0.5)``. These extra characters (including the
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internal quotes) now cause a ValueError to be raised.
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`.SymLogNorm` now has a *base* parameter
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Previously, `.SymLogNorm` had no *base* kwarg, and defaulted to ``base=np.e``
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whereas the documentation said it was ``base=10``. In preparation to make
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the default 10, calling `.SymLogNorm` without the new *base* kwarg emits a
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deprecation 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),
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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

Lines changed: 1 addition & 1 deletion
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,
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vmin=-1.0, vmax=1.0),
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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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‎lib/matplotlib/colors.py

Lines changed: 26 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1202,8 +1202,8 @@ class SymLogNorm(Normalize):
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*linthresh* allows the user to specify the size of this range
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(-*linthresh*, *linthresh*).
12041204
"""
1205-
def __init__(self, linthresh, linscale=1.0,
1206-
vmin=None, vmax=None, clip=False):
1205+
def __init__(self, linthresh, linscale=1.0, vmin=None, vmax=None,
1206+
clip=False, *, base=None):
12071207
"""
12081208
Parameters
12091209
----------
@@ -1213,14 +1213,29 @@ def __init__(self, linthresh, linscale=1.0,
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linscale : float, default: 1
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This allows the linear range (-*linthresh* to *linthresh*) to be
12151215
stretched relative to the logarithmic range. Its value is the
1216-
number of decades to use for each half of the linear range. For
1217-
example, when *linscale* == 1.0 (the default), the space used for
1218-
the positive and negative halves of the linear range will be equal
1219-
to one decade in the logarithmic range.
1216+
number of powers of *base* (decades for base 10) to use for each
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half of the linear range. For example, when *linscale* == 1.0
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(the default), the space used for the positive and negative halves
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of the linear range will be equal to a decade in the logarithmic
1220+
range if ``base=10``.
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base : float, default: None
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For v3.2 the default is the old value of ``np.e``, but that is
1223+
deprecated for v3.3 when base will default to 10. During the
1224+
transition, specify the *base* kwarg to avoid a deprecation
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warning.
12201226
"""
12211227
Normalize.__init__(self, vmin, vmax, clip)
1228+
if base is None:
1229+
self._base = np.e
1230+
cbook.warn_deprecated("3.3", message="default base will change "
1231+
"from np.e to 10. To suppress this warning specify the base "
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"kwarg.")
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else:
1234+
self._base = base
1235+
self._log_base = np.log(self._base)
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self.linthresh = float(linthresh)
1223-
self._linscale_adj = (linscale / (1.0 - np.e ** -1))
1238+
self._linscale_adj = (linscale / (1.0 - self._base ** -1))
12241239
if vmin is not None and vmax is not None:
12251240
self._transform_vmin_vmax()
12261241

@@ -1255,7 +1270,8 @@ def _transform(self, a):
12551270
with np.errstate(invalid="ignore"):
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masked = np.abs(a) > self.linthresh
12571272
sign = np.sign(a[masked])
1258-
log = (self._linscale_adj + np.log(np.abs(a[masked]) / self.linthresh))
1273+
log = (self._linscale_adj +
1274+
np.log(np.abs(a[masked]) / self.linthresh) / self._log_base)
12591275
log *= sign * self.linthresh
12601276
a[masked] = log
12611277
a[~masked] *= self._linscale_adj
@@ -1265,7 +1281,8 @@ def _inv_transform(self, a):
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"""Inverse inplace Transformation."""
12661282
masked = np.abs(a) > (self.linthresh * self._linscale_adj)
12671283
sign = np.sign(a[masked])
1268-
exp = np.exp(sign * a[masked] / self.linthresh - self._linscale_adj)
1284+
exp = np.power(self._base,
1285+
sign * a[masked] / self.linthresh - self._linscale_adj)
12691286
exp *= sign * self.linthresh
12701287
a[masked] = exp
12711288
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
@@ -398,7 +398,7 @@ def test_SymLogNorm():
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"""
399399
Test SymLogNorm behavior
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"""
401-
norm = mcolors.SymLogNorm(3, vmax=5, linscale=1.2)
401+
norm = mcolors.SymLogNorm(3, vmax=5, linscale=1.2, base=np.e)
402402
vals = np.array([-30, -1, 2, 6], dtype=float)
403403
normed_vals = norm(vals)
404404
expected = [0., 0.53980074, 0.826991, 1.02758204]
@@ -408,16 +408,30 @@ def test_SymLogNorm():
408408
_mask_tester(norm, vals)
409409

410410
# Ensure that specifying vmin returns the same result as above
411-
norm = mcolors.SymLogNorm(3, vmin=-30, vmax=5, linscale=1.2)
411+
norm = mcolors.SymLogNorm(3, vmin=-30, vmax=5, linscale=1.2, base=np.e)
412412
normed_vals = norm(vals)
413413
assert_array_almost_equal(normed_vals, expected)
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415+
# test something more easily checked.
416+
norm = mcolors.SymLogNorm(1, vmin=-np.e**3, vmax=np.e**3, base=np.e)
417+
nn = norm([-np.e**3, -np.e**2, -np.e**1, -1,
418+
0, 1, np.e**1, np.e**2, np.e**3])
419+
xx = np.array([0., 0.109123, 0.218246, 0.32737, 0.5, 0.67263,
420+
0.781754, 0.890877, 1.])
421+
assert_array_almost_equal(nn, xx)
422+
norm = mcolors.SymLogNorm(1, vmin=-10**3, vmax=10**3, base=10)
423+
nn = norm([-10**3, -10**2, -10**1, -1,
424+
0, 1, 10**1, 10**2, 10**3])
425+
xx = np.array([0., 0.121622, 0.243243, 0.364865, 0.5, 0.635135,
426+
0.756757, 0.878378, 1.])
427+
assert_array_almost_equal(nn, xx)
428+
415429

416430
def test_SymLogNorm_colorbar():
417431
"""
418432
Test un-called SymLogNorm in a colorbar.
419433
"""
420-
norm = mcolors.SymLogNorm(0.1, vmin=-1, vmax=1, linscale=1)
434+
norm = mcolors.SymLogNorm(0.1, vmin=-1, vmax=1, linscale=1, base=np.e)
421435
fig = plt.figure()
422436
mcolorbar.ColorbarBase(fig.add_subplot(111), norm=norm)
423437
plt.close(fig)
@@ -428,7 +442,7 @@ def test_SymLogNorm_single_zero():
428442
Test SymLogNorm to ensure it is not adding sub-ticks to zero label
429443
"""
430444
fig = plt.figure()
431-
norm = mcolors.SymLogNorm(1e-5, vmin=-1, vmax=1)
445+
norm = mcolors.SymLogNorm(1e-5, vmin=-1, vmax=1, base=np.e)
432446
cbar = mcolorbar.ColorbarBase(fig.add_subplot(111), norm=norm)
433447
ticks = cbar.get_ticks()
434448
assert sum(ticks == 0) == 1
@@ -905,9 +919,10 @@ def __add__(self, other):
905919
mydata = data.view(MyArray)
906920

907921
for norm in [mcolors.Normalize(), mcolors.LogNorm(),
908-
mcolors.SymLogNorm(3, vmax=5, linscale=1),
922+
mcolors.SymLogNorm(3, vmax=5, linscale=1, base=np.e),
909923
mcolors.Normalize(vmin=mydata.min(), vmax=mydata.max()),
910-
mcolors.SymLogNorm(3, vmin=mydata.min(), vmax=mydata.max()),
924+
mcolors.SymLogNorm(3, vmin=mydata.min(), vmax=mydata.max(),
925+
base=np.e),
911926
mcolors.PowerNorm(1)]:
912927
assert_array_equal(norm(mydata), norm(data))
913928
fig, ax = plt.subplots()

‎tutorials/colors/colormapnorms.py

Lines changed: 1 addition & 1 deletion
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@@ -98,7 +98,7 @@
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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')
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