matplotlib-users Mailing List for matplotlib (Page 8)

Chris Withers wrote:
> Michael Droettboom wrote:
>>> That's cool'n'all, but when is svn going to make it into a Windows 
>>> binary release? ;-)
>>> 
>> I suspect your question is somewhat rhetorical, but... it will 
>> probably be a while ;) 
> 
> Why is that? Who cranks out the binary releases on Windows and what 
> compiler do they use?
> 
>> I know a lot of people (myself included) have had success with MinGW. 
> 
> What's the "official" compiler used, though?
> 
>> It's a good learning experience, and there's lots on this list willing 
>> to help. If we can get more SVN Windows users on board, more crazy 
>> Windows-only bugs will get found and squashed sooner... ;)
> 
> Well, tell me how to get the svn trunk and how to compile and I'll give 
> it a go :-)
Assuming you have svn installed on your machine, start here:
http://sourceforge.net/svn/?group_id=80706
You will probably want to modify the checkout command slightly, 
something like this:
svn co 
https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/matplotlib 
mpl_svn
(That should be all one line, but the mailer may have broken it.)
There are some Windows-related compilation hints in the INSTALL.txt file 
and in setupext.py. I think the basic idea is that once you have all 
prerequisites in place, complete with header files, then the standard 
"python setup.py install" will do the right thing. The hard part is 
probably getting all the prerequisites installed. I've never tried on 
Win, so I don't know.
Charlie Moad does the Windows releases. I don't know what compiler he uses.
It would be nice if some people who have successfully built on Windows 
could collectively assemble a step-by-step account of how to go from a 
bare Win box to a working mpl (preferably compiled with mingw); but 
maybe this would take more effort than it is worth. I am on shaky 
ground suggesting it, because it is not something I can help with at 
all, and I don't even have a clear picture of what it would require. I 
gather a similar account would be useful for OS X.
Eric
> 
> cheers,
> 
> Chris
> 

> Out of interest, how does one tell MPL to "start a new figure and forget 
> everything that's gone before"?
You can minimize the amount of package and module-level state 
information by using the oo interface: see examples/agg_oo.py. If you 
change any rcParams dictionary entries, typically using the rc function, 
then you can restore the dictionary to its default condition with the 
rcdefaults() function.
Eric

Hi. I'm making scientific graphs again, so i just got back on this 
mailing list after a two year hiatus.
I am using:
matplotlib-0.90.0-py2.5-macosx-10.4-fat.egg
Here is a simple program:
#!/usr/bin/python
#
# Do our plots with matplotlib
import matplotlib
matplotlib.use('Agg')
from pylab import *
fig = figure(num=1,figsize=(6.5,4))
ax = fig.add_axes([.15,.3,.8,.65])
ax.set_title("Why is the Y axes upside down?")
ax.set_yscale('log')
ax.set_ylabel('Queries per second')
ax.bar(1,1000,.5,color='r')
ax.bar(2,5000,.5,color='b')
ax.bar(3,55000,.5,color='g')
fig.savefig("broken_log_demo.png")
Here is the plot with a PNG:

Charlie Moad wrote:
> I agree you are not using a universal build of python to compile 
> matplotlib. You cannot pass in the "-arch i386 -arch ppc" flags. 
> Only pass the architecture of your computer.
Actually, I think the OP IS using a universal python, thus both flags -- 
he isn't manually passing in any flags at all. The problem is that it's 
trying to link in a jpeg lib that isn't Universal.
Is there a Universal Binary egg that will work with MacPython 2.5?
Note to OP -- maybe you'd have better luck with Apple's Python 2.5 -- it 
seems that that's what more people are using with Leopard.
-Chris
-- 
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Chr...@no... 

Pierre,
I was interested in learning more about TimeSeries, and had a few
questions...
Your data is indexed in time, right ? Your x-axis is a date object ?
Just to be clear on the language: "indexed in time" means data for which
the x-axis is a series of dates, correct? But I am not sure what is meant
by the "x-axis being a date object"--wouldn't it be a axis object with the
values comprising it being date objects? I'm not trying to split hairs, I'm
just unclear about the way this is typically described and it would be
useful for me to be clear about it.
Then use
> scikits.timeseries
> http://scipy.org/scipy/scikits/wiki/TimeSeries
> That package was designed to take missing dates/data into account. That
> way,
> you can plot your data with the gaps already taken into account: we have
> written a specific matplotlib interface, you'll find the details following
> the link above.
I've looked at the link. Could you explain what TimeSeries does that the
mpl modules dates and dateutil don't do, or when one would use one versus
the other?
For my part, I need to simply plot values with dates (and yes with some
dates missing no doubt) as the x-axis and am looking for various ways to do
it well.
Thank you.

I agree you are not using a universal build of python to compile matplotlib.
 You cannot pass in the "-arch i386 -arch ppc" flags. Only pass the
architecture of your computer.
- Charlie
On Thu, Mar 20, 2008 at 7:13 PM, Christopher Barker <Chr...@no...>
wrote:
> Andrew Charles wrote:
> > Compiling Matplotlib from source, or easy_installing the egg
>
> >>From the egg:
> > ld: in /sw/lib/libJPEG.dylib, file is not of required architecture for
>
> hmm -- odd, I wouldn't think the egg should be linked against what looks
> like a macports libJPEG -- are you sure it isn't trying to build the
> egg when you easy_install?
>
> > And from source:
>
> > ld: in /sw/lib/libJPEG.dylib, file is not of required architecture for
> > architecture ppc
>
> It's trying to link against a macports libJPEG. However, macports
> doesn't build universal binaries, and the MacPython tries to build them,
> and hence the problem.
>
> I'd try to find another libJPEG -- The UnixImageIO Frameworks form
> KyngChaos are a good choice, though I don't know off the top of my head
> how to get MPL to find them.
>
> http://www.kyngchaos.com/wiki/software:frameworks
>
>
> -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...
>
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Chris,
My 2c:
Your data is indexed in time, right ? Your x-axis is a date object ? Then use 
scikits.timeseries
http://scipy.org/scipy/scikits/wiki/TimeSeries
That package was designed to take missing dates/data into account. That way, 
you can plot your data with the gaps already taken into account: we have 
written a specific matplotlib interface, you'll find the details following 
the link above. I must admit we didn't implement poly_between for timeseries. 
Most likely, we'd have to implement it for regular masked arrays first, as 
mentioned by Eric.
What you could do is to fill your array with some kind of baseline, such as 0, 
or your minimum data, or wtvr. That's just a quick trick and no fix.

Hi Brook,
FG> Can you give me a simple example to show how to set the figure's
FG> interactive property to on? I appreciate!
 >>> import pylab
 >>> pylab.ion()
-- 
Chris

I've searched the user manual (and this forum) but I don't see anything that
helps.
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<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'>Can you give me a simple example to show how to set the figure's interactive property to on? I appreciate!<br><br>--Brook<br><br><br>--- On <b>Fri, 3/21/08, Christopher Brown <i>&lt;c-...@as...&gt;</i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">From: Christopher Brown &lt;c-...@as...&gt;<br>Subject: Re: [Matplotlib-users] How to close the figure after show it?<br>To: gnu...@ya...<br>Cc: mat...@li...<br>Date: Friday, March 21, 2008, 12:19 AM<br><br><pre>Hi,<br><br>&gt; Hi Mike,thanks for your reply. I tried f=figure() and pylab.close(f),<br>&gt; but the figure can not be closed automatically. Seems that<br> &gt; time.sleep(3) doesn't be called until I close the figure manually.<br><br>Maybe try setting the figure's interactive property to on?<br><br>--
 <br>Chris</pre></blockquote></td></tr></table><br>
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Hi,
> Hi Mike,thanks for your reply. I tried f=figure() and pylab.close(f),
> but the figure can not be closed automatically. Seems that
 > time.sleep(3) doesn't be called until I close the figure manually.
Maybe try setting the figure's interactive property to on?
-- 
Chris

<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'>Hi Mike,thanks for your reply. I tried f=figure() and pylab.close(f), but the figure can not be closed automatically. Seems that <span style="font-weight: bold;">time.sleep(3) </span>doesn't be called until I close the figure manually. The test code is attached below.<br><br>Thanks,<br>Brook<br>&nbsp;<br>==================================<br>from pylab import *<br>from matplotlib import *<br>from pylab import figure, close, show, nx<br>from matplotlib.figure import Figure<br>import time<br><br>x=arange(10)<br>y=[2, 4, 6, 8, 10, 12, 14, 16, 18, 20]<br>x2=arange(20)<br>y2=arange(20)<br><br>f=figure()&nbsp;&nbsp;&nbsp; <br>hold(True)<br>plot(x,y)<br>plot(x2,y2)<br>grid()<br>pylab.show()<br>time.sleep(3)<br>pylab.close(f)<br></td></tr></table><br>
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Andrew Charles wrote:
> Compiling Matplotlib from source, or easy_installing the egg
>>From the egg:
> ld: in /sw/lib/libJPEG.dylib, file is not of required architecture for
hmm -- odd, I wouldn't think the egg should be linked against what looks 
like a macports libJPEG -- are you sure it isn't trying to build the 
egg when you easy_install?
> And from source:
> ld: in /sw/lib/libJPEG.dylib, file is not of required architecture for
> architecture ppc
It's trying to link against a macports libJPEG. However, macports 
doesn't build universal binaries, and the MacPython tries to build them, 
and hence the problem.
I'd try to find another libJPEG -- The UnixImageIO Frameworks form 
KyngChaos are a good choice, though I don't know off the top of my head 
how to get MPL to find them.
http://www.kyngchaos.com/wiki/software:frameworks
-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...

Michael Droettboom wrote:
>> That's cool'n'all, but when is svn going to make it into a Windows 
>> binary release? ;-)
>> 
> I suspect your question is somewhat rhetorical, but... it will probably 
> be a while ;) 
Why is that? Who cranks out the binary releases on Windows and what 
compiler do they use?
> I know a lot of people (myself included) have had success with MinGW. 
What's the "official" compiler used, though?
> It's a good learning experience, and there's lots on this list willing 
> to help. If we can get more SVN Windows users on board, more crazy 
> Windows-only bugs will get found and squashed sooner... ;)
Well, tell me how to get the svn trunk and how to compile and I'll give 
it a go :-)
cheers,
Chris
-- 
Simplistix - Content Management, Zope & Python Consulting
 - http://www.simplistix.co.uk

[re-adding in the list]
Eric Firing wrote:
> It looks like you have hit a bug that has been fixed. I don't know when 
> it was fixed, but your example works with svn.
As I said elsewhere, with all the fixes, maybe it's time for a new 
release? ;-)
> Also, you can call bar repeatedly; I think it will just keep adding the 
> new bars, resizing the plot as needed. Everything has to be done before 
> the show() command, though. 
I don't think I was clear enough.. I want to do all the plotting at one 
time, but looking at the example, it appears that you have to do much 
more work as a user if you want bar charts where the bars are 
side-by-side than if you use a line plot.
Are bar charts a relatively new addition? They feel less slick to use 
than the other options :-S
cheers,
Chris
-- 
Simplistix - Content Management, Zope & Python Consulting
 - http://www.simplistix.co.uk

Eric Firing wrote:
> If you are referring to scripts in the matplotlib/examples/ subdirectory 
> then you must have a version in which some of those scripts had not been 
> brought up to date with the rest of matplotlib. 
You should turn them into unit tests as well as examples.
I'm about to try and do this, time permiting, for xlwt (small plug - 
it's great for generating formatted excel files from raw data, just as 
xlrd is for extracting data and formatting from excel files, sadly, 
neither can do charting with excel, which is why I'm learning to love 
and hate numpy and matplotlib ;-) )
Out of interest, does MPL have unit tests? It should ;-)
cheers,
Chris
-- 
Simplistix - Content Management, Zope & Python Consulting
 - http://www.simplistix.co.uk

Eric Firing wrote:
> In general, I don't think mpl is threadsafe at all; it uses global 
> variables, such as all the rc parameters, that could easily be modified 
> by one thread while being used by another. 
Yep, I guessed as much, BFL it is then ;-)
> I think that great care 
> would be needed if one wanted to have multiple threads making plots. 
> Having one plotting thread and any number of threads doing other things, 
> however, should be OK.
Out of interest, how does one tell MPL to "start a new figure and forget 
everything that's gone before"?
> At the very least, I think we would have to take all the global state 
> information and put it in a class instance, so there could be multiple 
> plotting machines. 
Yes.
cheers,
Chris
-- 
Simplistix - Content Management, Zope & Python Consulting
 - http://www.simplistix.co.uk

Michael Droettboom wrote:
> At least the Agg backend *looks* to be reasonably threadsafe -- there 
> are no obvious gotchas like global variables etc. Note, though, that 
> multithreading may not gain much in the way of performance since the 
> global interpreter lock is never released around long-running C blocks.
It's not performance I'm looking for, it's making sure that MPL apps 
served from multi-threaded wsgi servers don't screw each others charts 
up ;-)
cheers,
Chris
-- 
Simplistix - Content Management, Zope & Python Consulting
 - http://www.simplistix.co.uk

Giorgio F. Gilestro wrote:
> 
> import numpy as np
> a = ['','','',1.1,2.2]
> mask_a = [i == '' for i in a]
> b = np.ma.MaskedArray(a, mask=mask_a)
Not very efficient, though, is it?
cheers,
Chris
-- 
Simplistix - Content Management, Zope & Python Consulting
 - http://www.simplistix.co.uk

Eric Firing wrote:
> Both with respect to documentation and functionality, what you are 
> encountering is the historical aspect of masked arrays as a tacked-on 
> part of python numeric packages, and of matplotlib.
*sigh* I feel lucky ;-)
> Support and 
> integration are improving, but still far from perfect. 
I wish I could help, but my knowledge is lacking...
> Now with respect to your particular case here, trying to plot a filled 
> line with gaps: poly_between has no notion of masked arrays at present. 
> If it did, how should it behave? 
Well, what I actually settled on was juat doing using:
my_masked_array.filled(0)
...to plot with.
> At the very least, additional 
> arguments are needed to specify what should happen for fill-type 
> plotting with missing values. 
Indeed, what I personally would have liked was a complete gap where the 
data is missing, but I guess that would have to return multiple 
polygons, and I don't know how that would work?
> provide them in mpl. I would be happy to fix this gap in mpl's handling 
> of gappy data, 
...heh ;-)
> but I can't make it a priority use of my time right now.
No, I understand :-)
cheers,
Chris
-- 
Simplistix - Content Management, Zope & Python Consulting
 - http://www.simplistix.co.uk

Hi Folks,
I'm having some trouble installing Matplotlib on a Macbook pro running Leopard.
I installed macpython 2.5.2, and I have numpy and scipy installed from
source for the 2.5.2 installation.
Compiling Matplotlib from source, or easy_installing the egg
(matplotlib-0.91.2-py2.5-macosx-10.3-fat.egg) both fail with the same
error:
>From the egg:
-------------------------------------------------------------------
........
ld: in /sw/lib/libJPEG.dylib, file is not of required architecture for
architecture ppc
collect2: ld returned 1 exit status
lipo: can't open input file: /var/tmp//ccG9WQI9.out (No such file or directory)
error: Setup script exited with error: command 'g++' failed with exit status 1
Exception exceptions.OSError: (2, 'No such file or directory',
'src/image.cpp') in <bound method CleanUpFile.__del__ of
<setupext.CleanUpFile instance at 0x1b5f4b8>> ignored
Exception exceptions.OSError: (2, 'No such file or directory',
'src/transforms.cpp') in <bound method CleanUpFile.__del__ of
<setupext.CleanUpFile instance at 0x1b5ccd8>> ignored
Exception exceptions.OSError: (2, 'No such file or directory',
'src/backend_agg.cpp') in <bound method CleanUpFile.__del__ of
<setupext.CleanUpFile instance at 0x1b5f030>> ignored
--------------------------
And from source:
----------------------
...
building 'matplotlib.ft2font' extension
g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g
-bundle -undefined dynamic_lookup
build/temp.macosx-10.3-i386-2.5/src/ft2font.o
build/temp.macosx-10.3-i386-2.5/src/mplutils.o
build/temp.macosx-10.3-i386-2.5/CXX/cxx_extensions.o
build/temp.macosx-10.3-i386-2.5/CXX/cxxsupport.o
build/temp.macosx-10.3-i386-2.5/CXX/IndirectPythonInterface.o
build/temp.macosx-10.3-i386-2.5/CXX/cxxextensions.o -L/usr/X11/lib
-L/usr/local/lib -L/usr/lib -L/sw/lib -L/usr/X11R6/lib -lfreetype -lz
-lstdc++ -lm -o build/lib.macosx-10.3-i386-2.5/matplotlib/ft2font.so
-Wl,-framework,CoreServices,-framework,ApplicationServices
ld: in /sw/lib/libJPEG.dylib, file is not of required architecture for
architecture ppc
collect2: ld returned 1 exit status
lipo: can't open input file: /var/tmp//ccMIVHPU.out (No such file or directory)
error: command 'g++' failed with exit status 1
------------------
Has anyone else hit up against this before. Do I need to update
libJPEG, or modify setup.py?
Cheers,
-------------------------
Andrew Charles

I think f = figure();
...
pylab.close(f);
should work.
--Mike
On Mar 20, 2008, at 2:14 PM, Fans Gnu wrote:
> Hi All,
>
> I am using matplotlab to plot some figure. I would like to close 
> the figure after show it 5 sec. My code is pasted below. However, I 
> can not close the figure automatically. Can anyone help me to fix it?
>
> Thanks,
> Brook
>
> ==========================
> import time
> from pylab import *
> from matplotlib import *
> x=**
> y=**
> x2=**
> y2=***
> figure()
> hold(True)
> plot(x,y)
> plot(x2,y2,'g^')
> axis([0, 100, 0, 100])
> title('Pylab plot')
> xlabel('X')
> ylabel('Y')
> grid()
> pylab.show()
> time.sleep(5)
> pylab.close()
>
>
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<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'>Hi All,<br><br>I am using matplotlab to plot some figure. I would like to close the figure after show it 5 sec. My code is pasted below. However, I can not close the figure automatically.&nbsp; Can anyone help me to fix it?<br><br>Thanks,<br>Brook<br><br>==========================<br>import time<br>from pylab import *<br>from matplotlib import *<br>x=**<br>y=**<br>x2=**<br>y2=***<br>figure()<br>hold(True)<br>plot(x,y)<br>plot(x2,y2,'g^')<br>axis([0, 100, 0, 100])<br>title('Pylab plot')<br>xlabel('X')<br>ylabel('Y')<br>grid()<br>pylab.show()<br>time.sleep(5)<br>pylab.close()<br><br></td></tr></table><br>
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On 2008年3月20日, Eric Firing wrote:
> Sorry, but those options are not presently available at the rc level. Mpl 
> simply does not have easy support for that style of plot. It is on the wish 
> list.
Eric,
 I'm surprised because this is quite common ... at least in my needs over
the years.
> To get rid of the upper and right sides of the box I think you would have
> to do something like "box('off')" and then use hline and vline calls or
> methods to manually put in the lower and left boundaries.
 I use:
 p.p.box(on=False)
 p.axhline(linewidth=1, xmin=0, color='black')
 p.axvline(linewidth=1, ymin=0, color='black')
but the frameless display now has negative values (x = -10, y = -0.2) when
the scales should be x = [0, 50] and y = [0.0, 1.0].
 I want to learn how to get these correct before addressing the grid lines.
Actually, I can turn off the grid lines and use axhline for each one I want.
Thanks,
Rich
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Rich Shepard wrote:
> I've read the users guide and API (both as pdf and on the web site), and
> do not see how to configure the axes for only left and bottom, and the grid
> for only horizontal lines.
> 
> The axes(rect, w) is used to specify the position of the left and bottom
> lines plus the width and height of the box. What do I put in
> ~/.matplotlib/matplotlibrc to specify no top or right axes, and no vertical
> grid lines?
> 
> Rich
> 
Sorry, but those options are not presently available at the rc level. 
Mpl simply does not have easy support for that style of plot. It is on 
the wish list.
Here is one way of turning off vertical grid lines:
xgl = ax.xaxis.get_gridlines()
for l in gl:
 l.set_visible(False)
To get rid of the upper and right sides of the box I think you would 
have to do something like "box('off')" and then use hline and vline 
calls or methods to manually put in the lower and left boundaries.
Eric