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Hi, I have a script witch saves to graphs to SVG. The script works on 2 of my computer (ArchLinux and Gentoo) but the SVG saves doesn't on Fedora Core 3. The 3 uses matplotlib v0.87.4. The error I get is : > Traceback (most recent call last): > File "src/affichage/affichage_E.py", line 1091, in ? > main() > File "src/affichage/affichage_E.py", line 262, in main > updatefig() > File "src/affichage/affichage_E.py", line 427, in updatefig > p.savefig(filename, dpi=100) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/pylab.py", line 811, in savefig > return fig.savefig(*args, **kwargs) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/figure.py", line 661, in savefig > self.canvas.print_figure(*args, **kwargs) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_gtkagg.py", line 113, in print_figure > orientation, **kwargs) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_agg.py", line 481, in print_figure > orientation, **kwargs) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_svg.py", line 289, in print_figure > self.figure.draw(renderer) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/figure.py", line 532, in draw > for a in self.axes: a.draw(renderer) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/axes.py", line 1045, in draw > a.draw(renderer) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/image.py", line 189, in draw > renderer.draw_image(l, b, im, self.axes.bbox) > File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_svg.py", line 154, in draw_image > image64 = base64.b64encode (imfile.read()) > AttributeError: 'module' object has no attribute 'b64encode' Is there something I'm missing ? Thank you.
hey guys i got the subversion from the site and I am trying to install it on windows. I changed dir into the matplotlib dir that includes the setup.py file. run python setup.py install, and im getting a wierd error. i left the topmost lines along with the error. has anyone seen anything like this before? building 'matplotlib.enthought.traits.ctraits' extension creating build\temp.win32-2.4\Release\lib creating build\temp.win32-2.4\Release\lib\matplotlib creating build\temp.win32-2.4\Release\lib\matplotlib\enthought creating build\temp.win32-2.4\Release\lib\matplotlib\enthought\traits C:\Program Files\Microsoft Visual Studio .NET 2003\Vc7\bin\cl.exe /c /nologo /Ox /MD /W3 /GX /DNDEBUG -Ic:\Python24\include -Ic:\Python24\PC /Tclib/matplotlib/e nthought/traits/ctraits.c /Fobuild\temp.win32-2.4\Release\lib/matplotlib/enthoug ht/traits/ctraits.obj C:\Program Files\Microsoft Visual Studio .NET 2003\Vc7\bin\link.exe /DLL /nologo /INCREMENTAL:NO /LIBPATH:c:\Python24\libs /LIBPATH:c:\Python24\PCBuild /EXPORT: initctraits build\temp.win32-2.4\Release\lib/matplotlib/enthought/traits/ctraits .obj /OUT:build\lib.win32-2.4\matplotlib\enthought\traits\ctraits.pyd /IMPLIB:bu ild\temp.win32-2.4\Release\lib/matplotlib/enthought/traits\ctraits.lib building 'matplotlib.backends._tkagg' extension C:\Program Files\Microsoft Visual Studio .NET 2003\Vc7\bin\cl.exe /c /nologo /Ox /MD /W3 /GX /DNDEBUG -Iwin32_static/include/tcl84 -I. -Isrc -Iswig -Iagg23/incl ude -I. -I. -Iwin32_static/include/tcl84\freetype2 -I.\freetype2 -Isrc\freetype2 -Iswig\freetype2 -Iagg23/include\freetype2 -I.\freetype2 -I.\freetype2 -Ic:\Pyt hon24\include -Ic:\Python24\PC /Tpsrc/_tkagg.cpp /Fobuild\temp.win32-2.4\Release \src/_tkagg.obj _tkagg.cpp src\_tkagg.cpp(28) : fatal error C1083: Cannot open include file: 'tk.h': No suc h file or directory error: Command ""C:\Program Files\Microsoft Visual Studio .NET 2003\Vc7\bin\cl.e xe" /c /nologo /Ox /MD /W3 /GX /DNDEBUG -Iwin32_static/include/tcl84 -I. -Isrc - Iswig -Iagg23/include -I. -I. -Iwin32_static/include/tcl84\freetype2 -I.\freetyp e2 -Isrc\freetype2 -Iswig\freetype2 -Iagg23/include\freetype2 -I.\freetype2 -I.\ freetype2 -Ic:\Python24\include -Ic:\Python24\PC /Tpsrc/_tkagg.cpp /Fobuild\temp .win32-2.4\Release\src/_tkagg.obj" failed with exit status 2
You're right, Jeff. When I use numpy in the test script, I don't see the leak. Alternatively, moving the basemap object creation outside of the loop (even with Numeric 24.2) makes it faster and doesn't produce the leak. Thanks for showing me the way. Gerald Jeff Whitaker wrote: > Gerald John M. Manipon wrote: >> Hi all, >> >> I'm trying to generate a plot that contains 3 subplots: >> 2 line plots and a basemap plot showing location. I'm >> generating about 200 such plots however my script >> doesn't get to complete because it encounters a MemoryError. >> >> I found the test script at >> http://matplotlib.sourceforge.net/faq.html#LEAKS (which >> BTW generates a plot with 4 subplots) and it succeeded >> beautifully with no memory issues. However I changed the >> last subplot to be a basemap plot and I was able to see >> the memory leak. Below is the modified leak test script >> I used and the abbreviated output from it. I would truly >> appreciate any help on this. >> >> Thanks, >> >> Gerald >> >> ################################################ >> #memory leak test >> ################################################ >> import os, sys, time >> import matplotlib >> matplotlib.use('Agg') >> from pylab import * >> from matplotlib.toolkits.basemap import Basemap >> >> def report_memory(i): >> pid = os.getpid() >> a2 = os.popen('ps -p %d -o rss,sz' % pid).readlines() >> print i, ' ', a2[1], >> return int(a2[1].split()[1]) >> >> >> >> # take a memory snapshot on indStart and compare it with indEnd >> indStart, indEnd = 30, 150 >> for i in range(indEnd): >> ind = arange(100) >> xx = rand(len(ind)) >> >> figure(1) >> subplot(221) >> plot(ind, xx) >> >> subplot(222) >> X = rand(50,50) >> >> imshow(X) >> subplot(223) >> scatter(rand(50), rand(50)) >> subplot(224) >> #pcolor(10*rand(50,50)) >> m = Basemap(0, -85, 360, 85) >> m.plot((50,), (20,), 'ro', markersize=12, label='gps') >> m.drawcoastlines() >> >> savefig('tmp%d' % i, dpi = 75) >> close(1) >> >> >> val = report_memory(i) >> # wait a few cycles for memory usage to stabilize >> if i==indStart: start = val >> >> end = val >> print 'Average memory consumed per loop: %1.4fk bytes ' % \ >> ((end-start)/float(indEnd-indStart)) >> >> >> ################################################ >> #abbreviated results >> ################################################ >> 0 42724 12739 >> 1 65068 18359 >> 2 83036 22924 >> 3 100980 27463 >> 4 118928 32027 >> 5 136872 36577 >> 6 154828 41129 >> 7 172784 45681 >> 8 190736 50156 >> 9 208692 54711 >> 10 226644 59272 >> 11 244592 63824 >> 12 262548 68375 >> 13 280496 72926 >> 14 298440 77478 >> 15 316392 81964 >> . >> . >> . >> 143 1771824 663458 >> 144 1788924 668010 >> 145 1791316 672561 >> 146 1771104 677112 >> 147 1775644 681599 >> 148 1787288 686166 >> 149 1791604 690718 >> Average memory consumed per loop: 4505.0833k bytes >> > > Gerald: One way to workaround the memory leak with Numeric is to move > the Basemap instance creation > > m = Basemap(0, -85, 360, 85) > > outside the loop. There's no need to recreate it each time. > > As a bonus, the script runs many times faster too. > > -Jeff >
>>>>> "Esdras" == Esdras Caleb <ach...@gm...> writes: Esdras> I have esperimental data here and i want plot them to do a Esdras> grafic and cut the poits who are too out but whem i use Esdras> plot(Array1,Array2,+) i obtaim a perfect line and i do it Esdras> in gnu plot and see the ploted points arent a perfect Esdras> line, someone can tell me how I can simple draw the points Esdras> in the grafic using mathplot? Try using a mask, eg examples/masked_demo.py. Using nan should work as well from pylab import figure, show, nx x = nx.arange(0.0, 10.0) y = x**2 x[3] = nx.nan fig = figure() ax = fig.add_subplot(111) ax.plot(x, y) show() JDH
Hi, It's pretty hard to figure out exactly what your problem is without more info. Did you check that the scaling was identical in gnuplot and matplotlib ? matplotlib will set the axes so that all data are included in the figure, so if you have large outliers, the scaling will be too large and its probable that your data will look like a perfect line. Try modifying the scaling of the graph, using ylim(y1, y2) or xlim(x1, x2). David 2006年9月1日, Esdras Caleb <ach...@gm...>: > > I have esperimental data here and i want plot them to do a grafic and cut > the poits who are too out but whem i use plot(Array1,Array2,+) i obtaim a > perfect line and i do it in gnu plot and see the ploted points arent a > perfect line, someone can tell me how I can simple draw the points in the > grafic using mathplot? > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users > > >
I have esperimental data here and i want plot them to do a grafic and cut the poits who are too out but whem i use plot(Array1,Array2,+) i obtaim a perfect line and i do it in gnu plot and see the ploted points arent a perfect line, someone can tell me how I can simple draw the points in the grafic using mathplot?
Hello, I am writing a little GUI with PyQT4 and matplotlib. So it is embeded. I want that feature for the user : he can decided after ploting some data to synchronize 2 graph with the x axis for the zoom. So this method would be very useful for me. Maybe I can write it. Do you have a idea of all the variables involved in the sharex feature ? Thank you Samuel Eric Firing wrote: > Samuel, > > Trying to manipulate variables with leading underscores is > discouraged--that is the meaning of the leading underscores. > > Changing the shared status of axes involves changes in additional > variables. This could be encapsulated in a single method. It might be > very easy, or complexities and gotchas might turn up. How important is > it? What is the problem with setting the shared status when you make > the axes, as in your first example? > > Eric > > Samuel GARCIA wrote: > >> Hi all, >> is there a possibility to change the sharex and sharey after creating a >> axes ? >> >> For example this perfectitly work : >> >> import pylab >> fig = pylab.figure() >> ax1 = fig.add_subplot(121) >> ax2 = fig.add_subplot(122, sharex=ax1) >> ax1.plot(rand(5)) >> ax2.plot(rand(5)) >> pylab.show() >> >> But when I try naively to change _sharex and _masterx after creating >> the axes it doesn't work : >> >> >> import pylab >> fig = pylab.figure() >> ax1 = fig.add_subplot(121) >> ax2 = fig.add_subplot(122) >> ax1.plot(rand(5)) >> ax2.plot(rand(5)) >> ax2._sharex = ax1 >> ax1._masterx = True >> pylab.show() >> >> What 's the solution ? >> thank you >> >> Samuel >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> Using Tomcat but need to do more? Need to support web services, security? >> Get stuff done quickly with pre-integrated technology to make your job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Matplotlib-users mailing list >> Mat...@li... >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >> > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >
Gerald John M. Manipon wrote: > Hi all, > > I'm trying to generate a plot that contains 3 subplots: > 2 line plots and a basemap plot showing location. I'm > generating about 200 such plots however my script > doesn't get to complete because it encounters a MemoryError. > > I found the test script at > http://matplotlib.sourceforge.net/faq.html#LEAKS (which > BTW generates a plot with 4 subplots) and it succeeded > beautifully with no memory issues. However I changed the > last subplot to be a basemap plot and I was able to see > the memory leak. Below is the modified leak test script > I used and the abbreviated output from it. I would truly > appreciate any help on this. > > Thanks, > > Gerald > > ################################################ > #memory leak test > ################################################ > import os, sys, time > import matplotlib > matplotlib.use('Agg') > from pylab import * > from matplotlib.toolkits.basemap import Basemap > > def report_memory(i): > pid = os.getpid() > a2 = os.popen('ps -p %d -o rss,sz' % pid).readlines() > print i, ' ', a2[1], > return int(a2[1].split()[1]) > > > > # take a memory snapshot on indStart and compare it with indEnd > indStart, indEnd = 30, 150 > for i in range(indEnd): > ind = arange(100) > xx = rand(len(ind)) > > figure(1) > subplot(221) > plot(ind, xx) > > subplot(222) > X = rand(50,50) > > imshow(X) > subplot(223) > scatter(rand(50), rand(50)) > subplot(224) > #pcolor(10*rand(50,50)) > m = Basemap(0, -85, 360, 85) > m.plot((50,), (20,), 'ro', markersize=12, label='gps') > m.drawcoastlines() > > savefig('tmp%d' % i, dpi = 75) > close(1) > > > val = report_memory(i) > # wait a few cycles for memory usage to stabilize > if i==indStart: start = val > > end = val > print 'Average memory consumed per loop: %1.4fk bytes ' % \ > ((end-start)/float(indEnd-indStart)) > > > ################################################ > #abbreviated results > ################################################ > 0 42724 12739 > 1 65068 18359 > 2 83036 22924 > 3 100980 27463 > 4 118928 32027 > 5 136872 36577 > 6 154828 41129 > 7 172784 45681 > 8 190736 50156 > 9 208692 54711 > 10 226644 59272 > 11 244592 63824 > 12 262548 68375 > 13 280496 72926 > 14 298440 77478 > 15 316392 81964 > . > . > . > 143 1771824 663458 > 144 1788924 668010 > 145 1791316 672561 > 146 1771104 677112 > 147 1775644 681599 > 148 1787288 686166 > 149 1791604 690718 > Average memory consumed per loop: 4505.0833k bytes > Gerald: One way to workaround the memory leak with Numeric is to move the Basemap instance creation m = Basemap(0, -85, 360, 85) outside the loop. There's no need to recreate it each time. As a bonus, the script runs many times faster too. -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 NOAA/OAR/CDC R/PSD1 FAX : (303)497-6449 325 Broadway Boulder, CO, USA 80305-3328
Gerald John M. Manipon wrote: > Hi all, > > I'm trying to generate a plot that contains 3 subplots: > 2 line plots and a basemap plot showing location. I'm > generating about 200 such plots however my script > doesn't get to complete because it encounters a MemoryError. > > I found the test script at > http://matplotlib.sourceforge.net/faq.html#LEAKS (which > BTW generates a plot with 4 subplots) and it succeeded > beautifully with no memory issues. However I changed the > last subplot to be a basemap plot and I was able to see > the memory leak. Below is the modified leak test script > I used and the abbreviated output from it. I would truly > appreciate any help on this. > > Thanks, > > Gerald > > ################################################ > #memory leak test > ################################################ > import os, sys, time > import matplotlib > matplotlib.use('Agg') > from pylab import * > from matplotlib.toolkits.basemap import Basemap > > def report_memory(i): > pid = os.getpid() > a2 = os.popen('ps -p %d -o rss,sz' % pid).readlines() > print i, ' ', a2[1], > return int(a2[1].split()[1]) > > > > # take a memory snapshot on indStart and compare it with indEnd > indStart, indEnd = 30, 150 > for i in range(indEnd): > ind = arange(100) > xx = rand(len(ind)) > > figure(1) > subplot(221) > plot(ind, xx) > > subplot(222) > X = rand(50,50) > > imshow(X) > subplot(223) > scatter(rand(50), rand(50)) > subplot(224) > #pcolor(10*rand(50,50)) > m = Basemap(0, -85, 360, 85) > m.plot((50,), (20,), 'ro', markersize=12, label='gps') > m.drawcoastlines() > > savefig('tmp%d' % i, dpi = 75) > close(1) > > > val = report_memory(i) > # wait a few cycles for memory usage to stabilize > if i==indStart: start = val > > end = val > print 'Average memory consumed per loop: %1.4fk bytes ' % \ > ((end-start)/float(indEnd-indStart)) > > > ################################################ > #abbreviated results > ################################################ > 0 42724 12739 > 1 65068 18359 > 2 83036 22924 > 3 100980 27463 > 4 118928 32027 > 5 136872 36577 > 6 154828 41129 > 7 172784 45681 > 8 190736 50156 > 9 208692 54711 > 10 226644 59272 > 11 244592 63824 > 12 262548 68375 > 13 280496 72926 > 14 298440 77478 > 15 316392 81964 > . > . > . > 143 1771824 663458 > 144 1788924 668010 > 145 1791316 672561 > 146 1771104 677112 > 147 1775644 681599 > 148 1787288 686166 > 149 1791604 690718 > Average memory consumed per loop: 4505.0833k bytes > Gerald: No leak here [jsw@Macintosh:/Users/jsw/python] python memleak.py 0 27856 89672 1 32672 92620 2 33200 92620 3 33200 92620 4 33168 92612 5 33196 92620 6 33196 92620 7 33164 92616 8 33200 92620 9 33184 92616 10 33196 92620 11 33184 92616 12 33176 92616 13 33204 92620 MacOS 10.4.7, matplotlib 0.87.4, basemap latest svn, numpy 1.0b2. However, if I use Numeric 24.2 [jsw@Macintosh:/Users/jsw/python] python memleak.py --Numeric 0 44472 102496 1 67140 123932 2 85376 141308 3 103200 159728 4 120992 177104 5 138800 194496 it leaks! No idea why - but I doubt it has much to do with basemap. -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 NOAA/OAR/CDC R/PSD1 FAX : (303)497-6449 325 Broadway Boulder, CO, USA 80305-3328
Scott, This is fixed now in svn. (I will probably go back shortly and make another change to improve efficiency.) There was a one-line bug in contour.py, but the fundamental problem was that colors.ColorConverter (which handles color inputs for collections, among other things) was stripping off the alpha value and replacing it with 1.0. Thanks for highlighting the bug. Eric Scott Ransom wrote: > Hi Eric, > > This shows what I'm talking about: > > -------------------- > from pylab import * > > delta = 0.025 > x = arange(-3.0, 3.0, delta) > y = arange(-2.0, 2.0, delta) > X, Y = meshgrid(x, y) > Z1 = bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0) > Z2 = bivariate_normal(X, Y, 1.5, 0.5, 1, 1) > # difference of Gaussians > Z = 10.0 * (Z2 - Z1) > > contourf(X, Y, sin(Y)*cos(X), > alpha=0.2) > hot() > contour(X, Y, Z, 6, > linewidths=4, > colors=('r', 'green', 'blue', (1,1,0), '#afeeee', '0.5'), > alpha=0.4) > show() > > ------------------- > > On Thursday 31 August 2006 13:50, Eric Firing wrote: >> Scott, >> >> Please send a minimal example that I can use as a test case. This >> sounds vaguely familiar. >> >> Thanks. >> >> Eric >> >> Scott Ransom wrote: >>> Hi All, >>> >>> I'm using matplotlib (with agg backends) from recent svn: >>> >>> In [63]: matplotlib.__version__ >>> Out[63]: '0.87.4' >>> >>> and I can't seem to get contour() or contourf() to utilize the >>> alpha keyword. No matter what value I set, alpha=1.0 on the >>> output. Alpha in general works fine, as the scatter_demo2.py >>> example gives very nicely alpha-channeled output. >>> >>> Any ideas? Thanks a bunch, >>> >>> Scott >
Hi all, I'm trying to generate a plot that contains 3 subplots: 2 line plots and a basemap plot showing location. I'm generating about 200 such plots however my script doesn't get to complete because it encounters a MemoryError. I found the test script at http://matplotlib.sourceforge.net/faq.html#LEAKS (which BTW generates a plot with 4 subplots) and it succeeded beautifully with no memory issues. However I changed the last subplot to be a basemap plot and I was able to see the memory leak. Below is the modified leak test script I used and the abbreviated output from it. I would truly appreciate any help on this. Thanks, Gerald ################################################ #memory leak test ################################################ import os, sys, time import matplotlib matplotlib.use('Agg') from pylab import * from matplotlib.toolkits.basemap import Basemap def report_memory(i): pid = os.getpid() a2 = os.popen('ps -p %d -o rss,sz' % pid).readlines() print i, ' ', a2[1], return int(a2[1].split()[1]) # take a memory snapshot on indStart and compare it with indEnd indStart, indEnd = 30, 150 for i in range(indEnd): ind = arange(100) xx = rand(len(ind)) figure(1) subplot(221) plot(ind, xx) subplot(222) X = rand(50,50) imshow(X) subplot(223) scatter(rand(50), rand(50)) subplot(224) #pcolor(10*rand(50,50)) m = Basemap(0, -85, 360, 85) m.plot((50,), (20,), 'ro', markersize=12, label='gps') m.drawcoastlines() savefig('tmp%d' % i, dpi = 75) close(1) val = report_memory(i) # wait a few cycles for memory usage to stabilize if i==indStart: start = val end = val print 'Average memory consumed per loop: %1.4fk bytes ' % \ ((end-start)/float(indEnd-indStart)) ################################################ #abbreviated results ################################################ 0 42724 12739 1 65068 18359 2 83036 22924 3 100980 27463 4 118928 32027 5 136872 36577 6 154828 41129 7 172784 45681 8 190736 50156 9 208692 54711 10 226644 59272 11 244592 63824 12 262548 68375 13 280496 72926 14 298440 77478 15 316392 81964 . . . 143 1771824 663458 144 1788924 668010 145 1791316 672561 146 1771104 677112 147 1775644 681599 148 1787288 686166 149 1791604 690718 Average memory consumed per loop: 4505.0833k bytes