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golden_ratio = (math.sqrt(5) - 1) / 2
if not height:
height = int(width * golden_ratio)
if plt is None:
import matplotlib.pyplot as plt
import importlib
mod = importlib.import_module("palettable.colorbrewer.%s" %
color_cycle[0])
colors = getattr(mod, color_cycle[1]).mpl_colors
from cycler import cycler
plt.figure(figsize=(width, height), facecolor="w", dpi=dpi)
ax = plt.gca()
ax.set_prop_cycle(cycler('color', colors))
else:
fig = plt.gcf()
fig.set_size_inches(width, height)
plt.xticks(fontsize=ticksize)
plt.yticks(fontsize=ticksize)
ax = plt.gca()
ax.set_title(ax.get_title(), size=width * 4)
labelsize = int(width * 3)
ax.set_xlabel(ax.get_xlabel(), size=labelsize)
ax.set_ylabel(ax.get_ylabel(), size=labelsize)
return plt
"""
if by_period:
df = pd.DataFrame(tab[1:],
columns = tab[0]).set_index(ind).transpose()
stack = False
num_col = int(n_data)/10
else:
df = pd.DataFrame(tab[1:], columns = tab[0]).set_index(ind)
stack = True
num_col = int(n_data)/2
fig = plt.figure()
inv_ax = fig.add_subplot(111)
inv_ax.grid(b=False)
# You have to play with the color map and the line style list to
# get enough combinations for your particular plot
inv_ax.set_prop_cycle(cycler('color',
[color_map(i/n_data) for i in range(0, n_data+1)]))
# To locate the legend: "loc" is the point of the legend for which you
# will specify coordinates. These coords are specified in
# bbox_to_anchor (can be only 1 point or couple)
inv_plot = df.plot(kind='bar', ax=inv_ax,
stacked=stack).legend(loc='lower left', fontsize=8,
bbox_to_anchor=(0.,1.015,1.,1.015), ncol=num_col, mode="expand")
if by_period:
plt.xticks(rotation=0, fontsize=10)
fname = summaries_dir+'/'+name+'.pdf'
else:
plt.xticks(rotation=90, fontsize=9)
fname = summaries_dir+'/'+name+'_stacked_by_p.pdf'
plt.savefig(fname, bbox_extra_artists=(inv_plot,), bbox_inches='tight')
plt.close()
def beautify_axes(axes):
try:
from cycler import cycler
axes.set_prop_cycle(
cycler('color', [to01(x) for x in plot.graph_colors]))
except (ImportError, KeyError):
axes.set_color_cycle(list(map(to01, plot.graph_colors)))
xa = axes.get_xaxis()
ya = axes.get_yaxis()
for attr in ('labelpad', 'LABELPAD'):
if hasattr(xa, attr):
setattr(xa, attr, xa.get_label().get_fontsize())
setattr(ya, attr, ya.get_label().get_fontsize())
break
('dashdotted', (0, (3, 5, 1, 5))),
('densely dashdotted', (0, (3, 1, 1, 1))),
('dashdotdotted', (0, (3, 5, 1, 5, 1, 5))),
('loosely dashdotdotted', (0, (3, 10, 1, 10, 1, 10))),
('densely dashdotdotted', (0, (3, 1, 1, 1, 1, 1)))]
# color maps for potential and concentration plots
cmap_u = plt.get_cmap('Reds')
cmap_c = [plt.get_cmap('Oranges'), plt.get_cmap('Blues')]
# general line style cycler
line_cycler = cycler( linestyle = [ s for _,s in linestyle_tuple ] )
# potential anc concentration cyclers
u_cycler = cycler( color = cmap_u( np.linspace(0.4,0.8,N) ) )
u_cycler = len(line_cycler)*u_cycler + len(u_cycler)*line_cycler
c_cyclers = [ cycler( color = cmap( np.linspace(0.4,0.8,N) ) ) for cmap in cmap_c ]
c_cyclers = [ len(line_cycler)*c_cycler + len(c_cycler)*line_cycler for c_cycler in c_cyclers ]
# https://matplotlib.org/3.1.1/tutorials/intermediate/constrainedlayout_guide.html
fig, (ax1,ax2,ax3) = plt.subplots(
nrows=1, ncols=3, figsize=[24,7], constrained_layout=True)
ax1.set_xlabel('z (nm)')
ax1.set_ylabel('potential (V)')
ax2.set_xlabel('z (nm)')
ax2.set_ylabel('concentration (mM)')
ax3.set_xlabel('z (nm)')
ax3.set_ylabel('concentration (mM)')
# ax1.axvline(x=pnp.lambda_D()*1e9, label='Debye Length', color='grey', linestyle=':')
import math
import imp # for reload
import json
from itertools import cycle
from cycler import cycler
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy
import pandas
# NB linestyle cycler broken in matplotlib 2.0.2
plt.rc("axes", prop_cycle=(cycler("color", ['r', 'g', 'b', 'y' ] )+
cycler("linestyle", ["-","--","-.",":"])))
plt.rc("savefig", dpi=300)
plt.rc("path", simplify=True)
plt.rc("font", family="serif")
plt.rc("mathtext", fontset ="custom")
plt.rc("text", usetex=True)
for x in ["xtick", "ytick"]:
plt.rc(x+".major", size=6, width=1)
plt.rc(x+".minor", size=3, width=1)
plt.rc("lines", markeredgewidth= 1)
plt.rc("legend", numpoints=1, frameon= False, handletextpad= 0.3)
zorder=-1, transform=a.transAxes, ha='center', va='top')
a.titleleft = a.text(0+titlepad/a.width, 1-titlepad/a.height, '',
zorder=-1, transform=a.transAxes, ha='left', va='top')
a.titleright = a.text(1-titlepad/a.width, 1-titlepad/a.height, '',
zorder=-1, transform=a.transAxes, ha='right', va='top')
# ABC labeling
a.abcinside = a.text(abcpad/a.width, 1-abcpad/a.height, ascii_uppercase[i],
# bbox=dict(facecolor='w', edgecolor=None, alpha=1),
transform=a.transAxes, ha='left', va='top', visible=False)
a.abc = a.text(0, 1, ascii_uppercase[i],
transform=a.title._transform, ha='left', va='baseline', visible=False) # copies the a.title transform
# Property cycling
# To print current cycle, use list(next(ax._get_lines.prop_cycler)['color'] for i in range(10))
colors = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b', '#e377c2', '#7f7f7f', '#bcbd22', '#17becf']
a.set_prop_cycle(cycler('color', [colors[i%10] for i in range(40)])
+ cycler('linestyle', [i for i in ('-','--','--','--') for n in range(10)])
+ cycler('dashes', [i for i in (tuple(), (1,1), (3,2), (6,3)) for n in range(10)]))
# Method overrides; plotting (e.g. to fix white lines between polygons), and formatting
for a in ax:
# Formatting function
a.format = MethodType(_format, a) # MethodType approach
# Mapped overrides
if projection is not None and package=='basemap':
# Setup basemap
a.m = mbasemap.Basemap(projection=projection, ax=a, **projection_kw)
a.m.drawmapboundary() # **settings().line)
# must be set before-hand, otherwise this wonky set_axes method automatically draws two mapboundary Patch objects
# when you plot something, one for fill and the other for the edges; then, since the patch object in
# _mapboundarydrawn is only the fill-version, calling drawmapboundar() again will replace only ***that one***,
# but the original visible edges is still drawn; if you instead call drawmapboundary right away, calling it again will ***replace*** the object
# First, set up new methods that fix white edges
def add(self,name="plot"):
page = Plot(self.nb)
self.nb.AddPage(page,name)
page.figure.gca().set_prop_cycle(
cycler('color', ['r', 'g', 'b', 'y', 'm', 'c']) *
cycler('linestyle', ['-', '--', '-.'])
)
return page.figure
if kwargs:
warnings.warn(f'Ignoring keyword args {kwargs}.')
elif all(isinstance(arg, cycler.Cycler) for arg in args):
# Merge cycler objects
if kwargs:
warnings.warn(f'Ignoring keyword args {kwargs}.')
if len(args) == 1:
return args[0]
else:
props = {}
for arg in args:
for key,value in arg.by_key():
if key not in props:
props[key] = []
props[key].extend([*value])
return cycler.cycler(**props)
else:
# Construct and register ListedColormap
if args and isinstance(args[-1], Number):
args, samples = args[:-1], args[-1] # means we want to sample existing colormaps or cycles
kwargs.setdefault('fade', 90)
kwargs.setdefault('listmode', 'listed')
cmap = Colormap(*args, **kwargs) # the cmap object itself
if isinstance(cmap, mcolors.ListedColormap):
N = samples
colors = cmap.colors[:N] # if samples is None, does nothing
else:
samples = _notNone(samples, 10)
if isinstance(samples, Integral):
samples = np.linspace(0, 1, samples) # from edge to edge
elif np.iterable(samples) and all(isinstance(item,Number) for item in samples):
samples = np.array(samples)
mcm.cmap_d[name] = cmap
# Save the cycle
if save:
basename = f'{name}.hex'
filename = os.path.join(DATA_USER_CYCLES, basename)
with open(filename, 'w') as f:
f.write(','.join(mcolors.to_hex(color) for color in cmap.colors))
print(f'Saved color cycle to "{basename}".')
# Add to property dict
nprops = max(nprops, len(colors))
props['color'] = cmap.colors # save the tupled version!
# Build cycler, make sure lengths are the same
for key,value in props.items():
if len(value) < nprops:
value[:] = [value[i%len(value)] for i in range(nprops)] # make loop double back
return cycler.cycler(**props)
prefix = '# ' if comment else ''
data = []
for key, pair in rcdict.items():
# Optionally append description
if description and isinstance(pair, tuple): # add commented out description
value = pair[0]
descrip = '# ' + pair[1]
else:
descrip = ''
if isinstance(pair, tuple):
value = pair[0]
else:
value = pair
# Translate object to string
if isinstance(value, cycler.Cycler): # special case!
value = repr(value)
elif isinstance(value, (str, numbers.Number, NoneType)):
value = str(value)
elif isinstance(value, (list, tuple, np.ndarray)) and all(
isinstance(val, (str, numbers.Number)) for val in value
):
value = ', '.join(str(val) for val in value)
else:
warnings._warn_proplot(
f'Failed to write rc setting {key} = {value!r}. Must be string, '
'number, or list or tuple thereof, or None or a cycler.'
)
continue
if value[:1] == '#': # e.g. HEX string
value = repr(value)
data.append((key, value, descrip))