matplotlib-users Mailing List for matplotlib (Page 2)

Hello matplotlib users, 

I just recently started using the matplot library for generating simple
graphs instead of using R. The problem i'm experiencing are the following. 

On my work station i had to enable x11 forwarding to be able to run a script
generating plots on a server . The problem now is that my own computer is a
mac and normally when i use the x11 app to connect to a server x forwarding
is suited to run all script that use a x11 window. 

when i start a development server ( in Django ) from the my linux computer
it works but from apple it doesn't
In this case i get a error saying that i miss the DISPLAY variable. 

I talked to our sys administrator because i was thinking how it would
respond when i put the version in production in this case it would be behind
apache instead of a development server that i manually start in Django. He
told me that that could be a problem because apache doesn't connects to any
x11 display. 

Does anyone had some experience with using apache and matplot lib together,
if so could you share the experiences you had installing everything. 

I'd like to know before i continue developing these features of the
application.

Any help would be greatly appreciated. 

Regards, 

Richard Mendes
-- 
View this message in context: http://www.nabble.com/matplotlib-x11-usage-tp17536252p17536252.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

I've consistently been able to build matplotlib on OS X. Just make
sure you have all the dependencies installed. Personally, I have lbpng
and whatnot installed in /usr/local instead of /usr/X11. I don't know
if that'll help. Also, I use the GCC 4.2 that Apple has available for
download on developer.apple.com. Then you just change the Makefile in
the /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/config/
directory to not use Wno-long-double or no-cpp-precomp. I also took
out all the ppc arch flags since it was causing some issues there with
my versions of libpng and whatnot technically not being universal
binaries. If you don't want to build univeral binary versions of your
dependencies or use the ones alread provided in /usr/X11 (which are
universal I think), you should make Python only build for your
architecture, which is what I did.

My only issue with matplotlib thusfar seems to be the inability to do
the plot3d examples from the scipy website, but I'm told that stuff is
officially unsupported anyway.

Josh

On Wed, May 28, 2008 at 3:35 PM, Eric Firing <ef...@ha...> wrote:
> Christopher Barker wrote:
>> Tommy Grav wrote:
>>>> I
>>>> don't know that it has ever all been consolidated into one easy-to-
>>>> find, easy-to-use set of instructions that will work for just about anyone.
>>
>> no, it hasn't.
> And one of the reasons may be that it is very complicated in practice,
> with all the possible variations of OSX versions, Xcode versions,
> processor architectures, and styles of build for python itself and
> various libraries.  It seems to require learning a whole new jargon.
>>
>> However, I think:
>>
>> $ easy-install matplotlib
>>
>> should work, at least with the python.org python2.5
>>
>>>> Maybe someone can provide, or has provided, a universal binary of
>>>> 0.91.2  built against numpy 1.1?
>>
>> does it need to be "built against" numpy at all? I didn't think it was a
>> build-time dependency -- that is, any MPL 0.91.2 should do, and you can
>> drop a new numpy into it. I don't know if there is one yet, though...
>
> _backend_gdk.c and nxutils.c both call into the numpy C API; maybe some
> c++ code does also.  It is not entirely clear to me whether 1.1 is
> sufficiently binary-compatible that this is safe.
>
>
>> There are essentially two options:
>>
>> 1) built it just for yourself -- I think the instructions John H. posted
>> are pretty easy to follow.
>
> That's the way they look, but having watched someone try it, I can
> testify that looks are deceptive.  I would say that with 95%
> probability, if Tommy tried to follow John's instructions, he would not
> succeed.
>
> Eric
>
> -------------------------------------------------------------------------
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>

Christopher Barker wrote:
> Tommy Grav wrote:
>>> I
>>> don't know that it has ever all been consolidated into one easy-to- 
>>> find, easy-to-use set of instructions that will work for just about anyone.
> 
> no, it hasn't.
And one of the reasons may be that it is very complicated in practice, 
with all the possible variations of OSX versions, Xcode versions, 
processor architectures, and styles of build for python itself and 
various libraries.  It seems to require learning a whole new jargon.
> 
> However, I think:
> 
> $ easy-install matplotlib
> 
> should work, at least with the python.org python2.5
> 
>>> Maybe someone can provide, or has provided, a universal binary of  
>>> 0.91.2  built against numpy 1.1?
> 
> does it need to be "built against" numpy at all? I didn't think it was a 
> build-time dependency -- that is, any MPL 0.91.2 should do, and you can 
> drop a new numpy into it. I don't know if there is one yet, though...

_backend_gdk.c and nxutils.c both call into the numpy C API; maybe some 
c++ code does also.  It is not entirely clear to me whether 1.1 is 
sufficiently binary-compatible that this is safe.


> There are essentially two options:
> 
> 1) built it just for yourself -- I think the instructions John H. posted 
> are pretty easy to follow.

That's the way they look, but having watched someone try it, I can 
testify that looks are deceptive.  I would say that with 95% 
probability, if Tommy tried to follow John's instructions, he would not 
succeed.

Eric

Tommy Grav wrote:
>> I
>> don't know that it has ever all been consolidated into one easy-to- 
>> find, easy-to-use set of instructions that will work for just about anyone.

no, it hasn't.

However, I think:

$ easy-install matplotlib

should work, at least with the python.org python2.5

>> Maybe someone can provide, or has provided, a universal binary of  
>> 0.91.2  built against numpy 1.1?

does it need to be "built against" numpy at all? I didn't think it was a 
build-time dependency -- that is, any MPL 0.91.2 should do, and you can 
drop a new numpy into it. I don't know if there is one yet, though...

> I seemed to remember that I had similar problems with 0.91.1, but used
> the super-scipy package to install it. Of course that package is now  
> only for intel macs :(

There was talk of making it Universal, but I don't know what came of that.

There are essentially two options:

1) built it just for yourself -- I think the instructions John H. posted 
are pretty easy to follow.

2) Built so that it is re-distributable, as part of a py2app *.app, for 
instance. In this case, you need to find or build the dependencies as 
Universal static libs, then make sure that those are linked when you 
build. You should also probably use the python.org build of python, 
rather than Apple's one. I don't know that there are easy instructions 
for this anywhere, but Russel Owen did post some somewhere a while back.

2b) built against the Universal Frameworks found here:

http://www.kyngchaos.com/wiki/software:frameworks
(I think FreeType and UnixImageIO should do it).

That will give you a Universal build that you can use with py2app, but 
if anyone else wants to use that build, they'll need to install those 
frameworks too.

-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

Chr...@no...

On May 28, 2008, at 2:27 PM, John Hunter wrote:

> On Wed, May 28, 2008 at 1:21 PM, Eric Firing <ef...@ha...>  
> wrote:
>
>> Maybe someone can provide, or has provided, a universal binary of  
>> 0.91.2
>> built against numpy 1.1?
>
> Does it need to be built against numpy 1.1?  I thought the 1.1 release
> was binary compatible.
> If it is, this egg should work:
>
> http://downloads.sourceforge.net/matplotlib/matplotlib-0.91.2-py2.5-macosx-10.3-fat.egg?use_mirror=internap
>
> JDH

The problem with the egg is that it installs it in /Library/Python/2.5/ 
site-packages. This is only valid
for the standard apple python version. But with

easy_install -d /Library/Frameworks/Python.framework/Versions/Current/ 
lib/python2.5/site-packages matplotlib-0.91.2-py2.5-macosx-10.3-fat.egg

I was able to get 0.91.2 on my system :)

Thanks
   Tommy

Which version of matplotlib are you using?  Can you provide the set of 
compiler options you ultimately arrived at?  Also, can you provide the 
build output?

Cheers,
Mike

Steve Smith wrote:
> Hi all,
> I've been running into this one and tried compiling it a number of 
> ways.  Unfortunately the way it's fitting into our infrastructure, it's 
> gotta be 64-bit.  Here's the script:
>
> #!/usr/bin/python/bin/python
> from pylab import *
>
> plot([1,2,3,4])
> savefig('secondfig')
> show()
>
> I comment out the the "savefig" line and all works just fine.
>
> The truss output I have is:
>
> resolvepath("/usr/sfw/lib/libfreetype.so.6", 
> "/usr/sfw/lib/libfreetype.so.6", 1023) = 29
> open("/usr/sfw/lib/libfreetype.so.6", O_RDONLY)    = 8
> mmap(0xFFFFFFFF76500000, 32768, PROT_READ|PROT_EXEC, 
> MAP_PRIVATE|MAP_FIXED, 8, 0) = 0xFFFFFFFF76500000
> close(8)                    = 0
> stat("/opt/SUNWspro/lib/rw7/v9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) 
> Err#2 ENOENT
> stat("/opt/SUNWspro/lib/sparcvis2/64/libfreetype.so.6", 
> 0xFFFFFFFF7FFF7A30) Err#2 ENOENT
> stat("/opt/SUNWspro/lib/v9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 
> ENOENT
> stat("/usr/ccs/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 
> ENOENT
> stat("/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 ENOENT
> stat("/usr/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 ENOENT
> mmap(0x00000000, 8192, PROT_READ|PROT_WRITE|PROT_EXEC, 
> MAP_PRIVATE|MAP_ANON, -1, 0) = 0xFFFFFFFF74700000
> munmap(0xFFFFFFFF76500000, 32768)        = 0
> lseek(7, 0, SEEK_CUR)                = 0
> close(7)                    = 0
> lseek(6, 0, SEEK_CUR)                = 0
> close(6)                    = 0
> brk(0x101116C00)                = 0
> brk(0x10111AC00)                = 0
> brk(0x10111AC00)                = 0
> brk(0x10111EC00)                = 0
>
>
> Any ideas what my problem could be?  I'm happy to provide any additional 
> info as requested.  Thanks
>
> -Steve
>
> -------------------------------------------------------------------------
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> Defy all challenges. Microsoft(R) Visual Studio 2008.
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>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

On May 28, 2008, at 2:21 PM, Eric Firing wrote:

> Building on the Mac seems to be a nightmare.  There are various emails
> and howto writeups (including one of John's) floating around, but I
> don't know that it has ever all been consolidated into one easy-to- 
> find,
> easy-to-use set of instructions that will work for just about anyone.
>
> Maybe someone can provide, or has provided, a universal binary of  
> 0.91.2
>  built against numpy 1.1?

I seemed to remember that I had similar problems with 0.91.1, but used
the super-scipy package to install it. Of course that package is now  
only
for intel macs :(

Hopefully someone else can shed some light on the issue. I will play  
around
in the mean time and maybe I will stumble upon something :)

Cheers
   Tommy

On Wed, May 28, 2008 at 1:21 PM, Eric Firing <ef...@ha...> wrote:

> Maybe someone can provide, or has provided, a universal binary of 0.91.2
>  built against numpy 1.1?

Does it need to be built against numpy 1.1?  I thought the 1.1 release
was binary compatible.
If it is, this egg should work:

http://downloads.sourceforge.net/matplotlib/matplotlib-0.91.2-py2.5-macosx-10.3-fat.egg?use_mirror=internap

JDH

Tommy Grav wrote:
> On May 28, 2008, at 1:54 PM, Eric Firing wrote:
> 
>> Tommy,
>>
>> That's right.  If you upgrade numpy you need to upgrade mpl to  
>> 0.91.2 or later.
>>
>> Eric
> 
> I am trying to build matplotlib from svn, but run into this error:

> ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libJPEG.dylib,  
> file is not of required architecture for architecture i386
> collect2: ld returned 1 exit status
> lipo: can't open input file: /var/folders/+9/+9BDgtoTFv4AaU0pWhEE4+++ 
> +TI/-Tmp-//ccUnfmnm.out (No such file or directory)
> error: command 'g++' failed with exit status 1
> [skathi:~/Downloads/matplotlib-0.91.2] tgrav%
> 
> I am on a PPC running mac os x 10.5.2. How can I configure g++ to drop  
> the -arch i386 flag,
> or is there something else wrong here?

Building on the Mac seems to be a nightmare.  There are various emails 
and howto writeups (including one of John's) floating around, but I 
don't know that it has ever all been consolidated into one easy-to-find, 
easy-to-use set of instructions that will work for just about anyone.

Maybe someone can provide, or has provided, a universal binary of 0.91.2 
  built against numpy 1.1?

Eric

On May 28, 2008, at 1:54 PM, Eric Firing wrote:

> Tommy,
>
> That's right.  If you upgrade numpy you need to upgrade mpl to  
> 0.91.2 or later.
>
> Eric

I am trying to build matplotlib from svn, but run into this error:

running build
running build_py
copying lib/matplotlib/mpl-data/matplotlibrc -> build/lib.macosx-10.3- 
fat-2.5/matplotlib/mpl-data
copying lib/matplotlib/mpl-data/matplotlib.conf -> build/ 
lib.macosx-10.3-fat-2.5/matplotlib/mpl-data
running build_ext
building 'matplotlib.ft2font' extension
g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk - 
bundle -undefined dynamic_lookup 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/usr/local/lib -L/usr/local/lib -L/usr/lib -L/usr/ 
X11R6/lib -lfreetype -lz -lstdc++ -lm -o build/lib.macosx-10.3-fat-2.5/ 
matplotlib/ft2font.so -Wl,-framework,CoreServices,- 
framework,ApplicationServices
ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libJPEG.dylib,  
file is not of required architecture for architecture i386
collect2: ld returned 1 exit status
lipo: can't open input file: /var/folders/+9/+9BDgtoTFv4AaU0pWhEE4+++ 
+TI/-Tmp-//ccUnfmnm.out (No such file or directory)
error: command 'g++' failed with exit status 1
[skathi:~/Downloads/matplotlib-0.91.2] tgrav%

I am on a PPC running mac os x 10.5.2. How can I configure g++ to drop  
the -arch i386 flag,
or is there something else wrong here?

Cheers
   Tommy

Tommy,

That's right.  If you upgrade numpy you need to upgrade mpl to 0.91.2 or 
later.

Eric

Tommy Grav wrote:
> [skathi:~/Work/myCode/pyS3M] tgrav% python
> ActivePython 2.5.1.1 (ActiveState Software Inc.) based on
> Python 2.5.1 (r251:54863, May  1 2007, 17:40:00)
> [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import numpy
>  >>> numpy.__version__
> '1.1.0'
>  >>> import pylab
> Traceback (most recent call last):
>    File "<stdin>", line 1, in <module>
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/pylab.py", line 1, in <module>
>      from matplotlib.pylab import *
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/matplotlib/pylab.py", line 206, in <module>
>      from matplotlib.numerix import npyma as ma
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/matplotlib/numerix/__init__.py", line 166, in  
> <module>
>      __import__('ma', g, l)
>    File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/matplotlib/numerix/ma/__init__.py", line 16,  
> in <module>
>      from numpy.core.ma import *
> ImportError: No module named ma
>  >>> import matplotlib
>  >>> matplotlib.__version__
> '0.91.1'
> 
> 
> 
> -------------------------------------------------------------------------
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> Defy all challenges. Microsoft(R) Visual Studio 2008.
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On Wed, May 28, 2008 at 12:37 PM, Tommy Grav <gr...@if...> wrote:
> [skathi:~/Work/myCode/pyS3M] tgrav% python
> ActivePython 2.5.1.1 (ActiveState Software Inc.) based on
> Python 2.5.1 (r251:54863, May  1 2007, 17:40:00)
> [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import numpy
>  >>> numpy.__version__
> '1.1.0'>  >>> import matplotlib
>  >>> matplotlib.__version__
> '0.91.1'

The latest release of matplotlib (0.91.2) should work with the latest
release of numpy (1.1.0).  Please test that configuration.

Thanks,
JDH

[skathi:~/Work/myCode/pyS3M] tgrav% python
ActivePython 2.5.1.1 (ActiveState Software Inc.) based on
Python 2.5.1 (r251:54863, May  1 2007, 17:40:00)
[GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy
 >>> numpy.__version__
'1.1.0'
 >>> import pylab
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/pylab.py", line 1, in <module>
     from matplotlib.pylab import *
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/pylab.py", line 206, in <module>
     from matplotlib.numerix import npyma as ma
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/numerix/__init__.py", line 166, in  
<module>
     __import__('ma', g, l)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/numerix/ma/__init__.py", line 16,  
in <module>
     from numpy.core.ma import *
ImportError: No module named ma
 >>> import matplotlib
 >>> matplotlib.__version__
'0.91.1'

On Wed, May 28, 2008 at 10:17 AM, Margherita Vittone wiersma
<vi...@fn...> wrote:

> thank for your reply; i made a typo when i cut and paste my example which was
> longer and i just trimmed it down to email it. So even with the correct formatter defined,
> on the plot i only see 00:00:00 for the time portion of the label

Well that is a different problem.  In your original post you wrote "I
don't see the time portion of it, just the date" so I misunderstood
your problem.  With 00:00:00, you are seing the time portion of the
*tick locations*.  As I wrote in a previous post, you are seeing the
format strings for the locations of the ticks, not the data points.
The default tick locator tries to put the ticks on even days.  If you
want the ticks to be on the data points, you need to do:

   ax.set_xticks(dates)

to put ticks explicitly where you want them.

JDH

Hello,
thank for your reply; i made a typo when i cut and paste my example which was
longer and i just trimmed it down to email it. So even with the correct formatter defined,
on the plot i only see 00:00:00 for the time portion of the label; i am wondering
if it could related to the version of matplotlib i am using:

matplotlib-0.87.7-py2.5

thanks again

Margherita

On Wed, May 28, 2008 at 7:10 AM, New2Python <new...@li...> wrote:

> One issue that I find now is that the removed marker is not redrawn as
> removed, in other words, all the original markers remain drawn whether or
> not the datapoints exist in the array. How can I remove the marker I don't
> want anymore withought doing a clf() call because I can have over 300,000
> datapoints and the redraw will take ages

You will need to do some extra work here.  I would have a "picking
mode" which is enabled by a key-stroke or button press, and when the
mode is enabled, you can copy the background using the
copy_background/restore region/blit techniques discussed at
http://www.scipy.org/Cookbook/Matplotlib/Animations.  Then you can
mark your vertices and just draw the vertex marker line over the
background.  Alternatively, you can use the clipped line approach I
pointed you to in my prior post to only plot the vertices in the
viewport.  You will have to do a little bookkeeping to translate the
marked vertices in the viewport to the ones in the original dataset.

Unfortunately, I don't have time to write the complete example right now...

JDH

On Tue, May 27, 2008 at 6:29 AM, Johann Cohen-Tanugi
<co...@sl...> wrote:
> hello,
> when histogramming a distribution in log scale, I have some empty bins,
> which drives the y axis to 1e-100 as a lower limit, completely squashing
> the histogram....

I made changes to svn trunk so that zero area rectangles no longer
influence the autoscaling.  So this example scales correctly:

  import numpy as np
  import matplotlib.pyplot as plt

  x = np.random.rand(100)
  fig = plt.figure()
  ax = fig.add_subplot(111)
  n, bins, patches = ax.hist(x, 50, log=True)

  plt.show()

Thanks for the suggestion,
JDH

Thanks for that, the canvas.draw() function redraws the graph. I had to add
the "autoscale_on=False" to the add_subplot() to stop the graph from
autoscaling. 
 
One issue that I find now is that the removed marker is not redrawn as
removed, in other words, all the original markers remain drawn whether or
not the datapoints exist in the array. How can I remove the marker I don't
want anymore withought doing a clf() call because I can have over 300,000
datapoints and the redraw will take ages
 
Thanks for the link to the clipping code, that will come in handy. Much
appreciated


John Hunter-4 wrote:
> 
> On Mon, May 26, 2008 at 10:08 AM, John Hunter <jd...@gm...> wrote:
>> On Mon, May 26, 2008 at 7:01 AM, New2Python <new...@li...>
>> wrote:
>>
>>> I hope someone can give me a simple solution to my problem. I have a
>>> line
>>> plotted and I need to be able to mark selected data points on the line.
>>> I am
>>
>> If you are frequently changing the zoom level, as it looks like you
>> are, the copy background/restore region/blit idiom is probably not the
>> right one for you, since the background is assumed fixed.  You can
>> simply force a draw at any time by doing fig.canvas.draw() w/o having
>> to zoom out or resize to trigger a draw.  So after doing the
>> self.marker.set_data call, I would do fig.canvas.draw
> 
> I thought this would be a generally useful thing to do (maintain a
> list of toggleable selected vertices) so I added some support. Here is
> some example code to highlight the selected markers:
> 
> """
> The matplotlib.lines.VertexSelector maintains a list of selected line
> vertices using the line picker property. If an unselected vertex is
> clicked, it is selected, and if a selected vertex is clicked, it is
> unselectedit.
> 
> Classes which inherit from the VertexSelector should override the
> process_selected method to do something with the selected vertex. This
> example just highlights them with red markers.  If you don't have
> access to svn, I can send you a free-standing example.
> 
> 
> """
> The matplotlib.lines.VertexSelector maintains a list of selected line
> vertices using the line picker property. If an unselected vertex is
> clicked, it is selected, and if a selected vertex is clicked, it is
> unselectedit.
> 
> Classes which inherit from the VertexSelector should override the
> process_selected method to do something with the selected vertex. This
> example just highlights them with red markers.
> 
> """
> 
> import numpy as np
> import matplotlib.pyplot as plt
> import matplotlib.lines as lines
> 
> class HighlightSelected(lines.VertexSelector):
>     """
>     Highlight the selected vertices with a marker plot
>     """
>     def __init__(self, line, fmt='ro', **kwargs):
>         """
>         highlight the selected vertices of line with a marker plot.
>         The plot format string are given by fmt and the kwargs are
> additional
>         line properties
>         """
>         lines.VertexSelector.__init__(self, line)
>         self.markers, = self.axes.plot([], [], fmt, **kwargs)
> 
>     def process_selected(self, ind, xs, ys):
>         """
>         ind are the indices of the selected vertices.  xs and ys are
>         the coordinates of the selected vertices.
>         """
>         self.markers.set_data(xs, ys)
>         self.canvas.draw()
> 
> fig = plt.figure()
> ax = fig.add_subplot(111)
> x, y = np.random.rand(2, 30)
> line, = ax.plot(x, y, 'bs-', picker=5)
> 
> selector = HighlightSelected(line)
> plt.show()
> 
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Sent from the matplotlib - users mailing list archive at Nabble.com.

Reposting as it seems to have fallen through the cracks...
sorry in advance if it was not the case,
Johann

hello,
when histogramming a distribution in log scale, I have some empty bins, 
which drives the y axis to 1e-100 as a lower limit, completely squashing 
the histogram.... Bug or feature?
Johann

PS To be specific :
In [22]: entries, bins, patches = 
pl.hist(np.array(list1),bins=50,normed=1,log=True)

In [23]: entries
Out[23]:
array([  1.18347753e+00,   4.10926113e-01,   2.53989507e-01,
         1.84039145e-01,   1.27510992e-01,   9.21486321e-02,
         7.45965117e-02,   5.08495253e-02,   4.23315845e-02,
         3.43298825e-02,   2.78768971e-02,   1.83264787e-02,
         1.62615233e-02,   1.23897320e-02,   1.26478515e-02,
         7.74358253e-03,   4.38803010e-03,   5.93674661e-03,
         3.61367185e-03,   4.38803010e-03,   2.58119418e-03,
         1.29059709e-03,   7.74358253e-04,   1.03247767e-03,
         1.54871651e-03,   2.32307476e-03,   5.16238835e-04,
         2.58119418e-04,   1.03247767e-03,   2.58119418e-04,
         5.16238835e-04,   0.00000000e+00,   2.58119418e-04,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         2.58119418e-04,   2.58119418e-04,   2.58119418e-04,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   2.58119418e-04])

In [24]: bins
Out[24]:
array([  3.36150086e-09,   3.87417583e-01,   7.74835162e-01,
         1.16225274e+00,   1.54967032e+00,   1.93708790e+00,
         2.32450548e+00,   2.71192306e+00,   3.09934064e+00,
         3.48675822e+00,   3.87417580e+00,   4.26159338e+00,
         4.64901096e+00,   5.03642854e+00,   5.42384612e+00,
         5.81126370e+00,   6.19868128e+00,   6.58609885e+00,
         6.97351643e+00,   7.36093401e+00,   7.74835159e+00,
         8.13576917e+00,   8.52318675e+00,   8.91060433e+00,
         9.29802191e+00,   9.68543949e+00,   1.00728571e+01,
         1.04602746e+01,   1.08476922e+01,   1.12351098e+01,
         1.16225274e+01,   1.20099450e+01,   1.23973625e+01,
         1.27847801e+01,   1.31721977e+01,   1.35596153e+01,
         1.39470329e+01,   1.43344504e+01,   1.47218680e+01,
         1.51092856e+01,   1.54967032e+01,   1.58841208e+01,
         1.62715383e+01,   1.66589559e+01,   1.70463735e+01,
         1.74337911e+01,   1.78212087e+01,   1.82086262e+01,
         1.85960438e+01,   1.89834614e+01,   1.93708790e+01])


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On Tue, May 27, 2008 at 5:08 PM, John Hunter <jd...@gm...> wrote:
> On Tue, May 27, 2008 at 4:03 PM, C M <cmp...@gm...> wrote:
>
>> John, do you know why the times are coming out as 00:00:00 in your
>> example (and mine when I tried it), even though the actual times are
>> specified?
>
> Yes, these are the locations of the ticks, not the data points.  The
> default tick locator tries to put the ticks on even days.  If you want
> the ticks to be on the data points, you need to do:
>
>  ax.set_xticks(dates)
>
> Also, please respons on list since you may not be the only one with
> the same question and I may not be the only one with the answer!
>
> JDH

Thank you, John, and I'm sorry, I thought I was replying on-list but I
guess I have my mail settings set up differently than I thought.  I
always do intend to post to the list.

On Tue, May 27, 2008 at 4:03 PM, C M <cmp...@gm...> wrote:

> John, do you know why the times are coming out as 00:00:00 in your
> example (and mine when I tried it), even though the actual times are
> specified?

Yes, these are the locations of the ticks, not the data points.  The
default tick locator tries to put the ticks on even days.  If you want
the ticks to be on the data points, you need to do:

  ax.set_xticks(dates)

Also, please respons on list since you may not be the only one with
the same question and I may not be the only one with the answer!

JDH

Hi,

Here is what I get when using the verbose mode, since removing and 
installing over again Matplotlib didn't vhanged anything I suspect my 
LaTeX packages might be responsible,...

Thanks in advance for any help

$HOME=/home/fayette
CONFIGDIR=/home/fayette/.matplotlib
matplotlib data path /usr/lib/python2.5/site-packages/matplotlib/mpl-data
loaded rc file 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 0.91.2
verbose.level debug
interactive is False
units is False
platform is linux2
loaded modules: ['_bisect', 'xml.sax.urlparse', 'distutils', 'pylab', 
'datetime', 'matplotlib.tempfile', 'distutils.sysconfig', 
'encodings.encodings', '_numpy', 'xml', 'struct', 'tempfile', 
'xml.sax.urllib', 'pytz.os', 'matplotlib.matplotlib', 'string', 
'encodings.utf_8', 'matplotlib.__future__', 'pytz.tzinfo', 
'pytz.datetime', 'distutils.re', 'bisect', 'signal', 'Numeric', 'random', 
'xml.sax.xmlreader', 'matplotlib.pytz', 'ArrayPrinter', 'locale', 
'xml.sax.saxutils', 'encodings', 'umath', 'dateutil', 
'matplotlib.warnings', 'matplotlib.string', 'pytz.pytz', 'urllib', 
'matplotlib.sys', 're', 'new', 'math', 'numeric_version', 'fcntl', 
'UserDict', 'xml.sax.types', 'distutils.os', 'matplotlib', 'base', 
'codecs', 'paste', 'md5', '_locale', 'matplotlib.sre_constants', 
'matplotlib.os', 'thread', 'StringIO', 'weakref', 'itertools', 
'distutils.sys', 'os', 'marshal', '__future__', 'matplotlib.copy', 
'cStringIO', '_sre', '__builtin__', 'matplotlib.re', 'operator', 
'distutils.string', 'matplotlib.datetime', 'posixpath', 'errno', 
'_socket', 'binascii', 'Precision', 'sre_constants', 'matplotlib.md5', 
'types', 'pytz.sys', 'xml.sax.handler', 'xml.sax.os', 'matplotlib.xml', 
'multiarray', '_codecs', 'pytz', 'matplotlib.pyparsing', 'copy', 
'_struct', '_types', 'matplotlib.dateutil', 'hashlib', 'posix', 
'encodings.aliases', 'matplotlib.distutils', 'exceptions', 'sre_parse', 
'pytz.bisect', 'pickle', 'distutils.distutils', 'copy_reg', 'sre_compile', 
'xml.sax', '_hashlib', '_random', 'site', 'zipimport', '__main__', 
'shutil', 'matplotlib.weakref', 'strop', 'encodings.codecs', 'gettext', 
'matplotlib.rcsetup', 'pytz.sets', 'xml.sax._exceptions', 
'xml.sax.codecs', 'stat', '_ssl', 'warnings', 'encodings.types', 'sets', 
'sys', 'socket', 'xml.sax.sys', 'os.path', 'pytz.gettext', 
'matplotlib.fontconfig_pattern', '_weakref', 'distutils.errors', 
'urlparse', 'linecache', 'matplotlib.shutil', 'time']
numerix numpy 1.0.3.1
Using fontManager instance from 
/home/fayette/.matplotlib/fontManager.cache
backend GTKAgg version 2.12.0


==========================================================================================================
Matplotlib processing for  : 
/home/fayette/LaTeX/ASCII_data_files/2008-04--Wp_vs_Wm_test12/SL4_64_200Mo_std/ppb_up_wp_xx_phys01_pdf10150_mw00_yW_VS_ppb_up_wm_xx_phys01_pdf10150_mw00_yW.dat

   > Reading : 
/home/fayette/LaTeX/ASCII_data_files/2008-04--Wp_vs_Wm_test12/SL4_64_200Mo_std/ppb_up_wp_xx_phys01_pdf10150_mw00_yW_VS_ppb_up_wm_xx_phys01_pdf10150_mw00_yW.dat
   > Drawing !
   > Saving :  
./eps_pdf/ppb_up_wp_xx_phys01_pdf10150_mw00_yW_VS_ppb_up_wm_xx_phys01_pdf10150_mw00_yW.eps
Found dvipng version 1.5
 cd "/tmp" && latex -interaction=nonstopmode 
"/tmp/43f2d14607397712890028dfdf3f25ac.tex" > 
"/tmp/43f2d14607397712890028dfdf3f25ac.output"
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
entering extended mode
(/tmp/43f2d14607397712890028dfdf3f25ac.tex
LaTeX2e <2003/12/01>
Babel <v3.8d> and hyphenation patterns for american, french, german, 
ngerman, b
ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch, 
esperanto, e
stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk, 
polis
h, portuges, romanian, russian, serbian, slovak, slovene, spanish, 
swedish, tur
kish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf/tex/latex/base/article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/size10.clo))
(/usr/share/texmf/tex/latex/type1cm/type1cm.sty)
(/usr/share/texmf/tex/latex/psnfss/helvet.sty
(/usr/share/texmf/tex/latex/graphics/keyval.sty))
(/usr/share/texmf/tex/latex/psnfss/courier.sty)
(/usr/share/texmf/tex/latex/base/textcomp.sty
(/usr/share/texmf/tex/latex/base/ts1enc.def))
(/usr/share/texmf/tex/latex/geometry/geometry.sty
(/usr/share/texmf/tex/latex/geometry/geometry.cfg)

Package geometry Warning: Over-specification in `h'-direction.
    `width' (614.295pt) is ignored.


Package geometry Warning: Over-specification in `v'-direction.
    `height' (794.96999pt) is ignored.

) (/usr/share/texmf/tex/latex/psfrag/psfrag.sty
(/usr/share/texmf/tex/latex/graphics/graphics.sty
(/usr/share/texmf/tex/latex/graphics/trig.sty)
(/usr/share/texmf/tex/latex/graphics/graphics.cfg)
(/usr/share/texmf/tex/latex/graphics/dvips.def)))
(/usr/share/texmf/tex/latex/graphics/graphicx.sty)
(/usr/share/texmf/tex/latex/graphics/color.sty
(/usr/share/texmf/tex/latex/graphics/color.cfg)
(/usr/share/texmf/tex/latex/graphics/dvipsnam.def))
No file 43f2d14607397712890028dfdf3f25ac.aux.
(/usr/share/texmf/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/psnfss/ot1pnc.fd)
<43f2d14607397712890028dfdf3f25ac.eps>
(/usr/share/texmf/tex/latex/psnfss/ot1phv.fd) [1]
(./43f2d14607397712890028dfdf3f25ac.aux) )
Output written on 43f2d14607397712890028dfdf3f25ac.dvi (1 page, 5996 
bytes).
Transcript written on 43f2d14607397712890028dfdf3f25ac.log.

 cd "/tmp" && dvips -q -R0 -o "43f2d14607397712890028dfdf3f25ac.ps" 
"43f2d14607397712890028dfdf3f25ac.dvi" > 
"/tmp/43f2d14607397712890028dfdf3f25ac.output"

gs -dBATCH -dNOPAUSE -r6000 -sDEVICE=pswrite -sPAPERSIZE=letter 
-sOutputFile="/tmp/43f2d14607397712890028dfdf3f25ac.ps"                 
"/tmp/43f2d14607397712890028dfdf3f25ac" > 
"/tmp/43f2d14607397712890028dfdf3f25ac.output"
GPL Ghostscript 8.61 (2007-11-21)
Copyright (C) 2007 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Loading NimbusSanL-Regu font from 
/usr/share/fonts/default/Type1/n019003l.pfb... 2703240 1112639 2569336 
1264022 1 done.
Loading CenturySchL-Roma font from 
/usr/share/fonts/default/Type1/c059013l.pfb... 2746924 1245014 2589432 
1296705 1 done.

gs -dBATCH -dNOPAUSE -sDEVICE=bbox "/tmp/43f2d14607397712890028dfdf3f25ac"
%%BoundingBox: 15 188 578 615
%%HiResBoundingBox: 15.986742 188.125799 577.219975 614.267981

	findfont found Bitstream Vera Sans, normal, normal 400, normal, 
15.0
findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf
	findfont found Bitstream Vera Sans, normal, normal 400, normal, 
20.0
findfont returning 
/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf


On Tue, 27 May 2008, John Hunter wrote:

> On Tue, May 27, 2008 at 2:50 AM, Florent Fayette <fa...@lp...> wrote:
> 
> > Maybe it comes from LaTeX, does Matplotlib rely on the LaTeX software or
> > does it own his own version someh text.usetex         : Trueow hardcoded.
> 
> It does both.  If text.usetex     is False, we use our own fonts and
> text layout algorithms, which can look quite similar to latex because
> we ship some of the computer modern fonts.  If text.usetex is True, we
> call out to latex and dvipng.  If you post the output with the
> --verbose-debug flag set, we would know better what is going on on
> your system
> 
> > python simple_plot.py --verbose-debug > run.out
> 
> and post run.out.
> 
> JDH
> 
> 

On Tue, May 27, 2008 at 2:14 PM, Margherita Vittone wiersma
<vi...@fn...> wrote:

> id_list=[1,2,3,4,5,6]
> str_dates=['2006-07-29 11:01:01','2006-07-29 10:02:03','2006-07-31 00:00:00',
>          '2006-08-01 10:11:12','2006-08-02 09:09:09','2006-08-03 08:08:08']
>
> id_dates=datestr2num(str_dates)
>
> # It appears to ignore the formatting, it shows the month,day and year but not the time...
> formatter = DateFormatter('%m-%d-%y %H:%M:%S')
>
> ax = subplot(111)
> ax.plot_date(id_dates,id_list)
> ax.xaxis.set_major_formatter(dateFormatter)

"dateFormatter" is not defined -- I think you mean "formatter"

When I run this example with this change, I get tick labels with the
hour, minute and second as indicated...

Note recent versions of maptlotlib can takes dates explicitly (it will
handle the conversion for you).  I would write this example as
(fig.autofmt_xdate will handle the ticklabel rotation for you)

import datetime
import dateutil.parser
import matplotlib.dates as mpldates
import matplotlib.pyplot as plt

ids = [1,2,3,4,5,6]
str_dates = ['2006-07-29 11:01:01','2006-07-29 10:02:03','2006-07-31 00:00:00',
             '2006-08-01 10:11:12','2006-08-02 09:09:09','2006-08-03 08:08:08']

dates = [dateutil.parser.parse(s) for s in str_dates]

formatter = mpldates.DateFormatter('%m-%d-%y %H:%M:%S')

fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(dates, ids, 'o')
ax.xaxis.set_major_formatter(formatter)

fig.autofmt_xdate()
ax.set_title("test dates")
plt.show()



JDH

Hi all,
I've been running into this one and tried compiling it a number of 
ways.  Unfortunately the way it's fitting into our infrastructure, it's 
gotta be 64-bit.  Here's the script:

#!/usr/bin/python/bin/python
from pylab import *

plot([1,2,3,4])
savefig('secondfig')
show()

I comment out the the "savefig" line and all works just fine.

The truss output I have is:

resolvepath("/usr/sfw/lib/libfreetype.so.6", 
"/usr/sfw/lib/libfreetype.so.6", 1023) = 29
open("/usr/sfw/lib/libfreetype.so.6", O_RDONLY)    = 8
mmap(0xFFFFFFFF76500000, 32768, PROT_READ|PROT_EXEC, 
MAP_PRIVATE|MAP_FIXED, 8, 0) = 0xFFFFFFFF76500000
close(8)                    = 0
stat("/opt/SUNWspro/lib/rw7/v9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) 
Err#2 ENOENT
stat("/opt/SUNWspro/lib/sparcvis2/64/libfreetype.so.6", 
0xFFFFFFFF7FFF7A30) Err#2 ENOENT
stat("/opt/SUNWspro/lib/v9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 
ENOENT
stat("/usr/ccs/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 
ENOENT
stat("/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 ENOENT
stat("/usr/lib/sparcv9/libfreetype.so.6", 0xFFFFFFFF7FFF7A30) Err#2 ENOENT
mmap(0x00000000, 8192, PROT_READ|PROT_WRITE|PROT_EXEC, 
MAP_PRIVATE|MAP_ANON, -1, 0) = 0xFFFFFFFF74700000
munmap(0xFFFFFFFF76500000, 32768)        = 0
lseek(7, 0, SEEK_CUR)                = 0
close(7)                    = 0
lseek(6, 0, SEEK_CUR)                = 0
close(6)                    = 0
brk(0x101116C00)                = 0
brk(0x10111AC00)                = 0
brk(0x10111AC00)                = 0
brk(0x10111EC00)                = 0


Any ideas what my problem could be?  I'm happy to provide any additional 
info as requested.  Thanks

-Steve

Hello,
i am trying to plot information which will have on the x a timestamp imformation;
even if i specify the formatter i want(see code below) , it seems to be ingnored in the
labels, meaning, i don't see the time portion of it, just the date.
The code is very simple since i am just testing; thanks for suggestions in what 
i am doing wrong, best regards

Margherita

----------------------------------------------------------
from pylab import *
from pylab import figure, show, datestr2num, load
from matplotlib.dates import  DateFormatter
import datetime


id_list=[1,2,3,4,5,6]
str_dates=['2006-07-29 11:01:01','2006-07-29 10:02:03','2006-07-31 00:00:00',
          '2006-08-01 10:11:12','2006-08-02 09:09:09','2006-08-03 08:08:08']

id_dates=datestr2num(str_dates)

# It appears to ignore the formatting, it shows the month,day and year but not the time...
formatter = DateFormatter('%m-%d-%y %H:%M:%S')

ax = subplot(111)
ax.plot_date(id_dates,id_list)
ax.xaxis.set_major_formatter(dateFormatter)
labels = ax.get_xticklabels()

setp(labels, rotation=30, fontsize=8)
ax.set_title(" test dates")
show()