matplotlib-users Mailing List for matplotlib (Page 11)

On Tue, Jun 9, 2009 at 12:46 PM, Esmail <eb...@ho...> wrote:

> Sebastian Busch wrote:
> >
> >
> > Hey Esmail,
> >
> > there was the possibility for 3D plots in matplotlib:
> > http://www.scipy.org/Cookbook/Matplotlib/mplot3D
> >
> > however, the mayavi "mlab" interface was designed explicitly to be as
> > simple as pylab.
> >
> http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/mlab.html
> >
> > have fun 3D plotting,
> > sebastian.
>
> I'll give mayavi/mlab a try, I think there was a note to the
> effect that matplotlib quit supporting 3D plots and recommended
> mayavi.
>


There is still work going on to improve matplotlib 3d plotting
functionality. You can see matplotlib gallery or check-out the latest trunk
of matplotlib and experiment with the 3d examples.


>
> So much to learn, so little time :-)


Isn't that nice? Lifelong learning? Why are complaining? Are you not a
scientist or raising a kid something :)


>
>
> Thanks,
> Esmail
>
>

Sebastian Busch wrote:
>
> 
> Hey Esmail,
> 
> there was the possibility for 3D plots in matplotlib:
> http://www.scipy.org/Cookbook/Matplotlib/mplot3D
> 
> however, the mayavi "mlab" interface was designed explicitly to be as
> simple as pylab.
> http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/mlab.html
> 
> have fun 3D plotting,
> sebastian.

I'll give mayavi/mlab a try, I think there was a note to the
effect that matplotlib quit supporting 3D plots and recommended
mayavi.

So much to learn, so little time :-)

Thanks,
Esmail

Hi all,

I am looking for an autocrop function.

It should remove borders from an image.
Is it available in matplotlib ?

Any pointer would be appreciated.

Thanks in advance

                                                Nils


  

>
>> I am curious though why you prefer to alter the default color cycle
>> rather than just passing the color in to the plot command
[...]
>  I got tired of the extra code involved with this method and went  
> looking for a way to change the defaults.

I do something similar to enforce style/substance separation; the  
plotting is the simplest possible line at the end of the data  
analysis, and all the stylistic choices are somewhere else. Makes it  
easy to keep all plot styles consistent during a project, and makes it  
slightly harder to futz with font prettiness when I should be doing  
real work.

Chloe Lewis
Graduate student, Amundson Lab
Division of Ecosystem Sciences, ESPM
University of California, Berkeley
137 Mulford Hall - #3114
Berkeley, CA  94720-3114
ch...@na...

On Tue, Jun 9, 2009 at 10:22 AM, Hani Nakhoul<na...@gm...> wrote:
> Dear all,
> I'm running matplotlib 0.98.5.2 on a machine with Ubuntu Intrepid 8.10. It's
> worked well for me so far, but I encounter problems running matplotlib when
> trying to update the PYTHONPATH in the .bashrc file. Adding just the line
> "export PYTHONPATH=$PYTHONPATH", for example, gives the following:
>
> $ ipython -pylab
> Traceback (most recent call last):
>   File "/usr/bin/ipython", line 27, in <module>
>     IPython.Shell.start().mainloop()
>   File "/var/lib/python-support/python2.5/IPython/Shell.py", line 1219, in
> start
>     shell = _select_shell(sys.argv)
>   File "/var/lib/python-support/python2.5/IPython/Shell.py", line 1188, in
> _select_shell
>     backend = matplotlib.rcParams['backend']
> AttributeError: 'module' object has no attribute 'rcParams'

Most likely you are adding a directory to the path that has a
directory named matplotlib in it (eg the matplotlib src directory)
which is not the matplotlib install directory.  Try doing

>>> import matplotlib
>>> print matplotlib.__file__

when the PYTHONPATH is set to the troublesome value and then do an ls
on the directory that is reported by the __file__ printout.  Post the
listing here and we can advise further.

JDH

On Tue, Jun 9, 2009 at 10:18 AM, Jouni K. Seppänen<jk...@ik...> wrote:
> Chaitanya Krishna <ic...@gm...> writes:
>
>> On Tue, Jun 9, 2009 at 12:05 PM, Paul Anton Letnes <pau...@gm...> wrote:
>>>
>>> When I run the script below, the xlabel and ylabel do not show up. If I
>>> increase the figure size, it all works fine.
>>
>> I am not sure if it is a bug. But, it is usual that such a thing
>> happens when you are making small figures (like in your case).
>
> Arguably it is a bug, since it is reasonable to expect that when you set
> an xlabel or ylabel (or, say, large yticklabels), it shows up in the
> figure. There are at least two problems to solve here: what should the
> user interface be like, and how can it best be implemented?

These FAQs are also probably relevant:

http://matplotlib.sourceforge.net/faq/howto_faq.html#move-the-edge-of-an-axes-to-make-room-for-tick-labels
http://matplotlib.sourceforge.net/faq/howto_faq.html#automatically-make-room-for-tick-labels

JDH

Dear all,
I'm running matplotlib 0.98.5.2 on a machine with Ubuntu Intrepid 8.10. It's
worked well for me so far, but I encounter problems running matplotlib when
trying to update the PYTHONPATH in the .bashrc file. Adding just the line
"export PYTHONPATH=$PYTHONPATH", for example, gives the following:

$ ipython -pylab
Traceback (most recent call last):
  File "/usr/bin/ipython", line 27, in <module>
    IPython.Shell.start().mainloop()
  File "/var/lib/python-support/python2.5/IPython/Shell.py", line 1219, in
start
    shell = _select_shell(sys.argv)
  File "/var/lib/python-support/python2.5/IPython/Shell.py", line 1188, in
_select_shell
    backend = matplotlib.rcParams['backend']
AttributeError: 'module' object has no attribute 'rcParams'

On the other hand,

$ ipython

permits ipython to load seemingly normally, but in that case

In [1]: import matplotlib.pyplot as plt
ImportError: No module named pyplot

Any ideas on what might be wrong? I'd be grateful for any advice.

Thanks,
Hani Nakhoul

Chaitanya Krishna <ic...@gm...> writes:

> On Tue, Jun 9, 2009 at 12:05 PM, Paul Anton Letnes <pau...@gm...> wrote:
>>
>> When I run the script below, the xlabel and ylabel do not show up. If I
>> increase the figure size, it all works fine.
>
> I am not sure if it is a bug. But, it is usual that such a thing
> happens when you are making small figures (like in your case).

Arguably it is a bug, since it is reasonable to expect that when you set
an xlabel or ylabel (or, say, large yticklabels), it shows up in the
figure. There are at least two problems to solve here: what should the
user interface be like, and how can it best be implemented?

The user interface question seems difficult to me. If you set the figure
size to something small (as in this case) and then add labels, should
matplotlib reduce the area available for the plot? Or should it reduce
the font size of the labels and the tick labels, and perhaps the amount
of white space between the axes and the labels? Or some combination of
these?

The implementation question could also be somewhat hairy, since the
bounding box of text objects depends on the backend. If agg and pdf
disagree on the size of a label, is it OK to get different-looking
results in png and pdf?

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

On Tue, Jun 9, 2009 at 8:23 AM, Ulrich vor dem Esche<ulr...@we...> wrote:
> Greetings! I am new to matplotlib and python, and encountered a general problem:
> If i try to customize matplotlibrc, nothing changes. I changed the right thing:
> When i try
>
> import matplotlib
> matplotlib.matplotlib_fname()
>
> I get 'C:\\Python25\lib\\site-packages\\matplotlib\\mpl-data\\matplotlibrc'
> (as you see I'm in windows..)
>
> When I f.e. change
>
> #xtick.labelsize      : 14  (from '12')
> #xtick.direction      : out (from 'in')
>

By default, all lines are commented out.  You must remove the leading
'#" symbol to see your changes take effect

JDH

Ulrich vor dem Esche wrote:
> ...
> #xtick.labelsize      : 14  (from '12')
> #xtick.direction      : out (from 'in')
> 
> nothing changes ...
> I must have missed something very basic..

I guess that would be the "#" which declares everything behind as a comment.

Does it work when you remove the #?

Best,
Sebastian.

Greetings! I am new to matplotlib and python, and encountered a general problem:
If i try to customize matplotlibrc, nothing changes. I changed the right thing:
When i try

import matplotlib
matplotlib.matplotlib_fname()

I get 'C:\\Python25\lib\\site-packages\\matplotlib\\mpl-data\\matplotlibrc'
(as you see I'm in windows..)

When I f.e. change

#xtick.labelsize      : 14  (from '12')
#xtick.direction      : out (from 'in')

nothing changes at all. My program starts with 'import matplotlib.pyplot as plt', so
that actually matplotlibrc should be in use.. I tried to change other things in
\\matplotlib aswell, they were all ignored. I must have missed something very basic..
What did i miss?

Ulli
____________________________________________________________
Text: GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT!
Jetzt freischalten unter http://movieflat.web.de

On Tue, Jun 9, 2009 at 4:44 AM, Nan Dun<du...@yl...> wrote:
> Hello,
>
> Currently, in navigation window, the coordinates of cursor show like
> x = "%.1f", y="%.1f"
>
> Is it possible to custom these labels such that they show like
>
> my_x="%.3f", my_y="%.6f"


def my_x(x): return '%.3f'%x
def my_y(y): return '%.3f'%y

ax.fmt_xdata = my_x
ax.fmt_ydata = my_y

JDH

You may just want to start with the "custom_ticker1.py" example here:

http://matplotlib.sourceforge.net/examples/pylab_examples/custom_ticker1.html

The meat of it is just to provide a function that converts the incoming 
values (in your case pixel positions) into whatever you want to be 
displayed.

Cheers,
Mike

Jeremy Lewi wrote:
> I want to let matplotlib control where the tick marks go, but I want 
> to scale the value of the tick labels. For example,
> if my matrix has a 100 columns the tick marks might be [0,25,50,100].  
> I want to scale these tick labels by some value say .01 so that the 
> corresponding tick labels would be [0,.25,.5,1].
>
> Now say I zoom in on the image so that the xaxis limits are (0,50). 
> Lets suppose the tick marks are now [0,10,20,30,40,50]
> Then in this case the tick labels should be
> [0,.1,.2,.3,.4,.5]
>
> So how do I go about creating a custom formatter?
>
> Thanks
> Jeremy
>
> Michael Droettboom wrote:
>> What are you setting the x ticklabels to?  If you want to control how 
>> the numbers are displayed, you can create a custom formatter (which 
>> is basically a function to convert a floating-point number to a 
>> string).  If you want to control the number of ticks across the axis, 
>> you can make a custom ticker.
>>
>> If you can describe what your end goal is, I'm happy to describe the 
>> above options in more detail.
>>
>> Cheers,
>> Mike
>>
>> Jeremy Lewi wrote:
>>  
>>> Hi,
>>>     I'm using imshow to make an image of a 2-d matrix. I use 
>>> set_xticklabels to adjust the x-axis labels. The problem is that 
>>> when I then zoom in on the plot, the axis labels are not adjusted 
>>> appropriately. Does anyone suggestions on how I can fix this?
>>>
>>> Thanks
>>> Jeremy
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> Crystal Reports - New Free Runtime and 30 Day Trial
>>> Check out the new simplified licensing option that enables unlimited
>>> royalty-free distribution of the report engine for externally facing 
>>> server and web deployment.
>>> http://p.sf.net/sfu/businessobjects
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>       
>>
>>   
>

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

Hi Paul,

I am not sure if it is a bug. But, it is usual that such a thing
happens when you are making small figures (like in your case).

Try adjusting the following parameters in your rc file, in particular
increase the left space.
# The figure subplot parameters.  All dimensions are fraction of the
# figure width or height
#figure.subplot.left	: 0.125  # the left side of the subplots of the figure
#figure.subplot.right	: 0.9    # the right side of the subplots of the figure
#figure.subplot.bottom	: 0.1    # the bottom of the subplots of the figure
#figure.subplot.top	: 0.9    # the top of the subplots of the figure
#figure.subplot.wspace	: 0.2    # the amount of width reserved for
blank space between subplots
#figure.subplot.hspace	: 0.2    # the amount of height reserved for
white space between subplots

The other thing that you can try is to decrease the font size of the
axis labels.

It would be nice if we can rescale the left, right spacing depending
on the figure size.

Cheers,
Chaitanya


On Tue, Jun 9, 2009 at 12:05 PM, Paul Anton
Letnes<pau...@gm...> wrote:
> Dear all.
>
> When I run the script below, the xlabel and ylabel do not show up. If I
> increase the figure size, it all works fine. If I open the file in Adobe
> Illustrator, the x and ylabels are both there, but outside the canvas (or
> bounding box or whatever it is called). I believe this must be a bug?
>
> I moved my matplotlibrc file out of its usual location to make sure I don't
> have any funny settings which screws things up. I also deleted the tex cache
> to avoid any tex-related problems.
>
> Best regards,
> Paul.
> ######################
> import matplotlib
> matplotlib.rcParams['figure.figsize'] = [2.85, 2.20]
> matplotlib.use('pdf')
> from pylab import *
>
> xs = linspace(0, 2 * pi)
> ys = sin(xs)
> plot(xs, ys)
> xlabel(r'$T_{est}$')
> ylabel('y axis')
>
> savefig('test')
> show()
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Hello,

Currently, in navigation window, the coordinates of cursor show like
x = "%.1f", y="%.1f"

Is it possible to custom these labels such that they show like

my_x="%.3f", my_y="%.6f"

Thank you.

Nan

Dear all.

When I run the script below, the xlabel and ylabel do not show up. If  
I increase the figure size, it all works fine. If I open the file in  
Adobe Illustrator, the x and ylabels are both there, but outside the  
canvas (or bounding box or whatever it is called). I believe this must  
be a bug?

I moved my matplotlibrc file out of its usual location to make sure I  
don't have any funny settings which screws things up. I also deleted  
the tex cache to avoid any tex-related problems.

Best regards,
Paul.
######################
import matplotlib
matplotlib.rcParams['figure.figsize'] = [2.85, 2.20]
matplotlib.use('pdf')
from pylab import *

xs = linspace(0, 2 * pi)
ys = sin(xs)
plot(xs, ys)
xlabel(r'$T_{est}$')
ylabel('y axis')

savefig('test')
show()

Dear all.


When I run the script below, the xlabel and ylabel do not show up. If  
I increase the figure size, it all works fine. If I open the file in  
Adobe Illustrator, the x and ylabels are both there, but outside the  
canvas (or bounding box or whatever it is called). I believe this must  
be a bug?

I moved my matplotlibrc file out of its usual location to make sure I  
don't have any funny settings which screws things up. I also deleted  
the tex cache to avoid any tex-related problems.


Best regards,
Paul.

import matplotlib
matplotlib.rcParams['figure.figsize'] = [2.85, 2.20]
matplotlib.use('pdf')
from pylab import *

xs = linspace(0, 2 * pi)
ys = sin(xs)
plot(xs, ys)
xlabel(r'$T_{est}$')
ylabel('y axis')

savefig('test')
show()

I want to let matplotlib control where the tick marks go, but I want to 
scale the value of the tick labels. For example,
if my matrix has a 100 columns the tick marks might be [0,25,50,100].  I 
want to scale these tick labels by some value say .01 so that the 
corresponding tick labels would be [0,.25,.5,1].

Now say I zoom in on the image so that the xaxis limits are (0,50). Lets 
suppose the tick marks are now [0,10,20,30,40,50]
Then in this case the tick labels should be
[0,.1,.2,.3,.4,.5]

So how do I go about creating a custom formatter?

Thanks
Jeremy

Michael Droettboom wrote:
> What are you setting the x ticklabels to?  If you want to control how 
> the numbers are displayed, you can create a custom formatter (which is 
> basically a function to convert a floating-point number to a string).  
> If you want to control the number of ticks across the axis, you can make 
> a custom ticker.
>
> If you can describe what your end goal is, I'm happy to describe the 
> above options in more detail.
>
> Cheers,
> Mike
>
> Jeremy Lewi wrote:
>   
>> Hi,
>>     I'm using imshow to make an image of a 2-d matrix. I use 
>> set_xticklabels to adjust the x-axis labels. The problem is that when I 
>> then zoom in on the plot, the axis labels are not adjusted 
>> appropriately. Does anyone suggestions on how I can fix this?
>>
>> Thanks
>> Jeremy
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports - New Free Runtime and 30 Day Trial
>> Check out the new simplified licensing option that enables unlimited
>> royalty-free distribution of the report engine for externally facing 
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>   
>>     
>
>   

On Mon, Jun 8, 2009 at 2:14 PM, Gökhan SEVER<gok...@gm...> wrote:
> Hello,
>
> How do you add you automatically check-out new added files from matplotlib
> trunk? Is there a specific svn command for this?


Check out svn as indicated here::

  http://matplotlib.sourceforge.net/faq/installing_faq.html#install-from-svn

Once you have a checkout, you can get updates with ::

  > svn up

JDH

What are you setting the x ticklabels to?  If you want to control how 
the numbers are displayed, you can create a custom formatter (which is 
basically a function to convert a floating-point number to a string).  
If you want to control the number of ticks across the axis, you can make 
a custom ticker.

If you can describe what your end goal is, I'm happy to describe the 
above options in more detail.

Cheers,
Mike

Jeremy Lewi wrote:
> Hi,
>     I'm using imshow to make an image of a 2-d matrix. I use 
> set_xticklabels to adjust the x-axis labels. The problem is that when I 
> then zoom in on the plot, the axis labels are not adjusted 
> appropriately. Does anyone suggestions on how I can fix this?
>
> Thanks
> Jeremy
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing 
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>   

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

On Mon, Jun 8, 2009 at 2:16 PM, John Hunter <jd...@gm...> wrote:

> On Mon, Jun 8, 2009 at 2:14 PM, Gökhan SEVER<gok...@gm...> wrote:
> > Hello,
> >
> > How do you add you automatically check-out new added files from
> matplotlib
> > trunk? Is there a specific svn command for this?
>
>
> Check out svn as indicated here::
>
>
> http://matplotlib.sourceforge.net/faq/installing_faq.html#install-from-svn
>
> Once you have a checkout, you can get updates with ::
>
>  > svn up
>
> JDH
>


I need to issue a "python setup.py install" after each svn up, right?

Hello,

How do you add you automatically check-out new added files from matplotlib
trunk? Is there a specific svn command for this?

Another question: For example IPython has uses bzr and when I issue bzr
branch lp:ipython command I grab the latest development branch. I do a
development installation quoting from IPython documentation:

"Some users want to be able to follow the development branch as it changes.
If you have setuptools installed, this is easy. Simply replace the last step
by:

$ python setupegg.py develop


and one more step:

This creates links in the right places and installs the command line script
to the appropriate places. Then, if you want to update your IPython at any
time, just do:

$ bzr pull


No duplicated folders and bzr pulls the changes for me.

Could this be possible with matplotlib's VCS system?

Thank you

Gökhan

Hi,
    I'm using imshow to make an image of a 2-d matrix. I use 
set_xticklabels to adjust the x-axis labels. The problem is that when I 
then zoom in on the plot, the axis labels are not adjusted 
appropriately. Does anyone suggestions on how I can fix this?

Thanks
Jeremy

I ve a problem with the use of griddata.
I have a grid of x,y with value z. the grid have 4500 points
I would like to have a rigular grid of 1500 points.
I try the function zi = griddata(x,y,z,xi,yi)
but I have an error "too many indices". I don't understant why!!!
x,y,z,xi and yi are numpy array with 1 column.
Sorry for my bad english!!

Thanks

Josh Lawrence-2 wrote:
> 
> Greetings all,
> 
> In using the function griddata in mlab.py, I think I have found a bug.  
> The following line in mlab.py errors for me.
> I supply it an xi and yi that have shape (N,1). I have surface data,  
> but I only care about the variation in one direction. In mlab, when it  
> gets to this line (2956 in svn revision 7040):
> 
>           if min(xo[1:]-xo[0:-1]) < 0 or min(yo[1:]-yo[0:-1]) < 0:
>               raise ValueError, 'output grid defined by xi,yi must be  
> monotone increasing'
> 
> the result is an error. That is, I get the following:
> 
>           ValueError: min() arg is an empty sequence
> 
> A couple of things. First, if I make my variation in x to be 2 points  
> (x = 0 for the case I'm interested in--so I just have both values of x  
> be zero), I do not get this error and I believe the result works. So,  
> it seems that there should be some handling of the case that there are  
> only 1 point in either x or y direction.
> 
> Second, is it better to use the builtin python function min, or should  
> numpy.min be used instead?
> 
> Cheers,
> 
> Josh Lawrence
> Ph.D. Student
> Clemson University
> 
> 
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and 
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> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
> 

-- 
View this message in context: http://www.nabble.com/Griddata-tp23083610p23929245.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Esmail wrote:
> ...
> By the way, any idea how different the MayaVi interface is? I understand that
> matplotlib doesn't do 3D plots and I may want to plot some.
> ...

Hey Esmail,

there was the possibility for 3D plots in matplotlib:
http://www.scipy.org/Cookbook/Matplotlib/mplot3D

however, the mayavi "mlab" interface was designed explicitly to be as
simple as pylab.
http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/mlab.html

have fun 3D plotting,
sebastian.