Re: [Matplotlib-users] Memory usage
Hooo, well done! This is it. I didn't knew about caching... I was indeed using ipython, but I did led some test using the basic python interpreter,with same results, so I did not mention this point. In fact, python's basic interpreter still records the last three outputs. As my tests were really short (plt.close() ; mpl.cbook.report_memory() ; gc.collect() is only two lines before the collect, only o)ne o,f theme outputt ing something) even pyhton's caching was still at work, and the garbage collector could not free anything. Thanks a lot, and also thanks to Ben for taking interest ! Jules PS : Gary, sorry, for the duplicated mail... Le 14 janv. 2011 à 04:04, gary ruben a écrit : You're not doing this from ipython are you? It's cache hangs onto the plot object references and stops python's garbage collector from releasing them. If so, you can disable the cache as a workaround. A better option would be if ipython implemented an option to avoid caching references to matplotlib objects. Gary R. On Fri, Jan 14, 2011 at 2:59 AM, Benjamin Root ben.r...@ou.edu wrote: On Thu, Jan 13, 2011 at 7:54 AM, CASOLI Jules jules.cas...@cea.fr wrote: Hello to all, This is yet another question about matplotlib not freeing memory, when closing a figure (using close()). Here is what I'm doing (tried with several backends, on MacOSX and Linux, with similar results): import matplotlib as mpl from matplotlib import pylot as plt import numpy as np a = np.arange(100) mpl.cbook.report_memory() # - output: 54256 plt.plot(a) mpl.cbook.report_memory() # - output: 139968 plt.close() mpl.cbook.report_memory() # - output: 138748 Shouldn't plt.close() close the figure _and_ free the memory used by it? What am I doing wrong ? I tried several other ways to free the memory, such as f = figure(); ... ; del f, without luck. Any help appreciated ! P.S. : side question : how come the call to plot take so much memory (90MB for a 8MB array ?). I have read somewhere that each point is coded on three RGB floats, but it only means an approx. 12MB plot... (plus small overhead) Jules Jules, Which version of Matplotlib are you using and which backend? On my Linux install of matplotlib (development branch) using GTKAgg, the memory usage does get high during the call to show(), but returns to (near) normal amounts after I close. An interesting observation is that if the interactive mode is off, the memory usage returns back to just a few kilobytes above where it was before, but if interactive mode was turned on, the memory usage returned to being a few hundred kilobytes above where it started. Ben Root P.S. - As a side note, estimating the memory size of these plots from the given data isn't as straight-forward as multiplying by three (actually, it would be four because of the transparency value in addition to rgb). There are many other parts of the graph that needs to be represented (all having rgba values) but there are also a lot of simplifications that are done to reduce the amount of memory needed to represent these objects. -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] colorbar with Axes3D for a set of collections?
Hi Eric, thanks for your feedback, it helped a lot! I have some questions left, see below. 2011/1/14 Eric Firing efir...@hawaii.edu: Quick thoughts with no testing or concrete examples: 1) Don't set the cmap or norm for the colorbar; let it inherit those properties from the mappable to which it is connected. Am I doing this correctly in the attached code? It seems there are several ways of doing this... Which is the suggested one? How can I label the colorbar? 2) Ensure that the cmap and norm are the same for all collections. You are already taking care of the cmap, so the problem is that you are autoscaling the collections separately, which is setting vmin and vmax to different values for the different collections. Use the data to figure out the range (vmin, vmax) that you want the colors to span, and then for each collection, instead of col.autoscale(), use col.norm.vmin = vmin col.norm.vmax = vmax That was what I needed, see code :) (You could also make a single norm instance for all the collections to use, just as with the cmap, so that you only have to set vmin and vmax once.) And this I don't understandm could you please elaborate? Thanks a very lot in advance best regards from Austria, Daniel 3D_colorbar.py Description: Binary data -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Why no STIX fonts?
I have several machines running fedora f14. 2 of them produce plots fine with STIX, but 1 doesn't, but gives: /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeOneSym'] not found. Falling back to Bitstream Vera Sans (prop.get_family(), self.defaultFamily[fontext])) /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1252: UserWarning: findfont: Could not match :family=Bitstream Vera Sans:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0. Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf UserWarning) /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeThreeSym'] not found. Falling back to Bitstream Vera Sans (prop.get_family(), self.defaultFamily[fontext])) ... On that machine I have: Package stix-variants-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-pua-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-fonts-doc-1.0.0-1.fc14.noarch already installed and latest version Package stix-sizes-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-integrals-fonts-1.0.0-1.fc14.noarch already installed and latest version rpm -q python-matplotlib python-matplotlib-1.0.0-2.fc14.x86_64 Any ideas how to debug this? -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Axes3D:adjusting the parameters of the plot
Friends,
I sent the following mail to mpl users with a figure. Since the size was
bigger, it bounced back to my email. So i am fwd it again without attaching
the figure.
It seems that i can only set tick labels and limits of the axes using
set_xlabel and set_xlim3d functions.Basically i want to know how to
manipulate the x,y and z ticks intervals for a graph created with Axes3D.
On Fri, Jan 14, 2011 at 12:06 PM, Bala subramanian
bala.biophys...@gmail.com wrote:
Dear Friends, i used the following code to create a 3D plot (attached
figure). I manipulate the appearance of the graph. Someone please enlighten
me on the same. I dnt get what functions should i use to do the following
manipulations.
1) How to remove the blue shading in the grid
2) How to change the distance between the axis label and axis tick labels
3) How to set the interval of the axis ticks. For example the xlim varies
from -80 to 60. I want to set xticks at an interval of 30 rather than 20 as
in the plot.
My code.
import numpy as np
import matplotlib as mpl
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
FIG=plt.figure(figsize=(4.,3.27),dpi=200)
ax = Axes3D(FIG,azim=-60,elev=15)
x=np.reshape(np.loadtxt(data[0]),15000)
y=np.reshape(np.loadtxt(data[1]),15000)
z=np.reshape(np.loadtxt(data[2]),15000)
ax.scatter3D(x[::10],y[::10],z[::10],edgecolors=col[i],facecolors='white',marker=mar[i],s=5,alpha=0.7)
ax.set_xlabel('PC1',size=8)
ax.set_ylabel('PC2',size=8)
ax.set_zlabel('PC3',size=8)
ax.set_xlim3d(-80,60,30)
ax.set_ylim3d(-40,50,30)
ax.set_zlim3d(-40,40,30)
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Re: [Matplotlib-users] Axes3D:adjusting the parameters of the plot
On Fri, Jan 14, 2011 at 5:06 AM, Bala subramanian bala.biophys...@gmail.com
wrote:
Dear Friends, i used the following code to create a 3D plot (attached
figure). I manipulate the appearance of the graph. Someone please enlighten
me on the same. I dnt get what functions should i use to do the following
manipulations.
1) How to remove the blue shading in the grid
2) How to change the distance between the axis label and axis tick labels
Unfortunately, this is not possible to do with the current version of
matplotlib. I have been working on making this (somewhat) possible in the
next release. One thing you can do to make the axes labels look better is
to trigger mplot3d's internal logic to rotate the labels to be parallel to
the axes. mplot3d automatically rotates labels that have more than 4
characters in them. So, if you want PC1 to be rotated, set the axis label
to PC1 with spaces so that it will have 5 characters and get rotated.
3) How to set the interval of the axis ticks. For example the xlim varies
from -80 to 60. I want to set xticks at an interval of 30 rather than 20 as
in the plot.
My code.
import numpy as np
import matplotlib as mpl
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
FIG=plt.figure(figsize=(4.,3.27),dpi=200)
ax = Axes3D(FIG,azim=-60,elev=15)
x=np.reshape(np.loadtxt(data[0]),15000)
y=np.reshape(np.loadtxt(data[1]),15000)
z=np.reshape(np.loadtxt(data[2]),15000)
ax.scatter3D(x[::10],y[::10],z[::10],edgecolors=col[i],facecolors='white',marker=mar[i],s=5,alpha=0.7)
ax.set_xlabel('PC1',size=8)
ax.set_ylabel('PC2',size=8)
ax.set_zlabel('PC3',size=8)
ax.set_xlim3d(-80,60,30)
ax.set_ylim3d(-40,50,30)
ax.set_zlim3d(-40,40,30)
Passing '30' to set_xlim to set the tick intervals is not a feature in both
regular 2d plotting and 3d plotting, so I don't know how you expected that
to work. If you want to manually control the axis ticks, you can use axis
locators just like for 2D plots, keeping in mind that the axis objects for
3d plots are ax.w_xaxis, ax.w_yaxis, and ax.w_zaxis (where for a 2d plot, it
would be ax.xaxis, ax.yaxis, ax.zaxis).
I hope this helps!
Ben Root
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[Matplotlib-users] Only one colorbar for a figure?
Hi list; I am trying to do an imshow() comparison of four different data sets (astronomical photos), and since I want to show the differences in strength, I use fixed vmin and vmax. I would very much like one and only one colour bar for the entire figure, but I haven't been able to figure out how to do it without creating an entire subplot for it, and that is really kludgey and unhandy. I tried the Interwebz but have had no luck figuring it out. Cheers; Emil signature.asc Description: This is a digitally signed message part -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Why no STIX fonts?
You can try deleting matplotlib's font cache in ~/.matplotlib/fontList.cache. If that doesn't work, set the rcParam verbose.level to debug-annoying and send us the output... Mike On 01/14/2011 08:10 AM, Neal Becker wrote: I have several machines running fedora f14. 2 of them produce plots fine with STIX, but 1 doesn't, but gives: /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeOneSym'] not found. Falling back to Bitstream Vera Sans (prop.get_family(), self.defaultFamily[fontext])) /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1252: UserWarning: findfont: Could not match :family=Bitstream Vera Sans:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0. Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf UserWarning) /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeThreeSym'] not found. Falling back to Bitstream Vera Sans (prop.get_family(), self.defaultFamily[fontext])) ... On that machine I have: Package stix-variants-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-pua-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-fonts-doc-1.0.0-1.fc14.noarch already installed and latest version Package stix-sizes-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-integrals-fonts-1.0.0-1.fc14.noarch already installed and latest version rpm -q python-matplotlib python-matplotlib-1.0.0-2.fc14.x86_64 Any ideas how to debug this? -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Michael Droettboom Science Software Branch Space Telescope Science Institute Baltimore, Maryland, USA -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Only one colorbar for a figure?
2011/1/14 Thøger Emil Juul Thorsen thoe...@fys.ku.dk Hi list; I am trying to do an imshow() comparison of four different data sets (astronomical photos), and since I want to show the differences in strength, I use fixed vmin and vmax. I would very much like one and only one colour bar for the entire figure, but I haven't been able to figure out how to do it without creating an entire subplot for it, and that is really kludgey and unhandy. I tried the Interwebz but have had no luck figuring it out. Cheers; Emil Emil, I had this problem once before. You can use the axes_grid1 tool to do this: http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html Unfortunately, our documentation is a little broken on that page, but if you take a look at this source code example, you can see how to use AxesGrid to create a subplot grid that pre-allocates space for a single cbar automatically! http://matplotlib.sourceforge.net/plot_directive/mpl_toolkits/axes_grid/examples/demo_axes_grid.py I hope this helps! Ben Root -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Why no STIX fonts?
Seems that deleting fontList.cache did it. Michael Droettboom wrote: You can try deleting matplotlib's font cache in ~/.matplotlib/fontList.cache. If that doesn't work, set the rcParam verbose.level to debug-annoying and send us the output... Mike On 01/14/2011 08:10 AM, Neal Becker wrote: I have several machines running fedora f14. 2 of them produce plots fine with STIX, but 1 doesn't, but gives: /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeOneSym'] not found. Falling back to Bitstream Vera Sans (prop.get_family(), self.defaultFamily[fontext])) /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1252: UserWarning: findfont: Could not match :family=Bitstream Vera Sans:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0. Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf UserWarning) /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeThreeSym'] not found. Falling back to Bitstream Vera Sans (prop.get_family(), self.defaultFamily[fontext])) ... On that machine I have: Package stix-variants-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-pua-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-fonts-doc-1.0.0-1.fc14.noarch already installed and latest version Package stix-sizes-fonts-1.0.0-1.fc14.noarch already installed and latest version Package stix-integrals-fonts-1.0.0-1.fc14.noarch already installed and latest version rpm -q python-matplotlib python-matplotlib-1.0.0-2.fc14.x86_64 Any ideas how to debug this? -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] MemoryError with import matplotlib
Hi all, I tried to plot parts of a large 3D array with each 4 float64 entries. Loading the array with numpy.fromfile and performing a type conversion afterwards ends up in a MemoryError. The following code reproduces the error: *** import gc from os import path from numpy import zeros, empty, float32, float64, fromfile # With the imports of the next three lines a memory error occurs #import matplotlib #matplotlib.use(AGG) #import matplotlib.pylab as plt _filename = mt.dat if (path.exists(_filename)==False): print Write file ... _mtf = file(_filename, wb) _mtd = zeros( (300,300,300,4),dtype=float64) _mtd.tofile(_mtf) _mtf.close() _mtd = empty((0)) gc.collect(); print Try to read file ... _mtf = file(_filename, rb) # The memory error occurs with the type conversion to float 64, # but only if mathplotlib is imported! _mtd = fromfile(_mtf,float64).astype(float32) _mtf.close() print Successful read:,_mtd.shape # Here some plot stuff would be :) *** If the import of matplotlib is not included, no error occures otherwise it will not work. Perhaps anybody can help me (I tested it only on a Windows XP 32Bit). Best regards and thank you Stefan -- View this message in context: http://old.nabble.com/MemoryError-with-import-matplotlib-tp30674798p30674798.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] colorbar with Axes3D for a set of collections?
On 01/14/2011 02:02 AM, Daniel Mader wrote:
Hi Eric,
thanks for your feedback, it helped a lot! I have some questions left,
see below.
2011/1/14 Eric Firingefir...@hawaii.edu:
Quick thoughts with no testing or concrete examples:
1) Don't set the cmap or norm for the colorbar; let it inherit those
properties from the mappable to which it is connected.
Am I doing this correctly in the attached code? It seems there are
several ways of doing this... Which is the suggested one? How can I
label the colorbar?
The way you did it is fine. For the label, modify by keeping a reference
to the colorbar and then calling set_label:
cb = fig.colorbar(collist[-1], shrink=0.85,)#, aspect=5)
cb.set_label('whatever this is')
2) Ensure that the cmap and norm are the same for all collections. You
are already taking care of the cmap, so the problem is that you are
autoscaling the collections separately, which is setting vmin and vmax
to different values for the different collections. Use the data to
figure out the range (vmin, vmax) that you want the colors to span, and
then for each collection, instead of col.autoscale(), use
col.norm.vmin = vmin
col.norm.vmax = vmax
That was what I needed, see code :)
(You could also make a single norm instance for all the collections to
use, just as with the cmap, so that you only have to set vmin and vmax
once.)
And this I don't understandm could you please elaborate?
See attached modification.
Eric
Thanks a very lot in advance
best regards from Austria,
Daniel
import sys
import scipy,pylab
import matplotlib as mpl
from mpl_toolkits.mplot3d import Axes3D
##--
def closePolys(elements):
'''
close the open polygon elements by adding the first node of each poly again.
'''
closed = []
for nodes in elements:
i = nodes[0]
ii = list(nodes)
ii.append(i)
closed.append(ii)
return closed
elements = [ [ (0,0), (0,1), (1,1), (1,0) ],
[ (4,1), (2,3), (2,2), (3,1)],
[ (0,1), (2,3), (2,2), (1,1)],
[ (3,0), (3,1), (4,1), (4,0)]]
tmp = scipy.array([1,1.1,0.9,1])
data = [tmp, tmp*2, tmp*4]
## workaround for bug in mpl: close polys manually, no auto-closing!
polys = closePolys(elements)
##--
fig = pylab.figure()
ax = Axes3D(fig)
stacks = 3
zpos = scipy.arange(stacks)
vmin,vmax = scipy.amin(data), scipy.amax(data)
norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
cmap = mpl.cm.cool
collist = []
for i in range(stacks):
col = mpl.collections.PolyCollection(polys, linewidths=0.05, closed=False,
norm=norm, cmap=cmap)
col.set_array(data[i])
collist.append(col)
for i,col in enumerate(collist):
## get number of elements per collection
elemno = len(col.get_paths())
## create *iterable* for the 3D collection slices [z,z,z,...,z]
zs = [zpos[i]]*elemno
## collection transparency (opaque == 1), needed for projection bug workaround
col.set_alpha(0.3)
ax.add_collection3d(col, zs=zs, zdir='y')
#pylab.draw()
## colorbar:
cb = fig.colorbar(collist[-1], shrink=0.85,)#, aspect=5)
cb.set_label('whatever this is')
## axis limit settings:
ax.set_xlim3d(0,4)
ax.set_zlim3d(0,3)
ax.set_ylim3d(-0.1,stacks-1+0.1)
## labels:
ax.set_title('Transparency workaround')
ax.set_xlabel('x')
ax.set_ylabel('slice')
ax.set_zlabel('y')
##--
pylab.show()
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Re: [Matplotlib-users] MemoryError with import matplotlib
Works for me on Windows 7 64 bit with 32 bit Python. I believe you simply run out of memory. On a 32 bit Windows OS, Python can only use 2 GB, which it has to share with other all processes. zeros((300,300,300,4),dtype=float64) requires ~820MB of contiguous memory, which might not be available even if you have 1 GB free RAM. Better use a 64 bit OS and Python. Christoph On 1/14/2011 11:40 AM, sprobst wrote: Hi all, I tried to plot parts of a large 3D array with each 4 float64 entries. Loading the array with numpy.fromfile and performing a type conversion afterwards ends up in a MemoryError. The following code reproduces the error: *** import gc from os import path from numpy import zeros, empty, float32, float64, fromfile # With the imports of the next three lines a memory error occurs #import matplotlib #matplotlib.use(AGG) #import matplotlib.pylab as plt _filename = mt.dat if (path.exists(_filename)==False): print Write file ... _mtf = file(_filename, wb) _mtd = zeros( (300,300,300,4),dtype=float64) _mtd.tofile(_mtf) _mtf.close() _mtd = empty((0)) gc.collect(); print Try to read file ... _mtf = file(_filename, rb) # The memory error occurs with the type conversion to float 64, # but only if mathplotlib is imported! _mtd = fromfile(_mtf,float64).astype(float32) _mtf.close() print Successful read:,_mtd.shape # Here some plot stuff would be :) *** If the import of matplotlib is not included, no error occures otherwise it will not work. Perhaps anybody can help me (I tested it only on a Windows XP 32Bit). Best regards and thank you Stefan -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MemoryError with import matplotlib
On Fri, Jan 14, 2011 at 1:40 PM, sprobst stefanpro...@gmx.net wrote: Hi all, I tried to plot parts of a large 3D array with each 4 float64 entries. Loading the array with numpy.fromfile and performing a type conversion afterwards ends up in a MemoryError. The following code reproduces the error: *** import gc from os import path from numpy import zeros, empty, float32, float64, fromfile # With the imports of the next three lines a memory error occurs #import matplotlib #matplotlib.use(AGG) #import matplotlib.pylab as plt _filename = mt.dat if (path.exists(_filename)==False): print Write file ... _mtf = file(_filename, wb) _mtd = zeros( (300,300,300,4),dtype=float64) _mtd.tofile(_mtf) _mtf.close() _mtd = empty((0)) gc.collect(); print Try to read file ... _mtf = file(_filename, rb) # The memory error occurs with the type conversion to float 64, # but only if mathplotlib is imported! _mtd = fromfile(_mtf,float64).astype(float32) _mtf.close() print Successful read:,_mtd.shape # Here some plot stuff would be :) *** If the import of matplotlib is not included, no error occures otherwise it will not work. Perhaps anybody can help me (I tested it only on a Windows XP 32Bit). Best regards and thank you Stefan Stefan, I don't know if it would make a difference, but I see that you are importing matplotlib.pylab as plt. This is not a typical way of importing matplotlib. Try instead: import matplotlib.pyplot as plt Ben Root -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MemoryError with import matplotlib
Dear Christoph, It is not a memory problem, because before the programm starts I have more than 1.3 GB free memory left. And on the other hand it depends on the import line! There seems to be some interference of the packages. My Python version is 2.6 (needed by another programm), perhaps that also makes the difference. But thank you for the quick answer! Stefan -- View this message in context: http://old.nabble.com/MemoryError-with-import-matplotlib-tp30674798p30675089.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MemoryError with import matplotlib
The zeros(...) statement needs a contiguous block of 800 MB RAM and the conversion another contiguous block of 400 MB. Memory allocated during the matplotlib import statement could easily fragment the available memory such that no 800 + 400 MB blocks exist. Try monitoring your memory usage and import matplotlib after allocating/converting the array. Anyway, you'll be better off using a 64 bit system if you deal with such amount of data. Christoph On 1/14/2011 12:17 PM, sprobst wrote: Dear Christoph, It is not a memory problem, because before the programm starts I have more than 1.3 GB free memory left. And on the other hand it depends on the import line! There seems to be some interference of the packages. My Python version is 2.6 (needed by another programm), perhaps that also makes the difference. But thank you for the quick answer! Stefan -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] colorbar with Axes3D for a set of collections?
Thank you very much for your patience, your explanations helped me a very lot in getting beautiful plots for my thesis! Best regards, Daniel -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] specgram with zeros array
I am using Matplotlib version 1.0.1 and I get errors if I try the following:
import matplotlib.pyplot as plt
import numpy as np
plt.specgram(np.zeros(50))
I have pasted the error output below, but hopefully it would reproduce
in other systems. I'm not sure if this is intended behavior and was
wondering. I came across this when I was plotting the specgram of my
sound input, but my microphone was muted!
---
AttributeErrorTraceback (most recent call last)
/usr/local/lib/python2.6/dist-packages/matplotlib/backends/backend_wx.pyc in
_onPaint(self, evt)
1192 drawDC = wx.PaintDC(self)
1193 if not self._isDrawn:
- 1194 self.draw(drawDC=drawDC)
1195 else:
1196 self.gui_repaint(drawDC=drawDC)
/usr/local/lib/python2.6/dist-packages/matplotlib/backends/backend_wxagg.pyc
in draw(self, drawDC)
57
58 DEBUG_MSG(draw(), 1, self)
--- 59 FigureCanvasAgg.draw(self)
60
61 self.bitmap =
_convert_agg_to_wx_bitmap(self.get_renderer(), None)
/usr/local/lib/python2.6/dist-packages/matplotlib/backends/backend_agg.pyc
in draw(self)
392
393 self.renderer = self.get_renderer()
-- 394 self.figure.draw(self.renderer)
395
396 def get_renderer(self):
/usr/local/lib/python2.6/dist-packages/matplotlib/artist.pyc in
draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
--- 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/usr/local/lib/python2.6/dist-packages/matplotlib/figure.pyc in
draw(self, renderer)
796 dsu.sort(key=itemgetter(0))
797 for zorder, func, args in dsu:
-- 798 func(*args)
799
800 renderer.close_group('figure')
/usr/local/lib/python2.6/dist-packages/matplotlib/artist.pyc in
draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
--- 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/usr/local/lib/python2.6/dist-packages/matplotlib/axes.pyc in draw(self,
renderer, inframe)
1944
1945 for zorder, a in dsu:
- 1946 a.draw(renderer)
1947
1948 renderer.close_group('axes')
/usr/local/lib/python2.6/dist-packages/matplotlib/artist.pyc in
draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
--- 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/usr/local/lib/python2.6/dist-packages/matplotlib/image.pyc in
draw(self, renderer, *args, **kwargs)
352 warnings.warn(Image will not be shown
correctly with this backend.)
353
-- 354 im = self.make_image(renderer.get_image_magnification())
355 if im is None:
356 return
/usr/local/lib/python2.6/dist-packages/matplotlib/image.pyc in
make_image(self, magnification)
567 im, xmin, ymin, dxintv, dyintv, sx, sy = \
568 self._get_unsampled_image(self._A, [_x1, _x2, _y1,
_y2],
-- 569 transformed_viewLim)
570
571 fc = self.axes.patch.get_facecolor()
/usr/local/lib/python2.6/dist-packages/matplotlib/image.pyc in
_get_unsampled_image(self, A, image_extents, viewlim)
199 else:
200 if self._rgbacache is None:
-- 201 x = self.to_rgba(self._A, self._alpha)
202 self._rgbacache = x
203 else:
/usr/local/lib/python2.6/dist-packages/matplotlib/cm.pyc in
to_rgba(self, x, alpha, bytes)
191 pass
192 x = ma.asarray(x)
-- 193 x = self.norm(x)
194 x = self.cmap(x, alpha=alpha, bytes=bytes)
195 return x
/usr/local/lib/python2.6/dist-packages/matplotlib/colors.pyc in
__call__(self, value, clip)
809 if vmin vmax:
810 raise ValueError(minvalue must be less than or
equal to maxvalue)
-- 811 elif vmin==vmax:
812 result = 0.0 * val
813 else:
/usr/lib/python2.6/dist-packages/numpy/ma/core.pyc in __eq__(self, other)
3117 mask = np.all([[f[n].all() for n in
mask.dtype.names]
3118 for f in mask], axis=axis)
- 3119 check._mask = mask
3120 return check
3121 #
AttributeError: 'numpy.bool_' object has no attribute '_mask'
Re: [Matplotlib-users] MemoryError with import matplotlib
Problem solved ... even as orginally C++ or Java programmer it is strange, but a interpreted language makes it possible to obtain with an import at a different position a complety different behaviour during run-time. I just putted the import of mathplotlib and pylab after the file reading and after the type conversion and it works. :jumping: Comment to just switch to another system with 64bit. Sometimes if your are not admin of a machine, than it is hard to change the system ;-) Thank you anyhow, based on your comments I found the solution. Do you perhaps know if there is something like a memdefrag :-/? Have a nice weekend Stefan -- View this message in context: http://old.nabble.com/MemoryError-with-import-matplotlib-tp30674798p30676114.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
