In LogTransform, clip after log, not before.

anntzer · anntzer · commit 33efc48a4e56 · 2017-10-19T01:43:27.000-07:00
When clipping before taking the log, the clip value in the output array
cannot be beyond log(epsilon) ~ -300.  When clipping after taking the
log, the clip value can be much further (see comments regarding choice
of value).

This allows setting the default nonpos mode back to "clip".
diff --git a/lib/matplotlib/axes/_axes.py b/lib/matplotlib/axes/_axes.py
@@ -1618,6 +1618,7 @@ def semilogx(self, *args, **kwargs):
             self.cla()
         d = {'basex': kwargs.pop('basex', 10),
              'subsx': kwargs.pop('subsx', None),
+             'nonposx': kwargs.pop('nonposx', 'clip'),
              }
 
         self.set_xscale('log', **d)
@@ -1673,6 +1674,7 @@ def semilogy(self, *args, **kwargs):
             self.cla()
         d = {'basey': kwargs.pop('basey', 10),
              'subsy': kwargs.pop('subsy', None),
+             'nonposy': kwargs.pop('nonposy', 'mask'),
              }
         self.set_yscale('log', **d)
         b = self._hold
@@ -2851,11 +2853,6 @@ def errorbar(self, x, y, yerr=None, xerr=None,
             Valid kwargs for the marker properties are
 
             %(Line2D)s
-
-        Notes
-        -----
-        Error bars with negative values will not be shown when plotted on a
-        logarithmic axis.
         """
         kwargs = cbook.normalize_kwargs(kwargs, _alias_map)
         # anything that comes in as 'None', drop so the default thing
diff --git a/lib/matplotlib/axes/_base.py b/lib/matplotlib/axes/_base.py
@@ -2970,10 +2970,8 @@ def set_xscale(self, value, **kwargs):
 
         matplotlib.scale.LogisticTransform : logit transform
         """
-        # If the scale is being set to log, mask nonposx to prevent headaches
-        # around zero
-        if value.lower() == 'log' and 'nonposx' not in kwargs:
-            kwargs['nonposx'] = 'mask'
+        if value.lower() == "log":  # Avoid headaches around zero.
+            kwargs.setdefault("nonposx", "clip")
 
         g = self.get_shared_x_axes()
         for ax in g.get_siblings(self):
@@ -3292,10 +3290,8 @@ def set_yscale(self, value, **kwargs):
 
         matplotlib.scale.LogisticTransform : logit transform
         """
-        # If the scale is being set to log, mask nonposy to prevent headaches
-        # around zero
-        if value.lower() == 'log' and 'nonposy' not in kwargs:
-            kwargs['nonposy'] = 'mask'
+        if value.lower() == "log":  # Avoid headaches around zero.
+            kwargs.setdefault("nonposy", "clip")
 
         g = self.get_shared_y_axes()
         for ax in g.get_siblings(self):
diff --git a/lib/matplotlib/scale.py b/lib/matplotlib/scale.py
@@ -92,15 +92,19 @@ class LogTransformBase(Transform):
 
     def __init__(self, nonpos):
         Transform.__init__(self)
-        if nonpos == 'mask':
-            self._fill_value = np.nan
-        else:
-            self._fill_value = 1e-300
+        self._clip = {"clip": True, "mask": False}[nonpos]
 
     def transform_non_affine(self, a):
-        with np.errstate(invalid="ignore"):
-            a = np.where(a <= 0, self._fill_value, a)
-        return np.divide(np.log(a, out=a), np.log(self.base), out=a)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            out = np.log(a)
+        out /= np.log(self.base)
+        if self._clip:
+            # SVG spec says that conforming viewers must support values up
+            # to 3.4e38 (C float); however experiments suggest that Inkscape
+            # (which uses cairo for rendering) runs into cairo's 24-bit limit
+            # (which is apparently shared by Agg).  So pick a smaller value.
+            out[a <= 0] = -2 ** 23
+        return out
 
 
 class InvertedLogTransformBase(Transform):
@@ -432,18 +436,17 @@ class LogitTransform(Transform):
 
     def __init__(self, nonpos):
         Transform.__init__(self)
-        if nonpos == 'mask':
-            self._fill_value = np.nan
-        else:
-            self._fill_value = 1e-300
         self._nonpos = nonpos
+        self._clip = {"clip": True, "mask": False}[nonpos]
 
     def transform_non_affine(self, a):
         """logit transform (base 10), masked or clipped"""
-        with np.errstate(invalid="ignore"):
-            a = np.select(
-                [a <= 0, a >= 1], [self._fill_value, 1 - self._fill_value], a)
-        return np.log10(a / (1 - a))
+        with np.errstate(divide="ignore", invalid="ignore"):
+            out = np.log10(a / (1 - a))
+        if self._clip:  # See LogTransform for choice of clip value.
+            out[a <= 0] = -2 ** 23
+            out[1 <= a] = 2 ** 23
+        return out
 
     def inverted(self):
         return LogisticTransform(self._nonpos)
