Re: [Matplotlib-users] Where Do I Report MPL Guide Issues?

2010-02-15 Thread Philipp Bender
When I come back tonight I will try to fix the errors for you.

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Re: [Matplotlib-users] Where Do I Report MPL Guide Issues?

2010-02-15 Thread Philipp Bender
If you are interested in contributing to matplotlib check out this link:

http://matplotlib.sourceforge.net/faq/howto_faq.html#contributing-howto

The PDF is not the "original source", it's a product of the sphinx 
documentation system I think so contributing happens in simple plain text 
files. You can send a patch then.

Regards,
Philipp

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[Matplotlib-users] Trouble gridding irregularly spaced data

2010-02-15 Thread T J
Hi,

I'm trying to grid irregularly spaced data, such that the convex hull
of the data is not rectangular.  Specifically, all my data lies in an
equilateral triangle inside the unit circle.  I found:

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

and tried the suggested technique.  For my grid, I made a square of
the min and max of my data.  However, it had problems:

...
  File 
"/home/guest/.local/lib/python2.6/site-packages/matplotlib/delaunay/triangulate.py",
line 125, in _compute_convex_hull
hull.append(edges.pop(hull[-1]))
KeyError: 0


Should I expect matplotlib.mlab.griddata to work with a dataset like
this?  I know that I can use hexbin, but it'd be really nice to see
contours explicitly.

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Re: [Matplotlib-users] half-filled markers, two-colors

2010-02-15 Thread Chloe Lewis
 wrote:

> ...maybe dividing the markers up into 2, 3, or 4 sections would be  
> useful too.
> ...

There's a gallery example doing that in general, making pie-charts out  
of the markers:

http://matplotlib.sourceforge.net/examples/api/scatter_piecharts.html

although I think my demo of it shows off its data-representation better:

# Piechart markers from matplotlib gallery, thanks to Manuel Metz for  
the original example
# CPHLewis, 2010.

import math
import numpy as np
import matplotlib.pyplot as plt

def payoff(x,y):
 return x*y*400

def outcome_xwins(x,y):
 return x/(x+y)

def outcome_ywins(x,y):
 return y/(x+y)

x_cases = [ .25, .5, .75]
y_cases = [ .33, .5, .66]
outcomes = [('x wins', outcome_xwins, 'blue'),
 ('y wins', outcome_ywins, 'green')] #the name,  
calculation, and plotting color for categories of outcome

fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title('Small multiples: pie charts calculated based on (x,y)')
legend_once = True
#At each point in the plot we calculate everything about the outcomes.
for x in x_cases:
 for y in y_cases:
 size = payoff(x,y)
 start_at = 0
 for result in outcomes:
 result_share = result[1](x,y)
 xpt = [0] + np.cos(np.linspace(2*math.pi*start_at,  
2*math.pi*(result_share+start_at), 10)).tolist()
 ypt = [0] + np.sin(np.linspace(2*math.pi*start_at,  
2*math.pi*(result_share+start_at), 10)).tolist()
 xypt = zip(xpt, ypt)
 ax.scatter([x],[y], marker = (xypt, 0), s = size,  
facecolor = result[2], label=result[0])
 start_at = start_at + result_share
 if legend_once: ax.legend() #don't know why this isn't  
picking up the labels.
 legend_once = False
plt.show()






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Re: [Matplotlib-users] half-filled markers, two-colors

2010-02-15 Thread T J
On Mon, Feb 15, 2010 at 5:22 PM, John Hunter  wrote:
> Very nice and thorough work.  I think this should be included, but
> I'll wait to hear from other developers before committing.  Could you
> confirm that the unit tests pass?
>
 import matplotlib
 matplotlib.test()
>

Confirmed on rev 8133:

Ran 124 tests in 341.585s

FAILED (KNOWNFAIL=2, errors=2)

and the errors were something to do with hexbin extents and the figimage method.


> I think the markerangle would also be a useful contribution, though it
> would render some of the markers redundant (eg triangle left, right,
> etc, would all just be triangles with different angles...)
>

That was a concern I had as well, but I suppose > ^ v < (etc) could
just be considered shortcuts to particular angles.  Presumably, we
would not be removing them.  Correct?  Also, is the standard to have
the angle specified in degrees?  So what is more useful:  markerangle
or markerdeg?

The other difference is that when one specifies fillstyle='left', then
it would only apply to the marker at 0 degrees.  Whereas, marker='v',
fillstyle='left', markerangle=0  would correspond to marker='^',
fillstyle='right', markerangle=180   (or something like that).

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Re: [Matplotlib-users] turning off tick labels

2010-02-15 Thread Jan Strube
Hi Jeff,

thanks for your quick reply.
Unfortunately, the line you sent me doesn't have any effect on the plot,
either before or after turning off the tick labels.

Do you have another suggestion?

Cheers,
Jan

On Sun, Feb 14, 2010 at 11:28 PM, Jeffrey Blackburne  wrote:

>
> On Feb 14, 2010, at 5:41 PM, Jan Strube wrote:
>
>  Dear matplotters,
>>
>> I'm trying to follow
>> http://matplotlib.sourceforge.net/examples/pylab_examples/
>> ganged_plots.html
>> as an example how to turn of the ticks in the case of shared x axes.
>> The tick labels are gone, but unfortunately, matplotlib still plots a
>> '1e5' on the axis for which I have turned off the tick labels.
>> Please see the attached file for the problem
>>
>> How can I also switch of the exponent?
>>
>> Thanks,
>>Jan
>>
>
>
> Try this:
>
> ax.xaxis.set_major_formatter(mpl.ticker.ScalarFormatter(useOffset=False))
>
> where 'ax' is the name of the top subplot.
>
> Good luck,
> Jeff
>
>
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Re: [Matplotlib-users] graph suggestion

2010-02-15 Thread Stefaan Lippens
http://www.graphviz.org/ ?

On Sun, Feb 14, 2010 at 5:35 AM, Mag Gam  wrote:

> I manage 300 servers at my university lab. I would like to map out all
> the cron entries into a nice graph but I am not sure what would be
> appropriate. Can someone please suggest what would be ideal?
>
> TIA
>
>
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Re: [Matplotlib-users] half-filled markers, two-colors

2010-02-15 Thread John Hunter
On Mon, Feb 15, 2010 at 5:59 PM, T J  wrote:
> On Sun, Feb 14, 2010 at 2:49 PM, T J  wrote:
>> I ran across:
>>
>>    http://old.nabble.com/half-filled-markers-td24003576.html
>>
>> The name "fillstyle" can give the wrong impression about what is being
>> filled.  For example, see the comment here:
>>
>>   
>> http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg13074.html
>>
>> It's probably too late, but would "markerfillstyle" be a better name for 
>> this?
>>
>> Also, the current implementation fills half of the marker with the
>> markerfacecolor and doesn't fill the marker at all for the other half.
>>  I think a neat (and simple) feature would be for users to specify two
>> colors.  Perhaps 'markerfacecolor2'.   The change to the code is
>> minimal, but the functionality it brings is quite flexible.
>> markerfacecolor2 can default to 'none' to maintain current
>> functionality.
>>
>> Should I file a ticket for this?



>>
>
> I went ahead and implemented this.  The user can now specify
> 'markercoloralt'.  In the process, I finished the "half-marker" code
> for all remaining filled_markers.   The diff is attached, which also
> includes a fix for bug #560720:
>
>    
> https://sourceforge.net/tracker/?func=detail&aid=2952236&group_id=80706&atid=560720
>
> Please comment.  If there are no comments in a few days, I'll file a ticket.
>
> A picture demonstrating this functionality is attached.  Demos for all
> filled markers can be obtained here:
>
>    http://www.filedropper.com/filledmarkers
>
> Note, the diff contains the script used to generate the pictures. More
> generally, I wonder if there should be a 'markerangle' keyword. I can
> probably push through and implement this, but I'd like to hear what
> people think about it.

Very nice and thorough work.  I think this should be included, but
I'll wait to hear from other developers before committing.  Could you
confirm that the unit tests pass?

>>> import matplotlib
>>> matplotlib.test()

I think the markerangle would also be a useful contribution, though it
would render some of the markers redundant (eg triangle left, right,
etc, would all just be triangles with different angles...)

Many thanks,
JDH

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[Matplotlib-users] DateFormatter + Latex issue

2010-02-15 Thread Filipe Pires Alvarenga Fernandes
Hello list,

If I use DateFormatter with latex and lines breaks like this
>>> DateFormatter("\n \n %b") I get an latex error:

http://pastebin.com/m5b186ded

Although, if I do not use the line breaks,
>>> DateFormatter("%b")
The problem disappears.

Below is a script that reproduces what I'm talking about:

#Example:
from pylabimport *
from matplotlib   import rcParams
rcParams['text.usetex'] = True
fig = figure()
ax  = fig.add_subplot(111)
fig.subplots_adjust(bottom=0.2)
t = arange(100,110,.1)
u = sin(t)
v = cos(t)
quiver([t],[[0]*len(t)],u,v)
major  = DayLocator([10,04])
minor  = DayLocator()
majorF = DateFormatter("\n \n %b") # problem
#majorF = DateFormatter("%b") # no problem
minorF = DateFormatter('%d')
ax.xaxis.set_major_locator(major)
ax.xaxis.set_minor_locator(minor)
ax.xaxis.set_major_formatter(majorF)
ax.xaxis.set_minor_formatter(minorF)
gca().xaxis_date()
title(r"$\alpha \beta \gamma \delta$")
show()


I'm using the latest svn version with qt4 as backend.

Thanks, Filipe
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[Matplotlib-users] Pydot graphs in matplotlib?

2010-02-15 Thread Erik Tollerud
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.  I could easily
write out a png or something from pydot and then imshow it, but that
seems very kludgy.  Is there some way to load svg or other vector data
into matplotlib to be shown inside a figure?

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Re: [Matplotlib-users] half-filled markers, two-colors

2010-02-15 Thread PHobson
TJ,

I think this current implementation and adding a marker rotation key word would 
be wonderful. When I get stuck doing GIS work, I end up using split markers 
very often. It's quite useful.

Now's probably not the time, but maybe dividing the markers up into 2, 3, or 4 
sections would be useful too. 
But perhaps at that point it'd be easier to create half and quarter markers and 
then rotate accordingly as the user makes multiple calls to plot. I 
dunno...just thinking aloud.

This is a great contribution. Thanks a lot!
-paul

> -Original Message-
> From: T J [mailto:tjhn...@gmail.com]
> Sent: Monday, February 15, 2010 4:00 PM
> To: Matplotlib Users
> Subject: Re: [Matplotlib-users] half-filled markers, two-colors
> 
> On Sun, Feb 14, 2010 at 2:49 PM, T J  wrote:
> > I ran across:
> >
> >    http://old.nabble.com/half-filled-markers-td24003576.html
> >
> > The name "fillstyle" can give the wrong impression about what is being
> > filled.  For example, see the comment here:
> >
> >   http://www.mail-archive.com/matplotlib-
> us...@lists.sourceforge.net/msg13074.html
> >
> > It's probably too late, but would "markerfillstyle" be a better name
> for this?
> >
> > Also, the current implementation fills half of the marker with the
> > markerfacecolor and doesn't fill the marker at all for the other half.
> >  I think a neat (and simple) feature would be for users to specify two
> > colors.  Perhaps 'markerfacecolor2'.   The change to the code is
> > minimal, but the functionality it brings is quite flexible.
> > markerfacecolor2 can default to 'none' to maintain current
> > functionality.
> >
> > Should I file a ticket for this?
> >
> 
> I went ahead and implemented this.  The user can now specify
> 'markercoloralt'.  In the process, I finished the "half-marker" code
> for all remaining filled_markers.   The diff is attached, which also
> includes a fix for bug #560720:
> 
> 
> https://sourceforge.net/tracker/?func=detail&aid=2952236&group_id=80706&a
> tid=560720
> 
> Please comment.  If there are no comments in a few days, I'll file a
> ticket.
> 
> A picture demonstrating this functionality is attached.  Demos for all
> filled markers can be obtained here:
> 
> http://www.filedropper.com/filledmarkers
> 
> Note, the diff contains the script used to generate the pictures. More
> generally, I wonder if there should be a 'markerangle' keyword. I can
> probably push through and implement this, but I'd like to hear what
> people think about it.

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Re: [Matplotlib-users] Placing a marker at specific places where lines join?

2010-02-15 Thread Eric Firing
Tim Michelsen wrote:
> Hello,
> I have a similar problem to:
>> Suppose I plot a line from (0,0) to (1,1.5) to (2,2). Now I want to mark 
>> (1,1.5) with a green circle. How is that done?
> 

Your problem is not similar to the above; the problem above is solved 
with a simple call to "plot".

> I am performing a curve fit and also showing a distribution in my plot.
> In order to help the reader to evaluate the result I would like to draw 
> certain
> boundaries (vertical and horizontal line).
> While I am aware on how to draw such lines, I would like to know wheather 
> there
> are some functions in matplotlib which help me to retrieve the coordinates
> 
> a) at which two curves intersect
> b) at which a distribution reaches a certain value?
> 

I think this is strictly a computational problem, not a plotting 
problem, so I suggest you post the question to the numpy or scipy lists.

Eric

> Example:
> How do I get the y-axis value which is reached by the green curve in 
> http://matplotlib.sourceforge.net/_images/histogram_demo_extended_021.png
> a x-axis value of in 175?
> 
> I could proably use a solver from numpy like
> http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.solve.html#numpy.linalg.solve
> but if I plot a distribution, the equation of the envelove is unknown at the
> first place.
> 
> I'd appreciate your help or pointers to examples.
> 
> Thanks a lot in advance,
> Timmie
> 
> 
> 
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Re: [Matplotlib-users] save image from array?

2010-02-15 Thread Gary Ruben
Hi Nico,
I'm pretty sure the functionality is buried in there but unfortunately I 
couldn't figure out how to put it into the imsave function, so for now I 
think you have to resort to using PIL to do this.
Gary R.

Nico Schlömer wrote:
> Hi,
> 
> I see that with imsave() it's possible to save an image based on its
> cmap. Is there also functionality in matplotlib to to store a file
> based on RGB(alpha) information?
> 
> Cheers,
> Nico


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[Matplotlib-users] forcing a plot to appear

2010-02-15 Thread Ken Dere
Hi,

I am trying to develop an application that I can run inside the ipython 
shell.  One of my methods creates a plot, asks the user to make a choice 
based on that plot, and then creates another plot that displays the chosen 
set of information.

If the choices are made with a qt or wx dialogue, everything goes fine.  If 
I try to get the choice by asking the user to type the information into the 
shell, neither plot appears until after the choice is made.

I have tried show() and draw() but neither make any difference.

thanks for any help

Ken Dere



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Re: [Matplotlib-users] turning off tick labels

2010-02-15 Thread Jan Strube
Yes, yes!

what he said...
Thanks a lot JJ.

Dear developers, would it make sense to have
setp(axes1.get_xticklabels(), visible=False)
also automatically set
axes1.xaxis.offsetText.set_visible(False)
?

Cheers,
Jan


On Mon, Feb 15, 2010 at 5:10 PM, Jae-Joon Lee  wrote:

> Try
>
> ax1.xaxis.offsetText.set_visible(False)
>
> where ax1 is the upper axes.
>
> Regards,
>
> -JJ
>
>
> On Mon, Feb 15, 2010 at 4:50 AM, Jan Strube  wrote:
> > Hi Jeff,
> > thanks for your quick reply.
> > Unfortunately, the line you sent me doesn't have any effect on the plot,
> > either before or after turning off the tick labels.
> > Do you have another suggestion?
> > Cheers,
> > Jan
> > On Sun, Feb 14, 2010 at 11:28 PM, Jeffrey Blackburne 
> wrote:
> >>
> >> On Feb 14, 2010, at 5:41 PM, Jan Strube wrote:
> >>
> >>> Dear matplotters,
> >>>
> >>> I'm trying to follow
> >>>
> >>>
> http://matplotlib.sourceforge.net/examples/pylab_examples/ganged_plots.html
> >>> as an example how to turn of the ticks in the case of shared x axes.
> >>> The tick labels are gone, but unfortunately, matplotlib still plots a
> >>> '1e5' on the axis for which I have turned off the tick labels.
> >>> Please see the attached file for the problem
> >>>
> >>> How can I also switch of the exponent?
> >>>
> >>> Thanks,
> >>>Jan
> >>
> >>
> >> Try this:
> >>
> >>
> ax.xaxis.set_major_formatter(mpl.ticker.ScalarFormatter(useOffset=False))
> >>
> >> where 'ax' is the name of the top subplot.
> >>
> >> Good luck,
> >> Jeff
> >>
> >
> >
> >
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> >
> >
>
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[Matplotlib-users] agg_buffer_to_array.py

2010-02-15 Thread David Arnold
All,

This error:
The debugged program raised the exception unhandled AttributeError
"'FigureCanvasMac' object has no attribute 'buffer_rgba'"
File: 
/Users/darnold/Documents/temp/Matplotlib/PylabExamples/agg_buffer_to_array.py, 
Line: 16
is raised by the following script on my Macbook.

# agg_buffer_to_array.py
 
import matplotlib
matplotlib.use('macosx')
from pylab import figure, show
import numpy as np

# make an agg figure
fig = figure()
ax = fig.add_subplot(111)
ax.plot([1,2,3])
ax.set_title('a simple figure')
fig.canvas.draw()

# grab rhe pixel buffer and dumpy it into a numpy array
buf = fig.canvas.buffer_rgba(0,0)
l, b, w, h = fig.bbox.bounds
X = np.fromstring(buf, np.uint8)
X.shape = h,w,4

# now display the array X as an Axes in a new figure
fig2 = figure()
ax2 = fig2.add_subplot(111, frameon=False)
ax2.imshow(X)
show()

This is captured from:  
http://matplotlib.sourceforge.net/examples/pylab_examples/agg_buffer_to_array.html

With:

matplotlib.use('Agg')

Nothing happens at all. With --verbose-helpful, yields the following:

$HOME=/Users/darnold
CONFIGDIR=/Users/darnold/.matplotlib
matplotlib data path 
/Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/matplotlib/mpl-data
loaded rc file /Users/darnold/.matplotlib/matplotlibrc
matplotlib version 0.99.1.1
verbose.level helpful
interactive is False
units is False
platform is darwin
Using fontManager instance from /Users/darnold/.matplotlib/fontList.cache
backend agg version v2.2
findfont: Matching 
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
 to Bitstream Vera Sans 
(/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib-0.98.5.2n2-py2.5-macosx-10.3-fat.egg/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
 with score of 0.00
findfont: Matching 
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=large
 to Bitstream Vera Sans 
(/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib-0.98.5.2n2-py2.5-macosx-10.3-fat.egg/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
 with score of 0.00

Both

matplotlib.use('tkagg')

and

matplotlib.use('wxagg')

work as they should.

David.--
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Re: [Matplotlib-users] identification of color bars

2010-02-15 Thread Nico Schlömer
> As far as I can see, it is the other way around, i.e., mappables
> (e.g., images) know about the colorbar they are connected.

Well yeah, that'd be even better. I'll check out the API. -- Hints
would still be appreciated of course.

--Nico

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Re: [Matplotlib-users] Easy come easy go

2010-02-15 Thread Gökhan Sever
On Sun, Feb 14, 2010 at 10:36 PM, David Arnold wrote:

> All,
>
> This example:
> http://matplotlib.sourceforge.net/examples/event_handling/keypress_demo.html
>
> Raises this exception o my Macbook when the key 's' is pressed:
>
> The debugged program raised the exception unhandled TypeError
> "save_figure() takes exactly 1 argument (2 given)"
> File:
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/matplotlib/backend_bases.py,
> Line: 1703
>

I had reported this "s" key-handling issue before at
http://old.nabble.com/Assigning-%22k%22-key-for-xscaling-td27262672.html

(By the way, I and Matthias expanding the key-handling functionality a
little bit further -configuring and deassigning keys etc... Maybe by means
of this e-mail someone can review the patch at that mail and apply to the
trunk)

And yes I am getting a similar error when I hit "s" using Qt4Agg backend on
MPL svn8105

I[1]: plt.plot(range(10))
O[1]: []

I[2]:
---
TypeError Traceback (most recent call last)

/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/backends/backend_qt4.pyc
in keyPressEvent(self, event)
150 def keyPressEvent( self, event ):
151 key = self._get_key( event )
--> 152 FigureCanvasBase.key_press_event( self, key )
153 if DEBUG: print 'key press', key
154

/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/backend_bases.pyc
in key_press_event(self, key, guiEvent)
   1290 s = 'key_press_event'
   1291 event = KeyEvent(s, self, key, self._lastx, self._lasty,
guiEvent=guiEvent)
-> 1292 self.callbacks.process(s, event)
   1293
   1294 def key_release_event(self, key, guiEvent=None):

/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/cbook.pyc in
process(self, s, *args, **kwargs)
167 self._check_signal(s)
168 for func in self.callbacks[s].values():
--> 169 func(*args, **kwargs)
170
171

/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/backend_bases.pyc
in key_press(self, event)
   1890 self.canvas.toolbar.zoom()
   1891 elif event.key == s:
-> 1892 self.canvas.toolbar.save_figure(self.canvas.toolbar)
   1893
   1894 if event.inaxes is None:

TypeError: save_figure() takes exactly 1 argument (2 given)

[gse...@ccn various]$ python sysinfo.py

Platform :
Linux-2.6.31.9-174.fc12.i686.PAE-i686-with-fedora-12-Constantine
Python   : ('CPython', 'tags/r262', '71600')
IPython  : 0.10
NumPy: 1.5.0.dev8038
Matplotlib   : 1.0.svn (python setupegg.py develop newer shows
matplotlib.__version__ correctly :)


Thanks.


>
> David
>
> --
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Re: [Matplotlib-users] identification of color bars

2010-02-15 Thread Jae-Joon Lee
On Mon, Feb 15, 2010 at 12:25 PM, Nico Schlömer
 wrote:
> Well, it's related to the TikZ converter I'm writing. After having
> created the plot, the script is of course totally oblivious to what
> exact commands were used.
> I was thinking that there is still some sort of bond between the color
> bar and its parent plot after their creation, e.g., for when the color
> map of the main plot is changed. -- Is that not the case?

I doubt it.
As far as I can see, it is the other way around, i.e., mappables
(e.g., images) know about the colorbar they are connected. But I hope
some other developers can confirm (or dispute) this.
For this kind of work, you need to understand some of internals of
matplotlib, and I recommend you to go through the matplotlib sources.

Regards,

-JJ

>
>  --Nico
>
>
>
> On Mon, Feb 15, 2010 at 6:16 PM, Jae-Joon Lee  wrote:
>> Is there any reason that you need to find out which axes is a color
>> bar axes from the list of axes? Can you just keep references to
>> colorbars you create?
>>
>> cbar = colorbar()
>> cax = cbar.ax
>>
>> cax is the axes instance of the colobar you just created.
>>
>> Regards,
>>
>> -JJ
>>
>>
>> On Mon, Feb 15, 2010 at 12:04 PM, Nico Schlömer
>>  wrote:
>>> Hi,
>>>
>>> when plotting a color bar with a plot in matplotlib, the color bar
>>> gets treated internally as Axes.
>>>
>>> With two main plots, each of which comes with a color bar, one structurally 
>>> gets
>>>
>>> 
>>>    
>>>    
>>>    
>>>    
>>>
>>> (that is, a Figure has for childres Axes). To find out which one of
>>> those is a color bar, I basically inspect their children an look for
>>> Arrays with shape (256,), which is what color bars look like. That's
>>> ugly of course, but it kind of works(tm). :)
>>>
>>> I'm having problems, though, with associating color bars with the
>>> specific plot. Can I rely on the rule that an Axes -- if it has a
>>> color bar --, is immediately followed by the corresponding (color bar)
>>> Axes environment? Are there any other properties I could check to
>>> identify color bars? (Tried get_label to no avail.)
>>>
>>> Cheers,
>>> Nico
>>>
>>> --
>>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>
>

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Re: [Matplotlib-users] Easy come easy go

2010-02-15 Thread Jae-Joon Lee
I cannot reproduce this error both with 0.99.1 maintenance branch and
the current svn (with GtkAgg backend).
What version of matplotlib and what backend are you using?

http://matplotlib.sourceforge.net/faq/troubleshooting_faq.html

Regards,

-JJ


On Sun, Feb 14, 2010 at 11:36 PM, David Arnold
 wrote:
> All,
>
> This example:  
> http://matplotlib.sourceforge.net/examples/event_handling/keypress_demo.html
>
> Raises this exception o my Macbook when the key 's' is pressed:
>
> The debugged program raised the exception unhandled TypeError
> "save_figure() takes exactly 1 argument (2 given)"
> File: 
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/matplotlib/backend_bases.py,
>  Line: 1703
>
> David
> --
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
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>

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Re: [Matplotlib-users] Arrow question/request

2010-02-15 Thread Jae-Joon Lee
On Mon, Feb 15, 2010 at 2:32 AM, rcnelson  wrote:
> 1) Are there any plans or would it make sense to add another keyword to the
> pyplot.arrow function that allows you to choose the arrow class you would
> like to use? The default could be FancyArrow so that the original usage of
> pyplot.arrow will not be affected. The axes.arrow function - which it looks
> like it gets called by the pyplot.arrow function - could then convert the
> input arguments into the form necessary for the class you choose.
>

I recommend you to use "annotate" (see below). Because most of these
things are already addressed by "annotate", I don't see any immediate
need to enhance "arrow". But maybe it would be a good idea to mention
about "annotate" in the "arrow" documentation and vice versa.

> 2) Or... Is there a simple way that you can call the arrow function with
> start and end points in data coordinates, but have the arrow parameters
> calculated in normalized figure coordinates? I think FancyArrow calculates
> the head and body points using a line perpendicular to the line of the arrow
> in data coordinates, which I think is the source of my problem (? -- at
> least that is what I found doing some test calculations on my own). However,
> if I call the pyplot.arrow function with the following keywords,
> 'trasform=fig.transFigure, figure=fig' (as per the Artist tutorial, see
> below), then the arrow looks okay, but it needs to be positioned in
> normalized figure coordinates and it does not move when you zoom or
> translate the plot.
>

I guess you can just use "annotate" (with empty string) for your
purpose. See the the example below.

http://matplotlib.sourceforge.net/users/annotations_guide.html#annotating-with-arrow

Let me know if it does not fits your need.

Regards,

-JJ

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Re: [Matplotlib-users] identification of color bars

2010-02-15 Thread Nico Schlömer
Well, it's related to the TikZ converter I'm writing. After having
created the plot, the script is of course totally oblivious to what
exact commands were used.
I was thinking that there is still some sort of bond between the color
bar and its parent plot after their creation, e.g., for when the color
map of the main plot is changed. -- Is that not the case?

 --Nico



On Mon, Feb 15, 2010 at 6:16 PM, Jae-Joon Lee  wrote:
> Is there any reason that you need to find out which axes is a color
> bar axes from the list of axes? Can you just keep references to
> colorbars you create?
>
> cbar = colorbar()
> cax = cbar.ax
>
> cax is the axes instance of the colobar you just created.
>
> Regards,
>
> -JJ
>
>
> On Mon, Feb 15, 2010 at 12:04 PM, Nico Schlömer
>  wrote:
>> Hi,
>>
>> when plotting a color bar with a plot in matplotlib, the color bar
>> gets treated internally as Axes.
>>
>> With two main plots, each of which comes with a color bar, one structurally 
>> gets
>>
>> 
>>    
>>    
>>    
>>    
>>
>> (that is, a Figure has for childres Axes). To find out which one of
>> those is a color bar, I basically inspect their children an look for
>> Arrays with shape (256,), which is what color bars look like. That's
>> ugly of course, but it kind of works(tm). :)
>>
>> I'm having problems, though, with associating color bars with the
>> specific plot. Can I rely on the rule that an Axes -- if it has a
>> color bar --, is immediately followed by the corresponding (color bar)
>> Axes environment? Are there any other properties I could check to
>> identify color bars? (Tried get_label to no avail.)
>>
>> Cheers,
>> Nico
>>
>> --
>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
>> http://p.sf.net/sfu/solaris-dev2dev
>> ___
>> Matplotlib-users mailing list
>> Matplotlib-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>

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Re: [Matplotlib-users] identification of color bars

2010-02-15 Thread Jae-Joon Lee
Is there any reason that you need to find out which axes is a color
bar axes from the list of axes? Can you just keep references to
colorbars you create?

cbar = colorbar()
cax = cbar.ax

cax is the axes instance of the colobar you just created.

Regards,

-JJ


On Mon, Feb 15, 2010 at 12:04 PM, Nico Schlömer
 wrote:
> Hi,
>
> when plotting a color bar with a plot in matplotlib, the color bar
> gets treated internally as Axes.
>
> With two main plots, each of which comes with a color bar, one structurally 
> gets
>
> 
>    
>    
>    
>    
>
> (that is, a Figure has for childres Axes). To find out which one of
> those is a color bar, I basically inspect their children an look for
> Arrays with shape (256,), which is what color bars look like. That's
> ugly of course, but it kind of works(tm). :)
>
> I'm having problems, though, with associating color bars with the
> specific plot. Can I rely on the rule that an Axes -- if it has a
> color bar --, is immediately followed by the corresponding (color bar)
> Axes environment? Are there any other properties I could check to
> identify color bars? (Tried get_label to no avail.)
>
> Cheers,
> Nico
>
> --
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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>

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[Matplotlib-users] simple GTK agg animation with patches

2010-02-15 Thread John Jameson
Thought I would post this as a simple GTKagg animation 
with patches (after John Hunter fixed it for me :-):





import pygtk, gobject
import matplotlib
matplotlib.use('GTKAgg')
import numpy as np
import matplotlib.pyplot as plt
import pylab 
from matplotlib.patches import CirclePolygon, Polygon

fig = plt.figure(figsize=(10,6))
ax = fig.add_subplot(111, autoscale_on=False )
canvas = fig.canvas

plt.axis([-1, 7, -0.5, 2.2])

def update_line():
   global x, y
   print update_line.cnt_tot
   if update_line.background is None:
   update_line.background = canvas.copy_from_bbox(ax.bbox)
   canvas.restore_region(update_line.background)

   x_cir = 1.0 + 0.003*update_line.cnt

   if update_line.cir is None:
   cir =  CirclePolygon((x_cir, 1), 0.3, animated=True, \
   resolution=12, lw=2 )
   ax.add_patch(cir)
   update_line.cir = cir
   else:
   update_line.cir._xy = x_cir, 1
   update_line.cir._update_transform()
   ax.draw_artist(update_line.cir)

   canvas.blit(ax.bbox)

   if update_line.direction == 0:
   update_line.cnt += 1
   update_line.cnt_tot += 1 
   if update_line.cnt > 500:
   update_line.direction = 1
   else:
   update_line.cnt -= 1
   update_line.cnt_tot += 1 
   if update_line.cnt < 100:
   update_line.direction = 0

   return update_line.cnt<10


update_line.cnt = 0
update_line.cnt_tot = 0
update_line.direction = 0
update_line.background = None
update_line.cir = None

def start_anim(event):
gobject.idle_add(update_line)
canvas.mpl_disconnect(start_anim.cid)

start_anim.cid = canvas.mpl_connect('draw_event', start_anim)

plt.show()



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[Matplotlib-users] memory leak for GTKAgg animation

2010-02-15 Thread John Jameson
Hi John -
Yes thanks again!  This did it. Plus it is a valuable lesson
 - it never occurred to me to look at the base class to find 
more useful methods.  To make this cleaner I will post the
complete simple working example after this message.
best,
John  

-Original Message-
From: John Hunter [mailto:jdh2...@gmail.com] 
Sent: Sunday, February 14, 2010 7:39 PM
To: John Jameson
Cc: matplotlib-users@lists.sourceforge.net; Michael Droettboom
Subject: Re: [Matplotlib-users] memory leak for GTKAgg animation

On Sat, Feb 13, 2010 at 2:53 PM, John Jameson 
wrote:
> HI,
> I find the very basic animation below has a memory leak (my pagefile usage
> number keeps growing in the Windows XP Windows Task Manager Performance
> graph).I don't see this with the "animation_blit_gtk.py" example on:
>
> http://matplotlib.sourceforge.net/examples/index.html
>
> (which I used as a starting point for this). In "animation_blit_gtk.py"
the
> set_ydata() routine is used to update the line for the animation and this
> does not leak. But if you call plot again with the new y_data (instead of
> using set_ydata), this leaks too. Anyone have an idea on how to stop the
> leak?

This isn't a memory leak.  The problem is that you keep adding new
patches to the axes when you want just one with different data.  Eg,
in your loop, run this code, and you will see that the number of
patches is growing:


   x_cir = 1.0 + 0.003*update_line.cnt
   cir =  CirclePolygon((x_cir, 1), 0.3, animated=True, \
   resolution=12, lw=2 )
   ax.add_patch(cir)
   ax.draw_artist(cir)
   print 'num patches=%d, mem usage=%d'%(
   len(ax.patches), cbook.report_memory(update_line.cnt))
   canvas.blit(ax.bbox)

You should add just one patch and then manipulate the data.  In this
case, you are using a CirclePolygon which derives from RegularPolygon
and so you can update the "xy" property

 
http://matplotlib.sourceforge.net/api/artist_api.html#matplotlib.patches.Reg
ularPolygon

But on testing this it looks like there is a bug in that the set_xy
property setter is ignored.  I worked around this in the func below by
setting the private variable directly, but this looks like a bug we
need to fix (Michael, shouldn't we respect the xy passed in in
patches.RegularPolygon._set_xy ?).  In the meantime, the following
workaround should work for you w/o leaking

def update_line():
   global x, y
   print update_line.cnt
   if update_line.background is None:
   update_line.background = canvas.copy_from_bbox(ax.bbox)
   canvas.restore_region(update_line.background)

   x_cir = 1.0 + 0.003*update_line.cnt

   if update_line.cir is None:
   cir =  CirclePolygon((x_cir, 1), 0.3, animated=True, \
   resolution=12, lw=2 )
   ax.add_patch(cir)
   update_line.cir = cir
   else:
   update_line.cir._xy = x_cir, 1
   update_line.cir._update_transform()
   ax.draw_artist(update_line.cir)
   print 'num patches=%d, xy=%s, mem usage=%d'%(
   len(ax.patches), update_line.cir.xy,
cbook.report_memory(update_line.cnt))
   canvas.blit(ax.bbox)

   if update_line.direction == 0:
   update_line.cnt += 1
   if update_line.cnt > 500:
   update_line.direction = 1
   else:
   update_line.cnt -= 1
   if update_line.cnt < 100:
   update_line.direction = 0

   return update_line.cnt<100


update_line.cnt = 0
update_line.direction = 0
update_line.background = None
update_line.cir = None



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Re: [Matplotlib-users] turning off tick labels

2010-02-15 Thread Jae-Joon Lee
Try

ax1.xaxis.offsetText.set_visible(False)

where ax1 is the upper axes.

Regards,

-JJ


On Mon, Feb 15, 2010 at 4:50 AM, Jan Strube  wrote:
> Hi Jeff,
> thanks for your quick reply.
> Unfortunately, the line you sent me doesn't have any effect on the plot,
> either before or after turning off the tick labels.
> Do you have another suggestion?
> Cheers,
>     Jan
> On Sun, Feb 14, 2010 at 11:28 PM, Jeffrey Blackburne  wrote:
>>
>> On Feb 14, 2010, at 5:41 PM, Jan Strube wrote:
>>
>>> Dear matplotters,
>>>
>>> I'm trying to follow
>>>
>>> http://matplotlib.sourceforge.net/examples/pylab_examples/ganged_plots.html
>>> as an example how to turn of the ticks in the case of shared x axes.
>>> The tick labels are gone, but unfortunately, matplotlib still plots a
>>> '1e5' on the axis for which I have turned off the tick labels.
>>> Please see the attached file for the problem
>>>
>>> How can I also switch of the exponent?
>>>
>>> Thanks,
>>>    Jan
>>
>>
>> Try this:
>>
>> ax.xaxis.set_major_formatter(mpl.ticker.ScalarFormatter(useOffset=False))
>>
>> where 'ax' is the name of the top subplot.
>>
>> Good luck,
>> Jeff
>>
>
>
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>

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[Matplotlib-users] identification of color bars

2010-02-15 Thread Nico Schlömer
Hi,

when plotting a color bar with a plot in matplotlib, the color bar
gets treated internally as Axes.

With two main plots, each of which comes with a color bar, one structurally gets







(that is, a Figure has for childres Axes). To find out which one of
those is a color bar, I basically inspect their children an look for
Arrays with shape (256,), which is what color bars look like. That's
ugly of course, but it kind of works(tm). :)

I'm having problems, though, with associating color bars with the
specific plot. Can I rely on the rule that an Axes -- if it has a
color bar --, is immediately followed by the corresponding (color bar)
Axes environment? Are there any other properties I could check to
identify color bars? (Tried get_label to no avail.)

Cheers,
Nico

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[Matplotlib-users] tabbed figure browsing..

2010-02-15 Thread Nick Schurch
I have a script that calls several subroutines which each draw a
figure (TkAgg backend). When I call show() at the end of the script
all the figures pop up no problem, but when your producing 20+ figures
its a bit overwhelming! It'd be great if I could have just one plot
window with each figure as a tab in that window - is this possible
from matplotlib?

-- 
Cheers,

Nick Schurch

Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK

Tel: +44 1382 388707
Fax: +44 1382 345 893

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Re: [Matplotlib-users] turning off tick labels

2010-02-15 Thread Jeffrey Blackburne
Can you send a minimal working example that shows the problem?

On Feb 15, 2010, at 4:50 AM, Jan Strube wrote:

> Hi Jeff,
>
> thanks for your quick reply.
> Unfortunately, the line you sent me doesn't have any effect on the  
> plot, either before or after turning off the tick labels.
>
> Do you have another suggestion?
>
> Cheers,
> Jan
>
> On Sun, Feb 14, 2010 at 11:28 PM, Jeffrey Blackburne  
>  wrote:
>
> On Feb 14, 2010, at 5:41 PM, Jan Strube wrote:
>
> Dear matplotters,
>
> I'm trying to follow
> http://matplotlib.sourceforge.net/examples/pylab_examples/ 
> ganged_plots.html
> as an example how to turn of the ticks in the case of shared x axes.
> The tick labels are gone, but unfortunately, matplotlib still plots  
> a '1e5' on the axis for which I have turned off the tick labels.
> Please see the attached file for the problem
>
> How can I also switch of the exponent?
>
> Thanks,
>Jan
>
>
> Try this:
>
> ax.xaxis.set_major_formatter(mpl.ticker.ScalarFormatter 
> (useOffset=False))
>
> where 'ax' is the name of the top subplot.
>
> Good luck,
> Jeff
>
>
> -- 
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Re: [Matplotlib-users] Import bug for numpy >= 2.0

2010-02-15 Thread Robert Kern
On 2010-02-14 11:23 AM, Charles R Harris wrote:
> Lines 147-151 of __init__ need to be changed to
>
> import numpy
> nn = numpy.__version__.split('.')
> if not (int(nn[0]) > 1 or int(nn[0]) == 1 and int(nn[1]) >= 1):
>  raise ImportError(
> 'numpy 1.1 or later is required; you have %s' % numpy.__version__)

It's been noted and fixed in SVN.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth."
   -- Umberto Eco


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Re: [Matplotlib-users] Placing a marker at specific places where lines join?

2010-02-15 Thread Wayne Watson
Hi, Phillip. don't know why the mail would be returned. The address I 
see above is correct. sierra_mtni...@sbcglobal.net. The only thing I can 
think of is that yahoo mail wanted you to allow you to ask for 
permission. Beats me.

Frankly, I've never really liked the reply format of mail lists. I use 
Thunderbird on Win. Sometimes I see messages in my inbox from someone 
and wonder are they trying for a private comm or just sending me a 
courtesy msg so that I should follow up on the list.  Then there's Reply 
vs Reply All, and some filter  problems. The latter can produce what I 
call the boomerang effect. Mail intended for me goes right into the list 
folder. There are goblins out there. :-)

To me all this can be solved by one word, Forum. Not a mail list. Aside 
from the possible cost (to the Python Org?), comm is much clearer on 
them.  Perhaps one disadvantage is that some people apparently have some 
bizarre form of e-mail that is not suitable for them.   Otherwise, I 
have no idea why they are not more often used.

html not allowed? The rules just vary too much to follow this. Same with 
bottom vs top posting in NGs. My view, and I'm not trying to be 
unfriendly here, is if one doesn't like what they see,  ignore it, and 
don't respond.

+NG. Expect the unexpected. The warriors and self appointed moderators 
hang out there. Some are just begging for a fight.
+e-mail. If you aren't communicating with your friends, misunderstanding 
often prevail.
+Forums: Almost bliss. I must belong to 30 of them.

I must say that I am really puzzled by your comments about a footnote. I 
really don't use them much. I've probably posted thousands of msgs to 
NGs, forums, mail lists and I've never heard word one about footnotes. I 
use them as I see fit, and that's not very often. In fact, I like your 
use of the footnote below.

I'm not even going to touch etiquette. I'd be really impressed if anyone 
follows them. I'll just say this. Internet communication by any of the 
methods above is sometimes just plain weird. It takes patience to use 
these methods. That includes personal e-mail. Someone should write a 
book about it. Preferably a shrink of psychologist. IMHO, the internet 
is generally meant for easy and informal communications, and not studied 
carefully written posts. That doesn't mean some care isn't needed. I see 
matters as a running dialogs. Both  parties need to ask questions about 
clarity. Too much is often assumed.Maybe I'll write about it. Let's not 
hold  our breaths.

Hey, no footnotes used above. VBG

Cheers.


On 2/14/2010 1:39 PM, Philipp Bender wrote:
> Hi Wayne,
>
> (I wanted to answer you directly but the mail came back, don't know why)
> I have several points that
> you really should work on if you expect anyone to answer to your mails in
> future. First, you should check the destination of your messages. I got at
> least three of your messages addressed only for me, you obviously wanted to
> send them to the list but they only reached me. So I didn't answer because the
> mailing list should be an open and searchable discussion platform and I didn't
> want to forward your message to the list or something like that. Please check
> that carefully in future.
>
> The next thing is that everyone must have the feeling that you completely
> ignore replies. This link here should have been an alert for you:
>
> http://www.freebsd.org/doc/en/articles/mailing-list-faq/etiquette.html
>
> This was posted as reply to one of your mails. One thing explained there is to
> not
> cite the original mail after the own reply, instead you should cite the
> original issue at the beginning or in parts directly before the parts of the
> answer. See below:
>
>
>>> How to do foo bar?
>>>
> Just like that.
>
> You see? The same thing about your footnotes*.
>
> Another thing is the HTML I received from your adress two times -- HTML has
> neither benefit nor a good reputation in mailing lists. I delete HTML mails
> without reading it in most cases.
>
> And, but that's maybe more a personal thing, I find it very unfriendly to ask
> in the subject and write in the body something like "(see subject)" -- we take
> the time to read your message, in respect to that you also should take the
> time to ask a complete question.
>
> Please don't misunderstand this message -- I don't want to blame you, I want
> to help you and make sure that you get answers to your questions in future.
>
> Regards,
> Philipp
>
> * like this one here. They don't help you, they don't explain anything, they
> don't help me reading the message, they have absolutely no benefit.
>
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Re: [Matplotlib-users] 16bit tiff support?

2010-02-15 Thread Philipp Lies
Jeff Whitaker wrote:
> Philipp Lies wrote:
>> On 02/12/2010 07:49 PM, Eric Firing wrote:
>>  
>>> Philipp Lies wrote:
>>>
 Hi,

 is there a backend that supports 16bit tiff images?
   
> 
> The macosx backend supports tiff.
Thanks, but I need a linux backend :-/


>>> Can you just use png, and use the netpbm utilities or ImageMagick
>>> convert program to go to and from tiff?
>>> 
>> Would be 'dirty' but acceptable if matplotlib would support saving
>> uncompressed grayscale uint16 png files. But saving  nxm uint16 arrays
>> leads to nxmx3 float arrays which do not even closely resemble my
>> original data.
>> Example:
>> A
>> array([[47705, 11865,   739, 16941, 37700],
>> [64321, 26860, 49945, 63556, 13498],
>> [ 2676,  7720,  5995, 22399, 32735],
>> [56577, 34443,  6636, 23409, 61331],
>> [ 1020, 26013, 34677, 37262, 36136]], dtype=uint16)
>> imsave('t.png',A)
>> B = imread('t.png')
>> B[:,:,0]
>>
>> array([[ 1.,  0.,  0.,  0.,  0.74117649],
>> [ 0.49803922,  0.19607843,  1.,  0.5529412 ,  0. ],
>> [ 0.,  0.,  0.,  0.,  0.48627451],
>> [ 1.,  0.57647061,  0.,  0.01960784,  0.71372551],
>> [ 0.,  0.14509805,  0.58823532,  0.72941178,  0.6669]],
>> dtype=float32)
>>
>>
>>  
 According to the website GDK supports tiff but that's wrong:

  
>>> import matplotlib
>>> matplotlib.use('GDK')
>>> import matplotlib.pyplot as pyplot
>>> pyplot.imsave(arr=X, fname='test.tif')
>>> 
 Traceback (most recent call last):
 File "", line 1, in 
 File "/usr/lib/pymodules/python2.6/matplotlib/pyplot.py", line 1425,
 in imsave
 return _imsave(*args, **kwargs)
 File "/usr/lib/pymodules/python2.6/matplotlib/image.py", line 813, in
 imsave
 fig.savefig(fname, dpi=1, format=format)
 File "/usr/lib/pymodules/python2.6/matplotlib/figure.py", line 1033,
 in savefig
 self.canvas.print_figure(*args, **kwargs)
 File "/usr/lib/pymodules/python2.6/matplotlib/backend_bases.py", line
 1420, in print_figure
 '%s.' % (format, ', '.join(formats)))
 ValueError: Format "tif" is not supported.
 Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz.
  
>>> matplotlib.backends.backend
>>> 
 'gdk'

 matplotlib 0.99.0 python 2.6.4 ubuntu karmic x64

 If matplotlib cannot provide tiff support, does someone know an
 alternative? PIL doesn't work either, at least not intuitively.

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Re: [Matplotlib-users] 16bit tiff support?

2010-02-15 Thread Jeff Whitaker
Philipp Lies wrote:
> On 02/12/2010 07:49 PM, Eric Firing wrote:
>   
>> Philipp Lies wrote:
>> 
>>> Hi,
>>>
>>> is there a backend that supports 16bit tiff images?
>>>   

The macosx backend supports tiff.

-Jeff
>> Can you just use png, and use the netpbm utilities or ImageMagick
>> convert program to go to and from tiff?
>> 
> Would be 'dirty' but acceptable if matplotlib would support saving 
> uncompressed grayscale uint16 png files. But saving  nxm uint16 arrays 
> leads to nxmx3 float arrays which do not even closely resemble my 
> original data.
> Example:
> A
> array([[47705, 11865,   739, 16941, 37700],
> [64321, 26860, 49945, 63556, 13498],
> [ 2676,  7720,  5995, 22399, 32735],
> [56577, 34443,  6636, 23409, 61331],
> [ 1020, 26013, 34677, 37262, 36136]], dtype=uint16)
> imsave('t.png',A)
> B = imread('t.png')
> B[:,:,0]
>
> array([[ 1.,  0.,  0.,  0.,  0.74117649],
> [ 0.49803922,  0.19607843,  1.,  0.5529412 ,  0. ],
> [ 0.,  0.,  0.,  0.,  0.48627451],
> [ 1.,  0.57647061,  0.,  0.01960784,  0.71372551],
> [ 0.,  0.14509805,  0.58823532,  0.72941178,  0.6669]], 
> dtype=float32)
>
>
>   
>>> According to the website GDK supports tiff but that's wrong:
>>>
>>>   
>> import matplotlib
>> matplotlib.use('GDK')
>> import matplotlib.pyplot as pyplot
>> pyplot.imsave(arr=X, fname='test.tif')
>> 
>>> Traceback (most recent call last):
>>> File "", line 1, in 
>>> File "/usr/lib/pymodules/python2.6/matplotlib/pyplot.py", line 1425,
>>> in imsave
>>> return _imsave(*args, **kwargs)
>>> File "/usr/lib/pymodules/python2.6/matplotlib/image.py", line 813, in
>>> imsave
>>> fig.savefig(fname, dpi=1, format=format)
>>> File "/usr/lib/pymodules/python2.6/matplotlib/figure.py", line 1033,
>>> in savefig
>>> self.canvas.print_figure(*args, **kwargs)
>>> File "/usr/lib/pymodules/python2.6/matplotlib/backend_bases.py", line
>>> 1420, in print_figure
>>> '%s.' % (format, ', '.join(formats)))
>>> ValueError: Format "tif" is not supported.
>>> Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz.
>>>   
>> matplotlib.backends.backend
>> 
>>> 'gdk'
>>>
>>> matplotlib 0.99.0 python 2.6.4 ubuntu karmic x64
>>>
>>> If matplotlib cannot provide tiff support, does someone know an
>>> alternative? PIL doesn't work either, at least not intuitively.
>>>
>>> Cheers
>>>
>>> Philipp
>>>
>>>   
>
>   


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[Matplotlib-users] Looking for a Compiled Demo of MPL Graphics

2010-02-15 Thread Wayne Watson
Does anyone know where I can find a compiled demo that uses MPL grphics? 
I'd like, if possible, a Win version whose size is less than 10M, so 
that I can send it via e-mail, if necessary. It should use plot, so that 
someone can manipulate the plot with the navigation controls. At this 
point, I have no idea if that method is the fundamental graph tool or 
not. I suspect it is.

If a mailable demo isn't available, maybe there's a web site that one 
can download such examples from?
-- 
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news." -- Steven Pinker (and other sources) Why is this true, but yet 
the media says otherwise? The media knows very well how to manipulate us 
(see limbic, emotion, $$). -- WTW

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Re: [Matplotlib-users] Placing a marker at specific places where lines join?

2010-02-15 Thread Tim Michelsen
Hello,
I have a similar problem to:
> Suppose I plot a line from (0,0) to (1,1.5) to (2,2). Now I want to mark 
> (1,1.5) with a green circle. How is that done?

I am performing a curve fit and also showing a distribution in my plot.
In order to help the reader to evaluate the result I would like to draw certain
boundaries (vertical and horizontal line).
While I am aware on how to draw such lines, I would like to know wheather there
are some functions in matplotlib which help me to retrieve the coordinates

a) at which two curves intersect
b) at which a distribution reaches a certain value?

Example:
How do I get the y-axis value which is reached by the green curve in 
http://matplotlib.sourceforge.net/_images/histogram_demo_extended_021.png
a x-axis value of in 175?

I could proably use a solver from numpy like
http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.solve.html#numpy.linalg.solve
but if I plot a distribution, the equation of the envelove is unknown at the
first place.

I'd appreciate your help or pointers to examples.

Thanks a lot in advance,
Timmie



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Re: [Matplotlib-users] Enter Figure on Macs

2010-02-15 Thread Michiel de Hoon
I almost have a solution for this for the Mac OS X backend. I am stuck though 
at what I should pass to enter_notify_event and leave_notify_event for the 
guiEvent:

def leave_notify_event(self, guiEvent=None):
"""
Backend derived classes should call this function when leaving
canvas

*guiEvent*
the native UI event that generated the mpl event

"""

What are the requirements for guiEvent? If I call leave_notify_event without 
guiEvent, so guiEvent = None, then the example gives me the following error:

enter_figure Figure(640x480)
leave_figure
Traceback (most recent call last):
  File 
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/backend_bases.py",
 line 1416, in leave_notify_event
self.callbacks.process('figure_leave_event', LocationEvent.lastevent)
  File 
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/cbook.py",
 line 169, in process
func(*args, **kwargs)
  File "test.py", line 23, in leave_figure
print 'leave_figure', event.canvas.figure
AttributeError: 'NoneType' object has no attribute 'canvas'


So I guess I should pass some type of event object to enter|leave_notify_event.

--Michiel.

--- On Sun, 2/14/10, David Arnold  wrote:

> From: David Arnold 
> Subject: Re: [Matplotlib-users] Enter Figure on Macs
> To: "John Hunter" 
> Cc: "Michiel de Hoon" , 
> matplotlib-users@lists.sourceforge.net
> Date: Sunday, February 14, 2010, 11:50 PM
> John,
> 
> Only the wxagg worked. Here is the output:
> 
> $HOME=/Users/darnold
> CONFIGDIR=/Users/darnold/.matplotlib
> matplotlib data path
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/matplotlib/mpl-data
> loaded rc file /Users/darnold/.matplotlib/matplotlibrc
> matplotlib version 0.99.1.1
> verbose.level helpful
> interactive is False
> units is False
> platform is darwin
> Using fontManager instance from
> /Users/darnold/.matplotlib/fontList.cache
> backend WXAgg version 2.8.10.1
> findfont: Matching
> :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
> to Bitstream Vera Sans
> (/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib-0.98.5.2n2-py2.5-macosx-10.3-fat.egg/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
> with score of 0.00
> findfont: Matching
> :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
> to Bitstream Vera Sans
> (/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib-0.98.5.2n2-py2.5-macosx-10.3-fat.egg/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
> with score of 0.00
> enter_figure Figure(640x480)
> leave_figure Figure(640x480)
> enter_figure Figure(640x480)
> leave_figure Figure(640x480)
> enter_figure Figure(640x480)
> leave_figure Figure(640x480)
> enter_figure Figure(640x480)
> enter_axes Axes(0.125,0.536364;0.775x0.363636)
> leave_axes Axes(0.125,0.536364;0.775x0.363636)
> enter_axes Axes(0.125,0.1;0.775x0.363636)
> leave_axes Axes(0.125,0.1;0.775x0.363636)
> leave_figure Figure(640x480)
> 
> 
> Did not work with macosx:
> 
> $HOME=/Users/darnold
> CONFIGDIR=/Users/darnold/.matplotlib
> matplotlib data path
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/matplotlib/mpl-data
> loaded rc file /Users/darnold/.matplotlib/matplotlibrc
> matplotlib version 0.99.1.1
> verbose.level helpful
> interactive is False
> units is False
> platform is darwin
> Using fontManager instance from
> /Users/darnold/.matplotlib/fontList.cache
> backend MacOSX version unknown
> enter_axes Axes(0.125,0.536364;0.775x0.363636)
> leave_axes Axes(0.125,0.536364;0.775x0.363636)
> enter_axes Axes(0.125,0.1;0.775x0.363636)
> leave_axes Axes(0.125,0.1;0.775x0.363636)
> enter_axes Axes(0.125,0.1;0.775x0.363636)
> leave_axes Axes(0.125,0.1;0.775x0.363636)
> enter_axes Axes(0.125,0.536364;0.775x0.363636)
> leave_axes Axes(0.125,0.536364;0.775x0.363636)
> enter_axes Axes(0.125,0.1;0.775x0.363636)
> leave_axes Axes(0.125,0.1;0.775x0.363636)
> 
> 
> Did not work with tkagg:
> 
> $HOME=/Users/darnold
> CONFIGDIR=/Users/darnold/.matplotlib
> matplotlib data path
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/matplotlib/mpl-data
> loaded rc file /Users/darnold/.matplotlib/matplotlibrc
> matplotlib version 0.99.1.1
> verbose.level helpful
> interactive is False
> units is False
> platform is darwin
> Using fontManager instance from
> /Users/darnold/.matplotlib/fontList.cache
> backend TkAgg version 8.4
> findfont: Matching
> :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
> to Bitstream Vera Sans
> (/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/matplotlib-0.98.5.2n2-py2.5-macosx-10.3-fat.egg/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
> with score of 0.00
> findfont: Matching
> :family=sans-serif:style=normal

Re: [Matplotlib-users] 16bit tiff support?

2010-02-15 Thread Philipp Lies
On 02/12/2010 07:49 PM, Eric Firing wrote:
> Philipp Lies wrote:
>> Hi,
>>
>> is there a backend that supports 16bit tiff images?
>
> Can you just use png, and use the netpbm utilities or ImageMagick
> convert program to go to and from tiff?
Would be 'dirty' but acceptable if matplotlib would support saving 
uncompressed grayscale uint16 png files. But saving  nxm uint16 arrays 
leads to nxmx3 float arrays which do not even closely resemble my 
original data.
Example:
A
array([[47705, 11865,   739, 16941, 37700],
[64321, 26860, 49945, 63556, 13498],
[ 2676,  7720,  5995, 22399, 32735],
[56577, 34443,  6636, 23409, 61331],
[ 1020, 26013, 34677, 37262, 36136]], dtype=uint16)
imsave('t.png',A)
B = imread('t.png')
B[:,:,0]

array([[ 1.,  0.,  0.,  0.,  0.74117649],
[ 0.49803922,  0.19607843,  1.,  0.5529412 ,  0. ],
[ 0.,  0.,  0.,  0.,  0.48627451],
[ 1.,  0.57647061,  0.,  0.01960784,  0.71372551],
[ 0.,  0.14509805,  0.58823532,  0.72941178,  0.6669]], 
dtype=float32)


>> According to the website GDK supports tiff but that's wrong:
>>
>> >>>import matplotlib
>> >>>matplotlib.use('GDK')
>> >>>import matplotlib.pyplot as pyplot
>> >>>pyplot.imsave(arr=X, fname='test.tif')
>> Traceback (most recent call last):
>> File "", line 1, in 
>> File "/usr/lib/pymodules/python2.6/matplotlib/pyplot.py", line 1425,
>> in imsave
>> return _imsave(*args, **kwargs)
>> File "/usr/lib/pymodules/python2.6/matplotlib/image.py", line 813, in
>> imsave
>> fig.savefig(fname, dpi=1, format=format)
>> File "/usr/lib/pymodules/python2.6/matplotlib/figure.py", line 1033,
>> in savefig
>> self.canvas.print_figure(*args, **kwargs)
>> File "/usr/lib/pymodules/python2.6/matplotlib/backend_bases.py", line
>> 1420, in print_figure
>> '%s.' % (format, ', '.join(formats)))
>> ValueError: Format "tif" is not supported.
>> Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz.
>> >>>matplotlib.backends.backend
>> 'gdk'
>>
>> matplotlib 0.99.0 python 2.6.4 ubuntu karmic x64
>>
>> If matplotlib cannot provide tiff support, does someone know an
>> alternative? PIL doesn't work either, at least not intuitively.
>>
>> Cheers
>>
>> Philipp
>>
>

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Max Planck Institute for Biological Cybernetics
Computational Vision & Neuroscience Group
Spemannstr. 41
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Germany

Phone:  +49-7071-601-1788
Fax:+49-7071-601-552
E-Mail: philipp.l...@tuebingen.mpg.de
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Re: [Matplotlib-users] Enter Figure on Macs

2010-02-15 Thread John Hunter
On Mon, Feb 15, 2010 at 6:50 AM, Michiel de Hoon  wrote:
> I almost have a solution for this for the Mac OS X backend. I am stuck though 
> at what I should pass to enter_notify_event and leave_notify_event for the 
> guiEvent:
>
>    def leave_notify_event(self, guiEvent=None):
>        """
>        Backend derived classes should call this function when leaving
>        canvas
>
>        *guiEvent*
>            the native UI event that generated the mpl event
>
>        """
>
> What are the requirements for guiEvent? If I call leave_notify_event without 
> guiEvent, so guiEvent = None, then the example gives me the following error:

we don't make any assumptions about what kind of object the gui event
is.  We provide the GUI event because sometimes when using a specific
backend, the user wants to drill into the GUI native event (eg a
button press event) but we don't use it anywhere in the mpl frontend
because this would break the abstraction.  So if you have some event
that is being fired at the UI level on figure enter, pass that in.

It looks like you may be having a problem because the
leave_notify_event is getting called more than once, or is called for
a figure that has not been entered.  Check the logic in
backend_bases.FigureCanvasBase.leave_notify_event


def leave_notify_event(self, guiEvent=None):
"""
Backend derived classes should call this function when leaving
canvas

*guiEvent*
the native UI event that generated the mpl event

"""
self.callbacks.process('figure_leave_event', LocationEvent.lastevent)
LocationEvent.lastevent = None


It looks like your figure_leave_event is being triggered with
LocationEvent.lastevent = None (so it is not a problem with your
guiEvent).  This could happen if a leave event was processed *before*
and enter event (which sets the lastevent), or if a leave event was
processed twice.

Hopefully this will help you drill down into the source of the problem

JDH

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Re: [Matplotlib-users] tick labels in colorbar?

2010-02-15 Thread Nico Schlömer
> cb.ax.set_yticklabels((r'$-\pi$', '0', r'$\pi$'))

Works like a charm. Thanks!

--Nico

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Re: [Matplotlib-users] tick labels in colorbar?

2010-02-15 Thread Matthias Michler
On Monday 15 February 2010 09:28:10 Nico Schlömer wrote:
> Hi,
> thanks for the suggestion.
>
> > ax.set_xticks((-pi,pi))
> > ax.set_xticklabels(('$-\pi$','$\pi$'))
>
> I guess color bars are a little special in the sense that
>
>AttributeError: Colorbar instance has no attribute 'set_yticklabels'
>
> The tick positions are given not by set_yticks either, but as an option
>
>pylab.colorbar(ticks=(-pi,0,pi))
>
> at the instatiation of the bar. It would indeed be very handy if the
> bars acted like axes.

Hi Nico,

nontheless you can use the axes-method to display your preferred labels. The 
colorbar has its axes as attribute 'ax' (see also my small example below):

cb.ax.set_yticklabels((r'$-\pi$', '0', r'$\pi$'))

Kind regards,
Matthias

---
import matplotlib as mpl
mpl.rc('text', usetex=True)
import matplotlib.pyplot as plt
import numpy as np

ax = plt.axes()
plt.imshow(np.reshape(np.pi*np.arange(-2, 3, 0.5), (2, 5)))
cb = plt.colorbar()
cb.set_ticks((-np.pi, 0.0, np.pi))
cb.ax.set_yticklabels((r'$-\pi$', '0', r'$\pi$'))

plt.show()

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Re: [Matplotlib-users] How to draw a rectangle using event handler ?

2010-02-15 Thread Matthias Michler
Hi Yagua,

On Friday 12 February 2010 17:04:27 Yagua Rovi wrote:
> Hello world!
> I am displaying on my screen a set of data corresponding to points
> defined by a longitude and latitude.
> The display is fine with the command imshow (mydata ,...)
>
> I would like now associate to the application  a callback that draw a
> rectangle on two consecutive left mouse's button press defined by its two
> opposite vertices.
> (also returns points) and a right click button that erases the rectangle.

Why don't you want for select the rectangle using the rectangle selector?
I attached an example (modified version of example 'rectangle_selector.py') 
showing its usage. You can delete lines using the key 'd' or 'D'.

Furthermore I attached a script, which uses button_press_event s as you 
proposed above.

I hope at least one of the examples helps you.

Kind regards,
Matthias


draw_rectangle_using_button_press_events.py
Description: application/python


draw_rectangle_using_rectangle_selector.py
Description: application/python
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[Matplotlib-users] save image from array?

2010-02-15 Thread Nico Schlömer
Hi,

I see that with imsave() it's possible to save an image based on its
cmap. Is there also functionality in matplotlib to to store a file
based on RGB(alpha) information?

Cheers,
Nico

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Re: [Matplotlib-users] turning off tick labels

2010-02-15 Thread Jan Strube
Hi Jeff,

thanks for your quick reply.
Unfortunately, the line you sent me doesn't have any effect on the plot,
either before or after turning off the tick labels.

Do you have another suggestion?

Cheers,
Jan

On Sun, Feb 14, 2010 at 11:28 PM, Jeffrey Blackburne  wrote:

>
> On Feb 14, 2010, at 5:41 PM, Jan Strube wrote:
>
>  Dear matplotters,
>>
>> I'm trying to follow
>> http://matplotlib.sourceforge.net/examples/pylab_examples/
>> ganged_plots.html
>> as an example how to turn of the ticks in the case of shared x axes.
>> The tick labels are gone, but unfortunately, matplotlib still plots a
>> '1e5' on the axis for which I have turned off the tick labels.
>> Please see the attached file for the problem
>>
>> How can I also switch of the exponent?
>>
>> Thanks,
>>Jan
>>
>
>
> Try this:
>
> ax.xaxis.set_major_formatter(mpl.ticker.ScalarFormatter(useOffset=False))
>
> where 'ax' is the name of the top subplot.
>
> Good luck,
> Jeff
>
>
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Re: [Matplotlib-users] tick labels in colorbar?

2010-02-15 Thread Nico Schlömer
Hi,
thanks for the suggestion.

> ax.set_xticks((-pi,pi))
> ax.set_xticklabels(('$-\pi$','$\pi$'))

I guess color bars are a little special in the sense that

   AttributeError: Colorbar instance has no attribute 'set_yticklabels'

The tick positions are given not by set_yticks either, but as an option

   pylab.colorbar(ticks=(-pi,0,pi))

at the instatiation of the bar. It would indeed be very handy if the
bars acted like axes.

Cheers,
Nico

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