[Matplotlib-users] Problem with plotting fast spiking data
Hi, I work with neural models and I have problem with plotting fast spiking data. The spikes on the plot appear to have different hight which changes when I for example resize the plot window. The same problem is with saving data into files, especially in vector formats. I found the information about changing the join style, it helps a bit (rounded is the best) but doesn't solve the problem. For raster formats the workaround is to save the data in higher resolution, using DPI option. Below I included links to examples. Normal example (100 DPI): https://docs.google.com/leaf?id=0B3NZY3443E1VY2JjNTc3MjAtZDI5NC00OThjLTgwY2EtNTVhMDVkZWQ2YzIw&hl=en Example 300 DPI: https://docs.google.com/leaf?id=0B3NZY3443E1VNDdkMzUzNzAtMjdmNC00NjFmLTliMzMtODE5MzExMmNjNjQz&hl=en The problem is vector files (I'm especially interested in EPS) ignore DPI option. I've experimented with different backends and the problem is persistent on GUI and 'file-writting' back ends. I also tested it on Linux and Mac, and the outcome does't change. Creating larger figures sometimes helps a bit but not always solve the problem. Just to mention that plotting this kind of data is possible 'out of the box' in Matlab or XPPAut (which is not the most fancy plotting tool) I get a proper outcome. Maybe there should be a option to plot raw data in some sense, or join style function that deals with such a plots in a proper fashion. If you need some additional information do not hesitate to ask. Thanks for the help in advance. Cheers, Jakub -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problem with plotting fast spiking data
Dear John and Eric, Thank you for the fast response. I'm using version 0.99.1.1 (to be exact), the MacOSX binary release for Python 2.5. The fix with path.simplify: False in matplotlibrc works perfectly! I googled quite a lot beforehand in order to find a fix for this issue, but obviously failed to find this bug. Once more thank you very much for the help. Cheers, Jakub On 18 Feb 2010, at 22:39, John Hunter wrote: > On Thu, Feb 18, 2010 at 4:19 PM, Jakub Nowacki > wrote: >> Hi, >> >> I work with neural models and I have problem with plotting fast spiking >> data. The spikes on the plot appear to have different hight which changes >> when I for example resize the plot window. The same problem is with saving >> data into files, especially in vector formats. I found the information about >> changing the join style, it helps a bit (rounded is the best) but doesn't >> solve the problem. For raster formats the workaround is to save the data in >> higher resolution, using DPI option. Below I included links to examples. >> >> Normal example (100 DPI): >> https://docs.google.com/leaf?id=0B3NZY3443E1VY2JjNTc3MjAtZDI5NC00OThjLTgwY2EtNTVhMDVkZWQ2YzIw&hl=en >> >> Example 300 DPI: >> https://docs.google.com/leaf?id=0B3NZY3443E1VNDdkMzUzNzAtMjdmNC00NjFmLTliMzMtODE5MzExMmNjNjQz&hl=en >> >> The problem is vector files (I'm especially interested in EPS) ignore DPI >> option. I've experimented with different backends and the problem is >> persistent on GUI and 'file-writting' back ends. I also tested it on Linux >> and Mac, and the outcome does't change. Creating larger figures sometimes >> helps a bit but not always solve the problem. >> >> Just to mention that plotting this kind of data is possible 'out of the box' >> in Matlab or XPPAut (which is not the most fancy plotting tool) I get a >> proper outcome. Maybe there should be a option to plot raw data in some >> sense, or join style function that deals with such a plots in a proper >> fashion. >> >> If you need some additional information do not hesitate to ask. Thanks for >> the help in advance. > > > This is a known bug in the latest release of mpl that is fixed in svn. > We do need to get a new release out soon. > > It is easy to fix by uncomennting the > > path.simplify : False > > line in your matplotlibrc file (the default is True). Note that > path.simplify does work in the svn release of matplotlib -- it is > designed to reduce paths but be imperceptible to the eye at the > resolution plotted, but due to a bug in the released version it can > result in improper simplifications. > > > See http://matplotlib.sourceforge.net/users/customizing.html for > information on how to change your matplotlibrc settings. > > JDH -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Draw lines on the graph
Hi, If I understand right you want to redraw new trend lines when you zoom in (recalculated for the visible data). You then have to use event callbacks which usage example is shown here (view limits change example): http://matplotlib.sourceforge.net/examples/event_handling/viewlims.html For one trend line it's relatively easy, you just recalculate the beginning and the end points. In the case when you have to guess how many lines you have to use it begins to be quite tricky if you haven't got a proper algorithm for that. Hope it helps. Cheers, Jakub On 21 Feb 2010, at 08:48, logan wrote: > Hi, > > I'm plotting some graphs with matplotlib and I would like to do the following: > > Draw lines on the graph (match two points to show the up-trend or > down-trend line of a stock). I would want the lines drawn by me on the > graph resize accordingly as one zooms in or out of the graph. > > Can anyone kindly point me to the API's or examples on how to do this? > I have tried looking but couldn't get it working. > > Thanks, > Hitesh > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > Matplotlib-users mailing list > Matplotlib-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] mplot3d stays?
Hi, I have quite general question. Since mplot3d now back in matplotlib, the question is: is it going to stay there? Or is it some test release? I was just wondering cause sometimes I use 3d plotting and use Mayavi2 for that but in many cases it's like killing the spider with a shotgun, not mentioning that installation process can be quite tricky. Thanks for answer in advance. Cheers, Jakub -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] mplot3d stays?
Dear all, I don't know if creating full blown 3d library makes much sense. I think Reinier is right here that the current mplot3d creates quite satisfactory outcome with matplotlib look-and-feel we all like. In general, there are 3d libraries/packages out there (VTK, Mayavi2 etc.), which do most of the stuff one would need. The problem is many times using is not that trivial. Also, the installation process is usually much more complex, eg. setting up mayavi2 on snow leopard took me several days. I asked the question in the first place because in many cases I need rather simple 3d plotting tool, without al the massive rendering capabilities etc. Since I use matplotlib anyway, it would be nice to use the same tool and not be forced to install and learn something new just to plot not very complicated surface. Hence, I think the main goal here should be to have a relatively simple but usable plotting tool with matplotlib look-an-feel. BTW I didn't know that my simple question would generate such a discussion. :) Best wishes, Jakub -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Failure compiling MPL on Snow Leopard
Dear Jeremy, I'm not sure but I think it may be the problem with ppc, cause this architecture was dropped for Snow Leopard as far as I remember. So just delete "-arch ppc" and try again. In general you may try to use this description: http://blog.hyperjeff.net/?p=160 I've tested it and it works. Cheers, Jakub On 03/09/2010 04:54 AM, Jeremy Conlin wrote: > I am trying to compile MPL on Snow Leopard without success. I have a > fairly fresh system (10.6.2) with python.org 2.6.4 installed. I have > downloaded the MPL trunk with svn. I had to make a small change to > the make.osx file because there are some extra ". However I still > can't get MPL to compile/install; it fails when compiling zlib. The > change I made in the make.osx file is on line 11. It used to be: > > ARCH_FLAGS="-arch i386 -arch ppc -arch x86_64" > > and is now: > > ARCH_FLAGS=-arch i386 -arch ppc -arch x86_64 > > The error I get while compiling is copied below. Can anyone help me > figure out what is wrong? > > Thanks, > Jeremy > > x zlib-1.2.3/zutil.h > Checking for gcc... > Building static library libz.a version 1.2.3 with gcc. > Checking for unistd.h... No. > Checking whether to use vs[n]printf() or s[n]printf()... using s[n]printf() > Checking for snprintf() in stdio.h... No. >WARNING: snprintf() not found, falling back to sprintf(). zlib >can build but will be open to possible buffer-overflow security >vulnerabilities. > Checking for return value of sprintf()... No. >WARNING: apparently sprintf() does not return a value. zlib >can build but will be open to possible string-format security >vulnerabilities. > Checking for errno.h... No. > Checking for mmap support... No. > gcc -arch i386 -arch ppc -arch x86_64 -I/include -I/include/freetype2 > -isysroot /Developer/SDKs/MacOSX10.6u.sdk -DNO_snprintf > -DHAS_sprintf_void -DNO_ERRNO_H -c -o adler32.o adler32.c > gcc -arch i386 -arch ppc -arch x86_64 -I/include -I/include/freetype2 > -isysroot /Developer/SDKs/MacOSX10.6u.sdk -DNO_snprintf > -DHAS_sprintf_void -DNO_ERRNO_H -c -o compress.o compress.c > gcc -arch i386 -arch ppc -arch x86_64 -I/include -I/include/freetype2 > -isysroot /Developer/SDKs/MacOSX10.6u.sdk -DNO_snprintf > -DHAS_sprintf_void -DNO_ERRNO_H -c -o crc32.o crc32.c > In file included from crc32.c:29: > zutil.h:21:24: error: stddef.h: No such file or directory > zutil.h:23:22: error: string.h: No such file or directory > zutil.h:24:22: error: stdlib.h: No such file or directory > crc32.c:36:24: error: limits.h: No such file or directory > In file included from crc32.c:29: > zutil.h:21:24: error: stddef.h: No such file or directory > zutil.h:23:22: error: string.h: No such file or directory > zutil.h:24:22: error: stdlib.h: No such file or directory > crc32.c:36:24: error: limits.h: No such file or directory > In file included from crc32.c:29: > zutil.h:21:24: error: stddef.h: No such file or directory > zutil.h:23:22: error: string.h: No such file or directory > zutil.h:24:22: error: stdlib.h: No such file or directory > crc32.c:36:24: error: limits.h: No such file or directory > gcc -arch i386 -arch ppc -arch x86_64 -I/include -I/include/freetype2 > -isysroot /Developer/SDKs/MacOSX10.6u.sdk -DNO_snprintf > -DHAS_sprintf_void -DNO_ERRNO_H -c -o gzio.o gzio.c > lipo: can't figure out the architecture type of: /var/tmp//cc9xNLIP.out > make[1]: *** [crc32.o] Error 1 > make[1]: *** Waiting for unfinished jobs > gzio.c:10:19: error: stdio.h: No such file or directory > > > and more errors below. > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > Matplotlib-users mailing list > Matplotlib-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problem with plotting fast spiking data
Just to conclude the problem. I've just installed a fresh svn matplotlib (1.0-svn to be exact) and the problem with path optimisation disappeared, meaning with path.simplify False plots are correct as far as my data is concerned. BTW it very nicely builds out-of-the-box on 10.6 in 64-bit mode. Cheers, Jakub On 18 Feb 2010, at 22:37, Eric Firing wrote: > Jakub Nowacki wrote: >> Hi, >> I work with neural models and I have problem with plotting fast spiking >> data. The spikes on the plot appear to have different hight which changes >> when I for example resize the plot window. The same problem is with saving >> data into files, especially in vector formats. I found the information about >> changing the join style, it helps a bit (rounded is the best) but doesn't >> solve the problem. For raster formats the workaround is to save the data in >> higher resolution, using DPI option. Below I included links to examples. > > This sounds like a problem with the path simplification algorithm. If so, > the question is whether it is a bug that has been fixed or a new bug. What > mpl version are you using? Can you build and install from svn? > > Eric > >> Normal example (100 DPI): >> https://docs.google.com/leaf?id=0B3NZY3443E1VY2JjNTc3MjAtZDI5NC00OThjLTgwY2EtNTVhMDVkZWQ2YzIw&hl=en >> Example 300 DPI: >> https://docs.google.com/leaf?id=0B3NZY3443E1VNDdkMzUzNzAtMjdmNC00NjFmLTliMzMtODE5MzExMmNjNjQz&hl=en >> The problem is vector files (I'm especially interested in EPS) ignore DPI >> option. I've experimented with different backends and the problem is >> persistent on GUI and 'file-writting' back ends. I also tested it on Linux >> and Mac, and the outcome does't change. Creating larger figures sometimes >> helps a bit but not always solve the problem. Just to mention that plotting >> this kind of data is possible 'out of the box' in Matlab or XPPAut (which >> is not the most fancy plotting tool) I get a proper outcome. Maybe there >> should be a option to plot raw data in some sense, or join style function >> that deals with such a plots in a proper fashion. If you need some >> additional information do not hesitate to ask. Thanks for the help in >> advance. Cheers, >> Jakub -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] subplot grids with EPD
Hi, Personally I've tried to install Matplotlib 1.0.0 manually in EPD on Mac and Linux. For some reason on Linux it went totally OK from the first try (just had to define PREFIX correctly). On Mac I've tried to do the same but for some reason the libs are linked somehow differently and while the installation went OK (at least it didn't complain) mpl didn't work. I admit I don't have that much experience with Mac linking but it seems to be the issue. BTW have you tried to force 32-bit compilation using 'arch'? I was getting such messages when I've tired to run 64-bit module with 32-bit Python (didn't specify arch correctly). Best wishes, Jakub On 10/05/2010 03:26 PM, Robin wrote: > Hi, > > I am using EPD 6.2 (32 bit) on a mac. > > I would like to use subplot grids (matplotlib.gridspec) which seems to > require mpl 1.0.0. > > Is there anyway to install this and use it with EPD? So far I have > tried everything from the installation guide, but whatever I do I get > a bus error in ft2font. > > I can't get the wx backend to show up in the config stage (although wx > is installed in EPD). > I have tried building it myself, with the make.osx script, and with > the EPD guide on the installation page, both with gcc 4.0 and gcc 4.2 > but everything gives the same bus error. > I'm actually not sure what compiler is used for EPD so perhaps that is > the problem. > > Alternatively, is there a way to pick out the subplot grid features > and use them with the epd matplotlib? > > If anyone is interested this is the error I get: > > > Exception Type: EXC_BAD_ACCESS (SIGBUS) > Exception Codes: KERN_PROTECTION_FAILURE at 0x > Crashed Thread: 0 Dispatch queue: com.apple.main-thread > > Thread 0 Crashed: Dispatch queue: com.apple.main-thread > 0 ??? 00 0 + 0 > 1 libSystem.B.dylib 0x96f31108 > _Unwind_GetLanguageSpecificData + 24 > 2 libstdc++.6.dylib 0x97166d86 __gxx_personality_v0 + 120 > 3 libgcc_s.1.dylib 0x0040b476 > _Unwind_RaiseException_Phase2 + 102 (unwind.inc:68) > 4 libgcc_s.1.dylib 0x0040b890 _Unwind_Resume + 112 > (unwind.inc:238) > 5 ft2font.so0x04501a98 > FT2Font::FT2Font(std::string) + 4776 (ExtensionOldType.hxx:88) > 6 ft2font.so0x04501fd3 > ft2font_module::new_ft2font(Py::Tuple const&) + 515 (ft2font.cpp:1969) > 7 ft2font.so0x045041b6 > Py::ExtensionModule::invoke_method_varargs(void*, > Py::Tuple const&) + 102 (ExtensionModule.hxx:184) > 8 ft2font.so0x0450db87 method_varargs_call_handler > + 343 > 9 org.python.python 0x000cbfd5 PyEval_EvalFrameEx + 19429 > 10 org.python.python 0x000ce14d PyEval_EvalCodeEx + 2109 > 11 org.python.python 0x000cc1bc PyEval_EvalFrameEx + 19916 > 12 org.python.python 0x000ce14d PyEval_EvalCodeEx + 2109 > 13 org.python.python 0x0004b136 function_call + 166 > 14 org.python.python 0x00019b05 PyObject_Call + 85 > 15 org.python.python 0x0002c0e6 instancemethod_call + 422 > 16 org.python.python 0x00019b05 PyObject_Call + 85 > 17 org.python.python 0x000c642e > PyEval_CallObjectWithKeywords + 78 > 18 org.python.python 0x0002efb2 PyInstance_New + 114 > 19 org.python.python 0x00019b05 PyObject_Call + 85 > 20 org.python.python 0x000ca927 PyEval_EvalFrameEx + 13623 > 21 org.python.python 0x000cc956 PyEval_EvalFrameEx + 21862 > 22 org.python.python 0x000ce14d PyEval_EvalCodeEx + 2109 > 23 org.python.python 0x000ce2d7 PyEval_EvalCode + 87 > 24 org.python.python 0x000e5a3c PyImport_ExecCodeModuleEx + > 188 > 25 org.python.python 0x000e66dc load_source_module + 540 > 26 org.python.python 0x000e72fd import_submodule + 301 > 27 org.python.python 0x000e7559 load_next + 201 > 28 org.python.python 0x000e7f53 PyImport_ImportModuleLevel + > 419 > 29 org.python.python 0x000c09bf builtin___import__ + 159 > 30 org.python.python 0x00019b05 PyObject_Call + 85 > 31 org.python.python 0x000c642e > PyEval_CallObjectWithKeywords + 78 > 32 org.python.python 0x000c99c0 PyEval_EvalFrameEx + 9680 > 33 org.python.python 0x000ce14d PyEval_EvalCodeEx + 2109 > 34 org.python.python 0x000ce2d7 PyEval_EvalCode + 87 > 35 org.python.python 0x000e5a3c PyImport_ExecCodeModuleEx + > 188 > 36 org.python.python 0x000e66dc load_source_module + 540 > 37 org.python.python 0x000e72fd import_submodule + 301 > 38 org.python.python 0x000e78a7 ensure_fromlist + 439 > 39 org.python.pyt
[Matplotlib-users] Control over ticks in 3D plot
Dear All, I've found it impossible to get some control over ticks in a 3D plot (Axes3D, using with projection='3d' option) in Matplotlib 1.0.1 (EPD 7.1-1 linux 64-bit). Namely, I have one out of four subplots, that is 3D and it has much to many ticks (tick labels to be exact), which makes them unreadable (most of them overlay on one another, not mentioning axis labels are covered as well). Usually in such situations I used set_x(y)ticks with some values or ax.x(y)axis.get_major_locator()._nbins if I just wanted a certain number. But I've found that _nbins doesn't do anything (also, there is no zaxis object), set_zticks return an error 'AttributeError: 'Axes3DSubplot' object has no attribute 'set_zticks'' and set_x(y)ticks changes ticks of not 3d axis but 2d one. Is there any (other) way to influence the number of ticks? Thanks for the help in advance. Best wishes, Jakub -- Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Control over ticks in 3D plot
Thanks for the answers. Jakub, if possible, could you test out the latest matplotlib in development on github? I have been working hard in this. If not, you could also always operate directly through the axis objects themselves, such as: ax.zaxis (although, you might have to do ax.w_zaxis). OK, I can use axis through w_*axis to control them. The function set_ticks works(ish) in that case but the axes is for some reason flushed to the left (it filled the image before) as can be seen in the enclosed image. This behaviour has nothing to do with the ticks values nor the axis (brakes the same for x, y and z axis). The selected ticks are updated though, just the whole projection (?) brakes. The below suggestion by José works correctly without the effect shown in the image. a1.w_yaxis.set_major_locator(LinearLocator(5)) a1.w_zaxis.set_major_locator(LinearLocator(5)) As for the github version, I can try it out in some future but currently I don't have time. Also installing new stuff into EPD is not necessary too trivial. Thanks for the suggestions. Cheers, Jakub <>-- Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
