I have successfully done everything I need to do in order to plot a CDF (common data format, not a cumulative distribution function) file and have everything great. But I keep getting this when I type plt.show():
RuntimeError Traceback (most recent call last)
/usr/local/lib/python3.5/dist-packages/IPython/core/formatters.py in __call__(self, obj)
305 pass
306 else:
--> 307 return printer(obj)
308 # Finally look for special method names
309 method = get_real_method(obj, self.print_method)
/usr/local/lib/python3.5/dist-packages/IPython/core/pylabtools.py in <lambda>(fig)
238
239 if 'png' in formats:
--> 240 png_formatter.for_type(Figure, lambda fig: print_figure(fig, 'png', **kwargs))
241 if 'retina' in formats or 'png2x' in formats:
242 png_formatter.for_type(Figure, lambda fig: retina_figure(fig, **kwargs))
/usr/local/lib/python3.5/dist-packages/IPython/core/pylabtools.py in print_figure(fig, fmt, bbox_inches, **kwargs)
122
123 bytes_io = BytesIO()
--> 124 fig.canvas.print_figure(bytes_io, **kw)
125 data = bytes_io.getvalue()
126 if fmt == 'svg':
/usr/local/lib/python3.5/dist-packages/matplotlib/backend_bases.py in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs)
2190 orientation=orientation,
2191 dryrun=True,
-> 2192 **kwargs)
2193 renderer = self.figure._cachedRenderer
2194 bbox_inches = self.figure.get_tightbbox(renderer)
/usr/local/lib/python3.5/dist-packages/matplotlib/backends/backend_agg.py in print_png(self, filename_or_obj, *args, **kwargs)
543
544 def print_png(self, filename_or_obj, *args, **kwargs):
--> 545 FigureCanvasAgg.draw(self)
546 renderer = self.get_renderer()
547 original_dpi = renderer.dpi
/usr/local/lib/python3.5/dist-packages/matplotlib/backends/backend_agg.py in draw(self)
462
463 try:
--> 464 self.figure.draw(self.renderer)
465 finally:
466 RendererAgg.lock.release()
/usr/local/lib/python3.5/dist-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
61 def draw_wrapper(artist, renderer, *args, **kwargs):
62 before(artist, renderer)
---> 63 draw(artist, renderer, *args, **kwargs)
64 after(artist, renderer)
65
/usr/local/lib/python3.5/dist-packages/matplotlib/figure.py in draw(self, renderer)
1141
1142 mimage._draw_list_compositing_images(
-> 1143 renderer, self, dsu, self.suppressComposite)
1144
1145 renderer.close_group('figure')
/usr/local/lib/python3.5/dist-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, dsu, suppress_composite)
137 if not_composite or not has_images:
138 for zorder, a in dsu:
--> 139 a.draw(renderer)
140 else:
141 # Composite any adjacent images together
/usr/local/lib/python3.5/dist-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
61 def draw_wrapper(artist, renderer, *args, **kwargs):
62 before(artist, renderer)
---> 63 draw(artist, renderer, *args, **kwargs)
64 after(artist, renderer)
65
/usr/local/lib/python3.5/dist-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe)
2407 renderer.stop_rasterizing()
2408
-> 2409 mimage._draw_list_compositing_images(renderer, self, dsu)
2410
2411 renderer.close_group('axes')
/usr/local/lib/python3.5/dist-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, dsu, suppress_composite)
137 if not_composite or not has_images:
138 for zorder, a in dsu:
--> 139 a.draw(renderer)
140 else:
141 # Composite any adjacent images together
/usr/local/lib/python3.5/dist-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
61 def draw_wrapper(artist, renderer, *args, **kwargs):
62 before(artist, renderer)
---> 63 draw(artist, renderer, *args, **kwargs)
64 after(artist, renderer)
65
/usr/local/lib/python3.5/dist-packages/matplotlib/axis.py in draw(self, renderer, *args, **kwargs)
1136 ticks_to_draw = self._update_ticks(renderer)
1137 ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw,
-> 1138 renderer)
1139
1140 for tick in ticks_to_draw:
/usr/local/lib/python3.5/dist-packages/matplotlib/axis.py in _get_tick_bboxes(self, ticks, renderer)
1076 for tick in ticks:
1077 if tick.label1On and tick.label1.get_visible():
-> 1078 extent = tick.label1.get_window_extent(renderer)
1079 ticklabelBoxes.append(extent)
1080 if tick.label2On and tick.label2.get_visible():
/usr/local/lib/python3.5/dist-packages/matplotlib/text.py in get_window_extent(self, renderer, dpi)
965 raise RuntimeError('Cannot get window extent w/o renderer')
966
--> 967 bbox, info, descent = self._get_layout(self._renderer)
968 x, y = self.get_unitless_position()
969 x, y = self.get_transform().transform_point((x, y))
/usr/local/lib/python3.5/dist-packages/matplotlib/text.py in _get_layout(self, renderer)
351 tmp, lp_h, lp_bl = renderer.get_text_width_height_descent('lp',
352 self._fontproperties,
--> 353 ismath=False)
354 offsety = (lp_h - lp_bl) * self._linespacing
355
/usr/local/lib/python3.5/dist-packages/matplotlib/backends/backend_agg.py in get_text_width_height_descent(self, s, prop, ismath)
228 fontsize = prop.get_size_in_points()
229 w, h, d = texmanager.get_text_width_height_descent(s, fontsize,
--> 230 renderer=self)
231 return w, h, d
232
/usr/local/lib/python3.5/dist-packages/matplotlib/texmanager.py in get_text_width_height_descent(self, tex, fontsize, renderer)
674 else:
675 # use dviread. It sometimes returns a wrong descent.
--> 676 dvifile = self.make_dvi(tex, fontsize)
677 dvi = dviread.Dvi(dvifile, 72 * dpi_fraction)
678 try:
/usr/local/lib/python3.5/dist-packages/matplotlib/texmanager.py in make_dvi(self, tex, fontsize)
421 'string:\n%s\nHere is the full report generated by '
422 'LaTeX: \n\n' % repr(tex.encode('unicode_escape')) +
--> 423 report))
424 else:
425 mpl.verbose.report(report, 'debug')
RuntimeError: LaTeX was not able to process the following string:
b'lp'
Here is the full report generated by LaTeX:
I haven't an idea how to fix this nor could find a solution on the Internet, I'm thinking its something I haven't installed yet or something. Please advise, if helpful I'm running Ubuntu 16.04 LTS.
Respectfully, A
Full code below:
import spacepy as sp
from spacepy import pycdf
from pylab import *
from spacepy.toolbox import windowMean, normalize
from spacepy.plot.utils import annotate_xaxis
import pylab
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import matplotlib.mlab as mlab
import matplotlib.cbook as cbook
import matplotlib.ticker as ticker
from matplotlib.colors import LogNorm
from matplotlib.ticker import LogLocator
from matplotlib.dates import DateFormatter
from matplotlib.dates import DayLocator, HourLocator, MinuteLocator
from matplotlib import rc, rcParams
import matplotlib.dates as mdates
import datetime as dt
import bisect as bi
import seaborn as sea
import sys
import os
import multilabel as ml
import pandas as pd
sea.set_context('poster')
# sea.set_style('ticks',{'axes.facecolor':'yellow'})
sea.set_style('whitegrid')
sea.set_palette('muted',color_codes=True)
rc('text', usetex=True)
rc('font', family='Mono')
rcParams['text.latex.preamble']=[r'/usepackage{amsmath}']
MMS_1_HPCA_SURVEY_ION = pycdf.CDF(r'/home/ary/Desktop/Arya/Project/Data/MMS/1/HPCA/Survey/Ion/mms1_hpca_srvy_l2_ion_20151025120000_v1.0.0.cdf')
EPOCH_SURVEY_ION_1 = MMS_1_HPCA_SURVEY_ION['Epoch'][...]
H_Flux_SURVEY_ION_1 = MMS_1_HPCA_SURVEY_ION['mms1_hpca_hplus_flux'][...]
Ion_Energy_SURVEY_ION_1 = MMS_1_HPCA_SURVEY_ION['mms1_hpca_ion_energy'][...]
MMS_SURVEY_ION_1_Start_time = dt.datetime(2015, 10, 25, 12, 0, 0, 908117)
MMS_SURVEY_ION_1_Finish_time = dt.datetime(2015, 10, 25, 16, 22, 24, 403623)
dt_MMS = dt.timedelta(seconds = 15)
plt.close('all')
fig_MMS, axs_MMS = plt.subplots(2,sharex=True)
cmap = plt.get_cmap(cm.jet)
cmap.set_bad('black')
sidx_MMS_1_SURVEY_ION = bi.bisect_left(EPOCH_SURVEY_ION_1,MMS_SURVEY_ION_1_Start_time)
sidx_MMS_1_SURVEY_ION = int(sidx_MMS_1_SURVEY_ION-(sidx_MMS_1_SURVEY_ION/100))
lidx_MMS_1_SURVEY_ION = bi.bisect_left(EPOCH_SURVEY_ION_1, MMS_SURVEY_ION_1_Finish_time)
lidx_MMS_1_SURVEY_ION = int(lidx_MMS_1_SURVEY_ION+((len(EPOCH_SURVEY_ION_1)-lidx_MMS_1_SURVEY_ION)/100))
if MMS_SURVEY_ION_1_Start_time.date() == MMS_SURVEY_ION_1_Finish_time.date():
stopfmt = '%H:%M'
else:
stopfmt = '%-m/%-d/%y %H:%M'
title_1 = MMS_SURVEY_ION_1_Start_time.strftime('%m/%d/%y %H:%M')+' -'+MMS_SURVEY_ION_1_Finish_time.strftime(stopfmt)
if dt_MMS.seconds !=0:
title_1 = title_1 + ' with '+str(dt_MMS.seconds)+' second time averaging'
for j, ax in enumerate(axs_MMS.T.flatten()):
flix_1 = np.array(H_Flux_SURVEY_ION_1[sidx_MMS_1_SURVEY_ION:lidx_MMS_1_SURVEY_ION,
j, :].T)
if dt_MMS==dt.timedelta(0):
fluxwin_1 = flix_1
timewin_1 = EPOCH_SURVEY_ION_1[sidx_MMS_1_SURVEY_ION:lidx_MMS_1_SURVEY_ION]
else:
fluxwin_1=[[0 for y in range(len(flix_1))] for x_1 in range(len(flix_1))]
for i, flox in enumerate(flix_1):
fluxwin_1[i], timewin_1 = windowMean(flox, EPOCH_SURVEY_ION_1[sidx_MMS_1_SURVEY_ION:lidx_MMS_1_SURVEY_ION],
winsize=dt_MMS, overlap=dt.timedelta(0))
fluxwin_1[i] = np.array(fluxwin_1[i])
for x_1 in np.where(np.diff(EPOCH_SURVEY_ION_1[sidx_MMS_1_SURVEY_ION:lidx_MMS_1_SURVEY_ION])
>dt.timedelta(hours=1))[0]+sidx_MMS_1_SURVEY_ION:
fluxwin[i][bi.bisect_right(timewin_1, EPOCH_SURVEY_ION_1[x_1]):bi.bisect_right(timewin_1,
EPOCH_SURVEY_ION_1[x_1+1])]=0
fluxwin_1 = np.array(fluxwin_1)
fluxwin_1[np.where(fluxwin_1<=0)] = 0
x_1 = mdates.date2num(timewin_1)
pax_1 = ax.pcolormesh(x_1, Ion_Energy_SURVEY_ION_1, fluxwin_1, shading='turkey',cmap=cmap, vmin=1,
vmax=np.nanmax(H_Flux_SURVEY_ION_1[sidx_MMS_1_SURVEY_ION:lidx_MMS_1_SURVEY_ION,:,:]),
norm=LogNorm())
sax_1 = ax.twinx()
plt.setp(sax_1.get_yticklabels(), visible=False)
sax_1.tick_params(axis='y', right='off')
ax.set_xlim(MMS_SURVEY_ION_1_Start_time, MMS_SURVEY_ION_1_Finish_time)
ax.set_yscale('log')
ax.set_yticks([10, 100, 1000,10000])
#Allows non-log formatted values to be used for ticks
ax.yaxis.set_major_formatter(plt.ScalarFormatter())
axs_MMS[0].set_ylabel('Energy (eV)')
axs_MMS[0].set_title(title_1)
cbar_ax_1 = fig_MMS.add_axes([0.93, 0.15, 0.02, 0.7])
cb_MMS_1 = fig_MMS.colorbar(pax_1, cax=cbar_ax_1)
cb_MMS_1.set_label(r'Counts sec$^{-1}$ ster$^{-1}$ cm$^{-2}$ keV$^{-1}$')
#Sets the colorbar value range
cb_MMS_1.set_clim(1, np.nanmax(H_Flux_SURVEY_ION_1[sidx_MMS_1_SURVEY_ION:lidx_MMS_1_SURVEY_ION,:,:]))
#Redraws the colorbar
cb_MMS_1.draw_all()
Solved
The problem was that I had not installed all packages. For all users who use Ubuntu 16.04 LTS you will need to type the following commands into your terminal
sudo apt-get install dvipng
sudo apt-get install texlive-latex-extras
sudo apt-get install texlive-fonts-recommended
To be sure that your specific package is in a specific subgroup of latex and you need to install please refer to this page. Furthermore THE MOST IMPORT PART OF THE SOLUTION was the following:
Switching this:
[r'/usepackage{amsmath}']
To this:
[r'\usepackage{amsmath}']
Let this be a lesson for everyone that syntax is important and knowing whats on your computer.
Respectfully submitted, A
