from __future__ import (absolute_import, division, print_function, unicode_literals) from matplotlib.externals import six import numpy as np from numpy import ma from matplotlib.cbook import dedent from matplotlib.ticker import (NullFormatter, ScalarFormatter, LogFormatterMathtext, LogitFormatter) from matplotlib.ticker import (NullLocator, LogLocator, AutoLocator, SymmetricalLogLocator, LogitLocator) from matplotlib.transforms import Transform, IdentityTransform from matplotlib import docstring class ScaleBase(object): """ The base class for all scales. Scales are separable transformations, working on a single dimension. Any subclasses will want to override: - :attr:`name` - :meth:`get_transform` - :meth:`set_default_locators_and_formatters` And optionally: - :meth:`limit_range_for_scale` """ def get_transform(self): """ Return the :class:`~matplotlib.transforms.Transform` object associated with this scale. """ raise NotImplementedError() def set_default_locators_and_formatters(self, axis): """ Set the :class:`~matplotlib.ticker.Locator` and :class:`~matplotlib.ticker.Formatter` objects on the given axis to match this scale. """ raise NotImplementedError() def limit_range_for_scale(self, vmin, vmax, minpos): """ Returns the range *vmin*, *vmax*, possibly limited to the domain supported by this scale. *minpos* should be the minimum positive value in the data. This is used by log scales to determine a minimum value. """ return vmin, vmax class LinearScale(ScaleBase): """ The default linear scale. """ name = 'linear' def __init__(self, axis, **kwargs): pass def set_default_locators_and_formatters(self, axis): """ Set the locators and formatters to reasonable defaults for linear scaling. """ axis.set_major_locator(AutoLocator()) axis.set_major_formatter(ScalarFormatter()) axis.set_minor_locator(NullLocator()) axis.set_minor_formatter(NullFormatter()) def get_transform(self): """ The transform for linear scaling is just the :class:`~matplotlib.transforms.IdentityTransform`. """ return IdentityTransform() def _mask_non_positives(a): """ Return a Numpy array where all non-positive values are replaced with NaNs. If there are no non-positive values, the original array is returned. """ mask = a <= 0.0 if mask.any(): return np.where(mask, np.nan, a) return a def _clip_non_positives(a): a = np.array(a, float) a[a <= 0.0] = 1e-300 return a class LogTransformBase(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True def __init__(self, nonpos): Transform.__init__(self) if nonpos == 'mask': self._handle_nonpos = _mask_non_positives else: self._handle_nonpos = _clip_non_positives class Log10Transform(LogTransformBase): base = 10.0 def transform_non_affine(self, a): a = self._handle_nonpos(a * 10.0) return np.log10(a) def inverted(self): return InvertedLog10Transform() class InvertedLog10Transform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True base = 10.0 def transform_non_affine(self, a): return ma.power(10.0, a) / 10.0 def inverted(self): return Log10Transform() class Log2Transform(LogTransformBase): base = 2.0 def transform_non_affine(self, a): a = self._handle_nonpos(a * 2.0) return np.log2(a) def inverted(self): return InvertedLog2Transform() class InvertedLog2Transform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True base = 2.0 def transform_non_affine(self, a): return ma.power(2.0, a) / 2.0 def inverted(self): return Log2Transform() class NaturalLogTransform(LogTransformBase): base = np.e def transform_non_affine(self, a): a = self._handle_nonpos(a * np.e) return np.log(a) def inverted(self): return InvertedNaturalLogTransform() class InvertedNaturalLogTransform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True base = np.e def transform_non_affine(self, a): return ma.power(np.e, a) / np.e def inverted(self): return NaturalLogTransform() class LogTransform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True def __init__(self, base, nonpos): Transform.__init__(self) self.base = base if nonpos == 'mask': self._handle_nonpos = _mask_non_positives else: self._handle_nonpos = _clip_non_positives def transform_non_affine(self, a): a = self._handle_nonpos(a * self.base) return np.log(a) / np.log(self.base) def inverted(self): return InvertedLogTransform(self.base) class InvertedLogTransform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True def __init__(self, base): Transform.__init__(self) self.base = base def transform_non_affine(self, a): return ma.power(self.base, a) / self.base def inverted(self): return LogTransform(self.base) class LogScale(ScaleBase): """ A standard logarithmic scale. Care is taken so non-positive values are not plotted. For computational efficiency (to push as much as possible to Numpy C code in the common cases), this scale provides different transforms depending on the base of the logarithm: - base 10 (:class:`Log10Transform`) - base 2 (:class:`Log2Transform`) - base e (:class:`NaturalLogTransform`) - arbitrary base (:class:`LogTransform`) """ name = 'log' # compatibility shim LogTransformBase = LogTransformBase Log10Transform = Log10Transform InvertedLog10Transform = InvertedLog10Transform Log2Transform = Log2Transform InvertedLog2Transform = InvertedLog2Transform NaturalLogTransform = NaturalLogTransform InvertedNaturalLogTransform = InvertedNaturalLogTransform LogTransform = LogTransform InvertedLogTransform = InvertedLogTransform def __init__(self, axis, **kwargs): """ *basex*/*basey*: The base of the logarithm *nonposx*/*nonposy*: ['mask' | 'clip' ] non-positive values in *x* or *y* can be masked as invalid, or clipped to a very small positive number *subsx*/*subsy*: Where to place the subticks between each major tick. Should be a sequence of integers. For example, in a log10 scale: ``[2, 3, 4, 5, 6, 7, 8, 9]`` will place 8 logarithmically spaced minor ticks between each major tick. """ if axis.axis_name == 'x': base = kwargs.pop('basex', 10.0) subs = kwargs.pop('subsx', None) nonpos = kwargs.pop('nonposx', 'mask') else: base = kwargs.pop('basey', 10.0) subs = kwargs.pop('subsy', None) nonpos = kwargs.pop('nonposy', 'mask') if nonpos not in ['mask', 'clip']: raise ValueError("nonposx, nonposy kwarg must be 'mask' or 'clip'") if base == 10.0: self._transform = self.Log10Transform(nonpos) elif base == 2.0: self._transform = self.Log2Transform(nonpos) elif base == np.e: self._transform = self.NaturalLogTransform(nonpos) else: self._transform = self.LogTransform(base, nonpos) self.base = base self.subs = subs def set_default_locators_and_formatters(self, axis): """ Set the locators and formatters to specialized versions for log scaling. """ axis.set_major_locator(LogLocator(self.base)) axis.set_major_formatter(LogFormatterMathtext(self.base)) axis.set_minor_locator(LogLocator(self.base, self.subs)) axis.set_minor_formatter(NullFormatter()) def get_transform(self): """ Return a :class:`~matplotlib.transforms.Transform` instance appropriate for the given logarithm base. """ return self._transform def limit_range_for_scale(self, vmin, vmax, minpos): """ Limit the domain to positive values. """ return (vmin <= 0.0 and minpos or vmin, vmax <= 0.0 and minpos or vmax) class SymmetricalLogTransform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True def __init__(self, base, linthresh, linscale): Transform.__init__(self) self.base = base self.linthresh = linthresh self.linscale = linscale self._linscale_adj = (linscale / (1.0 - self.base ** -1)) self._log_base = np.log(base) def transform_non_affine(self, a): sign = np.sign(a) masked = ma.masked_inside(a, -self.linthresh, self.linthresh, copy=False) log = sign * self.linthresh * ( self._linscale_adj + ma.log(np.abs(masked) / self.linthresh) / self._log_base) if masked.mask.any(): return ma.where(masked.mask, a * self._linscale_adj, log) else: return log def inverted(self): return InvertedSymmetricalLogTransform(self.base, self.linthresh, self.linscale) class InvertedSymmetricalLogTransform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True def __init__(self, base, linthresh, linscale): Transform.__init__(self) symlog = SymmetricalLogTransform(base, linthresh, linscale) self.base = base self.linthresh = linthresh self.invlinthresh = symlog.transform(linthresh) self.linscale = linscale self._linscale_adj = (linscale / (1.0 - self.base ** -1)) def transform_non_affine(self, a): sign = np.sign(a) masked = ma.masked_inside(a, -self.invlinthresh, self.invlinthresh, copy=False) exp = sign * self.linthresh * ( ma.power(self.base, (sign * (masked / self.linthresh)) - self._linscale_adj)) if masked.mask.any(): return ma.where(masked.mask, a / self._linscale_adj, exp) else: return exp def inverted(self): return SymmetricalLogTransform(self.base, self.linthresh, self.linscale) class SymmetricalLogScale(ScaleBase): """ The symmetrical logarithmic scale is logarithmic in both the positive and negative directions from the origin. Since the values close to zero tend toward infinity, there is a need to have a range around zero that is linear. The parameter *linthresh* allows the user to specify the size of this range (-*linthresh*, *linthresh*). """ name = 'symlog' # compatibility shim SymmetricalLogTransform = SymmetricalLogTransform InvertedSymmetricalLogTransform = InvertedSymmetricalLogTransform def __init__(self, axis, **kwargs): """ *basex*/*basey*: The base of the logarithm *linthreshx*/*linthreshy*: The range (-*x*, *x*) within which the plot is linear (to avoid having the plot go to infinity around zero). *subsx*/*subsy*: Where to place the subticks between each major tick. Should be a sequence of integers. For example, in a log10 scale: ``[2, 3, 4, 5, 6, 7, 8, 9]`` will place 8 logarithmically spaced minor ticks between each major tick. *linscalex*/*linscaley*: This allows the linear range (-*linthresh* to *linthresh*) to be stretched relative to the logarithmic range. Its value is the number of decades to use for each half of the linear range. For example, when *linscale* == 1.0 (the default), the space used for the positive and negative halves of the linear range will be equal to one decade in the logarithmic range. """ if axis.axis_name == 'x': base = kwargs.pop('basex', 10.0) linthresh = kwargs.pop('linthreshx', 2.0) subs = kwargs.pop('subsx', None) linscale = kwargs.pop('linscalex', 1.0) else: base = kwargs.pop('basey', 10.0) linthresh = kwargs.pop('linthreshy', 2.0) subs = kwargs.pop('subsy', None) linscale = kwargs.pop('linscaley', 1.0) if base <= 1.0: raise ValueError("'basex/basey' must be larger than 1") if linthresh <= 0.0: raise ValueError("'linthreshx/linthreshy' must be positive") if linscale <= 0.0: raise ValueError("'linscalex/linthreshy' must be positive") self._transform = self.SymmetricalLogTransform(base, linthresh, linscale) self.base = base self.linthresh = linthresh self.linscale = linscale self.subs = subs def set_default_locators_and_formatters(self, axis): """ Set the locators and formatters to specialized versions for symmetrical log scaling. """ axis.set_major_locator(SymmetricalLogLocator(self.get_transform())) axis.set_major_formatter(LogFormatterMathtext(self.base)) axis.set_minor_locator(SymmetricalLogLocator(self.get_transform(), self.subs)) axis.set_minor_formatter(NullFormatter()) def get_transform(self): """ Return a :class:`SymmetricalLogTransform` instance. """ return self._transform def _mask_non_logit(a): """ Return a Numpy array where all values outside ]0, 1[ are replaced with NaNs. If all values are inside ]0, 1[, the original array is returned. """ mask = (a <= 0.0) | (a >= 1.0) if mask.any(): return np.where(mask, np.nan, a) return a def _clip_non_logit(a): a = np.array(a, float) a[a <= 0.0] = 1e-300 a[a >= 1.0] = 1 - 1e-300 return a class LogitTransform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True def __init__(self, nonpos): Transform.__init__(self) if nonpos == 'mask': self._handle_nonpos = _mask_non_logit else: self._handle_nonpos = _clip_non_logit self._nonpos = nonpos def transform_non_affine(self, a): """logit transform (base 10), masked or clipped""" a = self._handle_nonpos(a) return np.log10(1.0 * a / (1.0 - a)) def inverted(self): return LogisticTransform(self._nonpos) class LogisticTransform(Transform): input_dims = 1 output_dims = 1 is_separable = True has_inverse = True def __init__(self, nonpos='mask'): Transform.__init__(self) self._nonpos = nonpos def transform_non_affine(self, a): """logistic transform (base 10)""" return 1.0 / (1 + 10**(-a)) def inverted(self): return LogitTransform(self._nonpos) class LogitScale(ScaleBase): """ Logit scale for data between zero and one, both excluded. This scale is similar to a log scale close to zero and to one, and almost linear around 0.5. It maps the interval ]0, 1[ onto ]-infty, +infty[. """ name = 'logit' def __init__(self, axis, nonpos='mask'): """ *nonpos*: ['mask' | 'clip' ] values beyond ]0, 1[ can be masked as invalid, or clipped to a number very close to 0 or 1 """ if nonpos not in ['mask', 'clip']: raise ValueError("nonposx, nonposy kwarg must be 'mask' or 'clip'") self._transform = LogitTransform(nonpos) def get_transform(self): """ Return a :class:`LogitTransform` instance. """ return self._transform def set_default_locators_and_formatters(self, axis): # ..., 0.01, 0.1, 0.5, 0.9, 0.99, ... axis.set_major_locator(LogitLocator()) axis.set_major_formatter(LogitFormatter()) axis.set_minor_locator(LogitLocator(minor=True)) axis.set_minor_formatter(LogitFormatter()) def limit_range_for_scale(self, vmin, vmax, minpos): """ Limit the domain to values between 0 and 1 (excluded). """ return (vmin <= 0 and minpos or vmin, vmax >= 1 and (1 - minpos) or vmax) _scale_mapping = { 'linear': LinearScale, 'log': LogScale, 'symlog': SymmetricalLogScale, 'logit': LogitScale, } def get_scale_names(): names = list(six.iterkeys(_scale_mapping)) names.sort() return names def scale_factory(scale, axis, **kwargs): """ Return a scale class by name. ACCEPTS: [ %(names)s ] """ scale = scale.lower() if scale is None: scale = 'linear' if scale not in _scale_mapping: raise ValueError("Unknown scale type '%s'" % scale) return _scale_mapping[scale](axis, **kwargs) scale_factory.__doc__ = dedent(scale_factory.__doc__) % \ {'names': " | ".join(get_scale_names())} def register_scale(scale_class): """ Register a new kind of scale. *scale_class* must be a subclass of :class:`ScaleBase`. """ _scale_mapping[scale_class.name] = scale_class def get_scale_docs(): """ Helper function for generating docstrings related to scales. """ docs = [] for name in get_scale_names(): scale_class = _scale_mapping[name] docs.append(" '%s'" % name) docs.append("") class_docs = dedent(scale_class.__init__.__doc__) class_docs = "".join([" %s\n" % x for x in class_docs.split("\n")]) docs.append(class_docs) docs.append("") return "\n".join(docs) docstring.interpd.update( scale=' | '.join([repr(x) for x in get_scale_names()]), scale_docs=get_scale_docs().rstrip(), )