Re: [matplotlib-devel] Bus error using interactive plotting commands
On 7/13/07, Rob Hetland <[EMAIL PROTECTED]> wrote: > > Nope -- the same occurs in the regular terminal, so it's not > iPython's fault. > > Also, although I though I remembered this happening with qt4 (as > posted below), I do not seem to be able to reproduce this now.. > > Also, clearing and closing the figure works fine -- only clicking it > away triggers the bug. > So: Almost surely MPL, probably Tk, is my guess. Included below are our standard segfault instructions. The first thing to do is to make sure you blow away your build dir and installed mpl and get a clean build. Secondly, make sure you are using numpy and your rc numerix setting is numpy. Here are the instructions:: # How to diagnose where a segfault is occurring First thing to try is simply rm -rf the site-packages/matplotlib and build subdirs and get a clean install. Installing a new version over a pretty old version has been known to cause trouble, segfault, etc. Try importing these packages individually import matplotlib._image import matplotlib._transforms #one of these three depending on which numerix package you are using import matplotlib.backends._na_backend_agg # for numarray import matplotlib.backends._nc_backend_agg # for Numeric import matplotlib.backends._ns_backend_agg # for numpy import matplotlib.backends._tkagg import matplotlib._agg If the last two work and the others don't, it is likely you need to upgrade your gcc, because on some platforms (OS X for sure) old versions of gcc cannot compile new versions of pycxx, which matplotlib uses for building some but not all of it's extensions. Report back which if any work or segfault or raise tracebacks, If that shed additional light, again flush the build and install dirs, and try setting VERBOSE=True in setup.py before doing a clean install. The VERBOSE setting will generate lots of extra output and may help indicate where the segfault is occurring - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
Nope -- the same occurs in the regular terminal, so it's not iPython's fault. Also, although I though I remembered this happening with qt4 (as posted below), I do not seem to be able to reproduce this now.. Also, clearing and closing the figure works fine -- only clicking it away triggers the bug. So: Almost surely MPL, probably Tk, is my guess. -Rob On Jul 13, 2007, at 1:34 AM, Fernando Perez wrote: > On 7/12/07, Rob Hetland <[EMAIL PROTECTED]> wrote: >> >> I recently updated matplotlib, and I am now getting a bus error when >> plotting (any command) after I have already closed a matplotlib >> window. I can open as many windows as I want, but the first plot >> command executed after closing any window results in a bus error. >> >> Relavent things: >> >> OS: Mac OS X >> Backend: TkAgg (same bus error with qt4, though) >> very recent svn versions of numpy/mpl/ipython. > > The fact that you get this with Tk makes me suspect that for once, > it's not ipython's fault (since Tk does NOT activate the more > dangerous threading tricks). But it would be good to be 100% sure, by > trying in a pure python terminal > > from pylab import * > ion() > plot(...) > > and see if the crash persists. That would limit the likely culprits > to two out of three (and move this ball out of my court in the process > :) > > cheers, > > f > > -- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ___ > Matplotlib-devel mailing list > Matplotlib-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel Rob Hetland, Associate Professor Dept. of Oceanography, Texas A&M University http://pong.tamu.edu/~rob phone: 979-458-0096, fax: 979-845-6331 - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
FWIW, I'm able to reproduce this here. I have a hunch it may be related to my recent Tk memory leak "improvements". I'll look into this further and get back soon. Cheers, Mike John Hunter wrote: > On 7/13/07, Rob Hetland <[EMAIL PROTECTED]> wrote: > >> Nope -- the same occurs in the regular terminal, so it's not >> iPython's fault. >> >> Also, although I though I remembered this happening with qt4 (as >> posted below), I do not seem to be able to reproduce this now.. >> >> Also, clearing and closing the figure works fine -- only clicking it >> away triggers the bug. >> So: Almost surely MPL, probably Tk, is my guess. >> > > Included below are our standard segfault instructions. The first > thing to do is to make sure you blow away your build dir and installed > mpl and get a clean build. Secondly, make sure you are using numpy > and your rc numerix setting is numpy. Here are the instructions:: > > > # How to diagnose where a segfault is occurring > > First thing to try is simply rm -rf the site-packages/matplotlib and > build subdirs and get a clean install. Installing a new version over > a pretty old version has been known to cause trouble, segfault, etc. > > Try importing these packages individually > > import matplotlib._image > import matplotlib._transforms > > #one of these three depending on which numerix package you are using > import matplotlib.backends._na_backend_agg # for numarray > import matplotlib.backends._nc_backend_agg # for Numeric > import matplotlib.backends._ns_backend_agg # for numpy > > import matplotlib.backends._tkagg > import matplotlib._agg > > > If the last two work and the others don't, it is likely you need to > upgrade your gcc, because on some platforms (OS X for sure) old > versions of gcc cannot compile new versions of pycxx, which matplotlib > uses for building some but not all of it's extensions. Report back > which if any work or segfault or raise tracebacks, > > If that shed additional light, again flush the build and install dirs, > and try setting VERBOSE=True in setup.py before doing a clean install. > The VERBOSE setting will generate lots of extra output and may help > indicate where the segfault is occurring > > - > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ___ > Matplotlib-devel mailing list > Matplotlib-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
On Jul 13, 2007, at 9:14 AM, John Hunter wrote: > > Try importing these packages individually > > import matplotlib._image > import matplotlib._transforms > > #one of these three depending on which numerix package you are using > import matplotlib.backends._na_backend_agg # for numarray > import matplotlib.backends._nc_backend_agg # for Numeric > import matplotlib.backends._ns_backend_agg # for numpy > > import matplotlib.backends._tkagg > import matplotlib._agg I have done all the usual tricks (wipe build, get newest numpy/mpl, etc). I tried the suggestions above, and get an error for only one: >>> import matplotlib.backends._tkagg Traceback (most recent call last): File "", line 1, in ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/ lib/python2.5/site-packages/matplotlib/backends/_tkagg.so, 2): Symbol not found: _Tcl_AppendResult Referenced from: /Library/Frameworks/Python.framework/Versions/2.5/ lib/python2.5/site-packages/matplotlib/backends/_tkagg.so Expected in: dynamic lookup I think this is strange, because Tk works fine when I don't click- close a Tk window -- I.e., no errors when pylab starts, or plots, etc. -Rob Rob Hetland, Associate Professor Dept. of Oceanography, Texas A&M University http://pong.tamu.edu/~rob phone: 979-458-0096, fax: 979-845-6331 - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
This looks like that was introduced by a patching error when fixing the Tk save figure bug recently. The bug tracker added an extraneous newline to my patch submitted as a comment. (That's the last time I do that ;) http://sourceforge.net/tracker/index.php?func=detail&aid=1716732&group_id=80706&atid=560720 The segfault was happening because it was trying to blit to a window that had been destroyed (and the figure manager wasn't creating a new window as it should have.) I've committed a fix on the Python end, and also a check to the C side (_tkagg.cpp), so that if we get ourselves into that situation again, we'll get a Python exception rather than a segfault. If you still see crashes with the Qt backend, also let us know. This fix doesn't affect Qt at all. Cheers, Mike Michael Droettboom wrote: > FWIW, I'm able to reproduce this here. I have a hunch it may be related > to my recent Tk memory leak "improvements". I'll look into this further > and get back soon. > > Cheers, > Mike > > John Hunter wrote: > >> On 7/13/07, Rob Hetland <[EMAIL PROTECTED]> wrote: >> >> >>> Nope -- the same occurs in the regular terminal, so it's not >>> iPython's fault. >>> >>> Also, although I though I remembered this happening with qt4 (as >>> posted below), I do not seem to be able to reproduce this now.. >>> >>> Also, clearing and closing the figure works fine -- only clicking it >>> away triggers the bug. >>> So: Almost surely MPL, probably Tk, is my guess. >>> >>> >> Included below are our standard segfault instructions. The first >> thing to do is to make sure you blow away your build dir and installed >> mpl and get a clean build. Secondly, make sure you are using numpy >> and your rc numerix setting is numpy. Here are the instructions:: >> >> >> # How to diagnose where a segfault is occurring >> >> First thing to try is simply rm -rf the site-packages/matplotlib and >> build subdirs and get a clean install. Installing a new version over >> a pretty old version has been known to cause trouble, segfault, etc. >> >> Try importing these packages individually >> >> import matplotlib._image >> import matplotlib._transforms >> >> #one of these three depending on which numerix package you are using >> import matplotlib.backends._na_backend_agg # for numarray >> import matplotlib.backends._nc_backend_agg # for Numeric >> import matplotlib.backends._ns_backend_agg # for numpy >> >> import matplotlib.backends._tkagg >> import matplotlib._agg >> >> >> If the last two work and the others don't, it is likely you need to >> upgrade your gcc, because on some platforms (OS X for sure) old >> versions of gcc cannot compile new versions of pycxx, which matplotlib >> uses for building some but not all of it's extensions. Report back >> which if any work or segfault or raise tracebacks, >> >> If that shed additional light, again flush the build and install dirs, >> and try setting VERBOSE=True in setup.py before doing a clean install. >> The VERBOSE setting will generate lots of extra output and may help >> indicate where the segfault is occurring >> >> - >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> ___ >> Matplotlib-devel mailing list >> Matplotlib-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel >> >> > > > - > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ___ > Matplotlib-devel mailing list > Matplotlib-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
[matplotlib-devel] error with annotation arrows and panning
hello, I'm writing a program where the user can create annotations while interactively zooming and panning the graph. I kept getting errors when my panning would for the arrows to point toward the right. you can recreate the error by going to the example 'annotation_demo.py' and try to make the arrow in Figure 1 point toward the right. I looked in the source files and I think I've found the cause. A line in file patches.py, class YAArrow, function get_verts(self) needs to be changed from r = math.sqrt((y2-y1)**2. + (x2-x1)*2.) to r = math.sqrt((y2-y1)**2. + (x2-x1)**2.) This change seemed to fix the errors I was getting. Boonth - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] error with annotation arrows and panning
On 7/13/07, BOONTHANOME NOUANESENGSY <[EMAIL PROTECTED]> wrote: > r = math.sqrt((y2-y1)**2. + (x2-x1)**2.) > > This change seemed to fix the errors I was getting Fixed in svn. Thanks for the report. JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
[matplotlib-devel] [Fwd: Re: The STIX Fonts project]
John, Darren, Yes, the STIX schedule is still slip-sliding away... Eric --- Begin Message --- We will put you on the email notification list for when the beta fonts are available. Currently, it appears that 15 August is about the earliest that might occur. With best regards, Tim Ingoldsby Director of Strategic Initiatives and Business Development American Institute of Physics Phone: +1 516 576 2265 Fax: +1 516 576 2327 >>> <[EMAIL PROTECTED]> 7/11/07 5:47 PM >>> Name: Eric Firing Email: [EMAIL PROTECTED] Comments: I am a developer for the matplotlib plotting library, led by John D. Hunter (http://matplotlib.sourceforge.net/). We are interested in adding support for STIX fonts, and we have a new developer who may be able to work on this very soon. How can we obtain the "fully functional font sets and supporting information"? Thanks. Eric Firing Feedback submitted by user at IP 128.171.154.235 --- End Message --- - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
On 7/13/07, Tom Holroyd (NIH/NIMH) [E] <[EMAIL PROTECTED]> wrote: > import matplotlib as mpl > > and use mpl.artist, etc. I don't think this will work in this form. artist is a module, and it is not imported simply by importing matplotlib In [1]: import matplotlib as mpl In [2]: mpl.artist Traceback (most recent call last): File "", line 1, in ? AttributeError: 'module' object has no attribute 'artist' - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
John Hunter wrote: > from matplotlib import artist as mpl_artist > from matplotlib import agg as mpl_agg > from matplotlib import axis as mpl_axis > from matplotlib import cbook as mpl_cbook > from matplotlib import collections as mpl_collections > from matplotlib import colors as mpl_colors > from matplotlib import contour as mpl_contour might as well import matplotlib as mpl and use mpl.artist, etc. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
On 7/13/07, Ted Drain <[EMAIL PROTECTED]> wrote: > I think he means that the matplotlib/__init__.py file should be > changed to that those things are imported. but if __init__.py imports axes, and axes import matplotlib, don't we still have the problem of recursive imports? JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
I think he means that the matplotlib/__init__.py file should be changed to that those things are imported. At 01:12 PM 7/13/2007, John Hunter wrote: >On 7/13/07, Tom Holroyd (NIH/NIMH) [E] <[EMAIL PROTECTED]> wrote: > > > import matplotlib as mpl > > > > and use mpl.artist, etc. > >I don't think this will work in this form. artist is a module, and it >is not imported simply by importing matplotlib > >In [1]: import matplotlib as mpl > >In [2]: mpl.artist > >Traceback (most recent call last): > File "", line 1, in ? >AttributeError: 'module' object has no attribute 'artist' > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >___ >Matplotlib-devel mailing list >Matplotlib-devel@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/matplotlib-devel Ted Drain Jet Propulsion Laboratory [EMAIL PROTECTED] - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
[matplotlib-devel] numpification and imports
I just removed the last vestiges of the numerix extension code layer. The conditional imports are gone from the extension code, the -D flags are gone from the compile, as is the _ns_ module naming scheme. This is a fairly major change, so please blow away your install and build dirs after updating to r3513 I also numpified axes.py, by far the biggest and most complicated module, and fixed all of the imports as we discussed in an earlier thread. One problem I ran into. With the proposed from matplotlib import lines # and friends there is a lot of possibility for name clashes. Eg, in some places we also have a variable names "lines", which isn't life threatening but certainly can lead to confusion and bugs. Or for module legend, we also have an Axes function.legend. I decided to go with a foolish consistency that was unambiguous: from matplotlib import artist as mpl_artist from matplotlib import agg as mpl_agg from matplotlib import axis as mpl_axis from matplotlib import cbook as mpl_cbook from matplotlib import collections as mpl_collections from matplotlib import colors as mpl_colors from matplotlib import contour as mpl_contour and then mpl_cbook.iterable # and so on Because the mpl_ prefix occurs nowhere else, we can easily change this to whatever we want with a single search replace. I also added a module mpl which simply imports all the modules, so API or pylab users can >>> from pylab import mpl or >>> from matplotlib import mpl and have all of the API in one place (mpl.dates, mpl.figure, mpl.ticker, etc...) -- nice with tab completion an online help in ipython when you aren't sure where to find something I was hoping we could use this in the matplotlib code itself. Eg if axes could import mpl, then we could replace the somewhat ugly mpl_cbook with the nice and pretty mpl.cbook, but there is the problem of recursive imports. Is there a way to do this with some python magic, so that one "mpl" API module could serve all of the modules? Something in the back of my mind is telling me there is something in EGGS with an api module. Any ideas? JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
On Fri, Jul 13, 2007 at 03:06:45PM -0500, John Hunter wrote:
> Because the mpl_ prefix occurs nowhere else, we can easily change this
> to whatever we want with a single search replace.
I haven't sync'd with the repository yet so I can check this assertion:
h123063:~/src/matplotlib$ find . -name "*.py" | xargs grep mpl_ | wc
191 627 20498
These are mostly mpl_connect and mpl_disconnect, so not too bad.
The only other use of mpl_ is the following:
h123063:~/src/matplotlib$ find . -name "*.py" | xargs grep mpl_ | grep -v
mpl_connect | grep -v mpl_disconnect
./examples/mpl_with_glade.py:self.widgets =
gtk.glade.XML('mpl_with_glade.glade')
./lib/matplotlib/backends/backend_wx.py: - mpl_with_glade.py | N/A
(2) | N/A (2) |
./OME/python/matplotlib/backends/backend_wx.py: - mpl_with_glade.py |
N/A (2) | N/A (2) |
- Paul
-
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Re: [matplotlib-devel] Bus error using interactive plotting commands
First of all, Qt4 does appear to work fine. Second. I am trying to recompile, and I get the error attached below. Somebody had mentioned needing a recent version of gcc. Is this the problem here, or is it another bug? -Rob gcc -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 -DNDEBUG -g -O3 -Isrc -I. -I/Library/Frameworks/ Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/ include -I/usr/local/include -I/usr/include -I. -I/Library/Frameworks/ Python.framework/Versions/2.5/include/python2.5 -c src/transforms.cpp -o build/temp.macosx-10.3-fat-2.5/src/transforms.o src/transforms.cpp: In member function ‘Py::Object Bbox::update(const Py::Tuple&)’: src/transforms.cpp:478: error: ‘isnan’ was not declared in this scope src/transforms.cpp: In member function ‘Py::Object Bbox::update(const Py::Tuple&)’: src/transforms.cpp:478: error: ‘isnan’ was not declared in this scope src/transforms.cpp: In member function ‘Py::Object Bbox::update_numerix_xy(const Py::Tuple&)’: src/transforms.cpp:542: error: ‘isnan’ was not declared in this scopesrc/transforms.cpp: In member function ‘Py::Object Bbox::update_numerix_xy(const Py::Tuple&)’: src/transforms.cpp:542: error: ‘isnan’ was not declared in this scope src/transforms.cpp: In member function ‘Py::Object Bbox::update_numerix(const Py::Tuple&)’: src/transforms.cpp:616: error: ‘isnan’ was not declared in this scope src/transforms.cpp: In member function ‘Py::Object Bbox::update_numerix(const Py::Tuple&)’: src/transforms.cpp:616: error: ‘isnan’ was not declared in this scope src/transforms.cpp: In member function ‘Py::Object Transformation::nonlinear_only_numerix(const Py::Tuple&, const Py::Dict&)’: src/transforms.cpp:1258: error: ‘isnan’ was not declared in this scope src/transforms.cpp: In member function ‘Py::Object Transformation::nonlinear_only_numerix(const Py::Tuple&, const Py::Dict&)’: src/transforms.cpp:1258: error: ‘isnan’ was not declared in this scope lipo: can't figure out the architecture type of: /var/tmp//ccVkIyQR.out error: command 'gcc' failed with exit status 1 Rob Hetland, Associate Professor Dept. of Oceanography, Texas A&M University http://pong.tamu.edu/~rob phone: 979-458-0096, fax: 979-845-6331 - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
Yes - it doesn't solve or address the recursive import problem. My impression was that Tom was making a user interface assertion that doing: import matplotlib as mpl would be simpler for people than doing: from matplotlib import mpl of course I could be complete wrong as well :) I think the basic idea is that if I want to use MPL, I should import it and go and I should not have to import a sub-module out of MPL as the main API. At 01:25 PM 7/13/2007, John Hunter wrote: >On 7/13/07, Ted Drain <[EMAIL PROTECTED]> wrote: > > I think he means that the matplotlib/__init__.py file should be > > changed to that those things are imported. > >but if __init__.py imports axes, and axes import matplotlib, don't we >still have the problem of recursive imports? > >JDH > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >___ >Matplotlib-devel mailing list >Matplotlib-devel@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/matplotlib-devel Ted Drain Jet Propulsion Laboratory [EMAIL PROTECTED] - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
grr. that's probably my fault. I just fiddled with the definition of npy. I tested this on linux and thought I copied it pretty directly from numpy, so I assumed it would work elsewhere, but it's not. I'll see what I can do... Rob Hetland wrote: > First of all, Qt4 does appear to work fine. > > Second. I am trying to recompile, and I get the error attached > below. Somebody had mentioned needing a recent version of gcc. Is > this the problem here, or is it another bug? > > -Rob > > > > > > gcc -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 -DNDEBUG -g -O3 -Isrc -I. -I/Library/Frameworks/ > Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/ > include -I/usr/local/include -I/usr/include -I. -I/Library/Frameworks/ > Python.framework/Versions/2.5/include/python2.5 -c src/transforms.cpp > -o build/temp.macosx-10.3-fat-2.5/src/transforms.o > src/transforms.cpp: In member function ‘Py::Object Bbox::update(const > Py::Tuple&)’: > src/transforms.cpp:478: error: ‘isnan’ was not declared in this scope > src/transforms.cpp: In member function ‘Py::Object Bbox::update(const > Py::Tuple&)’: > src/transforms.cpp:478: error: ‘isnan’ was not declared in this scope > src/transforms.cpp: In member function ‘Py::Object > Bbox::update_numerix_xy(const Py::Tuple&)’: > src/transforms.cpp:542: error: ‘isnan’ was not declared in this > scopesrc/transforms.cpp: In member function ‘Py::Object > Bbox::update_numerix_xy(const Py::Tuple&)’: > src/transforms.cpp:542: error: ‘isnan’ was not declared in this scope > > src/transforms.cpp: In member function ‘Py::Object > Bbox::update_numerix(const Py::Tuple&)’: > src/transforms.cpp:616: error: ‘isnan’ was not declared in this scope > src/transforms.cpp: In member function ‘Py::Object > Bbox::update_numerix(const Py::Tuple&)’: > src/transforms.cpp:616: error: ‘isnan’ was not declared in this scope > src/transforms.cpp: In member function ‘Py::Object > Transformation::nonlinear_only_numerix(const Py::Tuple&, const > Py::Dict&)’: > src/transforms.cpp:1258: error: ‘isnan’ was not declared in this scope > src/transforms.cpp: In member function ‘Py::Object > Transformation::nonlinear_only_numerix(const Py::Tuple&, const > Py::Dict&)’: > src/transforms.cpp:1258: error: ‘isnan’ was not declared in this scope > lipo: can't figure out the architecture type of: /var/tmp//ccVkIyQR.out > error: command 'gcc' failed with exit status 1 > > > > > > Rob Hetland, Associate Professor > Dept. of Oceanography, Texas A&M University > http://pong.tamu.edu/~rob > phone: 979-458-0096, fax: 979-845-6331 > > > > - > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ___ > Matplotlib-devel mailing list > Matplotlib-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
Ted Drain wrote: > I think the basic idea is that if I want to use MPL, I should import > it and go and I should not have to import a sub-module out of MPL as > the main API. Yeah, about that, my typical usage is actually "from pylab import *". I guess I am unclear about the relationship between matplotlib and pylab. -- Tom Holroyd, Ph.D. "The fundamentally misconceived nature versus nurture debate should be abandoned: child development is inextricably both." -- Louann Brizendine - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
On 7/13/07, Andrew Straw <[EMAIL PROTECTED]> wrote: > grr. that's probably my fault. I just fiddled with the definition of > npy. I tested this on linux and thought I copied it pretty directly from > numpy, so I assumed it would work elsewhere, but it's not. I'll see what > I can do... It amy also be that he got a revision in an inconsistent state. At one point I committed some broken isnan stuff I was testing, so make sure you have the latest svn and try again. JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
John Hunter wrote: > On 7/13/07, Ted Drain <[EMAIL PROTECTED]> wrote: >> I think he means that the matplotlib/__init__.py file should be >> changed to that those things are imported. > > but if __init__.py imports axes, and axes import matplotlib, don't we > still have the problem of recursive imports? Yes, but that is not necessarily fatal. It depends on the order in which things are defined and imports are made: http://effbot.org/zone/import-confusion.htm Is there a significant performance penalty, however, in forcing every module to be imported every time any mpl script is run, regardless of whether the module is used in that script? Anyway, I *think* it is feasible to arrange matplotlib.__init__.py so that it imports all the modules, and then use import matplotlib as mpl ... mpl.cbook.is_iterable(x) ... both in scripts and within mpl modules. Whether this is the best approach is another question. Eric > > JDH > > - > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ___ > Matplotlib-devel mailing list > Matplotlib-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
Tom Holroyd (NIH/NIMH) [E] wrote: > > Ted Drain wrote: >> I think the basic idea is that if I want to use MPL, I should import >> it and go and I should not have to import a sub-module out of MPL as >> the main API. > > Yeah, about that, my typical usage is actually "from pylab import *". > I guess I am unclear about the relationship between matplotlib and pylab. > Tom, matplotlib is the object-oriented plotting library; pylab is a module within matplotlib that provides a matlab-style (state-machine) interface to the library. Eric - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
John Hunter wrote: > On 7/13/07, Andrew Straw <[EMAIL PROTECTED]> wrote: >> grr. that's probably my fault. I just fiddled with the definition of >> npy. I tested this on linux and thought I copied it pretty directly from >> numpy, so I assumed it would work elsewhere, but it's not. I'll see what >> I can do... > > It amy also be that he got a revision in an inconsistent state. At > one point I committed some broken isnan stuff I was testing, so make > sure you have the latest svn and try again. No, it looks like I screwed up - the top of numpy's umathmodule.c.src has a lot of stuff that would be really nice if numpy made available in a header file. This stuff is not necessary with my default compiler settings on my linux workstation, but on Mac OS X (and surely other platforms) it is. So, I've just reverted to our old way. I'll see if I can add isfinite() and also re-implement a couple cleanups I just took out after putting them in this morning. Rob, you should be able to compile now as of r3515. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
Eric Firing wrote: > Tom Holroyd (NIH/NIMH) [E] wrote: >> >> Ted Drain wrote: >>> I think the basic idea is that if I want to use MPL, I should import >>> it and go and I should not have to import a sub-module out of MPL as >>> the main API. >> >> Yeah, about that, my typical usage is actually "from pylab import *". >> I guess I am unclear about the relationship between matplotlib and pylab. >> > > Tom, > > matplotlib is the object-oriented plotting library; pylab is a module > within matplotlib that provides a matlab-style (state-machine) interface > to the library. > > Eric If I say >>> import matplotlib >>> help(matplotlib) (This is with 0.90.0 by the way) It basically gives me the help I'd expect for pylab. Oh, and it says "the" instead of "to". It's a little weird thinking of a library as the top level with the main interface as a module. I guess the interface is just another component of the library. Though when I >>> import pylab >>> help(pylab) I get what looks like help for numpy. Perhaps my installation is strange? -- Tom Holroyd, Ph.D. "The fundamentally misconceived nature versus nurture debate should be abandoned: child development is inextricably both." -- Louann Brizendine - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
Eric Firing wrote: > John Hunter wrote: >> On 7/13/07, Ted Drain <[EMAIL PROTECTED]> wrote: >>> I think he means that the matplotlib/__init__.py file should be >>> changed to that those things are imported. >> but if __init__.py imports axes, and axes import matplotlib, don't we >> still have the problem of recursive imports? > > Yes, but that is not necessarily fatal. It depends on the order in which > things are defined and imports are made: > > http://effbot.org/zone/import-confusion.htm > > Is there a significant performance penalty, however, in forcing every > module to be imported every time any mpl script is run, regardless of > whether the module is used in that script? > > Anyway, I *think* it is feasible to arrange matplotlib.__init__.py so > that it imports all the modules, and then use > > import matplotlib as mpl > ... mpl.cbook.is_iterable(x) ... > > both in scripts and within mpl modules. I have done a little experimentation, and I am pretty sure this will work. The problem I have run into so far is that in the initial orgy of importing, at the end of matplotlib/__init__, one has to be careful about the order so that kwdocd entries exist when they are needed. So, John, is this the direction you would like to go? It would mean that a long list of module imports at the top of each module would go away, replaced by the single "import matplotlib as mpl". This is simpler, but it removes the concise information about what modules a given module depends on. Eric > > Whether this is the best approach is another question. > > Eric >> JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
[matplotlib-devel] isnan issues resolved (hopefully)
I think I figured out and fixed the situation with isnan. >From http://lists.apple.com/archives/xcode-users/2005/Feb/msg00196.html > > Basically the story is this: > isnan() is a C99 extension to standard C. > Standard C++ is based on an older standard of C. > Hence isnan() is not part of standard C++ and may or may not work. But std::isnan() is part of standard C++ defined in . Since we use C++ (which numpy doesn't) we can drop our own isnan support and use std::isnan(). Which I just did. The cmath header also defines isfinite and isinf. So, John, go at the original change you wanted to make this morning, at least once the dust settle and we're happy this will work on all target platforms (now tested with gcc on Mac and Linux -- I'm afraid MSVC is beyond me right now). -Andrew - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
John Hunter wrote: > I don't think this will work in this form. artist is a module, and it > is not imported simply by importing matplotlib > > In [1]: import matplotlib as mpl > > In [2]: mpl.artist however, this seems to work (though it looks perhaps a bit odd) >>> import matplotlib as mpl >>> import matplotlib.artist >>> mpl.artist I do like this better -- names like mpl_*** rub me the wrong way. it looks like you really want a namespace -- and indeed you do! maybe the real solution is to have the matplotlib called "mpl" from the get go, like wxPython does: import wx wx.Whatever... I do wish that: >>> import matplotlib as mpl >>> import mpl.artist Traceback (most recent call last): File "", line 1, in ImportError: No module named mpl.artist worked. -Chris -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R(206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception [EMAIL PROTECTED] - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
Christopher Barker wrote: > John Hunter wrote: [...] > I do wish that: > import matplotlib as mpl import mpl.artist > Traceback (most recent call last): >File "", line 1, in > ImportError: No module named mpl.artist > > worked. The way I have it working now (on my machine, not in svn), when you import matplotlib as mpl You don't need to then import mpl.artist; it is already imported, ready for use. Eric > > -Chris > > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] numpification and imports
Tom Holroyd (NIH/NIMH) [E] wrote: [...] > If I say > import matplotlib help(matplotlib) > > (This is with 0.90.0 by the way) > > It basically gives me the help I'd expect for pylab. Oh, and it says > "the" instead of "to". It's a little weird thinking of a library as the > top level with the main interface as a module. I guess the interface is > just another component of the library. Though when I > import pylab help(pylab) > > I get what looks like help for numpy. Perhaps my installation is strange? > No, it is not your installation. You have identified an area that needs work, after we settle on a possibly new import and namespace strategy. Eric - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Bus error using interactive plotting commands
It seems to be working now. Thanks! This is a perfect example of quick response. I keep telling people that, sure, the scientific python suite has occasional bugs, but the community is *very* responsive. This is a perfect example. Thanks to everybody that helped, -Rob > Rob, you should be able to compile now as of r3515. Rob Hetland, Associate Professor Dept. of Oceanography, Texas A&M University http://pong.tamu.edu/~rob phone: 979-458-0096, fax: 979-845-6331 - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] isnan issues resolved (hopefully)
On 7/13/07, Andrew Straw <[EMAIL PROTECTED]> wrote: > I think I figured out and fixed the situation with isnan. > > >From http://lists.apple.com/archives/xcode-users/2005/Feb/msg00196.html > > > > > Basically the story is this: > > isnan() is a C99 extension to standard C. > > Standard C++ is based on an older standard of C. > > Hence isnan() is not part of standard C++ and may or may not work. > > But std::isnan() is part of standard C++ defined in . > > Since we use C++ (which numpy doesn't) we can drop our own isnan support > and use std::isnan(). Which I just did. We're not out of the woods yet. On my OS X 10.3 powerbook src/transforms.cpp: In member function `Py::Object Bbox::update(const Py::Tuple&)': src/transforms.cpp:476: error: `isnan' undeclared in namespace `std' src/transforms.cpp:476: error: `isnan' undeclared in namespace `std' John-Hunters-Computer:~/mpl> gcc --version gcc (GCC) 3.3 20030304 (Apple Computer, Inc. build 1495) JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] isnan issues resolved (hopefully)
Can you stick this in the top of src/_transforms.cpp and see if you still get the problem? #define _GLIBCPP_USE_C99 -Andrew John Hunter wrote: > On 7/13/07, Andrew Straw <[EMAIL PROTECTED]> wrote: >> I think I figured out and fixed the situation with isnan. >> >> >From http://lists.apple.com/archives/xcode-users/2005/Feb/msg00196.html >> >>> Basically the story is this: >>> isnan() is a C99 extension to standard C. >>> Standard C++ is based on an older standard of C. >>> Hence isnan() is not part of standard C++ and may or may not work. >> But std::isnan() is part of standard C++ defined in . >> >> Since we use C++ (which numpy doesn't) we can drop our own isnan support >> and use std::isnan(). Which I just did. > > We're not out of the woods yet. On my OS X 10.3 powerbook > > src/transforms.cpp: In member function `Py::Object Bbox::update(const >Py::Tuple&)': > src/transforms.cpp:476: error: `isnan' undeclared in namespace `std' > src/transforms.cpp:476: error: `isnan' undeclared in namespace `std' > > John-Hunters-Computer:~/mpl> gcc --version > gcc (GCC) 3.3 20030304 (Apple Computer, Inc. build 1495) > > JDH > > - > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ___ > Matplotlib-devel mailing list > Matplotlib-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] isnan issues resolved (hopefully)
OK, I reverted back to the tried and true MPL way... It hasn't been completely unproductive, however: I added tests for infinity (either sign) and finite-ness to MPL_isnan.h. (On top of which I now understand the IEEE 754 representations far better than I care to.) Now, this should work just like it did in the good old days... I mean it this time. :) John, commence using your infinity-finding powers! -Andrew - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
