[matplotlib-devel] mlab cohere_pairs patch
Hi, here is a suggested patch for mlab's cohere_pairs function. The old version was broken, due to some outdated code. Cheers, Ariel -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel mlab_cohere_pairs_patch.py Description: Binary data -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] mlab cohere_pairs patch
Hi - I would like to do that, but now, after I grabbed the most recent svn from main source and tried to build it (so that I can replicate the broken-ness of the code) I get this: ASR:matplotlib arokem$ python setup.py install BUILDING MATPLOTLIB matplotlib: 1.0.svn python: 2.5.2 |EPD 4.0.30001| (r252:60911, Sep 19 2008, 12:00:24) [GCC 4.0.1 (Apple Computer, Inc. build 5370)] platform: darwin REQUIRED DEPENDENCIES numpy: 1.3.0.dev5972 freetype2: 9.17.3 OPTIONAL BACKEND DEPENDENCIES libpng: 1.2.37 Tkinter: Tkinter: 50704, Tk: 8.4, Tcl: 8.4 wxPython: 2.8.7.1 * WxAgg extension not required for wxPython >= 2.8 Gtk+: no * Building for Gtk+ requires pygtk; you must be able * to "import gtk" in your build/install environment Mac OS X native: yes Qt: no Qt4: Qt: 4.5.2, PyQt4: 4.5.2 Cairo: no OPTIONAL DATE/TIMEZONE DEPENDENCIES datetime: present, version unknown dateutil: 1.4 pytz: 2008c OPTIONAL USETEX DEPENDENCIES dvipng: 1.9 ghostscript: 8.57 latex: 3.141592 [Edit setup.cfg to suppress the above messages] ... lots more output to the shell - everything looks OK... g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g -bundle -undefined dynamic_lookup build/temp.macosx-10.3-i386-2.5/src/ft2font.o build/temp.macosx-10.3-i386-2.5/src/mplutils.o build/temp.macosx-10.3-i386-2.5/CXX/cxx_extensions.o build/temp.macosx-10.3-i386-2.5/CXX/cxxsupport.o build/temp.macosx-10.3-i386-2.5/CXX/IndirectPythonInterface.o build/temp.macosx-10.3-i386-2.5/CXX/cxxextensions.o -L/opt/local/lib -L/usr/local/lib -L/usr/lib -L/sw/lib -lfreetype -lz -lz -lstdc++ -lm -o build/lib.macosx-10.3-i386-2.5/matplotlib/ft2font.so -Wl,-framework,CoreServices -Wl,-framework,ApplicationServices ld warning: in /opt/local/lib/libfreetype.dylib, file is not of required architecture ld warning: in /opt/local/lib/libz.dylib, file is not of required architecture ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libxml2.2.dylib, file is not of required architecture for architecture ppc collect2: ld returned 1 exit status ld warning: duplicate dylib /opt/local/lib/libz.1.dylib lipo: can't open input file: /var/folders/Qb/QbU9SmFNHoWnC7v-nTJYrE+++TI/-Tmp-//ccuiy1nA.out (No such file or directory) error: command 'g++' failed with exit status 1 Am I doing something wrong? I promise to follow your instructions, if I can make it work :-) Thanks, Ariel On Tue, Aug 11, 2009 at 5:14 PM, John Hunter wrote: > On Tue, Aug 11, 2009 at 5:02 PM, Ariel Rokem wrote: > > > here is a suggested patch for mlab's cohere_pairs function. The old > version > > was broken, due to some outdated code. > > Thanks Ariel for the patch. Could you explain your patch in words -- > what was broken before and how you fixed it. Also, while your patch > is particularly simple, since it is just a single function > replacement, we encourage people to submit svn diffs against HEAD or > the branch they are patching. It just makes life simpler for us, > since we (fortunately) get a lot of contributions. I strongly > encourage people to include a complete, free-standing example that I > can run unmodified which shows the undesired behavior pre-patch and > the desired behavior post-patch, with a clear verbal of what to look > for. I wrote this function 5 years ago, and while I remember it > pretty well, I will not be as familiar with it after such a long > hiatus as you are now. > > http://matplotlib.sourceforge.net/faq/howto_faq.html#contributing-howto > > JDH > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] mlab cohere_pairs patch
Resending, with CC to list. Thanks for the help! Nightmare of the living crash-test dummy... I tried following your instructions. Here's what that looks like: ASR:matplotlib arokem$ make build_os105 make: *** No rule to make target `build_os105'. Stop. ASR:matplotlib arokem$ cd release/osx ASR:osx arokem$ open README.txt I read the README - decide to skip reinstalling python and numpy, and skipped to the next step ... ASR:osx arokem$ unset PKG_CONFIG_PATH ASR:osx arokem$ make fetch_deps dependencies make: *** No rule to make target `fetch_deps'. Stop. ASR:osx arokem$ make fetch wget http://www.zlib.net/zlib-1.2.3.tar.gz &&\ wget http://internap.dl.sourceforge.net/sourceforge/libpng/libpng-1.2.33.tar.bz2&&\ wget http://download.savannah.gnu.org/releases/freetype/freetype-2.3.7.tar.bz2&&\ wget http://pypi.python.org/packages/source/b/bdist_mpkg/bdist_mpkg-0.4.4.tar.gz&&; \ tar xvfz bdist_mpkg-0.4.4.tar.gz &&\ echo "You need to to install bdist_mpkg-0.4.4 now" /bin/sh: wget: command not found make: *** [fetch] Error 127 I googled "wget" - downloaded wget source-code, installed wget. ASR:osx arokem$ make fetch seemed to work now, after fetch got everything, I continued with the crib sheet from the README.txt (which has an error in it, the 6th step there is 'cd ..'. That didn't work - instead I ran 'make deps' in the directory I previously ended up in '/release/osx/', that worked) Finally: ASR:osx arokem$ make installers unset PKG_CONFIG_PATH &&\ tar xvfz matplotlib-0.99.0.tar.gz && \ cd matplotlib-0.99.0 && \ rm -rf build && \ cp ../data/setup.cfg ../data/ReadMe.txt . &&\ export CFLAGS="-Os -arch ppc -arch i386 -I/Users/arokem/source/matplotlib/release/osx/zlib-1.2.3 -I/Users/arokem/source/matplotlib/release/osx/libpng-1.2.33 -I/Users/arokem/source/matplotlib/release/osx/freetype-2.3.7/include" &&\ export LDFLAGS="-arch ppc -arch i386 -L/Users/arokem/source/matplotlib/release/osx/zlib-1.2.3 -L/Users/arokem/source/matplotlib/release/osx/libpng-1.2.33 -L/Users/arokem/source/matplotlib/release/osx/freetype-2.3.7" &&\ /Library/Frameworks/Python.framework/Versions/2.6/bin/bdist_mpkg --readme=ReadMe.txt &&\ hdiutil create -srcdir dist/matplotlib-0.99.0-py2.6-macosx10.5.mpkg dist/matplotlib-0.99.0-py2.6-macosx10.5.dmg &&\ python2.6 setupegg.py bdist_egg tar (child): matplotlib-0.99.0.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error exit delayed from previous errors make: *** [installers] Error 2 But the version number I have here is matplotlib-1.0.svn (is that what I am supposed to have? I grabbed the svn as instructed on the webpage you linked to before), so I go and edit the Makefile, to reflect that. I run that again, it does a lot of stuff (I have the full output saved, if you want to see that). Then, finally: g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -bundle -undefined dynamic_lookup -arch ppc -arch i386 -L/Users/arokem/source/matplotlib/release/osx/zlib-1.2.3 -L/Users/arokem/source/matplotlib/release/osx/libpng-1.2.33 -L/Users/arokem/source/matplotlib/release/osx/freetype-2.3.7 -Os -arch ppc -arch i386 -I/Users/arokem/source/matplotlib/release/osx/zlib-1.2.3 -I/Users/arokem/source/matplotlib/release/osx/libpng-1.2.33 -I/Users/arokem/source/matplotlib/release/osx/freetype-2.3.7/include build/temp.macosx-10.3-fat-2.5/src/ft2font.o build/temp.macosx-10.3-fat-2.5/src/mplutils.o build/temp.macosx-10.3-fat-2.5/CXX/cxx_extensions.o build/temp.macosx-10.3-fat-2.5/CXX/cxxsupport.o build/temp.macosx-10.3-fat-2.5/CXX/IndirectPythonInterface.o build/temp.macosx-10.3-fat-2.5/CXX/cxxextensions.o -L/opt/local/lib -L/usr/local/lib -L/usr/lib -L/sw/lib -lfreetype -lz -lz -lstdc++ -lm -o build/lib.macosx-10.3-fat-2.5/matplotlib/ft2font.so -Wl,-framework,CoreServices -Wl,-framework,ApplicationServices ld warning: in /opt/local/lib/libfreetype.dylib, file is not of required architecture ld warning: in /opt/local/lib/libz.dylib, file is not of required architecture ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libxml2.2.dylib, file is not of required architecture for architecture ppc collect2: ld returned 1 exit status ld warning: duplicate dylib /opt/local/lib/libz.1.dylib lipo: can't open input file: /var/folders/Qb/QbU9SmFNHoWnC7v-nTJYrE+++TI/-Tmp-//ccp3hmVy.out (No such file or directory) error: command 'g++' failed with exit status 1 make: *** [installers] Error 1 So - I am back to square 1, it seems. Do you know where I should go from here? Cheers, Ariel On Tue, Aug 11, 2009 at 6:37 PM, John Hunter wrote: > On Tue, Aug 11, 2009 at 8:29 PM, Ariel Rokem wrote: > > > Am I doing something wrong? I promise
Re: [matplotlib-devel] mlab cohere_pairs patch
ate dylib /opt/local/lib/libz.1.dylib lipo: can't open input file: /var/folders/Qb/QbU9SmFNHoWnC7v-nTJYrE+++TI/-Tmp-//ccud2g4d.out (No such file or directory) error: command 'g++' failed with exit status 1 make: *** [installers] Error 1 Any ideas? Cheers, Ariel On Wed, Aug 12, 2009 at 3:42 AM, John Hunter wrote: > On Wed, Aug 12, 2009 at 2:26 AM, Fernando Perez > wrote: > > > By the way John, in this particular case, I don't think the change > > warrants a before/after example, because the before case is "it > > doesn't run" :) The code today makes calls to Numeric routines like > > typecode() that simply don't exist anymore, so it's totally broken: > > Great -- this is just the kind of explanation I need. Though if we had > an example, it is unlikely that the code would go so long w/o being > exercised. We do supply some eeg data with mpl -- see > examples/pylab_examples/mri_with_eeg.py, so Ariel may want to write a > simple cohere_pairs examples which just generates a scatter plot or > something else to show the output and then we can include it in > backend driver do it is will be unlikely to suffer bit rot going > forward. > > > Ariel, if you are still struggling with the binary build, since your > > changes are confined to a pure python file, you can submit the patch > > by simply running: > > > > - svn udpate > > - modify in-place mlab.py with your version of cohere_pairs > > - svn diff > mlab_cohere_pairs.diff > > udpate = update > > That will be fine -- I would like to help Ariel get his svn build > going, but if that is a distraction it doesn't need to slow the patch > down. For bugfixes we encourage patches against the release branch > > svn co > https://matplotlib.svn.sf.net/svnroot/matplotlib/branches/v0_99_maint > mpl99<https://matplotlib.svn.sf.net/svnroot/matplotlib/branches/v0_99_maint%0Ampl99> > > JDH > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] mlab cohere_pairs patch
Hi again - a string of strange things just happened. After this recent chain of failures, I decided to try to do some random attempts at making this work. First, I ran 'sudo python setup.py install' in the directory into which I had checked out the mpl source. After going through all of the above, that now went without a hitch(?!). I started ipython and imported matplotlib, but was disappointed to see that I was still importing 0.98.3, which is the version I previously had. I then ran: ASR:~ arokem$ easy_install matplotlib Searching for matplotlib Best match: matplotlib 0.99.0 Removing matplotlib 0.98.3.0001 from easy-install.pth file Adding matplotlib 0.99.0 to easy-install.pth file Using /Library/Frameworks/Python.framework/Versions/4.0.30001/lib/python2.5/site-packages Processing dependencies for matplotlib Finished processing dependencies for matplotlib Now, when I open ipython and import matplotlib, the version I have is 0.99, and it seems to work (opens plots and such). So - somehow the process worked, but how? Cheers, Ariel On Wed, Aug 12, 2009 at 10:08 AM, Ariel Rokem wrote: > Hi Fernando and John, > > regardless of the clunky way in which I was trying to introduce our patch, > I still want to be able to build MPL from source on my machine. It is a > distraction, but, hey, it's a distraction on top of a distraction on top of > a distraction, so at this point, I might as well be distracted. Besides, it > should end up being useful, and not only for me. Yesterday, there was > someone on the matplotlib-users list with exactly the same problem in > building MPL from source (sourceforge is not responding at the moment, so I > can't post a link to that message). If this is not a good time to > trouble-shoot this, let me know and we can come back to this in a couple of > weeks. It does seem like cohere_pairs has not gotten a lot of use, so the > patch can also languish for another couple of weeks andI can get stuff done > regardless of solving this problem, but I would love to be able to solve > this, with your help. > > So - I now checked out 0.99, running 'make build_osx105' (you do realize > the 'x' stands for '10', don't you?) didn't work, so I followed the > instructions in source/osx/README > > I still get exactly the same error as before: > > g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -bundle > -undefined dynamic_lookup -arch ppc -arch i386 > -L/Users/arokem/source/mpl99/release/osx/zlib-1.2.3 > -L/Users/arokem/source/mpl99/release/osx/libpng-1.2.33 > -L/Users/arokem/source/mpl99/release/osx/freetype-2.3.7 -Os -arch ppc -arch > i386 -I/Users/arokem/source/mpl99/release/osx/zlib-1.2.3 > -I/Users/arokem/source/mpl99/release/osx/libpng-1.2.33 > -I/Users/arokem/source/mpl99/release/osx/freetype-2.3.7/include > build/temp.macosx-10.3-fat-2.5/src/ft2font.o > build/temp.macosx-10.3-fat-2.5/src/mplutils.o > build/temp.macosx-10.3-fat-2.5/CXX/cxx_extensions.o > build/temp.macosx-10.3-fat-2.5/CXX/cxxsupport.o > build/temp.macosx-10.3-fat-2.5/CXX/IndirectPythonInterface.o > build/temp.macosx-10.3-fat-2.5/CXX/cxxextensions.o -L/opt/local/lib > -L/usr/local/lib -L/usr/lib -L/sw/lib -lfreetype -lz -lz -lstdc++ -lm -o > build/lib.macosx-10.3-fat-2.5/matplotlib/ft2font.so > -Wl,-framework,CoreServices -Wl,-framework,ApplicationServices > ld warning: in /opt/local/lib/libfreetype.dylib, file is not of required > architecture > ld warning: in /opt/local/lib/libz.dylib, file is not of required > architecture > ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libxml2.2.dylib, file > is not of required architecture for architecture ppc > collect2: ld returned 1 exit status > ld warning: duplicate dylib /opt/local/lib/libz.1.dylib > lipo: can't open input file: > /var/folders/Qb/QbU9SmFNHoWnC7v-nTJYrE+++TI/-Tmp-//cceiN12W.out (No such > file or directory) > error: command 'g++' failed with exit status 1 > make: *** [installers] Error 1 > > So - there is still some problem with the architecture. BTW - this closely > resembles errors I used to get when trying to install ETS, but in the recent > release of ETS, this problem seems to have been solved. Here's something > from enthought-dev, in that direction: > https://mail.enthought.com/pipermail/enthought-dev/2009-June/022153.html > > I tried following Robert Kern's suggestion and edited > /Library/Frameworks/Python.framework/Versions/Current/lib/python2.5/config/Makefile > in order to remove the '-arch ppc' flag from the CFLAGS and LDFLAGS > variables, and from one other place in that file, but that didn't seem to > help. Even though now g++ is called without the possibly offending '-arch > ppc' flag, somethow that flag is ge
Re: [matplotlib-devel] mlab cohere_pairs patch
Hi - scratch that. Only *seems* to be working. Actually it hangs when I run scripts that open figures. I am going to undo all this and forget I ever started down this path. Cheers, Ariel On Wed, Aug 12, 2009 at 11:10 AM, Ariel Rokem wrote: > Hi again - a string of strange things just happened. After this recent > chain of failures, I decided to try to do some random attempts at making > this work. > > First, I ran 'sudo python setup.py install' in the directory into which I > had checked out the mpl source. After going through all of the above, that > now went without a hitch(?!). I started ipython and imported matplotlib, but > was disappointed to see that I was still importing 0.98.3, which is the > version I previously had. > > I then ran: > > ASR:~ arokem$ easy_install matplotlib > Searching for matplotlib > Best match: matplotlib 0.99.0 > Removing matplotlib 0.98.3.0001 from easy-install.pth file > Adding matplotlib 0.99.0 to easy-install.pth file > > Using > /Library/Frameworks/Python.framework/Versions/4.0.30001/lib/python2.5/site-packages > Processing dependencies for matplotlib > Finished processing dependencies for matplotlib > > Now, when I open ipython and import matplotlib, the version I have is 0.99, > and it seems to work (opens plots and such). So - somehow the process > worked, but how? > > Cheers, > > Ariel > > > > On Wed, Aug 12, 2009 at 10:08 AM, Ariel Rokem wrote: > >> Hi Fernando and John, >> >> regardless of the clunky way in which I was trying to introduce our patch, >> I still want to be able to build MPL from source on my machine. It is a >> distraction, but, hey, it's a distraction on top of a distraction on top of >> a distraction, so at this point, I might as well be distracted. Besides, it >> should end up being useful, and not only for me. Yesterday, there was >> someone on the matplotlib-users list with exactly the same problem in >> building MPL from source (sourceforge is not responding at the moment, so I >> can't post a link to that message). If this is not a good time to >> trouble-shoot this, let me know and we can come back to this in a couple of >> weeks. It does seem like cohere_pairs has not gotten a lot of use, so the >> patch can also languish for another couple of weeks andI can get stuff done >> regardless of solving this problem, but I would love to be able to solve >> this, with your help. >> >> So - I now checked out 0.99, running 'make build_osx105' (you do realize >> the 'x' stands for '10', don't you?) didn't work, so I followed the >> instructions in source/osx/README >> >> I still get exactly the same error as before: >> >> g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -bundle >> -undefined dynamic_lookup -arch ppc -arch i386 >> -L/Users/arokem/source/mpl99/release/osx/zlib-1.2.3 >> -L/Users/arokem/source/mpl99/release/osx/libpng-1.2.33 >> -L/Users/arokem/source/mpl99/release/osx/freetype-2.3.7 -Os -arch ppc -arch >> i386 -I/Users/arokem/source/mpl99/release/osx/zlib-1.2.3 >> -I/Users/arokem/source/mpl99/release/osx/libpng-1.2.33 >> -I/Users/arokem/source/mpl99/release/osx/freetype-2.3.7/include >> build/temp.macosx-10.3-fat-2.5/src/ft2font.o >> build/temp.macosx-10.3-fat-2.5/src/mplutils.o >> build/temp.macosx-10.3-fat-2.5/CXX/cxx_extensions.o >> build/temp.macosx-10.3-fat-2.5/CXX/cxxsupport.o >> build/temp.macosx-10.3-fat-2.5/CXX/IndirectPythonInterface.o >> build/temp.macosx-10.3-fat-2.5/CXX/cxxextensions.o -L/opt/local/lib >> -L/usr/local/lib -L/usr/lib -L/sw/lib -lfreetype -lz -lz -lstdc++ -lm -o >> build/lib.macosx-10.3-fat-2.5/matplotlib/ft2font.so >> -Wl,-framework,CoreServices -Wl,-framework,ApplicationServices >> ld warning: in /opt/local/lib/libfreetype.dylib, file is not of required >> architecture >> ld warning: in /opt/local/lib/libz.dylib, file is not of required >> architecture >> ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libxml2.2.dylib, file >> is not of required architecture for architecture ppc >> collect2: ld returned 1 exit status >> ld warning: duplicate dylib /opt/local/lib/libz.1.dylib >> lipo: can't open input file: >> /var/folders/Qb/QbU9SmFNHoWnC7v-nTJYrE+++TI/-Tmp-//cceiN12W.out (No such >> file or directory) >> error: command 'g++' failed with exit status 1 >> make: *** [installers] Error 1 >> >> So - there is still some problem with the architecture. BTW - this closely >> resembles errors I used to get when trying to install ETS, but in the recent >> release of ETS, this
Re: [matplotlib-devel] Building matplotlib on os x
Resending with CC to list: D'oh. I forgot to do that. OK - now I went back and ran: env ARCHFLAGS='-arch i386' python setup.py install That also went with no hitches Then, in Python: >>> import matplotlib >>> matplotlib.__version__ '0.98.5.2' So - still no version update. I ran: 'easy_install matplotlib', which somehow seems to change the path setting to find the most recent version of things (maybe someone here can tell me how this happens?) now: >>> import matplotlib >>> matplotlib.__version__ '0.99.0' However, now, when I run a script that has plotting in it, in ipython, the script hangs after plotting. That is, it puts up the first figure in the script (a simple bar graph) and then doesn't do anything more. So - on the one hand, it doesn't crash while building and installing. On the other hand, it doesn't work. Cheers, Ariel On Thu, Aug 13, 2009 at 5:19 AM, Jeff Whitaker wrote: > Ariel Rokem wrote: >> >> Hi - that's interesting - I am actually on OS10.5. For some reason, >> the MPL libraries get built under a directory called >> "lib.macosx-10.3-fat-2.5" and the SDK set in the Python Makefile is >> /Developer/SDKs/MacOSX10.4u.sdk, which is why you see these mentioned >> in the output. >> >> Wondering if that is the cause of the problems, I reset the SDK in the >> Makefile to /Developer/SDKs/MacOSX10.5.sdk (in the definition of >> BASECFLAGS, as well as LDFLAGS). As before, I removed the '-arch ppc' >> (from these two places, as well) and ran 'env ARCHFLAGS='-arch i386' >> python setup.py build' >> >> This time I don't get any compilation errors at all. It just runs >> through. However, when I import matplotlib in python, I still get: >> > > Ariel: Did you run 'python setup.py install'? > > -Jeff > > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Building matplotlib on os x
Hi Jeff, > import matplotlib > matplotlib.__version__ > >> >> '0.98.5.2' >> > > Ariel: This tells me you really didn't install it, or you installed it in a > different version of python than you are trying to import it with. That does sound reasonable - but how do you explain what followed? >> So - still no version update. I ran: >> >> 'easy_install matplotlib', which somehow seems to change the path >> setting to find the most recent version of things (maybe someone here >> can tell me how this happens?) now: >> >> > > import matplotlib > matplotlib.__version__ > >> >> '0.99.0' > We'll need more details on this one - a simple script that triggers it and > what backend you're using, for starters. > Here's a simple script that triggers this behavior: from matplotlib import pylab pylab.plot([0,1]) pylab.show() When I run that from ipython, it hangs and doesn't respond to attempts to keyboard interrupt. When I run it from the terminal it also hangs, running it with --verbose-helpful, I get: backend MacOSX version unknown Is there another way to figure out which backend is being used? Cheers, Ariel -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Building matplotlib on os x
Hi Jeff,
>
> You are using the macosx backend. Can you try another backend, say TkAgg,
> by running:
>
> python test.py -dTkAgg ??
>
> -Jeff
tried that as well - it doesn't plot and produces the following traceback:
ASR:Desktop arokem$ python example.py -dTkAgg
Exception in Tkinter callback
Traceback (most recent call last):
File
"/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/lib-tk/Tkinter.py",
line 1414, in __call__
return self.func(*args)
File
"/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib/backends/backend_tkagg.py",
line 212, in resize
self.show()
File
"/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib/backends/backend_tkagg.py",
line 216, in draw
tkagg.blit(self._tkphoto, self.renderer._renderer, colormode=2)
File
"/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib/backends/tkagg.py",
line 19, in blit
tk.call("PyAggImagePhoto", photoimage, id(aggimage), colormode,
id(bbox_array))
TclError
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Re: [matplotlib-devel] Building matplotlib on os x
Hi - it was something to do with that. When I now *add*: ./matplotlib-0.98.5.2n2-py2.5-macosx-10.3-fat.egg, which was the version that EPD instaled, to easy-install.pth, I get back version 0.98.5 On Thu, Aug 13, 2009 at 9:25 AM, Gael Varoquaux wrote: > On Thu, Aug 13, 2009 at 09:30:22AM -0600, Jeff Whitaker wrote: >> Ariel Rokem wrote: >> > Resending with CC to list: > >> > D'oh. I forgot to do that. OK - now I went back and ran: > >> > env ARCHFLAGS='-arch i386' python setup.py install > >> > That also went with no hitches > >> > Then, in Python: > > >> >>>> import matplotlib >> >>>> matplotlib.__version__ > >> > '0.98.5.2' > > >> Ariel: This tells me you really didn't install it, or you installed it >> in a different version of python than you are trying to import it with. > >> > So - still no version update. I ran: > >> > 'easy_install matplotlib', which somehow seems to change the path >> > setting to find the most recent version of things (maybe someone here >> > can tell me how this happens?) now: > > > I am not sure that Ariel didn't install things right. He might be a > victim of setuptools' monkey patching of sys.path. Ariel, you should go > around in the various easy_install.pth in the different folder on you > Python path (that is the system ones as well as the ones in your > $PYTHONPATH) and make sure that any reference to matplotlib is removed. > > Gaël > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] building from SVN on Mac OS X 10.5
Hi folks -
just to add to the noise. Here is what eventually worked for me (with
OS 10.5.8 and EPD 4.3), with help from Mike McKerns:
0. I removed the ~/.matplotlib folder ("rm -rf ~/.matplotlib").
1. I edited
/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5/config/Makefile,
removing all occurrences of "-arch ppc" (3 occurrences), changing the
line "MACOSX_DEPLOYMENT_TARGET=10.3" to
"MACOSX_DEPLOYMENT_TARGET=10.5" and changing the occurrences of
"MacOSX10.54u.sdk" into "MacOSX10.5.sdk" (3 occurrences). Here is the
full diff:
60c60
< BASECFLAGS= -arch i386 -isysroot MacOSX10.5.sdk -fno-strict-aliasing
-Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic
---
> BASECFLAGS= -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd
> -fno-common -dynamic
66c66
< LDFLAGS= -arch i386 -isysroot MacOSX10.5.sdk -g -L/usr/local/lib
-L/Library/Frameworks/Python.framework/Versions/4.3.0/lib
---
> LDFLAGS= -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/4.3.0/lib
115c115
< UNIVERSALSDK=MacOSX10.5.sdk
---
> UNIVERSALSDK=/Developer/SDKs/MacOSX10.4u.sdk
123c123
< MACOSX_DEPLOYMENT_TARGET=10.5
---
> MACOSX_DEPLOYMENT_TARGET=10.3
405c405
< $(CC) -o $(LDLIBRARY) -arch i386 -dynamiclib \
---
> $(CC) -o $(LDLIBRARY) -arch i386 -arch ppc -dynamiclib \
2. In
/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5/site-packages/easy-install.pth,
I commented out the line containing the directory in which the
previous version of MPL was installed
("./matplotlib-0.98.5.2n2-py2.5-macosx-10.3-fat.egg", in my case). If
I don't do this, when I import matplotlib, it imports the previous
version I had of MPL and just ignores the new installation. This is a
setuptools problem, so if you didn't have setuptools, good for you and
ignore this.
3. I ran the attached shell-script ("sh ./install-matplotlib.sh"),
based on a script by Mike McKerns, in the directory in which I wanted
my source to be. This script sets some local variable (CFLAGS,
LDFLAGS, PKG_CONFIG_PATH, ARCHFLAGS), removes previous installations,
downloads the source, builds and installs it. The backend seems to be
set to MacOSX.
I would be happy if someone who's had similar problems to the ones I
have had could test this procedure and see if it works for them as
well.
Cheers,
Ariel
On Fri, Aug 21, 2009 at 9:15 AM, John Hunter wrote:
> On Fri, Aug 21, 2009 at 10:41 AM, Jouni K. Seppänen wrote:
>> Eric Bruning writes:
>>
>>> ld warning: in
>>> /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.10.4.dylib,
>>> missing required architecture ppc in file
>>> ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.1.dylib,
>>> missing required architecture ppc in file for architecture ppc
>>
>> Somehow your gcc is picking up libraries from /usr/local/lib, where you
>> have presumably installed an x86-only version of gcc (could be a side
>> effect of installing GNU Fortran). I don't know how to prevent that,
>> except perhaps by moving /usr/local away for the duration of the
>> compilation command, e.g.
>
> I think you should edit setupext.py and edit basedir directory, and
> remove all the /sw, /usr/local, etc from basedir in the 'darwin'
> entry, which reads:
>
> darwin' : ['/sw/lib/freetype2', '/sw/lib/freetype219', '/usr/local',
> '/usr', '/sw'],
>
> Then do a clean rebuild and see if that helps.
>
> JDH
>
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>
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Helen Wills Neuroscience Institute
University of California, Berkeley
http://argentum.ucbso.berkeley.edu/ariel
install-matplotlib.sh
Description: Bourne shell script
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Re: [matplotlib-devel] building from SVN on Mac OS X 10.5
Resending with CC to list: Hi - here is the diff with the suggested addition to the documentation. Cheers, Ariel On Sat, Aug 22, 2009 at 1:34 PM, John Hunter wrote: > On Sat, Aug 22, 2009 at 2:48 PM, Ariel Rokem wrote: >> Hi folks - >> >> just to add to the noise. Here is what eventually worked for me (with >> OS 10.5.8 and EPD 4.3), with help from Mike McKerns: > > Hey guys, this is great. Any chance I could twist your arm into > writing this up as a ReST FAQ and updating your script to do an svn > checkout instead of installing the last release. I would like to post > this on the FAQ on the website. > > JDH > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel mpl99doc_install_epd.diff Description: Binary data -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] mlab cohere_pairs patch
Hi - so - now, almost two weeks later, I can finally install MPL from source. On to submitting that patch. Here's what I get with mlab.cohere_pairs, as it is currently: In [1]: a=np.array([[1,2,3,4],[1,2,3,4]]) In [2]: b=([1,1],[0,0]) In [3]: mlab.cohere_pairs(a,b) --- NameError Traceback (most recent call last) /Users/arokem/ in () /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib/mlab.pyc in cohere_pairs(X, ij, NFFT, Fs, detrend, window, noverlap, preferSpeedOverMemory, progressCallback, returnPxx) 597 windowVals = window 598 else: --> 599 windowVals = window(np.ones((NFFT,), typecode(X))) 600 ind = range(0, numRows-NFFT+1, NFFT-noverlap) 601 numSlices = len(ind) NameError: global name 'typecode' is not defined So - as Fernando mentioned above, it is looking for something that doesn't exist anymore. With the patch (diff attached), this error no longer occurs. Cheers, Ariel On Wed, Aug 12, 2009 at 11:25 AM, Ariel Rokem wrote: > Hi - scratch that. Only *seems* to be working. Actually it hangs when I run > scripts that open figures. I am going to undo all this and forget I ever > started down this path. > > Cheers, > > Ariel > > On Wed, Aug 12, 2009 at 11:10 AM, Ariel Rokem wrote: >> >> Hi again - a string of strange things just happened. After this recent >> chain of failures, I decided to try to do some random attempts at making >> this work. >> >> First, I ran 'sudo python setup.py install' in the directory into which I >> had checked out the mpl source. After going through all of the above, that >> now went without a hitch(?!). I started ipython and imported matplotlib, but >> was disappointed to see that I was still importing 0.98.3, which is the >> version I previously had. >> >> I then ran: >> >> ASR:~ arokem$ easy_install matplotlib >> Searching for matplotlib >> Best match: matplotlib 0.99.0 >> Removing matplotlib 0.98.3.0001 from easy-install.pth file >> Adding matplotlib 0.99.0 to easy-install.pth file >> >> Using >> /Library/Frameworks/Python.framework/Versions/4.0.30001/lib/python2.5/site-packages >> Processing dependencies for matplotlib >> Finished processing dependencies for matplotlib >> >> Now, when I open ipython and import matplotlib, the version I have is >> 0.99, and it seems to work (opens plots and such). So - somehow the process >> worked, but how? >> >> Cheers, >> >> Ariel >> >> >> >> On Wed, Aug 12, 2009 at 10:08 AM, Ariel Rokem wrote: >>> >>> Hi Fernando and John, >>> >>> regardless of the clunky way in which I was trying to introduce our >>> patch, I still want to be able to build MPL from source on my machine. It is >>> a distraction, but, hey, it's a distraction on top of a distraction on top >>> of a distraction, so at this point, I might as well be distracted. Besides, >>> it should end up being useful, and not only for me. Yesterday, there was >>> someone on the matplotlib-users list with exactly the same problem in >>> building MPL from source (sourceforge is not responding at the moment, so I >>> can't post a link to that message). If this is not a good time to >>> trouble-shoot this, let me know and we can come back to this in a couple of >>> weeks. It does seem like cohere_pairs has not gotten a lot of use, so the >>> patch can also languish for another couple of weeks andI can get stuff done >>> regardless of solving this problem, but I would love to be able to solve >>> this, with your help. >>> >>> So - I now checked out 0.99, running 'make build_osx105' (you do realize >>> the 'x' stands for '10', don't you?) didn't work, so I followed the >>> instructions in source/osx/README >>> >>> I still get exactly the same error as before: >>> >>> g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk >>> -bundle -undefined dynamic_lookup -arch ppc -arch i386 >>> -L/Users/arokem/source/mpl99/release/osx/zlib-1.2.3 >>> -L/Users/arokem/source/mpl99/release/osx/libpng-1.2.33 >>> -L/Users/arokem/source/mpl99/release/osx/freetype-2.3.7 -Os -arch ppc -arch >>> i386 -I/Users/arokem/source/mpl99/release/osx/zlib-1.2.3 >>> -I/Users/arokem/source/mpl99/release/osx/libpng-1.2.33 >>> -I/Users/arokem/source/mpl99/release/osx/freetype-2.3.7/include >>> build/temp.macosx-10.3-fa
Re: [matplotlib-devel] mlab cohere_pairs patch
Hi - following up on this patch, as suggested, I have added a use-case of mlab.cohere_pairs to examples/pylab_examples/mri_with_eeg.py. Cheers, Ariel On Sat, Aug 22, 2009 at 4:27 PM, John Hunter wrote: > On Sat, Aug 22, 2009 at 6:00 PM, Ariel Rokem wrote: > >> so - now, almost two weeks later, I can finally install MPL from >> source. On to submitting that patch. > > Thanks for following up -- applied to the release branch, merged to trunk > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel pylab_example_cohere_pairs.diff Description: Binary data -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] building on OSX
Hi Eric, you could try making changes to your Python Makefile, as described here (in item 1): http://matplotlib.sourceforge.net/faq/installing_faq.html#building-and-installing-from-source-on-osx-with-epd Even if you are not installing on the basis of the EPD, it might still solve your issue. Cheers, Ariel On Mon, Aug 24, 2009 at 1:47 PM, Eric Bruning wrote: > For some reason, it's still picking up the gfortran-installed gcc in > /usr/local/lib, which is also listed in > /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib (along with everything > else in /usr/local/lib). I also still see -L /usr/local/lib even > though the darwin setupext.py key no longer includes it. > > I'm flummoxed. Apparently I should back up and try without gfortran > first, but that's a typical way to meet requirements for scipy that > I'd like to have around. > > -Eric > > g++ -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g > -bundle -undefined dynamic_lookup -arch i386 -arch ppc > -L/usr/local/matplotlib/lib > -syslibroot,/Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc > -I/usr/local/matplotlib/include > -I/usr/local/matplotlib/include/freetype2 -isysroot > /Developer/SDKs/MacOSX10.4u.sdk > build/temp.macosx-10.4-fat-2.6/src/ft2font.o > build/temp.macosx-10.4-fat-2.6/src/mplutils.o > build/temp.macosx-10.4-fat-2.6/CXX/cxx_extensions.o > build/temp.macosx-10.4-fat-2.6/CXX/cxxsupport.o > build/temp.macosx-10.4-fat-2.6/CXX/IndirectPythonInterface.o > build/temp.macosx-10.4-fat-2.6/CXX/cxxextensions.o -L/usr/local/lib > -lfreetype -lz -lstdc++ -lm -o > build/lib.macosx-10.4-fat-2.6/matplotlib/ft2font.so > ld warning: in > /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.10.4.dylib, > missing required architecture ppc in file > ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libgcc_s.1.dylib, > missing required architecture ppc in file for architecture ppc > collect2: ld returned 1 exit status > lipo: can't open input file: > /var/folders/RP/RPE-UjrSHZ4SQq6AJQBxqk+++TI/-Tmp-//ccAqigF2.out (No > such file or directory) > error: command 'g++' failed with exit status 1 > make: *** [mpl_build] Error 1 > > > On Sun, Aug 23, 2009 at 1:33 AM, John Hunter wrote: >> The problem of building on OSX, in particular the setupext basedir >> search path including /sw, /usr and /usr/local, appears so fraught >> with peril -- we don't know what kinds of libs built with what kinds >> of flags that we will find -- that I removed all the dirs from the >> basedir for darwin. Instead, I am hoping that the new makefile.osx >> Makefile I have added, which will fetch and build the required libs >> and install them into the PREFIX of your choice, will prove more >> supportable. >> >> I have tested this on a couple of platforms and it worked well, but >> there are other combinations that I do not have access to so please >> let me know if this is not viable. I am currently building with >> >> PREFIX=/Users/jdhunter/dev make -f makefile.osx fetch deps mpl_install >> >> Builds with enthought python make still be broken due to the issues in the >> FAQ: >> >> http://matplotlib.sourceforge.net/faq/installing_faq.html#building-and-installing-from-source-on-osx-with-epd >> >> Please kick the tires and give some feedback >> >> JDH >> >> -- >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> ___ >> Matplotlib-devel mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel >> > > -- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > Matplotlib-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel
Re: [matplotlib-devel] Question on sphinxext.plot_directive...
Hi Fernando and all, > > Speaking of sphinx for books, as I've mentioned before to John, the > last big problem is being able to cross-reference arbitrary text > elements like you can in latex, be they chapters or sections or > whatever, and get a number or something that's meaningful in print. > > I looked around, and apparently it's on the main docutils todo list: > > http://docutils.sourceforge.net/docs/dev/todo.html#object-numbering-and-object-references > > I hope we don't have to be the ones fixing that one... > I should also mention bibliography - using a bibtex bibliography is also still quite impossible at the moment, without going in and editing the .tex and running the tex (latex=>bibtex=>latex=>latex) commands on it yourself. Does anyone of the Sphinx mavens around here know anything about how to get Sphinx to do that for you? I am starting to believe that Sphinx can be made to do just about anything we would want it to for these kinds of uses. Cheers, Ariel -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
[matplotlib-devel] Comparison of mlab.csd and Matlab's cpsd
Hi everyone, Revisiting an issue which has already been discussed previously - in order to check whether mlab.csd really does exactly what Matlab's cpsd is doing, we wrote a couple of scripts, one in matlab and one in Python. They both run on the attached data. The comparison of the results show that they are very similar. However - two elements are off by a factor of approximately 2 - the very first element and the very last. The last one may be off just because it is very small, the difference between the two is tiny. But for the first one - this is not the case - there is actually a difference in the values. This is not only due to the fact that the DC component is very small, because even if I add a DC component to the time-series, there is still discrepancy of a factor of ~2 for that element. Does anyone have any idea why this would be the case? Thanks -- Ariel -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel 8.9429666e+00 5.0100717e+00 -2.6816087e+00 -7.1501559e+00 -8.0216237e+00 -8.4308386e+00 -8.7813313e+00 -7.1541340e+00 -3.1692794e+00 -3.1233587e-02 -8.6932796e-01 -3.2208590e+00 -2.7708292e+00 -1.1180497e+00 -1.1642218e+00 8.2827157e-01 7.7567196e+00 1.3427191e+01 1.2297869e+01 7.9463857e+00 4.3650450e+00 7.4513721e-01 -1.8071566e+00 -1.0494220e+00 2.7099914e-01 -6.0612992e-03 1.0650746e+00 2.7359840e+00 -2.3103312e-01 -5.4394070e+00 -5.6020012e+00 -2.8549610e+00 -3.9441985e+00 -6.5248611e+00 -5.5182498e+00 -3.5707725e+00 -3.3029199e+00 -1.4821612e+00 1.9829637e+00 2.9371484e+00 2.4922181e+00 4.6520641e+00 7.6516172e+00 7.9849900e+00 6.2872303e+00 3.0524810e+00 -2.6249618e+00 -8.4729269e+00 -1.1423490e+01 -1.1515627e+01 -8.0828989e+00 -6.1605087e-02 7.3546053e+00 7.3762039e+00 2.7203112e+00 9.7107193e-01 2.3389000e+00 2.3308435e+00 1.0908653e+00 1.3983531e+00 2.7507814e+00 3.1877024e+00 2.683e+00 2.0890036e+00 1.5431800e+00 2.6735579e-01 -2.8915636e+00 -6.9616787e+00 -7.7022941e+00 -2.6552425e+00 3.6478430e+00 4.5449371e+00 9.1741479e-01 -1.0349366e-01 3.1044471e+00 3.5481921e+00 -2.7689468e+00 -9.5888143e+00 -9.2968371e+00 -3.1434409e+00 1.4650620e+00 4.9126975e-02 -4.4859946e+00 -5.1590780e+00 1.6118592e-01 4.9388060e+00 4.1399337e+00 3.0802173e+00 7.1234314e+00 1.0353879e+01 6.3260927e+00 5.0624656e-01 -4.3675968e-01 -2.3225964e-01 -2.4186513e+00 -1.9095391e+00 2.5966116e+00 3.2187007e+00 -1.6422521e+00 -2.9320855e+00 1.4858112e+00 2.1743862e+00 -3.8657803e+00 -7.4941826e+00 -3.6778977e+00 1.4465903e+00 2.0995855e+00 -3.6925935e-01 -2.4488424e+00 -2.2657275e+00 -3.0767826e-01 -4.3447784e-02 -3.7835013e+00 -7.7710751e+00 -6.6156223e+00 -9.8452194e-01 3.6143927e+00 3.3559741e+00 -7.0214935e-01 -4.0464556e+00 -3.4005198e+00 3.1925151e-01 5.6106943e+00 1.2129909e+01 1.5598452e+01 1.0761346e+01 2.7808335e+00 1.6264690e+00 4.3371698e+00 6.9655189e-01 -6.4917108e+00 -7.1557533e+00 -3.2903321e+00 -2.5653037e+00 -2.8456560e+00 -3.8648126e-01 -3.4792857e-01 -5.4706976e+00 -8.4354584e+00 -4.7666552e+00 1.1698809e-01 1.4126243e+00 5.2560707e-01 -1.2557422e+00 -4.3464817e+00 -6.0548728e+00 -2.6022608e+00 3.4128104e+00 4.5097622e+00 -6.8046372e-01 -4.1244079e+00 -2.6499816e-02 6.5978997e+00 8.9300310e+00 8.9028673e+00 1.0882147e+01 1.1960235e+01 7.5608590e+00 3.1334125e-01 -4.6417949e+00 -6.9282767e+00 -7.4717365e+00 -4.8990327e+00 -5.8542748e-01 -8.4564434e-02 -4.8146391e+00 -8.9187473e+00 -8.1146069e+00 -5.1477694e+00 -3.292e+00 -7.1163877e-01 3.6409206e+00 6.6594649e+00 5.8487425e+00 3.7533921e+00 3.2460105e+00 2.9353594e+00 1.0668831e+00 -5.3054098e-01 -4.1149627e-01 -8.1327290e-01 -3.0706932e+00 -4.5485475e+00 -3.4206624e+00 -1.2170184e+00 9.6882742e-01 2.7440724e+00 1.8368024e+00 -1.5910131e+00 -2.0317113e+00 2.4423217e+00 5.2609099e+00 2.5027442e+00 -5.3925455e-01 3.6824003e-01 2.1030815e+00 1.6465455e+00 8.1607062e-02 -1.1482050e+00 -9.4266580e-01 1.0252083e+00 1.3283382e+00 -2.8992882e+00 -7.2661102e+00 -6.6027869e+00 -3.7400399e+00 -2.6018526e+00 -2.3601345e-01 5.1733118e+00 7.6959332e+00 3.2229165e+00 -3.2443397e+00 -5.6303607e+00 -3.8377406e+00 2.4645472e-01 5.0569136e+00 6.3004349e+00 1.3203384e+00 -3.1151906e+00 1.3232982e+00 9.5677298e+00 9.5030932e+00 1.5131090e+00 -3.8561271e+00 -4.4258970e+00 -5.7326471e+00 -7.0638856e+00 -4.7194733e+00 -2.2836642e+00 -3.3429743e+00 -2.5434213e+00 4.5252898e+00 1.1170906e+01 8.4467296e+00 -1.3827260e+00 -6.9978902e+00 -3.0066829e+00 2.8550972e+00 2.1056966e+00 -1.6739241e+00 -1.9125812e+00 -1.2343693e+00 -2.3238766e+00 3.4253954e-02 6.2718152e+00 8.340973
Re: [matplotlib-devel] Comparison of mlab.csd and Matlab's cpsd
Hi - thanks Ludwig. I don't think that a major reworking of the logic of the function is needed. Simply replacing the line you mentioned with: Pxy *= 1 / (np.abs(windowVals)**2).sum() Pxy[1:-1] *= scaling_factor if scale_by_freq: Pxy[[0,-1]] /= Fs seems to solve the 0 and NFFT/2 problem for the 'onesided' case (that is, the result is very similar to the Matlab result, patch attached) and still seems to work with twosided (because then the scaling factor is equal to 1 and it doesn't really do anything, except scale by frequency, if that is required). In the 'twosided' case, the output in matlab is fftshift-ed relative to the mlab output, but that's not crucial. What does become more apparent when I do that is that in frequency bands in which the power is rather small, the ratio discrepancies between the mlab result and the matlab result can be rather large, on the order of a factor of 2-2.5, even when the differences are tiny. Similarly, when the power is rather large, there can be non-negligible differences between the two results. Is there anything to do about that? Cheers, Ariel On Fri, Feb 5, 2010 at 11:53 PM, Ludwig Schwardt wrote: > Hi, > > > From: Ariel Rokem > > However - two elements are off by a factor of approximately 2 - the > > very first element and the very last. ... Does anyone have any idea > > why this would be the case? > > >From a quick look at the mlab code, it looks like a bug in > mlab._spectral_helper. > > The default spectrum is 'onesided' (same as for Matlab's cpsd). A > single-sided spectrum of a real signal has double the magnitude of a > double-sided spectrum, *except* at the origin (frequency index n = 0) > and Nyquist frequency (n = NFFT / 2), where it is the *same* as the > double-sided one [1]_. > > In the mlab code, all the spectral values are simply scaled by a > factor of 2 (among other factors) in this line: > ># Scale the spectrum by the norm of the window to compensate for ># windowing loss; see Bendat & Piersol Sec 11.5.2. Also include ># scaling factors for one-sided densities and dividing by the sampling ># frequency, if desired. >Pxy *= scaling_factor / (np.abs(windowVals)**2).sum() > > This should be easy to fix (although the function probably needs a > little rework). > > Regards, > Ludwig > > Quick reference from my bookshelf: > --- > .. [1] W. L. Briggs, V. E. Henson, "The DFT: An Owner's Manual for the > Discrete Fourier Transform," Section 1.3, Problem 6 (a), p. 13. > > > -- > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > ___ > Matplotlib-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel one_sided_spectrum_normalization.diff Description: Binary data -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Comparison of mlab.csd and Matlab's cpsd
Hi Ludwig (responding also to list), I don't think that the cause of the discrepancy is because of the hamming/hanning window difference. I do set the window in the matlab part to also be a hanning window of length nfft. Cheers, Ariel On Sun, Feb 7, 2010 at 7:45 AM, Ludwig Schwardt wrote: > Hi, > > On Sun, Feb 7, 2010 at 12:46 AM, Ariel Rokem wrote: > > I don't think that a major reworking of the logic of the function is > needed. > > Simply replacing the line you mentioned with: > > > > Pxy *= 1 / (np.abs(windowVals)**2).sum() > > Pxy[1:-1] *= scaling_factor > > if scale_by_freq: > > Pxy[[0,-1]] /= Fs > > I agree. I was hoping the first two lines above would be sufficient. > Then I saw scaling_factor also included Fs if scaling by frequency, > and Pxy is of shape (numFreqs,n), i.e. not a straightforward 1-D > array, which caused me to reserve my judgment a little bit... :-) > > > What does become more apparent when I do that is that in frequency bands > in > > which the power is rather small, the ratio discrepancies between the mlab > > result and the matlab result can be rather large, on the order of a > factor > > of 2-2.5, even when the differences are tiny. Similarly, when the power > is > > rather large, there can be non-negligible differences between the two > > results. Is there anything to do about that? > > Could this be because Matlab uses a Hamming window by default, while > mlab uses a *Hanning* window by default? Very similar-sounding names, > and also very similar windows numerically (but not exactly the > same)... > > Ludwig > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Comparison of mlab.csd and Matlab's cpsd
Hi - the maximal difference in this case is of about 6 (units?), which is an approximately 50% difference. This is in one point in the spectrum which has a relatively small value - the maximal peaks in the spectra are on the order of 1200, so in the grand scheme of things, not that horrible. Other large differences are on the order of 4, which is approximately 5% or less of those points. Thanks - Ariel PS for some reason, matplotlib-devel will not get your email unless you hit "reply all", so they have been getting my emails, but not yours. I am not sure whether that is what you intended, so I thought I would mention it. On Mon, Feb 8, 2010 at 1:24 AM, Ludwig Schwardt wrote: > Hi, > > On Mon, Feb 8, 2010 at 5:25 AM, Ariel Rokem wrote: > > I don't think that the cause of the discrepancy is because of the > > hamming/hanning window difference. I do set the window in the matlab part > to > > also be a hanning window of length nfft. > > I suspected you gave the same window to both, but I was just > checking... :-) To find those smaller discrepancies might be a bit > harder then, requiring a careful comparison of the various steps > involved. Just for interest's sake, how big are the differences we are > talking about? > > Regards, > Ludwig > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Comparison of mlab.csd and Matlab's cpsd
Hi everyone, Mystery solved (I think)! It turns out that matlab has two functions, one called "hann" and the other called "hanning". They both purport to produce the hanning window, but they produce two (slightly) different things. Only one of these (the one given by "hann") actually produces the hanning window as it is defined in the standard reference on this (Harris 1978. And also Wikipedia ;D). When using the "hann" function in Matlab in this little experiment, the difference between the python and the matlab results, is on the order of %10e-6. I think I am willing to live with that. The only mystery that remains (I think) is - what is Matlab's "hanning" supposed to be doing? Are there two different windows: hann and hanning (not "hamming" - I know that's a different one)? Cheers, Ariel On Mon, Feb 8, 2010 at 9:32 AM, Ariel Rokem wrote: > Hi - > > the maximal difference in this case is of about 6 (units?), which is an > approximately 50% difference. This is in one point in the spectrum which has > a relatively small value - the maximal peaks in the spectra are on the order > of 1200, so in the grand scheme of things, not that horrible. Other large > differences are on the order of 4, which is approximately 5% or less of > those points. > > Thanks - Ariel > > PS for some reason, matplotlib-devel will not get your email unless you hit > "reply all", so they have been getting my emails, but not yours. I am not > sure whether that is what you intended, so I thought I would mention it. > > > On Mon, Feb 8, 2010 at 1:24 AM, Ludwig Schwardt > wrote: > >> Hi, >> >> On Mon, Feb 8, 2010 at 5:25 AM, Ariel Rokem wrote: >> > I don't think that the cause of the discrepancy is because of the >> > hamming/hanning window difference. I do set the window in the matlab >> part to >> > also be a hanning window of length nfft. >> >> I suspected you gave the same window to both, but I was just >> checking... :-) To find those smaller discrepancies might be a bit >> harder then, requiring a careful comparison of the various steps >> involved. Just for interest's sake, how big are the differences we are >> talking about? >> >> Regards, >> Ludwig >> > > > > -- > Ariel Rokem > Helen Wills Neuroscience Institute > University of California, Berkeley > http://argentum.ucbso.berkeley.edu/ariel > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Comparison of mlab.csd and Matlab's cpsd
Hi - mea culpa - as pointed out by a colleague (and documented in the help document for "hanning" in Matlab), this function produces the same window, but without the first and last zero-weighted samples. Cheers -- Ariel On Tue, Feb 9, 2010 at 4:58 PM, Ariel Rokem wrote: > Hi everyone, > > Mystery solved (I think)! It turns out that matlab has two functions, one > called "hann" and the other called "hanning". They both purport to produce > the hanning window, but they produce two (slightly) different things. Only > one of these (the one given by "hann") actually produces the hanning window > as it is defined in the standard reference on this (Harris 1978. And also > Wikipedia ;D). When using the "hann" function in Matlab in this little > experiment, the difference between the python and the matlab results, is on > the order of %10e-6. I think I am willing to live with that. > > The only mystery that remains (I think) is - what is Matlab's "hanning" > supposed to be doing? Are there two different windows: hann and hanning (not > "hamming" - I know that's a different one)? > > Cheers, > > Ariel > > > On Mon, Feb 8, 2010 at 9:32 AM, Ariel Rokem wrote: > >> Hi - >> >> the maximal difference in this case is of about 6 (units?), which is an >> approximately 50% difference. This is in one point in the spectrum which has >> a relatively small value - the maximal peaks in the spectra are on the order >> of 1200, so in the grand scheme of things, not that horrible. Other large >> differences are on the order of 4, which is approximately 5% or less of >> those points. >> >> Thanks - Ariel >> >> PS for some reason, matplotlib-devel will not get your email unless you >> hit "reply all", so they have been getting my emails, but not yours. I am >> not sure whether that is what you intended, so I thought I would mention it. >> >> >> >> On Mon, Feb 8, 2010 at 1:24 AM, Ludwig Schwardt < >> [email protected]> wrote: >> >>> Hi, >>> >>> On Mon, Feb 8, 2010 at 5:25 AM, Ariel Rokem wrote: >>> > I don't think that the cause of the discrepancy is because of the >>> > hamming/hanning window difference. I do set the window in the matlab >>> part to >>> > also be a hanning window of length nfft. >>> >>> I suspected you gave the same window to both, but I was just >>> checking... :-) To find those smaller discrepancies might be a bit >>> harder then, requiring a careful comparison of the various steps >>> involved. Just for interest's sake, how big are the differences we are >>> talking about? >>> >>> Regards, >>> Ludwig >>> >> >> >> >> -- >> Ariel Rokem >> Helen Wills Neuroscience Institute >> University of California, Berkeley >> http://argentum.ucbso.berkeley.edu/ariel >> > > > > -- > Ariel Rokem > Helen Wills Neuroscience Institute > University of California, Berkeley > http://argentum.ucbso.berkeley.edu/ariel > -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ Matplotlib-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
