matplotlib-users Mailing List for matplotlib (Page 2)

On Mon, Feb 22, 2010 at 6:28 PM, Eric Firing <ef...@ha...> wrote:
> Yes.  You are looking at ColorbarBase, which does not have an associated
> mappable.  The derived Colorbar class does grab the cmap and norm from the
> mappable used in the initialization.  Is this somehow not working? Did you
> really need to specify the norm explicitly?

No, I didn't test this, I just read the code (apparently the wrong
code) and concluded I needed it.  I did just test w/o it and all is
well.  Sorry for the noise.

JDH

On Tue, Feb 23, 2010 at 4:12 AM, Jan Strube <cur...@gm...> wrote:
> Hi John,
> thanks for keeping at it. I have updated from svn
> But this script
>   File
> "/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/colorbar.py",
> line 278, in _config_axes
>     ticks, ticklabels, offset_string = self._ticker()
>   File
> "/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/colorbar.py",
> line 417, in _ticker
>     b = np.array(locator())
>   File
> "/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/ticker.py",
> line 1085, in __call__
>     vmin = self.axis.get_minpos()
> AttributeError: DummyAxis instance has no attribute 'get_minpos'

Take a look at the file name in the traceback: matplotlib-1.0.svn_r8037

The r8037 is the svn revision number.  According the svn log, I made
my commit on r8149, so you are not running HEAD.  You may have
multiple matplotlib's installed and are not picking up the right egg.
I recommend

  > rm -rf /Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib*

and then doing a clean install from mpl svn r8149 or later.

JDH

Hi,

has anyone a good idea how to interactively display the xy coordintes (as
whole numbers) and the pixel intensity using the mouse cursor. Here is the
code snippet:

...
fig = plt.figure()
ax1 = fig.add_subplot(111)
channel_select = 1
p = imread(filename) # normally I use TIFF file
if (p.ndim > 2):
    p1 = p[:,:,channel_select] # if more than 1 channel --> select
else:
    p1 = p

ax1.imshow(p1)
plt.show()
...

So far only the XY coordinates are displayed, but not as whole numbers and
even negative xy values are displayed, if the cursor is move to the corners
(???). And of course I would like the pixel intensity to be displayed ...

Thanks,

Sebi

I would like to use custom symbols (markers) on both line charts and scatter
charts. The symbols I would like to use are currently stored in PNG files.
Is there a way to convert these images to markers? Symbols are pretty simple
and contain only one colour, and the background should be transparent.

Hi all!

I am preparing a journal article and the figures should have a fixed width
of 3 inches, with as thin white border around as possible. The figure does
an imshow with *equal* axes:
My problem is: I do not know in advance the height of my figure to specify
figsize. The height should vary so that the whole figure (with ticks,
legends and colorbanr) fits tightly into a 3 x ? inch box.

I have already tried bbox_inches='tight' for savefig and looked at HowTo
FAQ: automatically make room for tick
labels<http://matplotlib.sourceforge.net/faq/howto_faq.html#automatically-make-room-for-tick-labels>for
possible ideas but do no have a clue yet.
Any suggestion is welcome.

Thx very much!

Kornel

Hi,

I'm using the Python(x,y) distribution which comes with matplotlib for
Windows. My OS is Windows XP with all updates and service packs on an
AMD Athlon 2600+ PC with ATI Radeon 9600 graiphics card.

Python will work fine for anything that doesn't import the pylab
component (I can import matplotlib itself no problem as well as numpy
etc) but if I try to import pylab I get:-

"An unhandled exception occured in pythonw.exe [3976]"

I've tied reinstalling Python(x,y) and even reinstalling windows then
Python(x,y) but to no avail. This seems odd to me as 2 other PCs at work
install Python(x,y) and run Pylab fine.

Any suggestions as to what I should check to track down this error?

Thanks

Jon



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Erik Tollerud-2 wrote:
> 
> I'm curious if anyone knows a good way to embed pydot
> (http://code.google.com/p/pydot/) graphs (or really, any
> graphviz-style graphs) inside matplotlib somehow. 
> 

The closest thing is probably NetworkX (http://networkx.lanl.gov/index.html)
and PyGraphviz (http://networkx.lanl.gov/pygraphviz/)

The above tools can at least provide the position of the nodes, but I don't
think they use the drawing information provided by Graphviz.

As mentioned in another post, it is not that hard to write a Graphviz to
Matplotlib converter. Graphviz can output very detailed rendering
information when using the xdot output format
(http://www.graphviz.org/doc/info/output.html#d:xdot) Sounds like a fun
weekend project :)

- Kjell Magne Fauske

-- 
View this message in context: http://old.nabble.com/Pydot-graphs-in-matplotlib--tp27602474p27701290.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Hi John,

thanks for keeping at it. I have updated from svn

But this script
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.ticker import LogFormatter
from matplotlib import colors

class LogFormatterHB(LogFormatter):
   def __call__(self, v, pos=None):
       vv = self._base ** v
       print vv
       return LogFormatter.__call__(self, vv, pos)

data = np.load('deltaR_parton_jet_109370.npz')
ptcut = np.logical_and(data['jetMomentum'] < 300000, data['jetMomentum']>0)
deltaRCut = data['deltaR']>0
cut = np.logical_and(ptcut, deltaRCut)
fig = plt.figure()
polycol = plt.hexbin(data['jetMomentum'][cut] / 1000, data['deltaR'][cut],
gridsize=50, norm=colors.LogNorm())
plt.title('deltaR between parton(eta<2.5) and jet(eta<2.5)')
plt.xlabel('jet pt (GeV)')
plt.ylabel('deltaR')
cb = plt.colorbar(norm=polycol.norm)
cb.set_label('# entries')
fig.savefig('hexbin_demo.png', dpi=100)
#plt.show()

gives me an error:

> python test.py
Traceback (most recent call last):
  File "test.py", line 24, in <module>
    cb = plt.colorbar(norm=polycol.norm)
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/pyplot.py",
line 1356, in colorbar
    ret = gcf().colorbar(mappable, cax = cax, ax=ax, **kw)
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/figure.py",
line 1104, in colorbar
    cb = cbar.Colorbar(cax, mappable, **kw)
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/colorbar.py",
line 649, in __init__
    ColorbarBase.__init__(self, ax, **kw)
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/colorbar.py",
line 240, in __init__
    self.draw_all()
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/colorbar.py",
line 251, in draw_all
    self._config_axes(X, Y)
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/colorbar.py",
line 278, in _config_axes
    ticks, ticklabels, offset_string = self._ticker()
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/colorbar.py",
line 417, in _ticker
    b = np.array(locator())
  File
"/Users/Jan/PYTHON/lib/python2.6/site-packages/matplotlib-1.0.svn_r8037-py2.6-macosx-10.6-universal.egg/matplotlib/ticker.py",
line 1085, in __call__
    vmin = self.axis.get_minpos()
AttributeError: DummyAxis instance has no attribute 'get_minpos'

Cheers,
    Jan



On Tue, Feb 23, 2010 at 12:26 AM, John Hunter <jd...@gm...> wrote:

> On Mon, Feb 22, 2010 at 4:33 PM, John Hunter <jd...@gm...> wrote:
> >  polycol = plt.hexbin(data['jetMomentum'][cut] / 1000,
> > data['deltaR'][cut],gridsize=50, norm=colors.LogNorm())
> >  cb = plt.colorbar(norm=colors.LogNorm())
> >
> > but this appears to be broken:
>
> I committed some changes to support this -- the following now works:
>
>  polycol = plt.hexbin(data['jetMomentum'][cut] / 1000,
> data['deltaR'][cut],gridsize=50, norm=colors.LogNorm())
>
>   cb = plt.colorbar(norm=polycol.norm)
>
> Eric - I was surprised the colorbar does not use the mappable norm by
> default (if passed norm=None).  Instead it uses ::
>
>  norm = colors.Normalize()
>
> is this a feature?
>
> JDH
>

David Goldsmith wrote:
> I've searched and searched the online docs...please help.
>
> DG
>   
If I understand your question correctly you probably need to look at
http://matplotlib.sourceforge.net/api/ticker_api.html#tick-formatting

ax.xaxis.set_major_formatter( xmajorFormatter )
ax.xaxis.set_minor_formatter( xminorFormatter )
 


- Steve

John Hunter wrote:
>
>
> On Mon, Feb 22, 2010 at 1:44 PM, Ben Axelrod <BAx...@co...
> <mailto:BAx...@co...>> wrote:
>
>     I noticed that there are many modules in the current code base
>     that are not listed at:
>     http://matplotlib.sourceforge.net/modindex.html.  I understand
>     that a few are new files and that the documentation for these will
>     be generated during the next release.  But I know that most of
>     these were in the last release so should have had their
>     documentation generated.  Am I missing something?  Can the
>     documentation for these modules be found somewhere else?
>
>
> You're not missing anything in terms of the html/pdf docs.  When we
> converted our documentation build system to sphinx/rest, we had to
> convert our docstrings to rest as well.  We made good headway for a
> while but the progress has stalled.  To add a module to the
> documentation system, you need to

Also, it's worth nothing that the docs from svn head are automatically
compiled and uploaded from svn on each commit:

HTML: http://matplotlib.sourceforge.net/trunk-docs/index.html
PDF: http://matplotlib.sourceforge.net/trunk-docs/Matplotlib.pdf

-Andrew

Hi David,

I found this one::

xticks( arange(5), ('Tom', 'Dick', 'Harry', 'Sally', 'Sue') )

On the page

http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.xticks

If I had that problem I would try to do something like that:

xvalues = linspace(0,100,1000)

xticks(xvalues, ["%.2f" % val for val in xvalues])

# or, with a lambda expression, but in #python they say 
# a list comprehension is better (faster)

xticks(xvalues, map(lambda i : "%.2f" % i, xvalues))

The side effect is, of course, that the tick is not exactly at the position he 
indicates. Maybe you better use "arange()" to get the right values for your 
ticks, just make sure that they cover the interval your xvalues are in.

If you find a better solution, please let me know.

Best regards,
Philipp

I've searched and searched the online docs...please help.

DG


      

John Hunter wrote:
> On Mon, Feb 22, 2010 at 4:33 PM, John Hunter <jd...@gm...> wrote:
>>  polycol = plt.hexbin(data['jetMomentum'][cut] / 1000,
>> data['deltaR'][cut],gridsize=50, norm=colors.LogNorm())
>>  cb = plt.colorbar(norm=colors.LogNorm())
>>
>> but this appears to be broken:
> 
> I committed some changes to support this -- the following now works:
> 
>   polycol = plt.hexbin(data['jetMomentum'][cut] / 1000,
> data['deltaR'][cut],gridsize=50, norm=colors.LogNorm())
> 
>   cb = plt.colorbar(norm=polycol.norm)
> 
> Eric - I was surprised the colorbar does not use the mappable norm by
> default (if passed norm=None).  Instead it uses ::
> 
>   norm = colors.Normalize()
> 
> is this a feature?

Yes.  You are looking at ColorbarBase, which does not have an associated 
mappable.  The derived Colorbar class does grab the cmap and norm from 
the mappable used in the initialization.  Is this somehow not working? 
Did you really need to specify the norm explicitly?

Eric
> 
> JDH