I am having two problems, both related to memory problems. The first case happens when there are about 5 resolvers used (see code and explanation below), the second when there are used about 15 resolvers. To the first problem there is a similar question on Stackoverflow. The solution to this problem was to clear the memory after each loop but I want to create mutliple datalines in a single graph, so this doesn't work for me.
Here is the code snippet where all that happens:
fig = plt.figure()
ax = fig.add_subplot(111)
def add_plot(resolver_name, results):
sum_results = sum(results)
norm = [float(i)/sum_results for i in results]
cy = np.cumsum(norm)
ax.plot(results, cy, label=resolver_name, linewidth=0.8)
for resolver in resolvers:
results = db.get_rt(resolver["ipv4"], tls)
add_plot(resolver["name"], results)
# Positioning of legend
box = ax.get_position()
ax.set_position([box.x0, box.y0, box.width * 0.8, box.height])
ax.legend(loc='center left', bbox_to_anchor=(1, 0.5))
fig.set_size_inches(10,5)
ax.set_xscale('log')
plt.title('CDF response time for '+('DNS-over-TLS measurements' if tls else 'DNS measurements'))
plt.xlabel("Response time (ms)")
plt.ylabel("CDF")
plt.grid(True)
png_name = V.base_directory+"/plots/rt_cdf.png"
if (tls):
png_name = V.base_directory+"/plots/rt_cdf_tls.png"
log.info("Plotting graph to "+png_name)
plt.savefig(png_name)
The variable resolvers contains some information about several public DNS resolvers. The variable results is a list of float values. All other unclear variables should not be relevant to this problem. But feel free to ask if you need further explanation.
Problem 1
As said this happens when there are used about 5 resolvers. The size of results varies between ~1 million and ~6 million entries. A MemoryError occurs at the last line:
Traceback (most recent call last):
File "plot_building/rt_cdf.py", line 63, in <module>
plt.savefig(png_name)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 695, in savefig
res = fig.savefig(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/figure.py", line 2062, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 2263, in print_figure
**kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 517, in print_png
FigureCanvasAgg.draw(self)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 437, in draw
self.figure.draw(self.renderer)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/figure.py", line 1493, in draw
renderer, self, artists, self.suppressComposite)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/image.py", line 141, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/axes/_base.py", line 2635, in draw
mimage._draw_list_compositing_images(renderer, self, artists)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/image.py", line 141, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/lines.py", line 756, in draw
tpath, affine = (self._get_transformed_path()
File "/usr/local/lib/python2.7/dist-packages/matplotlib/transforms.py", line 2848, in get_transformed_path_and_affine
self._revalidate()
File "/usr/local/lib/python2.7/dist-packages/matplotlib/transforms.py", line 2822, in _revalidate
self._transform.transform_path_non_affine(self._path)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/transforms.py", line 2492, in transform_path_non_affine
return self._a.transform_path_non_affine(path)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/transforms.py", line 1564, in transform_path_non_affine
x = self.transform_non_affine(path.vertices)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/transforms.py", line 2271, in transform_non_affine
return np.concatenate((x_points, y_points), 1)
MemoryError
Problem 2
This was a bit harder to figure out. At some point during the runtime the process just stopped. After some searching I found the following in var/log/syslog
[27578124.494907] Out of memory: Kill process 376 (python) score 897 or sacrifice child
[27578124.495020] Killed process 376 (python) total-vm:2081432kB, anon-rss:1833416kB, file-rss:1464kB
I think some other lines in the logfile might also belong to this problem but what I've found is that this problem is caused by having not enough RAM.
The script is running on a Ubuntu VM with 2GB RAM.
Any ideas how I could fix any of those problems?
Are you watching your system monitor whilst running this? Are you running out of RAM?
6 million points seems huge can you not just sample less?
Related
I am using maplotlib's Basemap to draw maps of the world and want to include longitude and latitude lines. This can be done using drawmeridians() and drawparallels(), but the linestyle of the corresponding lines can only be set via the keyword dashes. According to the documentation, see see here, is should work as follows:
dash pattern for meridians (default [1,1], i.e. 1 pixel on, 1 pixel off)
I tried dashes=[1,0] but that did not worked. Is there any simple way to have solid linestyle?
Here is my code:
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.basemap import Basemap
fig1, ax1 = plt.subplots(1,1)
map1 = Basemap( resolution='l', projection='mill',
llcrnrlat=-60., llcrnrlon=-180.,
urcrnrlat=90., urcrnrlon=180. )
map1.drawcoastlines()
map1.drawmapboundary( fill_color='aqua' )
map1.fillcontinents( color='coral', lake_color='aqua' )
# labels=[left,right,top,bottom]
map1.drawparallels( np.arange(-80.,81.,20.), labels=[True,True,False,False] )
map1.drawmeridians( np.arange(-180.,181.,40.), labels=[False,False,True,True] )
plt.show()
Here is the resulting map:
Edit 1: I just tried on a different computer and there it works, i.e. dashes=[1,0] results in solid linestyle. The version used on that computer are (according to a pip freeze)
basemap==1.2.0
matplotlib==2.2.3
As soon as I have access again to the original computer, I'll check what is going on there (and which versions are installed).
Edit 2: Being back at the computer where it did not worked, I can now tell a bit more. First, the following versions are used:
basemap==1.1.1
matplotlib==3.0.2
Then the error message (which I forgot to include previously):
ValueError: All values in the dash list must be positive
Edit 3: For the sake of completeness (and since it was partly helpful to hunt down the solution), here is the full Traceback:
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1540, in __call__
return self.func(*args)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_tkagg.py", line 280, in resize
self.show()
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_tkagg.py", line 351, in draw
FigureCanvasAgg.draw(self)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 464, in draw
self.figure.draw(self.renderer)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/figure.py", line 1143, in draw
renderer, self, dsu, self.suppressComposite)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/axes/_base.py", line 2409, in draw
mimage._draw_list_compositing_images(renderer, self, dsu)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/lines.py", line 822, in draw
drawFunc(renderer, gc, tpath, affine.frozen())
File "/usr/local/lib/python2.7/dist-packages/matplotlib/lines.py", line 1267, in _draw_lines
self._lineFunc(renderer, gc, path, trans)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/lines.py", line 1297, in _draw_dashed
gc.set_dashes(self._dashOffset, self._dashSeq)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 1007, in set_dashes
raise ValueError("All values in the dash list must be positive")
After some research on some bugreports on github I found the solution [1], dashes=(None,None):
map1.drawmeridians( np.arange(-180.,181.,40.), labels=[False,False,True,True], dashes=(None,None) )
[1] https://github.com/matplotlib/basemap/issues/173#issuecomment-68243710
I am using matplotlib(with LaTex enabled and agg backend) in order to display hydrodynamical simulations using the pcolormesh function.
System: Ubuntu 16.04
Python: Python 2.7.12
Matplotlib: 1.5.1-1ubuntu1
Im am also adding additional axis using twinx twiny After saving ~300 png images I get a crash pointing to a non-working dvi conversion command when processing the title. I am always using pylab.close("all") in order to close my figure after each saving process.
pylab.rc('text', usetex=True)
pylab.rc('text.latex', preamble=[r"\usepackage{amsmath}", r"\usepackage{amssymb}", r"\usepackage[alsoload=astronomy]{siunitx}"])
pylab.close("all")
f, ax = pylab.subplots(1)
cmap = pylab.cm.jet
cmap.set_bad('w',1.)
if in logquantity:
plot = ax.pcolormesh(x, y, quantity , vmax=maxvalue, vmin=minvalue, norm=LogNorm(vmax= maxvalue, vmin = minvalue), cmap=cmap)
else:
plot = ax.pcolormesh(x, y, quantity, vmax=maxvalue, vmin=minvalue, cmap=cmap)
ax.set_title("Title")
ax.set_aspect("equal")
ax.set_xscale("log")
ax.grid()
...<More Formatting stuff>
ax2 = ax.axes.twiny()
ax3 = ax.twinx()
...<Formatting labels, setting scales etc>
pylab.savefig("test.png", dpi = 800, bbox_inches='tight')
pylab.close("all")
pylab.savefig("test.png", dpi = 800, bbox_inches='tight')
File "/usr/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 689, in savefig
fig.canvas.draw_idle() # need this if 'transparent=True' to reset colors
File "/usr/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 2026, in draw_idle
self.draw(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 474, in draw
self.figure.draw(self.renderer)
File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 61, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/figure.py", line 1159, in draw
func(*args)
File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 61, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/axes/_base.py", line 2324, in draw
a.draw(renderer)
File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 61, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/text.py", line 792, in draw
mtext=mtext)
File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 253, in draw_tex
Z = texmanager.get_grey(s, size, self.dpi)
File "/usr/lib/python2.7/dist-packages/matplotlib/texmanager.py", line 583, in get_grey
pngfile = self.make_png(tex, fontsize, dpi)
File "/usr/lib/python2.7/dist-packages/matplotlib/texmanager.py", line 524, in make_png
'dvipng: \n\n' % dvifile + report)
RuntimeError: dvipng was not able to process the following file:
$HOME/.cache/matplotlib/tex.cache/2664bc1e879cb69289e1663e63a1c713.dvi
Here is the full report generated by dvipng:
No dvipng error report available.
If I check the mentioned .cache location I can perfectly find the dvi file mentioned. if I use dvipng on it I get the perfectly correctly rendered header it should put in the plot. I am assuming some kind of cache/buffer is running full. If it only concerns lineplots using plot,semilogy, semilogx and loglog I get this error after a much higher number of images. I can also provided the formatting details(or any other additional information) if anoyone thinks they are relevant for this problem.
Thank you in advance for your answers :-)
EDIT:
The string is $\rho$$\left[6.96e-20 \frac{\si{\gram}}{\si{\centi \meter \cubed}}\right]$, $t =\num{0.00e+00}\text{y}$, $n_R = \num{300}$, $n_{\varphi} = \num{50}$, $n_z = \num{401},\ [C.L.] = 1.14e+02\text{pc}$
Png Version of cached file
This is the result when I copy the cached file to another location and convert it to a png manually using dvipng.
The problem is not specific to this plot. It can happen with any plot. It works fine for whatever the first ~300 plots are. It is not always the same plot for which it crashes. That is one of the problems of looking into the problem.
There is a loop that runs through all quantities and then calls functions to plot
for quantityname in quantities:
quantitydict = quantities[quantityname]
quantity = quantitydict["data"]
There are 18 of these quantities per time-step.
EDIT2(More Information)
The error occurs more often when the machine it is run on does not have much free Main Memory(below 10GB, script uses roughly 1GB while running).
Also, sometimes manifests differently. It gives a LaTeX error. All the previous plots created in the run work just fine and I copy the line and compile it in LaTeX I get the correct result. Error Message:
pylab.savefig("test.png", dpi = 800, bbox_inches='tight')
File "/usr/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 688, in savefig
res = fig.savefig(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/figure.py", line 1565, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 2180, in print_figure
**kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 527, in print_png
FigureCanvasAgg.draw(self)
File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 474, in draw
self.figure.draw(self.renderer)
File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 61, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/figure.py", line 1159, in draw
func(*args)
File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 61, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/axes/_base.py", line 2324, in draw
a.draw(renderer)
File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 61, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/python2.7/dist-packages/matplotlib/text.py", line 749, in draw
bbox, info, descent = textobj._get_layout(renderer)
File "/usr/lib/python2.7/dist-packages/matplotlib/text.py", line 361, in _get_layout
ismath=ismath)
File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 229, in get_text_width_height_descent
renderer=self)
File "/usr/lib/python2.7/dist-packages/matplotlib/texmanager.py", line 675, in get_text_width_height_descent
dvifile = self.make_dvi(tex, fontsize)
File "/usr/lib/python2.7/dist-packages/matplotlib/texmanager.py", line 422, in make_dvi
report))
RuntimeError: LaTeX was not able to process the following string:
'CFL $\\\\Delta t_\\\\text{min}$$\\\\left[4.65e+05 \\\\text{yrs}\\\\right]$, $t =\\\\num{3.80e+03}\\\\text{y}$, $n_R = \\\\num{300}$, $n_{\\\\varphi} = \\\\num{50}$, $n_z = \\\\num{401},\\\\ [C.L.] = 1.14e+02\\\\text{pc}$'
Here is the full report generated by LaTeX:
No latex error report available.
I'm writing a lab report for uni and have decided to use pyplot to draw a graph for it. The units for one of my axes is V^(-1), but I can't seem to get matplotlib to write that with the power in superscript (it only superscripts the minus sign) when using the code:
plt.xlabel('$1/U (10^5 V ^-1 )$')
I'd also like to match the fonts used for the axes titles with that used for the values on the axes if at all possible. I've tried putting:
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
at the beginning of my code, but that gives me the error:
File "C:\Users\Sam\Documents\Uni\Labs\pytry.py", line 92, in <module>
plt.savefig("Xrayplot.png")
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\pyplot.py", line 561, in savefig
return fig.savefig(*args, **kwargs)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\figure.py", line 1421, in savefig
self.canvas.print_figure(*args, **kwargs)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\backends\backend_wxagg.py", line 85, in print_figure
FigureCanvasAgg.print_figure(self, filename, *args, **kwargs)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\backend_bases.py", line 2220, in print_figure
**kwargs)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\backends\backend_agg.py", line 505, in print_png
FigureCanvasAgg.draw(self)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\backends\backend_agg.py", line 451, in draw
self.figure.draw(self.renderer)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\artist.py", line 54, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\figure.py", line 1034, in draw
func(*args)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\artist.py", line 54, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\axes.py", line 2086, in draw
a.draw(renderer)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\artist.py", line 54, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\axis.py", line 1089, in draw
renderer)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\axis.py", line 1038, in _get_tick_bboxes
extent = tick.label1.get_window_extent(renderer)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\text.py", line 753, in get_window_extent
bbox, info, descent = self._get_layout(self._renderer)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\text.py", line 320, in _get_layout
ismath=False)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\backends\backend_agg.py", line 205, in get_text_width_height_descent
renderer=self)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\texmanager.py", line 666, in get_text_width_height_descent
dvifile = self.make_dvi(tex, fontsize)
File "C:\Users\Sam\AppData\Local\Enthought\Canopy\User\lib\site-packages\matplotlib\texmanager.py", line 413, in make_dvi
'LaTeX: \n\n' % repr(tex)) + report)
RuntimeError: LaTeX was not able to process the following string:
'lp'
Here is the full report generated by LaTeX:
Any help would be much appreciated.
For the superscript add { } around the text that should be super scripted. For the fonts i don't know the solution.
plt.xlabel('$1/U (10^5 V ^{-1} )$')
Just wanted to see if others thought that the following behaviour in matplotlib plot_date was buggy, or if it's just something I should put up with.
I have a multi-panel plot that I set up with sharex to facilitate zoom/pan on all axes, and I plot time series data in both panels. However, in the second panel, all of the data happens to be invalid (in this example I mask it).
from matplotlib.pyplot import figure,show
from datetime import datetime,timedelta
from numpy import sin,cos,linspace,pi,ma,array
fig=figure(figsize=(16,9))
ax1=fig.add_subplot(211)
ax2=fig.add_subplot(212,sharex=ax1)
# xdata is seconds
xdata=linspace(0,9999,10000)
tdata=array([datetime(2000,1,1)+timedelta(seconds=ss) for ss in xdata])
data1=ma.masked_array(sin(pi*xdata/300),mask=False)
data2=ma.masked_array(cos(pi*xdata/300),mask=True)
ax1.plot_date(tdata,data1,marker='',color='r')
ax2.plot_date(tdata,data2,marker='',color='b')
show()
I'd expect (prefer) it to just show up a blank panel, not to fail and give me a long unhelpful traceback. Is this the expected behaviour?
Notes:
This script also fails if I use ax.plot(...) instead of ax.plot_date(...)
It works fine (i.e. gives me an empty panel) if I just plot against xdata, not the datetime array tsdata (but I have to use ax1.set_xlim(xdata[0],xdata[-1]) to get a sensible domain displayed):
ax1.plot(xdata,data1,marker='',color='r')
ax2.plot(xdata,data2,marker='',color='b')
ax1.set_xlim(xdata[0],xdata[-1])
show()
I have just realised I can rescue the above plot by forcing the ax2 limits right before the show() command. I still think that the failure in the main example is inelegant:
ax2.set_xlim(tdata[0],tdata[-1])
show()
What do the experts think?
Thanks!
F.Y.I., This was on matplotlib 1.1.0, compiled from source on my PC.
Here is the traceback that I get:
Traceback (most recent call last):
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/backendsbackend_gtk.py", line 395, in expose_even
self._render_figure(self._pixmap, w, h)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py", line 75, in _render_f
FigureCanvasAgg.draw(self)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 401, in draw
self.figure.draw(self.renderer)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/figure.py", line 884, in draw
func(*args)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/axes.py", line 1983, in draw
a.draw(renderer)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/axis.py", line 1036, in draw
ticks_to_draw = self._update_ticks(renderer)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/axis.py", line 926, in _update_ticks
tick_tups = [ t for t in self.iter_ticks()]
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/axis.py", line 873, in iter_ticks
majorLocs = self.major.locator()
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/dates.py", line 749, in __call__
self.refresh()
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/dates.py", line 758, in refresh
dmin, dmax = self.viewlim_to_dt()
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/dates.py", line 530, in viewlim_to_dt
return num2date(vmin, self.tz), num2date(vmax, self.tz)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/dates.py", line 289, in num2date
if not cbook.iterable(x): return _from_ordinalf(x, tz)
File "/home/tchubb/local/lib/python2.7/site-packages/matplotlib/dates.py", line 203, in _from_ordinalf
dt = datetime.datetime.fromordinal(ix)
ValueError: ordinal must be >= 1
If you suspect this is an IPython bug, please report it at:
https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev#scipy.org
Yes, I would call this a bug, or at least an oversight which looks like it has been fixed (via #ali_m https://github.com/matplotlib/matplotlib/issues/162).
I was getting this exception, but that was on a version of 1.3.x from June (my bad, thought I had a more current version on this computer). Current master does not have this problem and #ali_m reports that it also works on 1.2.1 and 1.3.0 so I suspect the fix is to upgrade you version of matplotlib.
What looks like is going on is that there isn't a check in the code that sorts out where to put the ticks has no check to make sure you have given in non-empty data.
The reason that setting the limits explicitly prevents the error is that the code never tries to figure out what the range of your empty data is.
Please create a github issue for this (and include the trace back in the issue).
In [7]: Traceback (most recent call last):
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/backends/backend_qt4.py", line 366, in idle_draw
self.draw()
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/backends/backend_qt4agg.py", line 148, in draw
FigureCanvasAgg.draw(self)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/backends/backend_agg.py", line 440, in draw
self.figure.draw(self.renderer)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/artist.py", line 54, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/figure.py", line 1027, in draw
func(*args)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/artist.py", line 54, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 2088, in draw
a.draw(renderer)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/artist.py", line 54, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/axis.py", line 1076, in draw
ticks_to_draw = self._update_ticks(renderer)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/axis.py", line 938, in _update_ticks
tick_tups = [t for t in self.iter_ticks()]
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/axis.py", line 882, in iter_ticks
majorLocs = self.major.locator()
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/dates.py", line 785, in __call__
self.refresh()
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/dates.py", line 794, in refresh
dmin, dmax = self.viewlim_to_dt()
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/dates.py", line 560, in viewlim_to_dt
return num2date(vmin, self.tz), num2date(vmax, self.tz)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/dates.py", line 305, in num2date
return _from_ordinalf(x, tz)
File "/home/tcaswell/local_installs/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/dates.py", line 208, in _from_ordinalf
dt = datetime.datetime.fromordinal(ix)
ValueError: ordinal must be >= 1
I'm trying to set tick mark positions in matplotlib. I get errors when running the following minimal example:
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.ticker import MultipleLocator
x = 10.*np.random.randn(1000)
y = 10.*np.random.randn(1000)
fig = plt.figure()
ax = fig.add_subplot(1,1,1)
ax.scatter(x, y)
ax.xaxis.set_major_formatter(MultipleLocator(1.))
ax.yaxis.set_major_formatter(MultipleLocator(1.))
plt.show()
The error lies with the two lines that set the x- and y-axis tick marks. If I use NullFormatter() instead, or omit these lines entirely, the code runs fine and produces the expected plot. The above code, however, returns the following error:
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1413, in __call__
return self.func(*args)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 245, in resize
self.show()
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 248, in draw
FigureCanvasAgg.draw(self)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 394, in draw
self.figure.draw(self.renderer)
File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 798, in draw
func(*args)
File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 1946, in draw
a.draw(renderer)
File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/axis.py", line 971, in draw
tick_tups = [ t for t in self.iter_ticks()]
File "/usr/lib/pymodules/python2.7/matplotlib/axis.py", line 906, in iter_ticks
self.major.formatter.set_locs(majorLocs)
AttributeError: MultipleLocator instance has no attribute 'set_locs'
I've tried googling this error, but I can't find anyone else who has a similar problem. Any ideas as to why the use of locators is yielding errors?
MultipleLocator is a locator, not a formatter. You want to use
ax.xaxis.set_major_locator(MultipleLocator(1.))
ax.yaxis.set_major_locator(MultipleLocator(1.))
This works for me (doesn't look too pretty using 1, but it works).