Re: [Matplotlib-users] graphs in memory
i got that problem solved but i now have a new memory problem, the
error i get is
invalid command name *randomnumber*callit
while executing
*randomnumber*callit
(after script)
searched the internet and found that there is some variable stuck
somewhere, here is the def cousing the error, is designed to read some
files (getting them from the lists self.files and self.workspaces)
make a plot and save the plot
def save2dmulti(self):
try:
os.mkdir(self.save+/graph)
except:
pass
for x in range(0,1):
#fig = pyplot.figure()
for file in self.files:
ax = pyplot.subplot(111)#fig.add_subplot(111)
pyplot.hold(True)
for workspace in self.workspaces:
f = open(workspace+/alignment.iuf,r)
idlist = pickle.load(f)
f.close()
self.__newdict = {}
for item in idlist:
self.__newdict[idlist[item]] = item
for x in range(0,1):
try:
f =
open(workspace+/letters/letter_+self.__newdict[file]+.txt, r)
except:
print gene +file+ not found in
+workspace+ skipping this workspace
break
vals = pickle.load(f)
f.close()
base = []
basecount = []
for val in vals:
if val[0] == A:
base.append(A)
basecount.append(val[1])
elif val[0] == C:
base.append(C)
basecount.append(val[2])
elif val[0] == T:
base.append(T)
basecount.append(val[3])
elif val[0] == G:
base.append(G)
basecount.append(val[4])
N = len(base)
ind = numpy.arange(N)
width = 0.5
ax.plot(ind, basecount,'o-', label = workspace)
ax.set_xticks(ind)
ax.set_title(file)
pyplot.legend()
#print one
for workspacer in self.workspaces:
#print pretry
try:
#print opening file
f = open(workspacer+/alignment.iuf,r)
idlist = pickle.load(f)
f.close()
#print making dict
self.__newdict = {}
for item in idlist:
self.__newdict[idlist[item]] = item
f =
open(workspacer+/validated/+self.__newdict[file]+.fa,r)
text = f.read()
text = text.split(\n)
#print text, text[0], text[1]
f.close()
f = open(self.save+/temp.fa,w)
#print check OK+workspacer
t = text[0]+\n+text[1]+\n
f.write(t)
f.close()
output =
cline = centroid_fold +self.save+/temp.fa
test = subprocess.Popen(str(cline),stdout =
subprocess.PIPE,stderr = open(os.devnull))
output = test.communicate()[0]
#print output
output = output.split()
out = output[1]
out = out.split(\r\n)
#print out
xax = []
counter =0
for x in range(0,len(base)):
xax.append(str(vals[counter][0])+\n+out[2][counter])
counter = counter +1
ax.set_xticks(ind)
ax.set_xticklabels(xax)
sav = file
sav =
sav.replace(:,_).replace(\\,_).replace(-,_).replace(,)
#pyplot.show()
pyplot.savefig(self.save+/graph/+sav+.png)
os.remove(self.save+/temp.fa)
pyplot.clf()
break
except:
#print workspacer + failed
#print ERROR
pass
the code itself works and does what it needs to do, side effect is
that when i later make and show a graph all the graphs made by this
code are also shown and i get the error
2009/10/14 Ryan May rma...@gmail.com:
On Mon, Oct 12, 2009 at 8:09
[Matplotlib-users] graphs in memory
hi i am trying to use mathplot in a script that has to produce and store about 3000 graphs a time, the problem i have is that something inside mathplot keeps storing in the memory, (eigther the graph or the file to write to i guess...) so once it reached 1.5GB of ram it crashes i hope you can help me find a way to flush this memory usage already tried the .clf and .close options as well as the hold option regards Bas -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] graphs in memory
Bas, Send an example of how you're handling the plotting. I have had similar issues, but I've finally figured out how to work around it. Basically, look at the Object Oriented examples, rather than using pyplot. What I found to be most efficient was to reuse figures as much as possible, but delete the axes or just collections therein. -john bas pigmans wrote: hi i am trying to use mathplot in a script that has to produce and store about 3000 graphs a time, the problem i have is that something inside mathplot keeps storing in the memory, (eigther the graph or the file to write to i guess...) so once it reached 1.5GB of ram it crashes i hope you can help me find a way to flush this memory usage already tried the .clf and .close options as well as the hold option regards Bas -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- View this message in context: http://www.nabble.com/graphs-in-memory-tp25887905p25889534.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] graphs in memory
hi i am trying to use mathplot in a script that has to produce and store about 3000 graps a time, the problem i have is that something inside mathplot keeps stroring in the memmory, (eigther the graph or the file to write to i guess...) so once it reached 1.5GB of ram it crashes i hope you can help me find a way to flush this memory usage already tryed the .clf and .close options regards Bas -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] graphs in memory
On Mon, Oct 12, 2009 at 8:09 AM, bas pigmans mrnatr...@gmail.com wrote: hi i am trying to use mathplot in a script that has to produce and store about 3000 graps a time, the problem i have is that something inside mathplot keeps stroring in the memmory, (eigther the graph or the file to write to i guess...) so once it reached 1.5GB of ram it crashes i hope you can help me find a way to flush this memory usage already tryed the .clf and .close options In order to help you, we'll need to see a complete, minimal script that shows the problem you're having. Memory issues usually depend on the specifics of how you're doing something, Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
