Re: [Matplotlib-users] Figures missing from matplotlib documentation?

2008-10-14 Thread John Hunter
On Mon, Oct 13, 2008 at 6:56 PM, Eric Firing [EMAIL PROTECTED] wrote:

 However, unfortunately there appears to be some problem with the
 generation of the figures which are supposed to be embedded within that
 documentation - they're all appearing as nothing but blank white spaces,
 both in Firefox 3.0.3 on OS X 10.5.5, and when I download the files and view
 them with other programs.  Do other people see this problem?

 Yes, something is broken.  I don't know how to fix it, though.

It looks like either the rsync screwed up or sf is throttling us or
both.  I got this message in my cron job

  ssh: connect to host matplotlib.sf.net port 22: Connection refused
  rsync: connection unexpectedly closed (0 bytes received so far) [sender]
  rsync error: unexplained error (code 255) at io.c(453) [sender=2.6.9]
  ssh: connect to host matplotlib.sf.net port 22: Connection refused
  lost connection

when I check the images in the
http://matplotlib.sourceforge.net/doc/html/pyplots/ directory, they
are there but are smaller in filesize than they are in the directory
on the build machine, suggesting they were truncated in the transfer.
When I try and log into the sf shell server

   ssh -l jdh2358 shell.sf.net

it hangs.

Normally they send me an email when I am over file size quota, so I
would be surprised if they simply throttled us w/o a warning, but I
will file a ticket with the sf folks and see if they can help.

JDH

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Re: [Matplotlib-users] Figures missing from matplotlib documentation?

2008-10-14 Thread John Hunter
On Tue, Oct 14, 2008 at 7:35 AM, Michael Droettboom [EMAIL PROTECTED] wrote:
 I saw this blank image problem a couple of weeks ago, and I was seeing it in
 my local doc builds as well.

 It appeared then that this change broke inline plots:

 
 r6089 | jdh2358 | 2008-09-13 10:28:09 -0400 (Sat, 13 Sep 2008) | 1 line

 replaced ipython run magic with code.InteractiveConsole.runsource
 

 because InteractiveConsole injects a number of things in __builtin__ that
 interfere with recent SVN versions of Sphinx.

 
 r6137 | mdboom | 2008-09-30 16:07:54 -0400 (Tue, 30 Sep 2008) | 3 lines

 [ 2138392 ] API doc for add_subplot()
 Also fixing numerous problems with the documentation build.  It seems that
 the change in plot_directive.py to use the code module to run scripts
 interferes with i18n in Sphinx (due to the overloading of '_' as a symbol).
  Changed to use the fewer-moving-parts imp.load_module() instead.
 

 I changed this in SVN to just use imp.load_module instead, and this resolved
 the problem locally.  I had expected the doc buildbot to pick it up and run
 with it, but I never followed up to see if it ever did.  It's possible that
 this SF quota/login etc. problem has been blocking the updates all this
 time.  So it's not necessarily that the files are transferring incorrectly,
 merely that they haven't been transferring at all since Sept 30 or before.

Just checked my cron emails again and indeed, the last successful
update was in mid September.  I'll need to keep a closer eye on these.

Indeed, sourceforge revamped their shell services and I missed the
email.  Details are here

  http://sourceforge.net/community/forum/topic.php?id=3471pagereplies=2

Short answer: there is no longer any ssh shell access but sftp and
rsync over ssh are supported.  The new server is web.sf.net.  I
updated my makefile and synced the docs, so
http://matplotlib.sourceforge.net/doc/html/ is live again

JDH
JDH

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Re: [Matplotlib-users] Does anyone have an updated version of SentinelMap?

2008-10-14 Thread Michael Lerner
On Mon, Oct 13, 2008 at 3:59 PM, Eric Firing [EMAIL PROTECTED] wrote:
 Michael Lerner wrote:

 Hi,

 I'm trying to plot some data where certain values are marked by a
 sentinel, as per the Cookbook example:


 http://www.scipy.org/Cookbook/Matplotlib/Plotting_Images_with_Special_Values

 However, that code is fairly old, and doesn't work. A version that
 worked as of ~18 months ago was posted to the list:

 http://www.nabble.com/Re:-Trying-p8831162.html

 but it fails when I try to use it with matplotlib 0.98.3 and imshow.
 Does anyone have an updated version?

 Thanks,

 -michael


 Michael,

 In the mpl examples directory there is a script that might be directly
 relevant:

 examples/pylab_examples/image_masked.py

That's fantastic. I had tried using masked arrays before. They weren't
good enough because I need three different sentinels, and at least one
with a controllable alpha value. The combination of set_over,
set_under and set_bad gives me exactly what I need. Thanks!

-michael


 Eric




-- 
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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
http://www.umich.edu/~mlerner

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[Matplotlib-users] how to tell if a point is inside a polygon

2008-10-14 Thread Mathew Yeates
Is there a routine in matplotlib for telling whether  a point is inside a 
convex 4 sided polygon?

Mathew



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Re: [Matplotlib-users] plot chops off big Latex axis labels

2008-10-14 Thread Michael Droettboom
Can you send us some input and output that exhibits this problem, and 
some information about your versions and platform?

[EMAIL PROTECTED] wrote:
 The plot PDFs that matplotlib makes by default seem to be too tiny to contain
 my biggest axis labels and my poor Latex stuff is chopped in half.

 How fix?

 cs

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Re: [Matplotlib-users] how to tell if a point is inside a polygon

2008-10-14 Thread Mathew Yeates
Thanks! Thats exactly what I was looking for!

Mathew

Michael Droettboom wrote:
 If you can convert your polygon to a path, you can use the 
 contains_point method:

  from matplotlib import path
  p = path.Path([[0,0], [42, 3], [45, 23], [1, 32]])
  p.contains_point([5,5])
 1
  p.contains_point([72, 3])
 0

 Mike

 Mathew Yeates wrote:
 Is there a routine in matplotlib for telling whether  a point is 
 inside a convex 4 sided polygon?

 Mathew



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Re: [Matplotlib-users] how to tell if a point is inside a polygon

2008-10-14 Thread Eric Firing
Pierre GM wrote:
 Mathew,
 Have you tried the solution that was suggested by Angus yesterday on the 
 numpy 
 mailing list ?
 
 http://projects.scipy.org/pipermail/scipy-user/2008-February/015418.html
 
 import numpy as np
 import matplotlib.nxutils as nxutils
 polygon=np.array([(0,0),(0,1),(1,1),(1,0)])
 points = np.array([(0.5,0.5),(0.4,1.5)])
 nxutils.points_inside_poly(points, polygon)
 array([1, 0], dtype=int32)
 
 Meaning that the first point is, the second is not.

It seems to me that the output should be boolean, so the line

   mask = (PyArrayObject *)PyArray_SimpleNew(1,dimensions,PyArray_INT);

in nxutils.cpp would become

   mask = (PyArrayObject *)PyArray_SimpleNew(1,dimensions, NPY_BOOL);

Can anyone think of anything this would break, or any disadvantages?

Eric

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Re: [Matplotlib-users] zorder seems to cause problems when embed python in latex files

2008-10-14 Thread Jouni K . Seppänen
[EMAIL PROTECTED] writes:

 I also attached the final PDF since you asked for it.

You didn't mention your matplotlib version, but the embedded pdf file
seems to come from matplotlib 0.91.2. That version had a bug where the
graphics context was not always restored properly, which could very well
be the cause of your problem:

  2008-03-23 Fix a pdf backend bug which sometimes caused the outermost
 gsave to not be balanced with a grestore. - JKS
...
  2008-01-06 Released 0.91.2 at revision 4802

Can you upgrade to 0.91.4?

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Re: [Matplotlib-users] how to tell if a point is inside a polygon

2008-10-14 Thread John Hunter
On Tue, Oct 14, 2008 at 2:58 PM, Eric Firing [EMAIL PROTECTED] wrote:
  mask = (PyArrayObject *)PyArray_SimpleNew(1,dimensions,PyArray_INT);

 in nxutils.cpp would become

  mask = (PyArrayObject *)PyArray_SimpleNew(1,dimensions, NPY_BOOL);

 Can anyone think of anything this would break, or any disadvantages?

This looks better to me too - -I suggest testing it with the lasso
demo which was the example that motivated this code.

JDH

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Re: [Matplotlib-users] zorder seems to cause problems when embed python in latex files

2008-10-14 Thread chris
On Tue, Oct 14, 2008 at 03:00:05PM -0400, Michael Droettboom wrote:
 With the file you sent, I can see the messed up footer in xpdf, but not
 in acroread.  There are a number of times that I have seen xpdf not
 completely support the PDF spec, and this may be one of them.

I installed acroread and I was also able to view everything fine with it
whereas xpdf and evince showed the bug.


 Creating my own files, however, I'm not able to reproduce this here.

Hmmm.  This would imply that your versions somehow do something that makes xpdf
happy.

 When I compile your test.tex, I get an error, even though it seems to
 have loaded the python.sty file.  Not sure why (see attached log).

Looks like it doesn't know what \begin{python} means.  Did you put python.sty
in the same directory as text.tex?

 When I generate the plots offline, and then hack test.tex to simply
 include the files, everything works fine, and I don't see a problem with
 the footers with either xpdf or acroread.

I see the problem with xpdf when I simply include the plots which means that
python.sty was just a red herring.  python.sty isn't the problem.

 There was a recent bug discovered in matplotlib where PDF files weren't
 always getting flushed completely.  I don't *think* that's the cause of
 this, but if you could reproduce what I did (generate the plots
 independently of TeX and then load them), and that works for you, that
 might point to something like that.

xpdf still croaks for me.  Perhaps using the bleeding edge of matplotlib would
fix?  I'm using Ubuntu 8.04 which has python-matplotlib version
0.91.2-0ubuntu1.

 There was also a bug a few months back where xpdf didn't like the way
 matplotlib handled reusing the same graphic multiple times (which is
 used for markers).  That may be why you're seeing the footer bug and I'm
 not -- you didn't mention which version of matplotlib you're running, so
 it's hard to say.

 Here's my versions of all the various moving pieces:
 pdfTeX (Web2C 7.4.5) 3.14159-1.10b
 kpathsea version 3.4.5
 Copyright (C) 1997-2003 Han The Thanh.
 Beamer 3.00
 python 2.5.2
 matplotlib SVN (today)
 Acroread 8.1.1
 xpdf 3.00

Here is what I got:

Beamer 3.07-1
python 2.5.2
matplotlib  0.91.2-0ubuntu1
Acroread 8.1.2_SU1
xpdf 3.02-1.3ubuntu1

Ironically, all my stuff is newer than yours except for matplotlib.  Sounds
like bleeding edge of matplotlib must be tried next.

 That python.sty stuff looks really cool, by the way.  I haven't come
 across it before.

Glad I could help!

cs

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Re: [Matplotlib-users] zorder seems to cause problems when embed python in latex files

2008-10-14 Thread Jouni K . Seppänen
Jouni K. Seppänen [EMAIL PROTECTED] writes:

   2008-03-23 Fix a pdf backend bug which sometimes caused the outermost
  gsave to not be balanced with a grestore. - JKS

 Can you upgrade to 0.91.4?

Here's the relevant patch, in case applying it is more convenient than
upgrading:

Index: lib/matplotlib/backends/backend_pdf.py
===
--- lib/matplotlib/backends/backend_pdf.py	(revision 5017)
+++ lib/matplotlib/backends/backend_pdf.py	(revision 5018)
@@ -1159,7 +1159,7 @@
 self.tex_font_map = None
 
 def finalize(self):
-self.gc.finalize()
+self.file.output(*self.gc.finalize())
 
 def check_gc(self, gc, fillcolor=None):
 orig_fill = gc._fillcolor

-- 
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Re: [Matplotlib-users] how to tell if a point is inside a polygon

2008-10-14 Thread Mathew Yeates
Angus originally suggest matplotlib. The other proposed solutions are 
overkill, unless it turns out that performance is a problem

Thanks
Mathew

Pierre GM wrote:
 Mathew,
 Have you tried the solution that was suggested by Angus yesterday on the 
 numpy 
 mailing list ?

 http://projects.scipy.org/pipermail/scipy-user/2008-February/015418.html

   
 import numpy as np
 import matplotlib.nxutils as nxutils
 polygon=np.array([(0,0),(0,1),(1,1),(1,0)])
 points = np.array([(0.5,0.5),(0.4,1.5)])
 nxutils.points_inside_poly(points, polygon)
 
 array([1, 0], dtype=int32)

 Meaning that the first point is, the second is not.

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Re: [Matplotlib-users] how to tell if a point is inside a polygon

2008-10-14 Thread Michael Droettboom
If you can convert your polygon to a path, you can use the 
contains_point method:

  from matplotlib import path
  p = path.Path([[0,0], [42, 3], [45, 23], [1, 32]])
  p.contains_point([5,5])
1
  p.contains_point([72, 3])
0

Mike

Mathew Yeates wrote:
 Is there a routine in matplotlib for telling whether  a point is inside a 
 convex 4 sided polygon?

 Mathew



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Re: [Matplotlib-users] zorder seems to cause problems when embed python in latex files

2008-10-14 Thread Michael Droettboom
[EMAIL PROTECTED] wrote:
 LaTeX can accept embedded Python code with a python.sty file.

 This is handy to dynamically generate plots with Matplotlib for a LaTeX slide
 presentation.

 I successfully embedded lots of matplotlib plot code into my slides
 and then had problems with zorder.

 For some reason zorder seems to mess up the footer of my Beamer/LaTeX slides.
 (For some reason zorder setting make the footer shrink in size.)

 Is there any weirdness or side effects about zorder I should be aware of that
 would explain this?
   
My best guess is that when the elements of the plot are in a particular 
order, the last drawn element has some setting that is not getting 
reverted back when going back to the LaTeX part of the slide.  In 
general, matplotlib doesn't explicitly try to be careful about state in 
its output since it is really the embedding applications job (in this 
case Beamer/LaTeX) that is supposed to ensure that anything it embeds 
does not have external side effects.

But I've never tried this combination of python.sty/Beamer/LaTeX 
personally.  Can you send us the output of your plot on its own (ps or 
pdf...)?

Mike

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[Matplotlib-users] another noob question

2008-10-14 Thread Mathew Yeates
Any help appreciated

I am displaying a line on a map ala
--
m=Basemap(   )
xpt,ypt= m([],[])
outlines=m.plot(xpt,ypt,'r-')
-
and then in an update routine I do


def update(newxpts,newypts):
outlines[0].set_data(newxpst,newypts)
---

This works fine but now I want to add additional lines. I tried


m=Basemap(   )
xpt,ypt= m([],[])
outlines=m.plot(xpt,ypt,'r-')
slitlines=[]
for i in range(0,500):
slitlines.append(m.plot([],[],'b-'))


and


def update(newxpts,newypts,newslitx,newlity):
outlines[0].set_data(newxpst,newypts)
 for i in 
range(0,500):slitlines[i][0].set_data([startx[i],endx[i]],[starty[i],endy[i]])
-

but this doesn't work. Clearly I'm doing something wrong.
Whats the best way to do this?

Thanks
Mathew
 


   
   
   



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[Matplotlib-users] nevermind - Re: another noob question

2008-10-14 Thread Mathew Yeates
I had a bug in my code, when I fixed it I can now see the lines.
If there is a better way to do what I'm doing, and love to hear it.




Mathew Yeates wrote:
 Any help appreciated

 I am displaying a line on a map ala
 --
 m=Basemap(   )
 xpt,ypt= m([],[])
 outlines=m.plot(xpt,ypt,'r-')
 -
 and then in an update routine I do

 
 def update(newxpts,newypts):
 outlines[0].set_data(newxpst,newypts)
 ---

 This works fine but now I want to add additional lines. I tried

 
 m=Basemap(   )
 xpt,ypt= m([],[])
 outlines=m.plot(xpt,ypt,'r-')
 slitlines=[]
 for i in range(0,500):
 slitlines.append(m.plot([],[],'b-'))
 

 and

 
 def update(newxpts,newypts,newslitx,newlity):
 outlines[0].set_data(newxpst,newypts)
  for i in 
 range(0,500):slitlines[i][0].set_data([startx[i],endx[i]],[starty[i],endy[i]])
 -

 but this doesn't work. Clearly I'm doing something wrong.
 Whats the best way to do this?

 Thanks
 Mathew
  








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[Matplotlib-users] MPL on Windows x64 with Python 2.6

2008-10-14 Thread Dan Shechter
Hi,
I've successfully compiled NumPy for Python 2.6 on Windows x64 (amd64).
NumPy seems so pass most of the unit tests, except for a few minor ones
where it seems nose (the unit testing harness) seems to have problems with
python 2.6.

After compiling MPL for 2.6 on x64 (which was a LENGTHY process... phew!) I
do get a generally speaking working version but there seem to be quite a few
display issues... I have re-occuring cases of missing data points, for a
lack of a better name.
Feel free to look at a screenshot:
http://img101.imageshack.us/my.php?image=badsubloptswy1.png

Is MPL supported on Win x64? I someone working on this?

I would be happy to share my NumPy build and MPL dependencies + MPL build
with anyone that perhaps knowing a bit more than me about MPL :)
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Re: [Matplotlib-users] MPL on Windows x64 with Python 2.6

2008-10-14 Thread Charlie Moad
Could you please describe your build environment?  I am interested in what
compiler you used and what OS you are running.
- Charlie

On Tue, Oct 14, 2008 at 8:23 PM, Dan Shechter [EMAIL PROTECTED] wrote:

 Hi,
 I've successfully compiled NumPy for Python 2.6 on Windows x64 (amd64).
 NumPy seems so pass most of the unit tests, except for a few minor ones
 where it seems nose (the unit testing harness) seems to have problems with
 python 2.6.

 After compiling MPL for 2.6 on x64 (which was a LENGTHY process... phew!) I
 do get a generally speaking working version but there seem to be quite a few
 display issues... I have re-occuring cases of missing data points, for a
 lack of a better name.
 Feel free to look at a screenshot:
 http://img101.imageshack.us/my.php?image=badsubloptswy1.png

 Is MPL supported on Win x64? I someone working on this?

 I would be happy to share my NumPy build and MPL dependencies + MPL build
 with anyone that perhaps knowing a bit more than me about MPL :)

 -
 This SF.Net email is sponsored by the Moblin Your Move Developer's
 challenge
 Build the coolest Linux based applications with Moblin SDK  win great
 prizes
 Grand prize is a trip for two to an Open Source event anywhere in the world
 http://moblin-contest.org/redirect.php?banner_id=100url=/
 ___
 Matplotlib-users mailing list
 Matplotlib-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-users


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[Matplotlib-users] .show() documentation?

2008-10-14 Thread Nick Vaidyanathan
Does not exist here:
http://matplotlib.sourceforge.net/doc/html/api/pyplot_api.html

Which is curious, because it's plainly shown (PUNZ!) here:
http://matplotlib.sourceforge.net/doc/html/users/pyplot_tutorial.html

Now here's t3h sex: given the documentation, I kind of expect this to work:

---Python Code---
plotter.plot(xs,ys,'ro')
plotter.grid(True)
plotter.savefig('myresult.png')
plotter.show()
plotter.waitforbuttonpress(1)
plotter.close()
---End Python Code---

I would expect that would keep my window open for a second, or until I keyed
a button, and then close it. No dice.

...actually, I got my matplotlib through enthought, which has an old version
of the package (.91)...but a simple google search for matplotlib 0.91 api
doesn't show that package's docs on the front page...help?
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