
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
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__author__ = 'noe'

import numpy as _np
import matplotlib.pylab as _plt

def plot_implied_timescales(ITS, ax=None, outfile=None, xlog=False, ylog=True, confidence=0.95, refs=None):
    r""" Generate a pretty implied timescale plot

    Parameters
    ----------
    ITS : implied timescales object.
        Object whose data will be plotted. Must provide the functions: get_timescales() and get_timescales(i) where i is the
        the property samples_available
    ax : matplotlib Axes object, optional, default = None
        the axes to plot to. When set to None the default Axes object will be used.
    outfile : str, optional, default = None
        output file to write the figure to. When not given, the plot will be displayed
    xlog : bool, optional, default = False
        Iff true, the x-Axis is logarithmized
    ylog : bool, optional, default = True
        Iff true, the y-Axis is logarithmized
    confidence : float, optional, default = 0.95
        The confidence interval for plotting error bars (if available)
    refs : ndarray((m), dtype=float), optional, default = None
        Reference (exact solution or other reference) timescales if known. The number of timescales must match those
        in the ITS object

    Returns
    -------
    ax : Axes object containing the plot

    """
    # check input
    if (ax is None):
        ax = _plt.gca()
    colors = ['blue','red','green','cyan','purple','orange','violet']
    lags = ITS.lagtimes
    xmax = _np.max(lags)
    #ymin = min(_np.min(lags), _np.min(ITS.get_timescales()))
    #ymax = 1.5*_np.min(ITS.get_timescales())
    for i in range(ITS.number_of_timescales):
        # plot estimate
        ax.plot(lags, ITS.get_timescales(process=i), color = colors[i % len(colors)])
        # sample available?
        if (ITS.samples_available and ITS.sample_number_of_timescales > i):
            # plot sample mean
            ax.plot(ITS.sample_lagtimes, ITS.get_sample_mean(process=i), marker='o', color = colors[i % len(colors)], linestyle = 'dashed')
            (lconf, rconf) = ITS.get_sample_conf(confidence, i)
            ax.fill_between(ITS.sample_lagtimes, lconf, rconf, alpha=0.2, color=colors[i % len(colors)])
        # reference available?
        if (refs != None):
            tref = refs[i]
            ax.plot([0,min(tref,xmax)], [tref,tref], color='black', linewidth=1)
    # cutoff
    ax.fill_between(lags, ax.get_ylim()[0]*_np.ones(len(lags)), lags, alpha=0.5, color='grey')
    ax.plot(lags, lags, linewidth=2, color='black')
    ax.set_xlim([1,xmax])
    #ax.set_ylim([ymin,ymax])
    # formatting
    ax.set_xlabel('lag time (steps)')
    ax.set_ylabel('timescale (steps)')
    if (xlog):
        ax.set_xscale('log')
    if (ylog):
        ax.set_yscale('log')

    # show or save
    # if outfile is None:
    #    _plt.show()
    if outfile is not None:
        _plt.savefig(outfile)

    return ax
@@ -3664,10 +3664,14 @@
 efs 
-!=
+is not
  Non

fix comparision for None