def _fill_cbar_ax(self):
x = np.linspace(0, 1, 50).reshape((50, 1))
ax = self.cbar_ax
# Dummy image to get the colorbar
self._im = ax.imshow(x,
extent=[0, 1, 0, 1],
visible=False,
aspect='auto')
self._im.drawon = False
self.cbar = colorbar_factory(ax, self._im)
ax.yaxis.set_visible(True)
self.update()
def _fill_cbar_ax(self):
"""Put a colorbar-like image in the axes"""
x = np.linspace(0, 1, 50).reshape((50, 1))
ax = self.cbar_ax
# Dummy image to get the colorbar
self._im = ax.imshow(x,
extent=[0, 1, 0, 1],
visible=False,
aspect='auto')
self._im.drawon = False
self.cbar = colorbar_factory(ax, self._im)
ax.yaxis.set_visible(True)
self.update()
def colorbar(self, mappable, cax=None, ax=None, **kw):
"""
Create a colorbar for a ScalarMappable instance, *mappable*.
Documentation for the pylab thin wrapper:
%(colorbar_doc)s
"""
if ax is None:
ax = self.gca()
use_gridspec = kw.pop("use_gridspec", True)
if cax is None:
if use_gridspec and isinstance(ax, SubplotBase):
cax, kw = cbar.make_axes_gridspec(ax, **kw)
else:
cax, kw = cbar.make_axes(ax, **kw)
cax.hold(True)
cb = cbar.colorbar_factory(cax, mappable, **kw)
self.sca(ax)
return cb
def add_snapshot_subplot(ax, dir, start_file, do_cbar=False, figure_index=0, n_files=3, field='s', horiz_slice=False, plot_label=None, dims='$\mathrm{2D}$ | '):
plotter = MovieBuddy(dir, max_files=n_files, start_file=start_file)
plotter.add_subplot(field, 0, 0, zlabel="s'", sub_t_avg=True)
plotter.analyze_subplots()
slices = plotter.grab_whole_profile(plotter.local_files['slices'], plotter.local_writes_per_file,
subkey=['tasks'], profile_name=[field])
#max = plotter.ax[0]['mean']+stds*plotter.ax[0]['stdev']/2
#min = plotter.ax[0]['mean']-stds*plotter.ax[0]['stdev']/2
max = plotter.ax[0]['max_val']/3
min = -plotter.ax[0]['max_val']/3
if horiz_slice:
xs, ys = plotter.y_xx, plotter.y_yy
else:
xs, ys = plotter.xs, plotter.zs
if type(plotter.y) == type(None):
img = ax.pcolormesh(xs, ys, slices[field][figure_index,:,:]-plotter.ax[0]['t_avg'], cmap='RdBu_r',
vmin=min, vmax=max)
else:
if horiz_slice:
img = ax.pcolormesh(xs, ys, slices[field][figure_index,:,:][:,:,0]-np.mean(plotter.ax[0]['t_avg']), cmap='RdBu_r',
vmin=min, vmax=max)
else:
img = ax.pcolormesh(xs, ys, slices[field][figure_index,:,:][:,0,:]-plotter.ax[0]['t_avg'], cmap='RdBu_r',
vmin=min, vmax=max)
ax.set_xlim(np.min(xs), np.max(xs))
ax.set_ylim(np.min(ys), np.max(ys))
xticks = np.array([0, np.max(xs)/2, np.max(xs)])
xticklabels = [r'${:1.1f}$'.format(tick) for tick in xticks]
xticklabels[0] = r'${:1d}$'.format(0)
plt.xticks(xticks, xticklabels, fontsize=8)
yticks = np.array([0, np.max(ys)])
yticklabels = [r'${:1.1f}$'.format(tick) for tick in yticks]
yticklabels[0] = r'${:1d}$'.format(0)
plt.yticks(yticks, yticklabels, fontsize=8)
custom_label=True
if type(plot_label) == type(None):
custom_label=False
small_eps, small_ra = False, False
plot_label = '{:s}$\epsilon='.format(dims)
if plotter.atmosphere['epsilon'] < 0.1:
plot_label += '10^{'
plot_label += '{:1.0f}'.format(np.log10(plotter.atmosphere['epsilon']))
plot_label += '}$'
else:
plot_label += '{:1.1f}$'.format(plotter.atmosphere['epsilon'])
small_eps = True
ra_log = np.log10(plotter.atmosphere['rayleigh'])
plot_label += ' | $\mathrm{Ra} = 10^{'
if np.floor(ra_log) == ra_log:
plot_label += '{:1.0f}'.format(ra_log)
small_ra = True
else:
plot_label += '{:1.2f}'.format(ra_log)
plot_label += '}$'
plot_label = r'({:s})'.format(plot_label)
else:
plot_label = r'(${:s}$)'.format(plot_label)
# plt.annotate(plot_label, coords, size=9, color='white', path_effects=[PathEffects.withStroke(linewidth=1.2, foreground='black')])
if max > 0.1:
cbar_label = '$\pm {:1.2f}$'.format(max)
else:
str = '{:1.2e}'.format(max)
print(str)
if 'e+0' in str:
newstr = str.replace('e+0', '\\times 10^{')
elif 'e-0' in str:
newstr = str.replace('e-0', '\\times 10^{-')
else:
newstr = str.replace('e', '\\times 10^{')
newstr += '}'
cbar_label = '$\pm {:s}$'.format(newstr)
# cbar_label += ' ({:s})'.format(plot_label)
if do_cbar:
cax, kw = colorbar.make_axes(ax, fraction=0.15, pad=0.03, aspect=5, anchor=(0,0), location='top')
cbar = colorbar.colorbar_factory(cax, img, **kw)
for label in cax.xaxis.get_ticklabels():
label.set_visible(False)
cax.tick_params(axis=u'both', which=u'both',length=0)
trans = cax.get_yaxis_transform()
cax.annotate(r'{:s}'.format(cbar_label), (1.02,0.04), size=8, color='black', xycoords=trans)
cax.annotate(r'{:s}'.format(plot_label), (2.08,0.04), size=8, color='dimgrey', xycoords=trans)
else:
divider = make_axes_locatable(ax)
if horiz_slice:
cax = divider.append_axes('top', size='40%', pad=0.01)
cbx = divider.append_axes('bottom', size='30%', pad=0.01)
cbx.set_frame_on(False)
cbx.get_xaxis().set_visible(False)
cbx.get_yaxis().set_visible(False)
for xlabel in cbx.xaxis.get_ticklabels():
xlabel.set_visible(False)
for ylabel in cbx.yaxis.get_ticklabels():
ylabel.set_visible(False)
else:
cax = divider.append_axes('top', size='10%', pad=0.06)
cax.set_frame_on(False)
cax.get_xaxis().set_visible(False)
cax.get_yaxis().set_visible(False)
for xlabel in cax.xaxis.get_ticklabels():
xlabel.set_visible(False)
for ylabel in cax.yaxis.get_ticklabels():
ylabel.set_visible(False)
trans = ax.get_xaxis_transform() # x in data untis, y in axes fraction
ann = ax.annotate(cbar_label, xy=(-0.05, 1.05 ), size=8, color='black', xycoords=trans)
if not custom_label:
if np.floor(ra_log) != ra_log:
ann = ax.annotate(plot_label, xy=(xticks[-1]*0.48, 1.05 ), size=8, color='dimgrey', xycoords=trans)
elif small_eps:
ann = ax.annotate(plot_label, xy=(xticks[-1]*0.53, 1.05 ), size=8, color='dimgrey', xycoords=trans)
else:
ann = ax.annotate(plot_label, xy=(xticks[-1]*0.49, 1.05 ), size=8, color='dimgrey', xycoords=trans)
else:
ann = ax.annotate(plot_label, xy=(xticks[1]*1.25, 1.05 ), size=8, color='dimgrey', xycoords=trans)
elif species == "all2":
fig.subplots_adjust(right=0.8)
cax = fig.add_axes([0.9, 0.1, 0.03, 0.8])
elif species == "allRow":
fig.subplots_adjust(right=0.87, left=0.055, top=0.96, bottom=0.2, wspace=0.07)
cax = fig.add_axes([0.885, 0.2, 0.03, 0.76])
my_levels = np.logspace(10,20,11)
#print my_levels
CBpos = colorbar.ColorbarBase(cax,cmap=Cu_CS0.cmap,norm=Cu_CS0.norm, boundaries=my_levels, values=my_levels)
if species == "all":
cax2 = fig.add_axes([0.9, 0.1, 0.03, 0.8])
if qdens_CS2 != None: #Plot empty cbar in case of no negative charge density
CBneg = colorbar.colorbar_factory(cax2,qdens_CS2)
CBneg.values = my_levels
CBneg.boundaries = my_levels
CBneg.set_ticks(np.logspace(10,20,6))
# CBneg.update_ticks()
CBneg.config_axis()
CBneg.draw_all()
if species != "allRow":
plt.suptitle("Densities, time = %.3f [ns]" % (timestamp[i],))
else:
CBpos.set_label("Particle density [cm\\textsuperscript{-3}]")
plt.savefig(ofoldername + "/dens_log_%08d.png" %(outIdx,),dpi=DPI)
plt.savefig(ofoldername + "/dens_log_%08d.pdf" %(outIdx,))
plt.clf()
def __init__(self, ax, im):
AxesWidget.__init__(self, ax)
self.cbar = colorbar_factory(ax, im)
self.fmt = self.cbar.formatter = OffsetFormatter()
self.ax.yaxis.set_visible(True)
def plot_field(self, xs, zs, field, ax, field_name, cmap='RdYlBu_r', min=None, max=None,\
xlims=None, ylims=None, mod=None, plot_title=True, function='colormap',
bare=False):
'''
Plots a colormap of a given field.
xs -- a 2D grid of x-values
zs -- a 2D grid of z-values
field -- a 2D grid of values in the x-z plane for another parameter.
ax -- the Axis subplot on which to plot the field.
field_name -- The physical name that the numbers in 'field' represent
cmap -- the colormap of the plot
min, max -- the min and max values of the colormap to plot
xlims, ylims -- the boundaries on the x- and y- coordinates.
mod -- A modification on the field to alter the movie. Currently accepts:
"up" -- upflows
"down" -- downflows
"pos" -- Positive parts only
"neg" -- Negative parts only
bare -- If bare, then don't plot up any axis information (public talks, etc.)
'''
print(xs.shape, zs.shape, field.shape)
if self.idle: return
if max == None:
max = np.max(field)
if min == None:
min = np.min(field)
if function == 'colormap':
plot = ax.pcolormesh(xs, zs, field, cmap=cmap, vmin=min, vmax=max)
if not bare:
xticks = np.array([1, np.max(xs)/2, np.max(xs)])
yticks = np.array([1, np.max(zs)/2, np.max(zs)])
plt.xticks(xticks, [r'${:1.2f}$'.format(tick) for tick in xticks], fontsize=11)
plt.yticks(yticks, [r'${:1.2f}$'.format(tick) for tick in yticks], fontsize=11)
if self.atmosphere['atmosphere_name'] == 'single polytrope':
plot_label = '$\epsilon='
if self.atmosphere['epsilon'] < 0.1:
plot_label += '10^{'
plot_label += '{:1.0f}'.format(np.log10(self.atmosphere['epsilon']))
plot_label += '}$'
else:
plot_label += '{:1.1f}$'.format(self.atmosphere['epsilon'])
small_eps = True
ra_log = np.log10(self.atmosphere['rayleigh'])
plot_label += ' | $\mathrm{Ra} = 10^{'
if np.floor(ra_log) == ra_log:
plot_label += '{:1.0f}'.format(ra_log)
small_ra = True
else:
plot_label += '{:1.2f}'.format(ra_log)
plot_label += '}$'
plot_label = r'{:s}'.format(plot_label)
else:
print('ERROR: Unknown atmosphere type')
plot_label=''
if max > 0.1:
cbar_label = '$\pm {:1.2f}$'.format(max)
else:
str = '{:1.2e}'.format(max)
if 'e+0' in str:
newstr = str.replace('e+0', '\\times 10^{')
elif 'e-0' in str:
newstr = str.replace('e-0', '\\times 10^{-')
else:
newstr = str.replace('e', '\\times 10^{')
newstr += '}'
if min != 0:
cbar_label = '$\pm {:s}$'.format(newstr)
else:
cbar_label = '$min: 0 max: {:s}$'.format(newstr)
cbar_label += ' ({:s})'.format(plot_label)
cbar_label += ' {:s}'.format(field_name)
divider = make_axes_locatable(ax)
cax, kw = colorbar.make_axes(ax, fraction=0.07, pad=0.03, aspect=5, anchor=(0,0), location='top')
cbar = colorbar.colorbar_factory(cax, plot, **kw)
trans = cax.get_yaxis_transform()
cax.annotate(r'{:s}'.format(cbar_label), (1.02,0.01), size=11, color='black', xycoords=trans)
cax.tick_params(axis=u'both', which=u'both',length=0)
cax.set_xticklabels([])
cax.set_xticks([])
# for label in cax.xaxis.get_ticklabels():
# label.set_visible(False)
# for label in cax.yaxis.get_ticklabels():
# label.set_visible(False)
elif function == 'contour':
field[np.where(field > max)] = max
field[np.where(field < min)] = min
plot = ax.contour(xs, zs, field, 7, cmap=plt.cm.gray)
if xlims == None or len(xlims) != 2:
ax.set_xlim(np.min(xs), np.max(xs))
else:
ax.set_xlim(xlims[0], xlims[1])
if ylims == None or len(ylims) != 2:
ax.set_ylim(np.min(zs), np.max(zs))
else:
ax.set_ylim(ylims[0], ylims[1])
if bare:
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
wspace=0.07)
cax = fig.add_axes([0.885, 0.2, 0.03, 0.76])
my_levels = np.logspace(10, 20, 11)
#print my_levels
CBpos = colorbar.ColorbarBase(cax,
cmap=Cu_CS0.cmap,
norm=Cu_CS0.norm,
boundaries=my_levels,
values=my_levels)
if species == "all":
cax2 = fig.add_axes([0.9, 0.1, 0.03, 0.8])
if qdens_CS2 != None: #Plot empty cbar in case of no negative charge density
CBneg = colorbar.colorbar_factory(cax2, qdens_CS2)
CBneg.values = my_levels
CBneg.boundaries = my_levels
CBneg.set_ticks(np.logspace(10, 20, 6))
# CBneg.update_ticks()
CBneg.config_axis()
CBneg.draw_all()
if species != "allRow":
plt.suptitle("Densities, time = %.3f [ns]" % (timestamp[i], ))
else:
CBpos.set_label("Particle density [cm\\textsuperscript{-3}]")
plt.savefig(ofoldername + "/dens_log_%08d.png" % (outIdx, ), dpi=DPI)
plt.savefig(ofoldername + "/dens_log_%08d.pdf" % (outIdx, ))
plt.clf()
