matplotlib-devel Mailing List for matplotlib

Hi all,
I've come across an apparent bug in imshow when outputting to PDF and 
EPS files. (I haven't tested other vector formats.) It manifests as 
a small scaling error between the raster image and the axes coordinates.
I have attached a test script to illustrate the problem. The 
(correct) PNG output file shows a green 'X' at the common point 
between four pixels near the center of the raster image. The extent 
is chosen such that the coordinates refer to pixel centers. The PDF 
and EPS output files show a misalignment between the X and the pixel 
boundaries -- zoom in to see it clearly. Also, the topmost row and 
rightmost column appear truncated.
I am using svn r7395.
Thanks for the attention,
Mike

The segfault I reported on was on home computer. Today at work I tried 
the same installer and it works fine on my work machine. I performed 
the tests (though I doubt they're relevant since TkAgg works) and came 
up with:
>> python myscript.py -dTkAgg
works (at work)
>> python myscript.py -dWXAgg
I don't have wxPython installed so it fails as expected.
>> python myscript.py -dAgg
Works but I have no idea where the output goes.
>> python myscript.py -dmacosx
Works.
I can try more tests at home, but not until this evening. My *guess* 
based on past experience with matplotlib segfaults in TkAgg is that 
all those tests will pass except TkAgg, and that TkAgg will work if I 
move my /Library/Frameworks Tcl/Tk aside.
-- Russell
On Aug 5, 2009, at 3:27 AM, John Hunter wrote:
> On Tue, Aug 4, 2009 at 11:04 PM, Russell 
> Owen<rowen@u.washington.edu> wrote:
>
>> Thank you very much. Unfortunately it doesn't work for me. Trying 
>> to import
>> pylab results in a bus error (I appended the log in case it has 
>> anything
>> useful in it).
>>
>> My configuration:
>> - Intel Mac
>> - MacOS X 10.5.7
>> - Python 2.5.2 (in /Library/Frameworks... from python.org)
>> - Tcl/Tk 8.4.19 (in /Library/Frameworks... from ActiveState)
>> - this occurs with or without a ~/.matplotlib/matplotlibrc file 
>> (that uses
>> TkAgg) and with or without a ~/.matplotlib directory at all
>> I have confirmed that Tkinter works fine.\
>
> Can you create a small test script that creates an mpl figure and
> saves it with savefig, and run it with
>
>> python myscript.py -dTkAgg
>
>> python myscript.py -dWXAgg
>
>> python myscript.py -dAgg
>
>> python myscript.py -dmacosx
>
> and let me know if all segfault, and if not, which ones do?
>
> JDH

On Wed, Aug 5, 2009 at 10:53 AM, Russell Owen<ro...@uw...> wrote:
> The segfault I reported on was on home computer. Today at work I tried the
> same installer and it works fine on my work machine. I performed the tests
> (though I doubt they're relevant since TkAgg works) and came up with:
> I don't have wxPython installed so it fails as expected.
>
> python myscript.py -dAgg
If you made a call to savefig('somefile'), this will create somefile.png

On Wed, Aug 5, 2009 at 7:11 AM, John Hunter<jd...@gm...> wrote:
> Perhaps we could return a plain file handle pointing to the cached data?
OK, I've made a few changes to the code so Jouni you will probably
want to review them
* I renamed the svn repo and function to be "sample_data" rather than
"mpl_data" to avoid confusion with lib/matplotlib/mpl-data. The svn
repo, the examples and the cbook function have all been renamed. The
repo is ::
 svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/sample_data
 and the examples are::
 johnh@udesktop191:mpl> ls examples/misc/sam*.py
 examples/misc/sample_data_demo.py examples/misc/sample_data_test.py
* I added support for nested subdirs, so you can now do, as in
examples/misc/sample_data_test.py::
 datafile = 'testdir/subdir/testsub.csv'
 fh = cbook.get_sample_data(datafile)
* I commented out the random number appending, because I do not see
the use case, but we can re-add it when you enlighten me :-)
* I always return a file handle to the cached file, so seek works, and
is exercised in examples/misc/sample_data_test.py
It is probably worth doing a little more work to make the processor
plus the "get_sample_data" function all part of one class, so other
people can reuse it with other repos and other dirs. Eg, something
like the following in cbook::
 myserver = ViewVCCacheServer(mycachedir, myurlbase)
 get_sample_data = myserver.get_sample_data

On Wed, Aug 5, 2009 at 7:11 AM, John Hunter <jd...@gm...> wrote:
> >>> import matplotlib.mlab as mlab
> >>> import matplotlib.cbook as cbook
> >>> r = mlab.csv2rec( cbook.get_mpl_data('testdata.csv') )
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/Users/jdhunter/dev/lib/python2.6/site-packages/matplotlib/mlab.py",
> line 2108, in csv2rec
> fh = cbook.to_filehandle(fname)
> File
> "/Users/jdhunter/dev/lib/python2.6/site-packages/matplotlib/cbook.py",
> line 339, in to_filehandle
> raise ValueError('fname must be a string or file handle')
> ValueError: fname must be a string or file handle
>
> Perhaps we could return a plain file handle pointing to the cached data?
Another option is to use StringIO to create a new file-like object after
read()-ing in all the data.
Ryan
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

On Tue, Aug 4, 2009 at 2:45 PM, Jouni K. Seppänen<jk...@ik...> wrote:
> John Hunter <jd...@gm...> writes:
>
>>   # TODO: how to handle stale data in the cache that has been
>>   # updated from svn -- is there a clean http way to get the current
>>   # revision number that will not leave us at the mercy of html
>>   # changes at sf?
>
> The mod_dav_svn server sends an ETag header that happens to contain the
> revision number where the file was last modified, and a Last-Modified
> header that contains the date of that revision. The clean http way to
> make use of these is to make a conditional request - I hacked up a
> processor class for urllib2 that does this, and checked it in.
Also, it would be preferable for the returned file object which
supports the "seek" method. This is what cbook.to_filehandle checks
for, and what mlab.csv2rec uses to rewind the file after doing a data
introspection pass through to get the data types. Eg,
>>> import matplotlib.mlab as mlab
>>> import matplotlib.cbook as cbook
>>> r = mlab.csv2rec( cbook.get_mpl_data('testdata.csv') )
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/Users/jdhunter/dev/lib/python2.6/site-packages/matplotlib/mlab.py",
line 2108, in csv2rec
 fh = cbook.to_filehandle(fname)
 File "/Users/jdhunter/dev/lib/python2.6/site-packages/matplotlib/cbook.py",
line 339, in to_filehandle
 raise ValueError('fname must be a string or file handle')
ValueError: fname must be a string or file handle
Perhaps we could return a plain file handle pointing to the cached data?
JDH

On Tue, Aug 4, 2009 at 2:45 PM, Jouni K. Seppänen<jk...@ik...> wrote:
> The mod_dav_svn server sends an ETag header that happens to contain the
> revision number where the file was last modified, and a Last-Modified
> header that contains the date of that revision. The clean http way to
> make use of these is to make a conditional request - I hacked up a
> processor class for urllib2 that does this, and checked it in.
Wow, that is really clever and cool. Nicely done. I added
mpl_data/testdata.csv which is easier to modify than lena.png to test
the revision control and it worked beautifully
(examples/misc/mpl_data_test.py)
I didn't understand this part of the code:
 fn = rightmost
 while os.path.exists(self.in_cache_dir(fn)):
 fn = rightmost + '.' + str(random.randint(0,9999999))
when would there be a name clash that would require the randint appended?
Also, how hard would it be to add support for a directory structure?
I see you are getting the filename from the url as the last thing past
the '/'. Is there any way to generalize this so a relative path could
be supported in the svn repo and local cache dir?
JDH

On Tue, Aug 4, 2009 at 11:04 PM, Russell Owen<rowen@u.washington.edu> wrote:
> Thank you very much. Unfortunately it doesn't work for me. Trying to import
> pylab results in a bus error (I appended the log in case it has anything
> useful in it).
>
> My configuration:
> - Intel Mac
> - MacOS X 10.5.7
> - Python 2.5.2 (in /Library/Frameworks... from python.org)
> - Tcl/Tk 8.4.19 (in /Library/Frameworks... from ActiveState)
> - this occurs with or without a ~/.matplotlib/matplotlibrc file (that uses
> TkAgg) and with or without a ~/.matplotlib directory at all
> I have confirmed that Tkinter works fine.\
Can you create a small test script that creates an mpl figure and
saves it with savefig, and run it with
 > python myscript.py -dTkAgg
 > python myscript.py -dWXAgg
 > python myscript.py -dAgg
 > python myscript.py -dmacosx
and let me know if all segfault, and if not, which ones do?
JDH

On Aug 4, 2009, at 8:09 PM, John Hunter wrote:
> On Mon, Aug 3, 2009 at 2:58 PM, Russell E. Owen<ro...@uw...> wrote:
>
>> If you are using bdist_mpkg then it should do the right thing as 
>> long as
>> you build the python with your python.org python
>> (/Library/Frameworks...) instead of the system python.
>
> Following some of the suggestions in this thread and on the sf bug 
> report
>
> https://sourceforge.net/tracker/index.php?func=detail&aid=2831805&group_id=80706&atid=560720
>
> I rebuilt the OSX binaries from scratch, using a src framework build
> of python, and activetcl as suggested by Russell. The rc2 build
> candidates are at
>
> http://drop.io/xortel1#
>
> If anyone has a chance to test them, that would be great.
Thank you very much. Unfortunately it doesn't work for me. Trying to 
import pylab results in a bus error (I appended the log in case it has 
anything useful in it).
My configuration:
- Intel Mac
- MacOS X 10.5.7
- Python 2.5.2 (in /Library/Frameworks... from python.org)
- Tcl/Tk 8.4.19 (in /Library/Frameworks... from ActiveState)
- this occurs with or without a ~/.matplotlib/matplotlibrc file (that 
uses TkAgg) and with or without a ~/.matplotlib directory at all
I have confirmed that Tkinter works fine.
I'll see if I can build a binary, though perhaps I should first try 
using a conventional recipe, then if that works, compare it to the 
makefile.
-- Russell
Process: Python [2293]
Path: /Library/Frameworks/Python.framework/Versions/2.5/ 
Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: ??? (???)
Code Type: X86 (Native)
Parent Process: bash [2260]
Interval Since Last Report: 346695 sec
Crashes Since Last Report: 8
Per-App Interval Since Last Report: 0 sec
Per-App Crashes Since Last Report: 4
Date/Time: 2009年08月04日 20:58:49.631 -0700
OS Version: Mac OS X 10.5.7 (9J61)
Report Version: 6
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OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
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OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
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SecurityHI
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Library/Frameworks/vecLib.framework/Versions/A/vecLib
0xfffe8000 - 0xfffebfff libobjc.A.dylib ??? (???) /usr/lib/ 
libobjc.A.dylib
0xffff0000 - 0xffff1780 libSystem.B.dylib ??? (???) /usr/lib/ 
libSystem.B.dylib

On Mon, Aug 3, 2009 at 2:58 PM, Russell E. Owen<ro...@uw...> wrote:
> If you are using bdist_mpkg then it should do the right thing as long as
> you build the python with your python.org python
> (/Library/Frameworks...) instead of the system python.
Following some of the suggestions in this thread and on the sf bug report
 https://sourceforge.net/tracker/index.php?func=detail&aid=2831805&group_id=80706&atid=560720
I rebuilt the OSX binaries from scratch, using a src framework build
of python, and activetcl as suggested by Russell. The rc2 build
candidates are at
 http://drop.io/xortel1#
If anyone has a chance to test them, that would be great.
JDH