Matplotlib循环绘制时内存不足 [英] Matplotlib runs out of memory when plotting in a loop
问题描述
我有一个相当简单的绘图例程,如下所示:
I have a fairly simple plotting routine that looks like this:
from __future__ import division
import datetime
import matplotlib
matplotlib.use('Agg')
from matplotlib.pyplot import figure, plot, show, legend, close, savefig, rcParams
import numpy
from globalconstants import *
def plotColumns(columnNumbers, t, out, showFig=False, filenamePrefix=None, saveFig=True, saveThumb=True):
lineProps = ['b', 'r', 'g', 'c', 'm', 'y', 'k', 'b--', 'r--', 'g--', 'c--', 'm--', 'y--', 'k--', 'g--', 'b.-', 'r.-', 'g.-', 'c.-', 'm.-', 'y.-', 'k.-']
rcParams['figure.figsize'] = (13,11)
for i in columnNumbers:
plot(t, out[:,i], lineProps[i])
legendStrings = list(numpy.zeros(NUMCOMPONENTS))
legendStrings[GLUCOSE] = 'GLUCOSE'
legendStrings[CELLULOSE] = 'CELLULOSE'
legendStrings[STARCH] = 'STARCH'
legendStrings[ACETATE] = 'ACETATE'
legendStrings[BUTYRATE] = 'BUTYRATE'
legendStrings[SUCCINATE] = 'SUCCINATE'
legendStrings[HYDROGEN] = 'HYDROGEN'
legendStrings[PROPIONATE] = 'PROPIONATE'
legendStrings[METHANE] = "METHANE"
legendStrings[RUMINOCOCCUS] = 'RUMINOCOCCUS'
legendStrings[METHANOBACTERIUM] = "METHANOBACTERIUM"
legendStrings[BACTEROIDES] = 'BACTEROIDES'
legendStrings[SELENOMONAS] = 'SELENOMONAS'
legendStrings[CLOSTRIDIUM] = 'CLOSTRIDIUM'
legendStrings = [legendStrings[i] for i in columnNumbers]
legend(legendStrings, loc='best')
dt = datetime.datetime.now()
dtAsString = dt.strftime('%d-%m-%Y_%H-%M-%S')
if filenamePrefix is None:
filenamePrefix = ''
if filenamePrefix != '' and filenamePrefix[-1] != '_':
filenamePrefix += '_'
if saveFig:
savefig(filenamePrefix+dtAsString+'.eps')
if saveThumb:
savefig(filenamePrefix+dtAsString+'.png', dpi=300)
if showFig: f.show()
close('all')
当我在单次迭代中绘制它时,它可以正常工作.但是,当我将其放入循环中时,matplotlib发出了嘶嘶声……
When I plot this in single iterations, it works fine. However, the moment I put it in a loop, matplotlib throws a hissy fit...
Traceback (most recent call last):
File "c4hm_param_variation_h2_conc.py", line 148, in <module>
plotColumns(columnNumbers, timeVector, out, showFig=False, filenamePrefix='c
4hm_param_variation_h2_conc_'+str(hydrogen_conc), saveFig=False, saveThumb=True)
File "D:\phdproject\alexander paper\python\v3\plotcolumns.py", line 48, in plo
tColumns
savefig(filenamePrefix+dtAsString+'.png', dpi=300)
File "C:\Python25\lib\site-packages\matplotlib\pyplot.py", line 356, in savefi
g
return fig.savefig(*args, **kwargs)
File "C:\Python25\lib\site-packages\matplotlib\figure.py", line 1032, in savef
ig
self.canvas.print_figure(*args, **kwargs)
File "C:\Python25\lib\site-packages\matplotlib\backend_bases.py", line 1476, i
n print_figure
**kwargs)
File "C:\Python25\lib\site-packages\matplotlib\backends\backend_agg.py", line
358, in print_png
FigureCanvasAgg.draw(self)
File "C:\Python25\lib\site-packages\matplotlib\backends\backend_agg.py", line
314, in draw
self.figure.draw(self.renderer)
File "C:\Python25\lib\site-packages\matplotlib\artist.py", line 46, in draw_wr
apper
draw(artist, renderer, *kl)
File "C:\Python25\lib\site-packages\matplotlib\figure.py", line 773, in draw
for a in self.axes: a.draw(renderer)
File "C:\Python25\lib\site-packages\matplotlib\artist.py", line 46, in draw_wr
apper
draw(artist, renderer, *kl)
File "C:\Python25\lib\site-packages\matplotlib\axes.py", line 1735, in draw
a.draw(renderer)
File "C:\Python25\lib\site-packages\matplotlib\artist.py", line 46, in draw_wr
apper
draw(artist, renderer, *kl)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 374, in draw
bbox = self._legend_box.get_window_extent(renderer)
File "C:\Python25\lib\site-packages\matplotlib\offsetbox.py", line 209, in get
_window_extent
px, py = self.get_offset(w, h, xd, yd)
File "C:\Python25\lib\site-packages\matplotlib\offsetbox.py", line 162, in get
_offset
return self._offset(width, height, xdescent, ydescent)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 360, in findof
fset
return _findoffset(width, height, xdescent, ydescent, renderer)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 325, in _findo
ffset_best
ox, oy = self._find_best_position(width, height, renderer)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 817, in _find_
best_position
verts, bboxes, lines = self._auto_legend_data()
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 669, in _auto_
legend_data
tpath = trans.transform_path(path)
File "C:\Python25\lib\site-packages\matplotlib\transforms.py", line 1911, in t
ransform_path
self._a.transform_path(path))
File "C:\Python25\lib\site-packages\matplotlib\transforms.py", line 1122, in t
ransform_path
return Path(self.transform(path.vertices), path.codes,
File "C:\Python25\lib\site-packages\matplotlib\transforms.py", line 1402, in t
ransform
return affine_transform(points, mtx)
MemoryError: Could not allocate memory for path
这会在迭代2(从1开始)上发生,如果有区别的话.该代码在Windows XP 32位,python 2.5和matplotlib 0.99.1,numpy 1.3.0和scipy 0.7.1.上运行.
This happens on iteration 2 (counting from 1), if that makes a difference. The code is running on Windows XP 32-bit with python 2.5 and matplotlib 0.99.1, numpy 1.3.0 and scipy 0.7.1.
该代码现已更新,以反映崩溃实际上是在调用legend()
时发生的.评论出来可以解决问题,尽管很明显,我仍然希望能够在图上放一个图例...
The code has now been updated to reflect the fact that the crash actually occurs at the call to legend()
. Commenting that call out solves the problem, though obviously, I would still like to be able to put a legend on my graphs...
推荐答案
每个循环都应该生成一个新图形吗?我看不到您要关闭它或在循环之间创建新的图形实例.
Is each loop supposed to generate a new figure? I don't see you closing it or creating a new figure instance from loop to loop.
此调用将在循环结束后将其保存后清除当前图形:
This call will clear the current figure after you save it at the end of the loop:
pyplot.clf()
pyplot.clf()
不过,我会进行重构,并使您的代码更加面向对象,并在每个循环上创建一个新的图形实例:
I'd refactor, though, and make your code more OO and create a new figure instance on each loop:
from matplotlib import pyplot
while True:
fig = pyplot.figure()
ax = fig.add_subplot(111)
ax.plot(x,y)
ax.legend(legendStrings, loc = 'best')
fig.savefig('himom.png')
# etc....
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