I encountered a strange issue with the seaborn library. When generating barplot for data with ranging from very low to very high values, e.g.:
job duration type
0 1 83066.639344 A
1 2 820.700000 B
it fails with:
ValueError: cannot convert float NaN to integer
This looks like a bug in matplotlib and a duplicate of "pyplot.savefig fails with ValueError: cannot convert float NaN to integer". The latter has not been fixed yet. Is there a workaround for it?
Here's the minimal working example to reproduce the issue:
#!/usr/bin/env python3
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
d = {'job': [1, 2]),
'duration': [83066.639344, 820.700000],
'type': ['A', 'B']}
df = pd.DataFrame(d)
plot = sns.catplot(x="duration", y="job", data=df, hue='type',
color="b", kind="bar", height=3, aspect=4)
ax = plot.axes.flat[0]
for p in plt.gca().patches:
ax.text(p.get_width(),
p.get_y() + p.get_height() / 2,
p.get_width())
plot.savefig("barplot.png")
Some observations:
The problem does not occur when I do not differentiate between 'type' (no use ofhue='type').
Here's the full stacktrace:
posx and posy should be finite values
posx and posy should be finite values
/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/numpy/core/fromnumeric.py:83: RuntimeWarning: invalid value encountered in reduce
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
posx and posy should be finite values
posx and posy should be finite values
posx and posy should be finite values
Traceback (most recent call last):
File "/Users/dzieciou/projects/example/gocd/reproduce.py", line 31, in <module>
plot.savefig("barplot.png")
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/seaborn/axisgrid.py", line 37, in savefig
self.fig.savefig(*args, **kwargs)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/figure.py", line 2094, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 2075, in print_figure
**kwargs)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/backends/backend_agg.py", line 510, in print_png
FigureCanvasAgg.draw(self)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/backends/backend_agg.py", line 402, in draw
self.figure.draw(self.renderer)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/figure.py", line 1649, in draw
renderer, self, artists, self.suppressComposite)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/image.py", line 138, in _draw_list_compositing_images
a.draw(renderer)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 2610, in draw
mimage._draw_list_compositing_images(renderer, self, artists)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/image.py", line 138, in _draw_list_compositing_images
a.draw(renderer)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/axis.py", line 1185, in draw
ticks_to_draw = self._update_ticks(renderer)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/axis.py", line 1023, in _update_ticks
tick_tups = list(self.iter_ticks()) # iter_ticks calls the locator
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/axis.py", line 967, in iter_ticks
majorLocs = self.major.locator()
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/ticker.py", line 1985, in __call__
return self.tick_values(vmin, vmax)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/ticker.py", line 1993, in tick_values
locs = self._raw_ticks(vmin, vmax)
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/ticker.py", line 1932, in _raw_ticks
nbins = np.clip(self.axis.get_tick_space(),
File "/Users/dzieciou/virtualenvs/seaborn/lib/python3.7/site-packages/matplotlib/axis.py", line 2543, in get_tick_space
return int(np.floor(length / size))
ValueError: cannot convert float NaN to integer
Note that this is neither really a bug, nor is it related to the linked bug, which is indeed fixed.
One could argue that there should be a better error message when plotting text at nan coordinates though.
Before looking at the error, it seems you have another problem in your code, which is that you set the x coordinate of the text to the width of the bar. They are usually unrelated and you might have meant to use p.get_x() instead.
Now two options:
1. Don't position text at invalid coordinates.
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
d = {'job': list(range(1, 3)),
'duration': [83066.639344, 820.700000],
'type': ['A', 'B']}
df = pd.DataFrame(d)
plot = sns.catplot(x="duration", y="job", data=df, hue='type',
color="b", kind="bar", height=3, aspect=4)
ax = plot.axes.flat[0]
for p in plt.gca().patches:
height = np.nan_to_num(p.get_height(), 0)
ax.text(p.get_x(), p.get_y() + height/2., "My text")
plot.savefig("barplot.png")
plt.show()
2. Don't use bbox_inches="tight".
If you want to keep your code as it is, you may workaround this by not setting the bbox_inches="tight" options in seaborn's savefig.
plot.savefig("barplot.png", bbox_inches=None)
Or use matplotlib's savefig option
plot.fig.savefig("barplot.png")
Related
I'm trying to plot a pandas series, but I'm encountering an error when I attempt to format the x-axis date.
(A related issue was identified in the comments, but it appears that it was resolved in a much older version of pandas than what I'm using. So, it seems like this is a new problem.)
Consider a plot of the following pandas series:
import pandas as pd
d = {pd.Timestamp('2021-03-15 08:30:00'): -65.926651,
pd.Timestamp('2021-03-15 08:30:05'): -42.115551,
pd.Timestamp('2021-03-15 08:30:10'): -24.699627,
pd.Timestamp('2021-03-15 08:30:15'): -12.010081,
pd.Timestamp('2021-03-15 08:30:20'): -2.781321}
s = pd.Series(d)
ax = s.plot()
I seek to format the x-axis date on the plot using:
from matplotlib.dates import DateFormatter
format_str: str = '%H:%M:%S'
format_: DateFormatter = DateFormatter(format_str)
ax.xaxis.set_major_formatter(format_)
This results in the following error:
Traceback (most recent call last):
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/backends/backend_macosx.py", line 61, in _draw
self.figure.draw(renderer)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/figure.py", line 1863, in draw
mimage._draw_list_compositing_images(
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/image.py", line 131, in _draw_list_compositing_images
a.draw(renderer)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/cbook/deprecation.py", line 411, in wrapper
return func(*inner_args, **inner_kwargs)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 2747, in draw
mimage._draw_list_compositing_images(renderer, self, artists)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/image.py", line 131, in _draw_list_compositing_images
a.draw(renderer)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/axis.py", line 1164, in draw
ticks_to_draw = self._update_ticks()
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/axis.py", line 1022, in _update_ticks
major_labels = self.major.formatter.format_ticks(major_locs)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/ticker.py", line 250, in format_ticks
return [self(value, i) for i, value in enumerate(values)]
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/ticker.py", line 250, in <listcomp>
return [self(value, i) for i, value in enumerate(values)]
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/dates.py", line 605, in __call__
return num2date(x, self.tz).strftime(self.fmt)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/dates.py", line 511, in num2date
return _from_ordinalf_np_vectorized(x, tz).tolist()
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/numpy/lib/function_base.py", line 2108, in __call__
return self._vectorize_call(func=func, args=vargs)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/numpy/lib/function_base.py", line 2192, in _vectorize_call
outputs = ufunc(*inputs)
File "/Users/me/VirtualEnvironments/my_venv/lib/python3.9/site-packages/matplotlib/dates.py", line 331, in _from_ordinalf
np.timedelta64(int(np.round(x * MUSECONDS_PER_DAY)), 'us'))
OverflowError: int too big to convert
Interestingly, if I add a fractional offset to the timestamps, everything works:
s.index += pd.DateOffset(seconds=0.5)
When I examine x in the np.timedelta64 call, it corresponds to the number of days since the start of the unix epoch (1 Jan 1970) only if I add a fractional part to the timestamp. If there's no fractional part, the resulting integer is huge and seems to have no obvious relationship to the number of days since 1 Jan 1970.
What's wrong here?
Error occurred because data was given that exceeded the number range handled by DateFormatter.
Please refer to the official reference.
For example, the actual data for the first time series looks like this
s.index[0].value
1615797000000000000
This needs to be converted to numbers that can be handled by matplotlib.
s.index = mdates.date2num(s.index)
s
18701.354167 -65.926651
18701.354225 -42.115551
18701.354282 -24.699627
18701.354340 -12.010081
18701.354398 -2.781321
dtype: float64
update(I am on 3.6.3, so I am fixing it.)
ax = s.plot(style='o-')
import matplotlib.dates as mdates
format_str = '%H:%M:%S'
format_ = mdates.DateFormatter(format_str)
ax.xaxis.set_major_formatter(format_)
I had the same error message and I used this to resolve it.
import matplotlib.dates as mdates
ts = mdates.epoch2num(ts)
After that, I didn't have any error. I hope it will be help you.
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from sklearn.linear_model import LinearRegression
a = np.zeros((1000,3))
fig=plt.figure()
ax=fig.gca(projection='3d')
line1,=ax.plot(a[:,0], a[:,1], a[:,2], 'k')
ax.set_xlabel('$x_1_t$');ax.set_ylabel('$x_1_t-tau$');ax.set_zlabel('$x_1_t-2tau$')
plt.title('hello')
plt.show()
I use python2.x. The error message is the following. Anyone knows how to fix it?
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_macosx.py", line 83, in _draw
self.figure.draw(renderer)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/figure.py", line 1475, in draw
renderer, self, artists, self.suppressComposite)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/image.py", line 141, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 298, in draw
ax.draw(renderer)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mpl_toolkits/mplot3d/axis3d.py", line 306, in draw
self.label.draw(renderer)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/text.py", line 706, in draw
bbox, info, descent = textobj._get_layout(renderer)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/text.py", line 309, in _get_layout
ismath=ismath)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 237, in get_text_width_height_descent
self.mathtext_parser.parse(s, self.dpi, prop)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mathtext.py", line 3293, in parse
box = self._parser.parse(s, font_output, fontsize, dpi)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mathtext.py", line 2521, in parse
six.text_type(err)]))
ValueError:
^ Double subscript (at char 0), (line:1, col:1)
As the other answer suggests, the problem is trying to use double subscripts in the axis labels. The solution depends on how you would like the labels to look.
If you would like the 1 and the t to both be subscripts then you can use:
$x_{1t}$
If you want the first underscore to be an actual underscore then you can use
$x\_1_t$
The problem is in your labels, you are using a double subscripts:
$x_1_t$
If you change to just using single subscripts it should work (e.g):
$x_1t$
I have code to crawl through every file in a directory and plot every csv file it comes across. Each CSV has a header of the form
`Timestamp, P1rms (A), P2rms (A), P3rms (A), P4rms (A), P5rms (A), Vrms (V), P1 theta, P2 theta, P3 theta, P4 theta, P5 theta`.
Mon Sep 30 00:00:00 2013, 128, 128, 180, 177, 192, 43, 7, 7, 8, 8, 48
Mon Sep 30 00:00:01 2013, 127, 127, 182, 178, 193, 43, 8, 8, 8, 8, 49
# ect....
I am developing a fft visualization option, and I am running into an overflow error when I fft my data sets. here is my exact problem:
When I run my code:
#!/usr/bin/env python
from pandas import *
import matplotlib.pyplot as plt
import os
import sys
import platform
import numpy.fft as np
# name of plots folder
plotfold='plots'
# System specific info
if platform.system()=='Darwin':comsep="/"
else: comsep="\\"
# How many columns should I plot?
numcol=6
if len(sys.argv)<2:
print 'usage: ./canaryCrawler.py [-c] or [-f] rootdir'
quit()
if len(sys.argv)>2:
ylim=1500
root = sys.argv[2]
else:
ylim=1200
root = sys.argv[1]
for subdir, dirs, files in os.walk(root):
# plot each file
for file in files:
if str(file)[-4:]=='.csv':
print 'plotting '+str(file)+'...'
# load csv as data frame
df=pandas.io.parsers.read_csv(subdir+comsep+file)
for i in range(0,len(df.Timestamp)):
df.Timestamp[i] = datetime.strptime(df.Timestamp[i], '%a %b %d %H:%M:%S %Y')
# We only want the first 6 collumns
df = df.ix[:,0:numcol]
if len(sys.argv)>=2:
if sys.argv[1]=='-c' or sys.argv[1]=='-f':
plotfold='plots_Specialty'
df2 = df
df=pandas.DataFrame(df2.Timestamp)
df['Residence']=df2['P1rms (A)']+df2['P2rms (A)']
df['Specialty']=df2['P3rms (A)']+df2['P4rms (A)']
if sys.argv[1]=='-f':
df2['Residence']=np.fft(df['Residence'])
df2['Specialty']=np.fft(df['Specialty'])
df=df2
print 'Fourier Transformation Complete'
plotfold='plots_Specialty_fft'
# set up plot
plt.figure()
df.plot(df.Timestamp,alpha=0.6,linewidth=2.3) # add transparency to see overlapping colors
plt.tight_layout(pad=1.08)
plt.legend(loc='best') # add legend in non-intrusive location
plt.legend(loc=5,prop={'size':14}) #
plt.ylabel('Current')
plt.xlabel('Time')
plt.gcf().autofmt_xdate()
plt.gcf().set_size_inches(12.7,9.2)
plt.gca().set_ylim([0,ylim])
stamp = df.Timestamp[0]
day = datetime.strftime(stamp,'%a')
DOM=datetime.strftime(stamp,'%d')
month = datetime.strftime(stamp,'%b')
year = datetime.strftime(stamp,'%Y')
plt.title(subdir+' '+day+' '+month+' '+DOM+' '+year)
# keep plot
# check for existing plots folder,
# create one if it doesn't exist
if plotfold not in os.listdir(subdir):
print '** adding plots directory to ',subdir
os.mkdir(subdir+comsep+plotfold)
# save in plots directory
spsubs = str(subdir).split(comsep)
filnam=''
for piece in range(len(spsubs)-4,len(spsubs)-1):
filnam+='_'+spsubs[piece]
filnam+='_'+str(file)[:-4]
saveto=subdir+comsep+plotfold+comsep+filnam
print '**** saving plot to ',saveto
plt.savefig(saveto)
plt.close()
I get this error:
kilojoules$ ./canaryCrawler.py -f 35ca7/
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandas-0.14.0-py2.7-macosx-10.9-x86_64.egg/pandas/io/excel.py:626: UserWarning: Installed openpyxl is not supported at this time. Use >=1.6.1 and <2.0.0.
.format(openpyxl_compat.start_ver, openpyxl_compat.stop_ver))
plotting 2014Aug04.csv...
Fourier Transformation Complete
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-x86_64.egg/numpy/core/numeric.py:460: ComplexWarning: Casting complex values to real discards the imaginary part
return array(a, dtype, copy=False, order=order)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/tight_layout.py:225: UserWarning: tight_layout : falling back to Agg renderer
warnings.warn("tight_layout : falling back to Agg renderer")
**** saving plot to 35ca7/2014/Aug/plots_Specialty_fft/_Aug_35ca7_2014_2014Aug04
plotting 2014Aug05.csv...
Fourier Transformation Complete
**** saving plot to 35ca7/2014/Aug/plots_Specialty_fft/_Aug_35ca7_2014_2014Aug05
plotting 2014Aug07.csv...
Fourier Transformation Complete
**** saving plot to 35ca7/2014/Aug/plots_Specialty_fft/_Aug_35ca7_2014_2014Aug07
Traceback (most recent call last):
File "./canaryCrawler.py", line 97, in <module>
plt.savefig(saveto)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/pyplot.py", line 561, in savefig
return fig.savefig(*args, **kwargs)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/figure.py", line 1421, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 2220, in print_figure
**kwargs)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 505, in print_png
FigureCanvasAgg.draw(self)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 451, in draw
self.figure.draw(self.renderer)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/figure.py", line 1034, in draw
func(*args)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/axes.py", line 2086, in draw
a.draw(renderer)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/lines.py", line 562, in draw
drawFunc(renderer, gc, tpath, affine.frozen())
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/lines.py", line 938, in _draw_lines
self._lineFunc(renderer, gc, path, trans)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/lines.py", line 978, in _draw_solid
renderer.draw_path(gc, path, trans)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 145, in draw_path
self._renderer.draw_path(gc, path, transform, rgbFace)
OverflowError: Allocated too many blocks
I specified the agg.path.chunksize parameter in matplotlibrc to o agg.path.chunksize : 10000000. I only get this error when I run the -f fft option. How can I prevent this error?
Not sure but try pdf, svg backends
#!/usr/bin/env python
from pandas import *
import matplotlib.pyplot as plt # Insert just before import matplotlib as mpl
mpl.use('pdf') # Insert just before import matplotlib as mpl
import matplotlib as mpl
# ['pdf', 'pgf', 'Qt4Agg', 'GTK', 'GTKAgg', 'ps', 'agg',
# 'cairo', 'MacOSX', 'GTKCairo', 'WXAgg', 'template', 'TkAgg',
# 'GTK3Cairo', 'GTK3Agg', 'svg', 'WebAgg', 'CocoaAgg', 'emf', 'gdk', 'WX']
# (...)
plt.savefig('svg.pdf') # Consider file extension (!)
Following this answer's use of DateFormatter, I tried to plot a time series and label its x axis with years using pandas 0.15.0 and matplotlib 1.4.2:
import datetime as dt
import matplotlib as mpl
import matplotlib.pyplot as plt
import pandas.io.data as pdio
import scipy as sp
t1 = dt.datetime(1960, 1, 1)
t2 = dt.datetime(2014, 6, 1)
data = pdio.DataReader("GS10", "fred", t1, t2).resample("Q", how=sp.mean)
fig, ax1 = plt.subplots()
ax1.plot(data.index, data.GS10)
ax1.set_xlabel("Year")
ax1.set_ylabel("Rate (%)")
ax1.xaxis.set_major_formatter(mpl.dates.DateFormatter("%Y"))
fig.suptitle("10-yr Treasury Rate", fontsize=14)
fig.savefig('test.eps')
The final line throws an error: OverflowError: Python int too large to convert to C long
with this traceback:
C:\Anaconda3\lib\site-packages\IPython\core\formatters.py:239:
FormatterWarning: Exception in image/png formatter: Python int too
large to convert to C long FormatterWarning,
Traceback (most recent call
last):
File "", line 1, in
runfile('D:/username/latex_template/new_pandas_example.py', wdir='D:/username/latex_template')
File
"C:\Anaconda3\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
line 580, in runfile
execfile(filename, namespace)
File
"C:\Anaconda3\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
line 48, in execfile
exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)
File "D:/username/latex_template/new_pandas_example.py", line 18, in
fig.savefig('test.eps')
File "C:\Anaconda3\lib\site-packages\matplotlib\figure.py", line
1470, in savefig
self.canvas.print_figure(*args, **kwargs)
File "C:\Anaconda3\lib\site-packages\matplotlib\backend_bases.py",
line 2194, in print_figure
**kwargs)
File
"C:\Anaconda3\lib\site-packages\matplotlib\backends\backend_ps.py",
line 992, in print_eps
return self._print_ps(outfile, 'eps', *args, **kwargs)
File
"C:\Anaconda3\lib\site-packages\matplotlib\backends\backend_ps.py",
line 1020, in _print_ps
**kwargs)
File
"C:\Anaconda3\lib\site-packages\matplotlib\backends\backend_ps.py",
line 1110, in _print_figure
self.figure.draw(renderer)
File "C:\Anaconda3\lib\site-packages\matplotlib\artist.py", line 59,
in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "C:\Anaconda3\lib\site-packages\matplotlib\figure.py", line
1079, in draw
func(*args)
File "C:\Anaconda3\lib\site-packages\matplotlib\artist.py", line 59,
in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "C:\Anaconda3\lib\site-packages\matplotlib\axes_base.py", line
2092, in draw
a.draw(renderer)
File "C:\Anaconda3\lib\site-packages\matplotlib\artist.py", line 59,
in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "C:\Anaconda3\lib\site-packages\matplotlib\axis.py", line 1114,
in draw
ticks_to_draw = self._update_ticks(renderer)
File "C:\Anaconda3\lib\site-packages\matplotlib\axis.py", line 957,
in _update_ticks
tick_tups = [t for t in self.iter_ticks()]
File "C:\Anaconda3\lib\site-packages\matplotlib\axis.py", line 957,
in
tick_tups = [t for t in self.iter_ticks()]
File "C:\Anaconda3\lib\site-packages\matplotlib\axis.py", line 905,
in iter_ticks
for i, val in enumerate(majorLocs)]
File "C:\Anaconda3\lib\site-packages\matplotlib\axis.py", line 905,
in
for i, val in enumerate(majorLocs)]
File "C:\Anaconda3\lib\site-packages\matplotlib\dates.py", line 411,
in call
dt = num2date(x, self.tz)
File "C:\Anaconda3\lib\site-packages\matplotlib\dates.py", line 345,
in num2date
return _from_ordinalf(x, tz)
File "C:\Anaconda3\lib\site-packages\matplotlib\dates.py", line 225,
in _from_ordinalf
dt = datetime.datetime.fromordinal(ix)
OverflowError: Python int too large to convert to C long
Am I using DateFormatter incorrectly here? How can I easily put years (or any time format, since my time series might differ) on the a-axis of a matplotlib figure?
This is a 'regression' in pandas 0.15 (due to the refactor of Index), see https://github.com/matplotlib/matplotlib/issues/3727 and https://github.com/pydata/pandas/issues/8614, but is fixed in 0.15.1.
Short story: matplotlib now sees the pandas index as an array of datetime64[ns] values (which are actually very large int64s), instead of an array of Timestamps (which are subclass of datetime.datetime, and can be handled by matplotlib) in previous versions of pandas. So the underlying reason is that matplotlib does not handle datetime64 as date values but as ints.
For pandas 0.15.0 (but better upgrade to a newer version), there are two possible workarounds:
Register the datetime64 type, so it will also be handled as a date by matplotlib:
units.registry[np.datetime64] = pd.tseries.converter.DatetimeConverter()
Or convert the DatetimeIndex (with datetime64 values) to an array of datetime.datetime values with the to_pydatetime method, and plot this:
ax1.plot(data.index.to_pydatetime(), data.GS10)
related question: Plotting datetimeindex on x-axis with matplotlib creates wrong ticks in pandas 0.15 in contrast to 0.14
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).