"""
Generating and plotting on HC plane.
The class ``HCplots`` is used for plotting the HC plane and
for creating the bases of other plot formats that can be useful for
diagnostics, interpretation, and analysis with PECCARY.
"""
import numpy as np
import matplotlib.pylab as plt
from matplotlib.ticker import FormatStrFormatter
from functools import partial
from . import utils
__all__ = ["plotBoundsHC","HCplane","HCcurves"]
[docs]
def plotBoundsHC(ax, n=5, nsteps=1000, **kwargs):
"""
Plots region boundary lines on HC plane.
Parameters
----------
ax : Matplotlib axis
Axis on which to plot empty HC curves
n : int, optional
Sampling size, by default 5
nsteps : int, optional
Number of steps to use for generating HC bounding curves,
by default 1000
**kwargs : dict, optional
Style arguments passed to ``matplotlib.pyplot.plot``,
if none given uses PECCARY defaults
"""
minH, minC, maxH, maxC = utils.calcHCplane(n=n, nsteps=nsteps) # H and C values for HC min/max curves
minHVal = utils.HminPer(n=n) # Min. H value for periodic fnct
maxHVal = utils.HmaxPer(n=n) # Max. H value for periodic fnct
argMinH_CminCurve = np.argmin(np.abs(minH-minHVal)) # Min. H value argument for H values for min HC curve
argMinH_CmaxCurve = np.argmin(np.abs(maxH-minHVal)) # Min. H value argument for H values for max HC curve
argMaxH_CminCurve = np.argmin(np.abs(minH-maxHVal)) # Max. H value argument for H values for min HC curve
argMaxH_CmaxCurve = np.argmin(np.abs(maxH-maxHVal)) # Max. H value argument for H values for max HC curve
if 'lw' not in kwargs.keys():
kwargs['lw'] = 1.
if 'ls' not in kwargs.keys():
kwargs['ls'] = '--'
if 'color' not in kwargs.keys():
kwargs['color'] = 'k'
if 'alpha' not in kwargs.keys():
kwargs['alpha'] = 0.5
ax.plot(np.array([minHVal,minHVal]), np.array([minC[argMinH_CminCurve], maxC[argMinH_CmaxCurve]]), **kwargs)
ax.plot(np.array([maxHVal,maxHVal]), np.array([minC[argMaxH_CminCurve], maxC[argMaxH_CmaxCurve]]), **kwargs)
ax.plot(np.array([minHVal,maxHVal]), np.array([maxC[argMinH_CmaxCurve], maxC[argMaxH_CmaxCurve]]), **kwargs)
[docs]
def HCplane(H=None, C=None, ax=None, n=5, nsteps=1000, fontsize=12, showAxLabels=True, showBoundaries=True, annotatePlane=False,
savePlot=False, savePath='', kwargsFig={'figsize':(8,6)}, kwargsHC={'ls':'-','color':'k','zorder':0}, kwargsBnds={}, kwargsPts={}, annotateFontsize=None):
"""
Plot :math:`HC`-plane upper and lower allowed bounds, as well as
:math:`[H,C]` coordinates and/or region annotations, if specified.
If no Matplotlib axis is specified, it will return Matplotlib
figure and axis instances.
Parameters
----------
H : ndarray, optional
Permutation Entropy values, by default None
C : ndarray, optional
Statistical Complexity values, by default None
ax : Matplotlib axis
Axis on which to plot empty HC curves
n : int, optional
Sampling size, by default 5
nsteps : int, optional
Number of steps to use for generating HC bounding curves,
by default 1000
fontsize : integer or float, optional
Fontsize of axis labels, by default 12
showAxLabels : bool, optional
Show pre-defined axis labels, by default True
showBoundaries : bool, optional
Show HC plane boundary lines, by default True
annotatePlane : bool, optional
Annotate HC plane regions, by default False
savePlot : bool, optional
Saves HC plot if set to True, by default False
savePath : str, optional
Path to save plot if savePlot set to True, by default ''
Note: Use only forward slashes in savePath
kwargsFig : dict, optional
Style arguments for HC plane figure and axis passed to
``matplotlib.pyplot.subplots``, if none given uses PECCARY defaults
kwargsHC : dict, optional
Style arguments for HC plane envelope lines passed to
``matplotlib.pyplot.plot``, if none given uses PECCARY defaults
kwargsBnds : dict, optional
Style arguments for region boundary lines passed to
``matplotlib.pyplot.plot``, if none given uses PECCARY defaults
kwargsPts : dict, optional
Style arguments for [H,C] values plotted on HC-plane with
``matplotlib.pyplot.scatter``, if none given uses PECCARY defaults
annotateFontsize : float, optional
Fontsize for HC plane regions annotations, by default None
"""
# Calculate HC plane envelope
Cminx, Cminy, Cmaxx, Cmaxy = utils.calcHCplane(n=n, nsteps=nsteps)
# Check if an existing axis has been inputted
# Otherwise, create figure and subplot
if ax is None:
fig, ax = plt.subplots(1,1,**kwargsFig)
returnAx = True
else:
returnAx = False
# Plot HC envelope
ax.plot(Cminx,Cminy,**kwargsHC)
ax.plot(Cmaxx,Cmaxy,**kwargsHC)
# Check whether or not to plot HC plane boundaries
if showBoundaries:
plotBoundsHC(ax, **kwargsBnds)
else:
pass
# Check whether or not to include HC plane annotation
if annotatePlane:
if annotateFontsize is None:
annotateFontsize = fontsize
else:
pass
ax.text(0.30,0.27,'periodic',rotation=46., fontdict={'fontsize':annotateFontsize-4, 'color':'grey'})
ax.text(0.35,0.24,'regular',rotation=35., fontdict={'fontsize':annotateFontsize-1})
ax.text(0.56,0.36,'complex', fontdict={'fontsize':annotateFontsize-1})
ax.text(0.76,0.09,'stochastic',rotation=-53., fontdict={'fontsize':annotateFontsize-1})
else:
pass
# Check whether H and C values have been inputted
# If so, plot them
if (H is None) or (C is None):
pass
else:
ax.scatter(H, C, **kwargsPts)
# Check whether to include axis labels
if showAxLabels:
ax.set_xlabel(r"Normalized Permutation Entropy, $H$", fontsize=fontsize)
ax.set_ylabel(r"Statistical Complexity, $C$", fontsize=fontsize)
ax.tick_params(axis='both', labelsize=fontsize-2)
else:
pass
# Check whether to save plot
if savePlot:
ax.set(xlim=(0,1.0), ylim=(0,0.45))
ax.set_xticks(np.arange(0,1.1,0.1))
ax.set_yticks(np.arange(0,0.45,0.05))
if savePath.endswith('/'):
savefile=savePath + 'HCn5_blank'
else:
savefile=savePath + '/HCn5_blank'
plt.savefig(savefile+'.png')
elif returnAx:
return fig, ax
[docs]
def HCcurves(H=None, C=None, sampInts=None, axes=None, fontsize=12, showAxLabels=True,
savePlot=False, savePath='', kwargsFig={'figsize':(10,4)}, kwargsPts={},
orientation='horizontal', tPatAx=False, dt=None, n=5):
"""
Plots H- and C-curves or sets up blank figure for plotting H- and C- curves.
Parameters
----------
H : ndarray, optional
Permutation Entropy values corresponding to array of
sampling intervals, by default None
C : ndarray, optional
Statistical Complexity values corresponding to array of
sampling intervals, by default None
sampInts : ndarray, optional
Array of sampling intervals, by default None
axes : List of Matplotlib axess
Axes H- and C- curves
fontsize : integer or float, optional
Fontsize of axis labels, by default 12
showAxLabels : bool, optional
Show pre-defined axis labels, by default True
savePlot : bool, optional
Saves plot if set to True, by default False
savePath : str, optional
Path to save plot if savePlot set to True, by default ''
Note: Use only forward slashes in savePath
kwargsFig : dict, optional
Style arguments for figure and axis passed to
``matplotlib.pyplot.subplots``, if none given uses PECCARY defaults
kwargsPts : dict, optional
Style arguments for [H,C] values plotted on HC-plane with
``matplotlib.pyplot.scatter``, if none given uses PECCARY defaults
orientation : str, optional
Choose between 1 row x 2 column orientation ('horizontal') or
2 rows x 1 column (and shared x axis) orientation ('vertical'),
by default 'horizontal'
tPatAx : boolean, optional
Choose whether to plot secondary x-axis with pattern timescale values,
by default False
dt : float, optional
Timestep or timeseries resolution, only needed if tPatAx is True,
by default None
n : int, optional
Sampling size, only needed if tPatAx is True, by default 5
Raises
------
TypeError
If tPatAx is True, dt must be a float
"""
# Check if an existing axis has been inputted
# Otherwise, create figure and subplots
if axes is None:
if orientation.startswith('v'):
fig, axes = plt.subplots(2,1, sharex=True, **kwargsFig)
plt.subplots_adjust(hspace=0.)
axes[0].set_ylim(-0.1,1.1)
axes[0].yaxis.set_major_formatter(FormatStrFormatter('%.1f'))
axes[1].set_ylim(-0.02,utils.getMaxC())
returnAx = True
else:
fig, axes = plt.subplots(1,2,**kwargsFig)
plt.subplots_adjust(wspace=0.35)
axes[0].set_ylim(0,1.0)
axes[1].set_ylim(0,0.5)
returnAx = True
else:
returnAx = False
# Check whether H and C values have been inputted
# If so, plot them
if (H is None) or (C is None) or (sampInts is None):
pass
else:
axes[0].plot(sampInts, H, **kwargsPts)
axes[1].plot(sampInts, C, **kwargsPts)
# Check whether to include axis labels
if showAxLabels:
if orientation.startswith('v'):
axes[0].set_ylabel('Permutation Entropy, $H$', fontsize=fontsize)
axes[1].set_xlabel('Sampling interval', fontsize=fontsize)
axes[1].set_ylabel('Statistical Complexity, $C$', fontsize=fontsize)
else:
axes[0].set_ylabel(r"Permutation Entropy, $H$", fontsize=fontsize)
axes[1].set_ylabel(r"Statistical Complexity, $C$", fontsize=fontsize)
for axi in axes:
axi.set_xlabel(r"Sampling interval, $\ell$", fontsize=fontsize)
axi.tick_params(axis='both', labelsize=fontsize-2)
else:
pass
# Check whether secondary tPat axes should be created
if tPatAx and type(dt) != type(None):
if orientation.startswith('v'):
secAx = axes[0].secondary_xaxis('top', functions=(partial(utils.ell2tpat,n=5,dt=dt), partial(utils.tpat2ell,n=5,dt=dt,returnInt=False)))
secAx.set_xlabel('Pattern timescale', fontsize=fontsize)
secAx.tick_params(axis='both', which='major', labelsize=fontsize-2)
else:
for axi in axes:
secAx = axi.secondary_xaxis('top', functions=(partial(utils.ell2tpat,n=5,dt=dt), partial(utils.tpat2ell,n=5,dt=dt,returnInt=False)))
secAx.set_xlabel('Pattern timescale', fontsize=fontsize)
secAx.tick_params(axis='both', which='major', labelsize=fontsize-2)
elif tPatAx and type(dt) != float:
raise TypeError('If tPatAx is True, dt must be a float')
else:
pass
# Check whether to save plot
if savePlot:
if savePath.endswith('/'):
savefile=savePath + 'HCcurves'
else:
savefile=savePath + '/HCcurves'
plt.savefig(savefile+'.png')
elif returnAx:
return fig, axes
