matplotlib-users Mailing List for matplotlib

On 11/17/2010 01:28 PM, Ognjen Ilic wrote:
> Thanks for the help. However, when I change the matplotlibrc file I
> get the following message
> "Bad key "path.simplify" on line 267 in
> /HOME/.matplotlib/matplotlibrc.
> You probably need to get an updated matplotlibrc file from
> http://matplotlib.sf.net/matplotlibrc or from the matplotlib source
> distribution"
>
> I'd do the update but I don't have root access on the server
It sounds like you have an old enough version of mpl that it does not 
support rc configuration of the path simplification. If so, your only
option is to update mpl itself. It should be possible to build and 
install a local copy without root access, and put its location in your 
PYTHONPATH.
Eric
>
>
> On Wed, Nov 17, 2010 at 1:20 PM, Eric Firing<ef...@ha...> wrote:
>> On 11/17/2010 07:35 AM, Ognjen Ilic wrote:
>>> Hello all,
>>>
>>> I posted about this problem on another forum (with an image attachment)
>>> http://python-forum.org/pythonforum/viewtopic.php?f=18&t=21951&p=99290#p99290
>>>
>>> In the figure below white space that forms a trapezoid to the right
>>> (slope then constant) and tear-shape white space to the left (due to
>>> maxZ being too small) are expected and I have no issues with that.
>>> The weird things are the sharp white shapes to the left. They are very
>>> irregular and with a little different change in parameters they appear
>>> at different places.
>>
>> This looks like the path simplification bug that was fixed some time
>> before mpl 1.0. You can upgrade, or as a workaround you can turn off
>> path simplification by putting
>>
>> path.simplify : False
>>
>> in your matplotlibrc file, or by using
>> matplotlib.rcParams['path.simplify'] = False
>> in your script.
>>
>> Eric
>>
>>>
>>> Below are the relevant pieces of code
>>>
>>> Code: Select all
>>> import matplotlib.pyplot as plt
>>> import matplotlib.colors as colors
>>> ...
>>> z = numpy.transpose(z)
>>> z = numpy.ma.masked_where(z<=0, z)
>>> levels = numpy.linspace(0,maxZ,50)
>>> cset1=plt.contourf(x,y,z,levels,cmap=plt.get_cmap('jet',len(levels)-1))
>>> plt.colorbar(cset1)
>>> fname = 'pic.png'
>>> plt.savefig(fname)
>>>
>>>
>>>
>>> Above, z is the 2D array of values for different x and y (both lists
>>> have 400 elements each).
>>> Ths is really really confusing me. Any help is greatly appreciated!

Thanks for the help. However, when I change the matplotlibrc file I
get the following message
"Bad key "path.simplify" on line 267 in
/HOME/.matplotlib/matplotlibrc.
You probably need to get an updated matplotlibrc file from
http://matplotlib.sf.net/matplotlibrc or from the matplotlib source
distribution"
I'd do the update but I don't have root access on the server
On Wed, Nov 17, 2010 at 1:20 PM, Eric Firing <ef...@ha...> wrote:
> On 11/17/2010 07:35 AM, Ognjen Ilic wrote:
>> Hello all,
>>
>> I posted about this problem on another forum (with an image attachment)
>> http://python-forum.org/pythonforum/viewtopic.php?f=18&t=21951&p=99290#p99290
>>
>> In the figure below white space that forms a trapezoid to the right
>> (slope then constant) and tear-shape white space to the left (due to
>> maxZ being too small) are expected and I have no issues with that.
>> The weird things are the sharp white shapes to the left. They are very
>> irregular and with a little different change in parameters they appear
>> at different places.
>
> This looks like the path simplification bug that was fixed some time
> before mpl 1.0. You can upgrade, or as a workaround you can turn off
> path simplification by putting
>
> path.simplify : False
>
> in your matplotlibrc file, or by using
> matplotlib.rcParams['path.simplify'] = False
> in your script.
>
> Eric
>
>>
>> Below are the relevant pieces of code
>>
>> Code: Select all
>>   import matplotlib.pyplot as plt
>>   import matplotlib.colors as colors
>>   ...
>>   z = numpy.transpose(z)
>>   z = numpy.ma.masked_where(z<=0, z)
>>   levels = numpy.linspace(0,maxZ,50)
>>   cset1=plt.contourf(x,y,z,levels,cmap=plt.get_cmap('jet',len(levels)-1))
>>   plt.colorbar(cset1)
>>   fname = 'pic.png'
>>   plt.savefig(fname)
>>
>>
>>
>> Above, z is the 2D array of values for different x and y (both lists
>> have 400 elements each).
>> Ths is really really confusing me. Any help is greatly appreciated!
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3.
>> Spend less time writing and rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today
>> http://p.sf.net/sfu/msIE9-sfdev2dev
>>
>>
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
> Spend less time writing and rewriting code and more time creating great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Wed, Nov 17, 2010 at 1:54 PM, Eric Emsellem <eem...@es...> wrote:
> Dear Ben
> thanks a lot for this thoughful answer.
>
>
> When I use only "ipython" and not "ipython -pylab" IT WORKS!!!
>
> So this is a problem with "ipython -pylab" call...
> Any thought of why this is?
>
>
Possibly ipython is somehow configured to pull pylab from a different
location, thereby loading a different matplotlib (and under a different
name) from what mplot3d loads. Remember, python loads modules only once
during an execution, regardless of the number of times an import statement
appears. With ipython -pylab, it implicitly does these loads for you
(except for mplot3d because it is a separate toolkit). If ipython was
explicitly configured to look elsewhere for pylab, and then you come along
and tell it to import mplot3d using the normal python search path, it
*might* be possible that different matplotlibs got loaded. Again, though,
this is complete and utter speculation, and has little basis in fact nor
evidence.
> I provide more info below
>
> thanks for any help there.
>
> Eric
>
> P.S.: Here is the output of my setup:
>
> In [1]: matplotlib.__file__
> Out[1]: '/usr/lib64/python2.6/site-packages/matplotlib/__init__.pyc'
>
> In [6]: mpl_toolkits.mplot3d.__file__
> Out[6]:
> '/usr/lib64/python2.6/site-packages/mpl_toolkits/mplot3d/__init__.pyc'
>
>
Clarity is important here. Was this the same regardless of using '-pylab'?
Also, if you run "ipython -pylab", what is the value of pylab.__file__ and
how does it compare to matplotlib.__file__ and
mpl_toolkits.mplot3d.__file__?
> A funny one is that I have to import mpl_toolkits first and then mplot3d,
> and
> when I do this I get:
> In [5]: from mpl_toolkits import mplot3d
> try this
>
> I am not sure the "try this" is meant to be there....
>
>
It isn't, but I can not find it anywhere in the source files. I have
checked the source code for matplotlib from the OpenSUSE repos and from our
svn repos. It does not exist. That line must be coming from another
package or you may have forgotten you added it (this has happened to me
before).
>
> P.P.S.:
> Here is my detailed setup when I do ipython -pylab
>
> matplotlib data path /usr/lib64/python2.6/site-packages/matplotlib/mpl-data
> matplotlib version 1.0.0
> verbose.level helpful
> interactive is False
> units is False
> platform is linux2
> Your PyGtk has set_interactive(), so you can use the
> more stable single-threaded Gtk mode.
> See https://bugs.launchpad.net/ipython/+bug/270856
>
> backend GTKAgg version 2.17.0
> Python 2.6.5 (r265:79063, Jul 5 2010, 11:46:13)
>
>
> IPython 0.10 -- An enhanced Interactive Python.
>

Dear Ben
thanks a lot for this thoughful answer.
When I use only "ipython" and not "ipython -pylab" IT WORKS!!!
So this is a problem with "ipython -pylab" call...
Any thought of why this is?
I provide more info below
thanks for any help there.
Eric
P.S.: Here is the output of my setup:
In [1]: matplotlib.__file__
Out[1]: '/usr/lib64/python2.6/site-packages/matplotlib/__init__.pyc'
In [6]: mpl_toolkits.mplot3d.__file__
Out[6]: '/usr/lib64/python2.6/site-packages/mpl_toolkits/mplot3d/__init__.pyc'
A funny one is that I have to import mpl_toolkits first and then mplot3d, and
when I do this I get:
In [5]: from mpl_toolkits import mplot3d
try this
I am not sure the "try this" is meant to be there....
P.P.S.:
Here is my detailed setup when I do ipython -pylab
matplotlib data path /usr/lib64/python2.6/site-packages/matplotlib/mpl-data
matplotlib version 1.0.0
verbose.level helpful
interactive is False
units is False
platform is linux2
Your PyGtk has set_interactive(), so you can use the
more stable single-threaded Gtk mode.
See https://bugs.launchpad.net/ipython/+bug/270856
backend GTKAgg version 2.17.0
Python 2.6.5 (r265:79063, Jul 5 2010, 11:46:13)
IPython 0.10 -- An enhanced Interactive Python.

On Wed, Nov 17, 2010 at 2:32 AM, Eric Emsellem <eem...@es...> wrote:
> yes, it looks like this is the right file (when I look at
> matplotlib.__file__)
>
> Now tracing which routines are run when doing this, it looks like it looks
> for
> projection in projections/__init__.py
> after going through line 675 of figure.py
>
> It looks like add_subplot of plt.figure() is not compatible in my
> matplotlib.
>
> Eric
>
>
No, that code path is correct. The problem has to be that the registration
is not occurring correctly. I would double-check that the filepath for
matplotlib.__file__ and mpl_toolkits.mplot3d.__file__ matches. I am still
convinced that we have an installation issue. My bet is that -- somehow --
mplot3d is being loaded from one version, while matplotlib is being loaded
from another version.
Another thing that might be complicating things is the use of ipython
-pylab. If you aren't using pylab, then there really isn't much need to
call that. Did you fully un-install matplotlib before building matplotlib
from svn? If not, you might need to do a complete clean (package-wise and
build-wise) before trying again.
I notice that you are using OpenSUSE. We have been having a number of
reports of problems from OpenSUSE users in the past month. Almost all of
them appear to be packaging issues and not problems with matplotlib itself.
I don't know if this is the case here, but who knows?
I find this error to be fairly odd given how simple and fundamental the
algorithm is. It is essentially a python dictionary containing name/class
pairs. Kinda hard to break that. If you can verify that the Axes3D object
is registering itself, and then the projection can't be found later, then
there remains only two possibilities. First, that the dictionary being
checked is different from the dictionary used to register the Axes3D class.
Second, that the Axes3D entry got removed after being inserted.
Considering that I am unaware of any code that deregisters a projection, I
am inclined to believe that somehow we have different dictionary objects
being accessed. This is the basis for my theory that the matplotlib
installation is wonky because the matplotlib.pyplot that you import from
your script might -- somehow -- be different from the matplotlib that is
imported from mplot3d.
Again, it makes little sense, but that is what is going through my mind
right now. Anybody else have any thoughts?
Ben Root

On 11/17/2010 07:35 AM, Ognjen Ilic wrote:
> Hello all,
>
> I posted about this problem on another forum (with an image attachment)
> http://python-forum.org/pythonforum/viewtopic.php?f=18&t=21951&p=99290#p99290
>
> In the figure below white space that forms a trapezoid to the right
> (slope then constant) and tear-shape white space to the left (due to
> maxZ being too small) are expected and I have no issues with that.
> The weird things are the sharp white shapes to the left. They are very
> irregular and with a little different change in parameters they appear
> at different places.
This looks like the path simplification bug that was fixed some time 
before mpl 1.0. You can upgrade, or as a workaround you can turn off 
path simplification by putting
path.simplify : False
in your matplotlibrc file, or by using
matplotlib.rcParams['path.simplify'] = False
in your script.
Eric
>
> Below are the relevant pieces of code
>
> Code: Select all
> import matplotlib.pyplot as plt
> import matplotlib.colors as colors
> ...
> z = numpy.transpose(z)
> z = numpy.ma.masked_where(z<=0, z)
> levels = numpy.linspace(0,maxZ,50)
> cset1=plt.contourf(x,y,z,levels,cmap=plt.get_cmap('jet',len(levels)-1))
> plt.colorbar(cset1)
> fname = 'pic.png'
> plt.savefig(fname)
>
>
>
> Above, z is the 2D array of values for different x and y (both lists
> have 400 elements each).
> Ths is really really confusing me. Any help is greatly appreciated!
>
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3.
> Spend less time writing and rewriting code and more time creating great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hello all,
I posted about this problem on another forum (with an image attachment)
http://python-forum.org/pythonforum/viewtopic.php?f=18&t=21951&p=99290#p99290
In the figure below white space that forms a trapezoid to the right
(slope then constant) and tear-shape white space to the left (due to
maxZ being too small) are expected and I have no issues with that.
The weird things are the sharp white shapes to the left. They are very
irregular and with a little different change in parameters they appear
at different places.
Below are the relevant pieces of code
Code: Select all
 import matplotlib.pyplot as plt
 import matplotlib.colors as colors
 ...
 z = numpy.transpose(z)
 z = numpy.ma.masked_where(z<=0, z)
 levels = numpy.linspace(0,maxZ,50)
 cset1=plt.contourf(x,y,z,levels,cmap=plt.get_cmap('jet',len(levels)-1))
 plt.colorbar(cset1)
 fname = 'pic.png'
 plt.savefig(fname)
Above, z is the 2D array of values for different x and y (both lists
have 400 elements each).
Ths is really really confusing me. Any help is greatly appreciated!

There is numpy.histogram, which will give you the histogram without the plots.
But I have had little trouble using hist on log-log plots:
Try this (in ipython -pylab or with ">>> from pylab import *; import numpy"):
>>> x = numpy.random.lognormal(size=1e4)
>>> bins = logspace(-1.5, 1.5, 100)
>>> hist(x, histtype='step', bins=bins)
>>> xscale('log')
>>> yscale('log')
>>> show()
-Roban
On Wed, Nov 17, 2010 at 2:23 PM, Davide Fiocco <dav...@gm...> wrote:
> Hi folks,
>
> I want to bin sevaral arrays of data and superimpose them in a single plot.
> The simplest approach is to fire several times
>> hist(data_i, N)
>
> My problem is that I want to make a loglog plot (i.e. putting a
> logscale on the X axis too, something that hist doesn't allow me to
> do).
>
> So what I've done so far is extracting the bin coordinates from
> hist(data_i, N)[1], extract histogram values using hist(data_i, N)[0]
> and then a loglog plot them one against each other.
>
> The point is that I have to invoke at least once the command
> hist(data_i, N) in order to do so, and this draws patches on my figure
> which I don't want to appear on my final plot.
>
> How do I delete the histogram bars? In other words, how to I delete an
> entire histogram from my plot?
>
> Other suggestions to have this sort of "loglog histogram" in a few
> lines of code are more than welcome, of course.
>
> Cheers,
>
> Davide
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
> Spend less time writing and rewriting code and more time creating great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
-- 
Roban Hultman Kramer | Zwicky Fellow | Institute for Astronomy
ETH Zürich (Swiss Federal Institute of Technology)

On Wed, Nov 17, 2010 at 5:45 AM, Matthias Plum
<pl...@ph...>wrote:
> Hi
>
> I am trying to plot data on the sphere and use the hammer projection.
> The data ploting works fine, but the angular grid isn't shown correctly.
> In the attached picture you can see the error(mouse pointer is on the
> position 60 E 30 S). Can anyone help me on this subject? Thanks.
>
> Matthias
>
>
Matthias,
Looking at the transform equation for Hammer, it looks like there might be a
mistake in the calculation. Can you include the script you used to make
that figure so I can test the fix?
Thanks,
Ben Root

Hi folks,
I want to bin sevaral arrays of data and superimpose them in a single plot.
The simplest approach is to fire several times
> hist(data_i, N)
My problem is that I want to make a loglog plot (i.e. putting a
logscale on the X axis too, something that hist doesn't allow me to
do).
So what I've done so far is extracting the bin coordinates from
hist(data_i, N)[1], extract histogram values using hist(data_i, N)[0]
and then a loglog plot them one against each other.
The point is that I have to invoke at least once the command
hist(data_i, N) in order to do so, and this draws patches on my figure
which I don't want to appear on my final plot.
How do I delete the histogram bars? In other words, how to I delete an
entire histogram from my plot?
Other suggestions to have this sort of "loglog histogram" in a few
lines of code are more than welcome, of course.
Cheers,
Davide

On Wed, Nov 17, 2010 at 2:29 AM, Tim Åberg <qw...@ho...> wrote:
> Hello!
>
> I have now been tampering with a custom formatter and the more i think about
> it the more i feel there must be a more easy soulution. I have a set of
> values that are plotted over time (i use date2num, to get the conversion
> from date to num), i also have a list with dates that corresponds to these
> values;
> ['2010-11-05 10:27:45.605000', '2010-11-05 10:27:50.576000', '2010-11-05
> 10:27:55.913000'], this to not have to do a conversion back, i imagine its
> the most effective way to do it.
>
> Now to the question;
>
> The only two values in the datelist that is vital is the first and the last,
> in between i really just want to have values that corresponds lineary. Thats
> brings me to resoulution, if the values are far far in between, say weeks or
> even moth the time (h:s:ms) isnt so important and vice versa.
>
> Is there any formatter that do this sort of things? eg. takes in two
> values(dates) and format it by itself.
Take a look at this example
http://matplotlib.sourceforge.net/examples/api/date_index_formatter.html
It's trying to solve a different but related problem: in financial
time series you only have data on Monday - Friday, and you don't want
to plot the gaps on weekends. So you plot the data linearly with an
index, and use a custom locator and formatter to set and format the
ticks.
JDH

Hi
I am trying to plot data on the sphere and use the hammer projection.
The data ploting works fine, but the angular grid isn't shown correctly.
In the attached picture you can see the error(mouse pointer is on the
position 60 E 30 S). Can anyone help me on this subject? Thanks.
Matthias

I just checked it up, and it had some nice function, the timeseries 
looked nice and maybe i can use it in some way (time_series looked 
interesting) . I dont want to go away from Linecollection way of 
plotting due to its speed or is the timeseries-way a fast way of 
plotting? 
Date: 2010年11月17日 09:55:13 +0100
Subject: Re: [Matplotlib-users] Formatter dates
From: pgm...@gm...
To: qw...@ho...
Tim, have you tried the scikits.timeseries package? Its plotting capacities, albeit limited, may be helpful in your case... 
On Nov 17, 2010 9:31 AM, "Tim Åberg" <qw...@ho...> wrote:
> 
> Hello!
> 
> I have now been tampering with a custom formatter and the more i think about it the more i feel there must be a more easy soulution. I have a set of values that are plotted over time (i use date2num, to get the conversion from date to num), i also have a list with dates that corresponds to these values;
> ['2010-11-05 10:27:45.605000', '2010-11-05 10:27:50.576000', '2010-11-05 10:27:55.913000'], this to not have to do a conversion back, i imagine its the most effective way to do it. 
> 
> Now to the question; 
> 
> The only two values in the datelist that is vital is the first and the last, in between i really just want to have values that corresponds lineary. Thats brings me to resoulution, if the values are far far in between, say weeks or even moth the time (h:s:ms) isnt so important and vice versa.
> 
> Is there any formatter that do this sort of things? eg. takes in two values(dates) and format it by itself.
> 
> // Tim
> 		 	 		 
 		 	 		 

yes, it looks like this is the right file (when I look at matplotlib.__file__)
Now tracing which routines are run when doing this, it looks like it looks for
projection in projections/__init__.py
after going through line 675 of figure.py
It looks like add_subplot of plt.figure() is not compatible in my matplotlib.
Eric
> Strange indeed. Ok, what does matplotlib.__file__ say? Does the
> filename match the path you are expecting? At this point, I would also
> try putting print statements in the register code at the end of
> axes3d.py to see if that code path gets executed (can't see why not).
> 
> Ben Root
>

Hello!
I have now been tampering with a custom formatter and the more i think about it the more i feel there must be a more easy soulution. I have a set of values that are plotted over time (i use date2num, to get the conversion from date to num), i also have a list with dates that corresponds to these values;
['2010-11-05 10:27:45.605000', '2010-11-05 10:27:50.576000', '2010-11-05 10:27:55.913000'], this to not have to do a conversion back, i imagine its the most effective way to do it. 
Now to the question; 
The only two values in the datelist that is vital is the first and the last, in between i really just want to have values that corresponds lineary. Thats brings me to resoulution, if the values are far far in between, say weeks or even moth the time (h:s:ms) isnt so important and vice versa.
Is there any formatter that do this sort of things? eg. takes in two values(dates) and format it by itself.
// Tim
 		 	 		 

Hi,
I spent a fair amount of time today debugging what I thought was a bug
in the scaling of psd() when I was using NFFT to specify zero-padding.
 This was a mis-use of the code on my part, where I should have been
using pad_to to get zero-padding. Most embarassing about this is that
I'm basically the maintainer of record for this code and responsible
for the most recent changes, part of which improved 0-padding. (> 2
years ago)
I've come to the conclusion that if I was able to get it wrong, it's
likely that this issue has bitten and will bite other users. The
problem stems from the fact that the code underlying psd (and csd,
etc.) will gladly pad your data to NFFT if len(x) < NFFT. The extra
0's added here throw off the scaling (whereas using pad_to does not).
[Aside for the curious: The NFFT-padding code pre-dates the use of
pad_to for zero-padding and was left so-as not to break code, not
realizing that leaving it was still wrong.] Options:
1) Rip out the code that does the zero-padding based on NFFT and raise
an exception in the case that len(x) < NFFT.
2) Issue a warning on len(x) < NFFT for awhile, and then rip it out.
3) ?
I'm really tempted to just go with 1), with an exception that details
the problem and the fix. While this would break existing code, this
code is almost 100% guaranteed to be broken and silently producing the
incorrect answer (unless code was already hacking around our
broken-ness, which wouldn't be easy.)
I still need to go through and convince myself that there's not some
use-case where NFFT > len(x) would produce correct and desired
behavior, which isn't covered by pad_to. What I'm looking for is
thoughts from devs on breaking backwards compatibility and from users,
whose code may or may not be broken by such a change.
Ryan
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma