Re: [Matplotlib-users] [matplotlib-devel] License, freetype

[Goyo]

I usually install the matplotlib binaries from pipy and I don't
remember doing a separate installation of freetype.

2017-02-18 17:20 GMT+01:00 Paul Hobson :
> Especially on Windows, I always install freetype from conda.
> -p
>
> On Sat, Feb 18, 2017 at 6:24 AM, CAB  wrote:
>>
>> Hi, Gents,
>>
>> Many thanks for your thoughtful responses!  Freetype is indeed available
>> under a BSD-like licensse.  But when I tried to install freetype on my
>> Windows system using the binary provided from GnuWin32, it attempts to force
>> me to accept the GPL3, which I cannot.  Freetype's link to another binary
>> supplied by GTK+ is broken.  So, I guess I have two choices; compile
>> freetype from the source, or download something like Anaconda, which I'd
>> rather not do because I have Python already installed.
>>
>> If you have any other ideas, I'd be happy to hear them.
>>
>> Best,
>> Chad
>>
>>
>> 
>> From: Joe Kington 
>> To: Paul Hobson 
>> Cc: CAB ; Matplotlib Development List
>> ; Matplotlib Users
>> 
>> Sent: Friday, February 17, 2017 5:03 PM
>> Subject: Re: [matplotlib-devel] [Matplotlib-users] License, freetype
>>
>> Well, if Freetype were only distributed under the GPL, you couldn't
>> distribute matplotlib in binary form without providing the source code.
>>
>> However, Freetype is distributed under more than one license.  (see:
>> https://www.freetype.org/license.html )
>>
>> Because it's distributed under a BSD-style license in addition to the GPL,
>> it can be distributed in binary form, subject to an accreditation clause:
>> http://git.savannah.gnu.org/cgit/freetype/freetype2.git/tree/docs/FTL.TXT
>>
>> In the past, I have gotten approval from corporate lawyers at a very large
>> company to use freetype (and matplotlib) in an application that was being
>> distributed in binary form.  The dual-licensing of freetype was key in that
>> particular case.
>>
>> Or that's my take on it, anyway.  I'm not a Lawyer, so don't consider this
>> legal advice in any way.
>> Cheers!
>> -Joe
>>
>> On Fri, Feb 17, 2017 at 4:52 PM, Paul Hobson  wrote:
>>
>> Chad,
>>
>> My recollections is that matplotlib doesn't distribute the source code to
>> FreeType, it only uses it as a dependency. As such, MPL is in the clear with
>> its more permissive licensing.
>> -Paul
>>
>> On Fri, Feb 17, 2017 at 12:45 PM, CAB  wrote:
>>
>> Hi, All,
>>
>> I just went to install matplotlib version 2.0.0, and it has a dependency
>> called "freetype". This software appears to be licensed under GPL3.  My
>> reading of that latter license is that, if someone wanted to distribute a
>> compiled version of a program requiring matplotlib, that entire program
>> would fall under the GPL3 license.  I'm sure that would be a non-starter for
>> many, many projects.
>>
>> Does anyone have any takes on this?
>>
>> Chad
>>
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Re: [Matplotlib-users] Fixing axes for imshow plot on top of a figure

[Goyo]

I do not think fig.add_axes([0.1, 1, 1, 1]) makes any sense. The docstring says:

fig.add_axes(*args, **kwargs)

Add an axes at position *rect* [*left*, *bottom*, *width*,
*height*] where all quantities are in fractions of figure
width and height.

If bottom and height are both 1 you need the height of the figure to
be 2 in fractions of figure height. This means 1 must equal 2 and then
Bertrand Russel must be the Pope[1].

Goyo

[1] 
http://ceadserv1.nku.edu/longa//classes/mat385_resources/docs/russellpope.html

2015-05-20 13:43 GMT+02:00 aradand arada...@gmail.com:
 I'm trying to plot an image on top of a Figure, but imshow seems to always
 distort the size of the axes. What I want is that the lower part of the top
 image stay always in the same position, for any image height

 This minimal example shows my issue

 import matplotlib.pyplot as plt
 import numpy as np

 fig = plt.figure()
 ax = fig.add_axes([0.1, 0, 1, 1])

 # Top figure aligned with the bottom figure
 # keeping the same width (?)
 ax2 = fig.add_axes([0.1, 1, 1, 1])
 ax2.set_xticks([])

 # Depending on the number of rows or columns
 # the top image will be moved further to the top
 # or will be stretched if rows  columns
 # I dont know how to control this to stay always
 # with the same separation with respect
 # to the bottom figure and keeping the same width
 # (so the frame is the same width than the bottom figure)
 im = np.random.rand(10, 30)
 ax2.imshow(im)
 plt.plot()

 If it is possible to

 I would prefer to avoid using subplots or grid, since I have already
 specified a lot of things using the add_axes method.



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Re: [Matplotlib-users] installation problem

[Goyo]

2014-07-04 8:30 GMT+02:00 Rachana Katkam katkam.rach...@gmail.com:
 Hey, even I had similar issue.
 Later I learnt python2.7 could support matplotlib version1.0.1 only.

 So if you want to upgrade your matplotlib, you first need to upgrade your
 python.

matplotlib 1.3.1 works quite well with python 2.7.

Goyo

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Re: [Matplotlib-users] Undefined color model and inconsistencies between backends

[Goyo]

FWIW I can't tell any difference between colors in different backends.
I tried agg, cairo, several interactive backends and ipython inline in
Ubuntu.

Goyo

2014-05-17 6:14 GMT+02:00 Michael Goerz go...@physik.uni-kassel.de:
 On Fri, 16 May 2014, Eric Firing wrote:
 On 2014/05/16 4:41 PM, Michael Goerz wrote:
 While playing around for an afternoon with colors in matplotlib, I came
 across some inconsistencies. I was trying to define colors in sRGB (my
 understanding is that sRGB as a standardized color space is
 device-independent). Giving RGB values to matplotlib, I checked the
 output with a color picker -- Color Maker from the Mac App Store, set
 to the sRGB mode, but the built-in DigitalColor Meter gives the same
 result. It turns out that the colors I see in the output are not what I
 specified. This makes playing around with colors, a bit difficult:
 http://nbviewer.ipython.org/gist/goerz/9aab94f5322d5a457625
 As far as I can tell, Matplotlib does not specify in
 which color model in interprets RGB values (this should ideally be
 stated in the documentation). Also, the output in different backends
 (IPython notebook, and interactive GUI) gave different results. As a
 minimal example, consider the following:
 Matplotlib doesn't interpret RGB values; that is left to the display
 device.  Matplotlib simply writes the RGB values in a file,
 unmodified, or sends them via a GUI backend to a display, also
 unmodified *by mpl*.  What you put in, is what it puts out.

 Thanks for pointing out the DigitalColor Meter--I hadn't noticed it.

 What I see with your example is that the MacOSX backend *display* is
 interpreting RGB as sRGB, and the qt4agg backend *display* is
 interpreting RGB as native values (based on matching with
 DigitalColor Meter).

 I haven't tried this with inline plots in the notebook, but mpl is
 merely feeding RGB values to the browser, just as would occur when
 displaying a png, and it is up to the browser to decide how to
 convert them into pixel intensity.

 I don't see that there is a bug here.
 Fair enough, so that would imply that there is a difference between the
 png streams produced by matplotlib and the direct PIL image. I might
 be seeing the problems discussed here: https://hsivonen.fi/png-gamma/
 It might be that the matplotlib png stream is untagged, whereas the
 PIL image is tagged properly as sRGB. I'd have to decode the base64
 data from the notebook to check this.

 Beyond that it seems quite tricky to understands how in a given
 application, or matplotlib backend in this case, a given RGB color
 input yields a specific output on my screen, and how to make this
 consistent (consistency obviously being more important than
 accurateness with respect to some real color model). Maybe this just
 goes to show what I realized these last couple of days, that colors are
 a huge can of worms.


  import pylab
  import numpy as np
  import matplotlib
  #%matplotlib inline
  # draw line with sRGB color 228, 26, 28
  pylab.plot(np.linspace(0,10, 10), np.linspace(0,20,10), linewidth=10,
 color=(0.894, 0.102, 0.110))
  pylab.show()
  # Colorpicker shows 210, 46, 13 in GUI view
  # Colorpicker shows 229, 39, 27 in iPython Notebook
 
 In the IPython notebook, direct PIL graphics do seem to give the right
 colors cf. In [5] in the linked IPython notebook (even though PIL also
 does not explicitly specify its color model). Just matplotlib seems
 off. Of course, I'm doing some slightly crazy stuff in the Notebook,
 displaying every matplotlib output through PIL, but I cecked that
 `%matplotlib inline` actually produces the same colors.
 
 Should I file this on github as a bug report?
 
 Best,
 Michael
 
 P.S.: please CC for direct replies

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Re: [Matplotlib-users] how to reduce the file size of plots generated with matplotlib

[Goyo]

2014-03-22 20:23 GMT+01:00 Christopher Kuhlman ckuhl...@vbi.vt.edu:
[...]
 For example, most recently, I am plotting 3 data sets; each data set has 
 about 90,000 points.  If I plot all three sets in one PDF figure, the file 
 size is over 2MB.
 This seems absurd to me.  I used R plotting for many years (again, my own 
 homegrown code, for 6 years) and never had this issue, and I was making these 
 kinds of plots/figures.

 I thought it may be a vector/raster issue, but the following web page says 
 that PDF are generated as vector image, which, to my understanding (which 
 could be wrong), is the more compact format.
 http://matplotlib.org/faq/usage_faq.html
[...]

Roughly speaking, size of vector files depend on the number of points
while size of raster files depends on the number of pixels. For your
use case (many points, small images) raster output should be more
compact.

Goyo

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Re: [Matplotlib-users] how to reduce the file size of plots generated with matplotlib

[Goyo]

2014-03-22 21:38 GMT+01:00 Christopher Kuhlman ckuhl...@vbi.vt.edu:
 Thank you both for your fast replies.  (Just an aside, plotting all the 
 points is a quick way to detect outliers.)

 Before I sent the email, I tried to find a simple raster command in 
 matplotlib to do just that (convert the image to raster), but I could not 
 find one in my search.  Is there such a thing?

outfile = basefile + .png

Goyo

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Re: [Matplotlib-users] Access to color cycle?

[Goyo]

2014-03-05 21:13 GMT+01:00 Adam Hughes hughesada...@gmail.com:
 Thanks Andreas.  That is correct; however, I'd rather not make this change
 global.  I only want a subset of my plots to have this behavior.  I feel
 like changing the rcparams would change this globally and probably confuse
 users who don't know this is being called.

Try using rc_context:

with plt.rc_context(rc={'axes.color_cycle': ['orange', default_cycle[1::]]}):
plt.plot(...)

This should change the color cycle only within the scope of the with
clause (not tested with this particular rcparam).

Goyo

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Re: [Matplotlib-users] twinx and grid

[Goyo]

2014-02-09 2:29 GMT+01:00 garyr ga...@fidalgo.net:
 The script below labels both the left and right x-axes and shows a grid. Is
 there a way to force the horizontal grid lines to line up with the tic marks 
 on
 the left axis (ax1)?

 import numpy as np
 import matplotlib.pyplot as plt
 fig = plt.figure()
 ax1 = fig.add_subplot(111)
 t = np.arange(0.01, 10.0, 0.01)
 s1 = np.exp(t)
 ax1.plot(t, s1, 'b-')
 ax2 = ax1.twinx()
 s2 = np.sin(2*np.pi*t)
 ax2.plot(t, s2, 'r')
 plt.grid()
 plt.show()

plt.grid() affects the current axes so calling it before creating the
second one should do. I think it would be more consistent if you used
the method ax1.grid() though.

Goyo

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Re: [Matplotlib-users] Memory leak when using pyplot.ion() ?

[Goyo]

2013/10/14 Mark Lawrence breamore...@yahoo.co.uk:
 On 14/10/2013 13:51, OCuanachain, Oisin (Oisin) wrote:
 Hi,

 I am having problems with a script. It runs a number of iterations and
 plots and saves a number of plots on each iteration. After the plots
 have been saved I issue the pyplot.close(‘all’) command so despite many
 plots being created only 4 should be open at any given time which should
 not cause any memory problems. When I run the script however I see the
 RAM usage gradually growing without bound and eventually causing the
 script to crash. Interestingly I have found if I comment out the
 pyplot.ion()  and pyplot.ioff() the problem vanishes. So I do have a
 workaround but it would still be good to have this fixed in case I
 forget about it in future and loose another weekend’s work.

 My OS is Windows XP Service Pack 3
 Python 2.6
 Matplotlib 1.0.1


 Is this actually a matplotlib problem or could it be a Windows problem
 as discussed here http://bugs.python.org/issue19246 ?

I think this is different. That bug report is not about RAM usage
growing without bound but memory allocation failing with plenty of RAM
available.

Goyo

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Re: [Matplotlib-users] x axis non-uniform labeling (KURT PETERS)

[Goyo]

2013/10/1 KURT PETERS petersk...@msn.com:
 here's what SHOULD be happening

 | 0   1   5  9 13 18 21 24 25 28
  3 | x
 |x  x
 |   xx
 |   x x
 -1|_x__x_
12  3   4  56   7   8   9  10

 How can I make that happen?  Instead, MPL is autoranging the top axis.  I
 don't want that   I just want the actual labels to occur up there.

Then just set the ticks and the tick labels of the axis:

import numpy as np
import matplotlib.pyplot as plt
xdat=np.arange(1,11)
simtimedata = np.array([0, 1, 5, 9, 13, 18, 21, 24, 25, 28])
idatanp = np.array([-1,0, 1, 2, 3, 2, 1, 0, -1, -2])
ax1 = plt.subplot(111)
ax1.plot(xdat,idatanp)
ax2 = ax1.twiny()
ax2.set_xticks(range(len(xdat)))
ax2.set_xticklabels(simtimedata)
plt.show()

Goyo

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Re: [Matplotlib-users] Broken clabel manual=True in 1.3.0

[Goyo]

2013/9/28 Felix Patzelt fe...@neuro.uni-bremen.de:
 Dear all,

 manually placing labels when using clabel seems to be broken in Matplotlib 
 1.3.0.

 I'm on OS X 10.8.5 and have Matplotlib installed via macports. Today I 
 updated all installed ports and thereby got the new version of Matplotlib. 
 Now manually placing cline labels creates weird artefacts. I attached a demo 
 script at the bottom and uploaded a screenshot at 
 http://i.imgur.com/u6BLcRB.png . As you can see there is also a depreciation 
 warning. Now I downgraded to Matoplotlib 1.2.1 again (keeping all other 
 updates in place) and the problem is gone. I currently have very little time 
 for bug hunting and therefore will just stay away from updates for a while. 
 Maybe someone can figure out what's going wrong.


FWIW, I can confirm this issue in Ubuntu Raring with the development
version of matplotlib packaged in ppa:takluyver/matplotlib-daily.

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Re: [Matplotlib-users] datestr2num of year and month

[Goyo]

2013/9/19 Mark Bakker mark...@gmail.com:
 Hello List,

 When I use datestr2num('2010-05') it nicely converts that to a number
 representing the date.
 When I convert that number back with num2date, it turns out it sets the day
 to the 19th of the month. The dime is 0:00:00.
 Any reason it is set to the 19th instead of the first?
 Maybe because today it the 19th, or is that just a coincidence?

datestr2num calls dateutil.parser.parse, which by default uses the
current date at 00:00:00 for missing fields. The dateutil function
also can use a default argument to change this bahavoir but it is
not available in datestr2num.

http://labix.org/python-dateutil#head-a23e8ae0a661d77b89dfb3476f85b26f0b30349c

Goyo

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Re: [Matplotlib-users] Matplotlib installation issues

[Goyo]

2013/9/3 Michael Droettboom md...@stsci.edu:

 That's correct.  We could probably do a better job reporting that to the
 user, though.  Would you mind creating an issue for that?

https://github.com/matplotlib/matplotlib/issues/2379

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Re: [Matplotlib-users] Matplotlib installation issues

[Goyo]

2013/8/31 Dino Bektešević ljet...@gmail.com:
 Hello,

 After a little mishap from ubuntu 12.04 after which I reinstalled the
 OS, on this fresh install I did:

sudo apt-get install python-numpy python-scipy python-matplotlib ipython 
ipython-notebook python-pandas python-sympy python-nose

 as per scipy stack installation instructions and
 everything went more or less as it should have no errors reported
 during installation that I saw. Keep in mind the entire install like
 this had ~500MB or so and I wasn't always paying attention.
 I ran python, and did numpy.test(), returned:
Ran 3161 tests in 50.667s
OK (KNOWNFAIL=3, SKIP=4)
nose.result.TextTestResult run=3161 errors=0 failures=0

 did scipy.test(), returned:
Ran 3780 tests in 74.809s
FAILED (KNOWNFAIL=11, SKIP=13, failures=2)
nose.result.TextTestResult run=3780 errors=0 failures=2

 I send a mail to scipy mailing list couple of days ago, but still no answer,
 if someone knows how bad those 2 failures are please share and then
 did matplotlib.test() which was disasterous:
Ran 1065 tests in 284.956s
FAILED (KNOWNFAIL=267, errors=772)

With mpl 1.3.0 (packaged for Raring by Thomas Kluyver):

Ran 1465 tests in 402.499s
FAILED (KNOWNFAIL=1, SKIP=5, errors=1331)

But matplotlib itself is working pretty well. The output is full with
error messages like:

IOError: Baseline image
'/home/goyo/result_images/test_triangulation/tripcolor1-expected.svg'
does not exist.

It maybe that distro packages do not ship with baseline images. Looks
sensible to me since there must be an awful lot of them and most users
do not need them.

Goyo

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Re: [Matplotlib-users] Graph ticks label missing !

[Goyo]

2013/7/19 Nicolas Mailhot nicolas.mail...@laposte.net:
 Le Mer 17 juillet 2013 14:56, Michael Droettboom a écrit :
 Can you please provide a completely standalone example?  The following
 code has undefined variables etc.

 Here it is, I'm afraid this testcase intent is less clear than what I
 pasted previously (I replaced variables with precomputed values)

 As shown in the attached png, the bottom tick labels (month names) are
 missing. It worked in matplotlib ≤ 1.2.0

I can confirm the issue with 1.2.1 but it works with a recent
development version (output attached) so it must have been fixed at
some point.

Goyo
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Re: [Matplotlib-users] Setting right spine position to 'zero' locates spine at +1

[Goyo]

2013/4/26 Chad Parker parker.char...@gmail.com

 Hi all-

 I've been working on a plot that puts the bottom and right spines at zero
 (adapting some code from the example at
 http://matplotlib.org/examples/pylab_examples/spine_placement_demo.html)
 , and I've discovered that setting the position of the right spine to
 'zero' seems to locate it at x=1.

 Is this a bug? Or is there something that I'm missing?


It looks like a bug to me, set_position('data', x) puts the spine at x + 1
instead of x.

Goyo
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Re: [Matplotlib-users] plot_surface in pylab mode?

[Goyo]

2013/4/2 Benjamin Root ben.r...@ou.edu:


 I would suggest bringing this issue up with them (that the figure
 gets destroyed at the end of each cell).

The default behaviour of the inline backend is closing figures after cell
execution, but this is configurable[1]

That said you should be able to use the OO approach with oneliners like
this:

surf = plt.gca(projection='3d').plot_surface(...)

Or write you own pyplot-style function. Adding 3d plotting functions to
pyplot might or might not be a good thing, I can't tell. Or there might be
a separate, pyplot-like module for 3d. Does that make sense?

http://ipython.org/ipython-doc/stable/interactive/qtconsole.html#pylab-inline

Goyo
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Re: [Matplotlib-users] Matplotlib, Tk, and multithreading

[Goyo]

2013/3/14 Oliver King oliver.afr...@gmail.com:
 [...]
 I tried doing as you suggested [don't import Tk directly and change the 
 backend to Agg] but it still crashes with the same TkAqua message.

You must set the desired backend from the very begining and before
importing pylab o pyplot.

Goyo

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Re: [Matplotlib-users] ticklabels

[Goyo]

2013/3/14 Andrew H. Jaffe a.h.ja...@gmail.com:
 Dear all,

 None of the obvious ways for changing ticklabels seem to work for the current 
 version of Matplotlib (1.2.0 for me). At present, 
 ax.yaxis.get_ticklabels().get_text() returns empty strings, as does 
 ax.get_yticklabels(), and the equivalent set_* functions don't seem to have 
 any effect.

It seems to be working for me. I'm using a development version but I
don't thing this has changed.

In [1]: import matplotlib.pyplot as plt

In [2]: plt.get_backend()
Out[2]: 'TkAgg'

In [3]: plt.plot([1, 2])
Out[3]: [matplotlib.lines.Line2D at 0x424c310]

In [4]: plt.draw()

In [5]: labels = plt.gca().get_yticklabels()

In [6]: map(lambda x: x.get_text(), labels)
Out[6]: [u'1.0', u'1.2', u'1.4', u'1.6', u'1.8', u'2.0', u'2.2', '']

In [7]: plt.gca().set_yticklabels(['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h'])
Out[7]:
[matplotlib.text.Text at 0x3e97bd0,
 matplotlib.text.Text at 0x3ea2390,
 matplotlib.text.Text at 0x42bed90,
 matplotlib.text.Text at 0x42c0390,
 matplotlib.text.Text at 0x42c05d0,
 matplotlib.text.Text at 0x42c0c50,
 matplotlib.text.Text at 0x42c1310,
 matplotlib.text.Text at 0x42c1990]

In [8]: map(lambda x: x.get_text(), labels)
Out[8]: ['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h']

Goyo

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Re: [Matplotlib-users] confused by savefig.dpi and how can I set the dpi of jpeg format?

[Goyo]

2013/3/11 Chao YUE chaoyue...@gmail.com:
 Dear all,

 I searched the internet but still get confused by how can I save a figure
 with high dpi value to jpeg format.

 I am using matplotlib 1.2.0 with ubuntu system.
 In [14]: mat.__version__
 Out[14]: '1.2.0'

 I tried both setting the flag savefig.dpi flag in matplotlibrc as 300,
 and use fig.savefig('temp.jpg',dpi=300) when saving the figure.
 But when I checked the figure dpi with GIMP, it says 72.

I can replicate this, but saving as png I get the correct dpi. I don't
know if this is a bug or a limitation of the jpg format.

Anyway, the jpg and png images are made of the same number of pixels
hence the dpi should not be an issue provided you can scale the image
in your publishing software. And the png format will do better in many
cases.

Goyo

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Re: [Matplotlib-users] Incorrect ylabel placement in twinx

[Goyo]

2013/1/9 Goyo goyod...@gmail.com:
 I'm using matplotlib master from
 https://launchpad.net/%7Etakluyver/+archive/matplotlib-daily, ubuntu
 12.10 and python 2.7 and sometimes I get misplaced y labels for twinx
 plots. I file a bug at github with a sample script and figure images:
 https://github.com/matplotlib/matplotlib/issues/1608
 A guy commented there saying he can't replicate the issue. I wonder if
 anyone using ubuntu 12.10 can try my code with the matplotlib version
 from that repo and share the output.


Follow up: there's a PR for an older bug which works for me:
https://github.com/matplotlib/matplotlib/issues/1608#issuecomment-12071708

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[Matplotlib-users] Incorrect ylabel placement in twinx

[Goyo]

I'm using matplotlib master from
https://launchpad.net/%7Etakluyver/+archive/matplotlib-daily, ubuntu
12.10 and python 2.7 and sometimes I get misplaced y labels for twinx
plots. I file a bug at github with a sample script and figure images:
https://github.com/matplotlib/matplotlib/issues/1608
A guy commented there saying he can't replicate the issue. I wonder if
anyone using ubuntu 12.10 can try my code with the matplotlib version
from that repo and share the output.

Best regards

Goyo

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Re: [Matplotlib-users] bug with empty values dates

[Goyo]

2012/11/22 Jeffrey Melloy jmel...@gmail.com:
 I'm graphing data from a web service, and seem to have stumbled upon a
 bug when dates are graphed without any values.

 Here's a minimum repro:

 import datetime
 import matplotlib.pyplot as plt

 fig = plt.figure()
 ax = fig.add_subplot(111)

 x = []
 st = datetime.datetime(2012,11,21)
 while st  datetime.datetime(2012,11,21, 16, 00):
 x.append(st)
 st = st + datetime.timedelta(minutes=30)
 y = [None] * len(x)

 ax.plot(x,y)
 fig.autofmt_xdate()
 plt.show()


 The stack trace I get:

 Traceback (most recent call last):
   File min_mpl.py, line 15, in module
 fig.autofmt_xdate()
   File c:\python26\lib\site-packages\matplotlib\figure.py, line 318,
 in autofmt_xdate
 for label in ax.get_xticklabels():
   File c:\python26\lib\site-packages\matplotlib\axes.py, line 2507,
 in get_xticklabels
 self.xaxis.get_ticklabels(minor=minor))
   File c:\python26\lib\site-packages\matplotlib\axis.py, line 1104,
 in get_ticklabels
 return self.get_majorticklabels()
   File c:\python26\lib\site-packages\matplotlib\axis.py, line 1088,
 in get_majorticklabels
 ticks = self.get_major_ticks()
   File c:\python26\lib\site-packages\matplotlib\axis.py, line 1186,
 in get_major_ticks
 numticks = len(self.get_major_locator()())
   File c:\python26\lib\site-packages\matplotlib\dates.py, line 749,
 in __call__
 self.refresh()
   File c:\python26\lib\site-packages\matplotlib\dates.py, line 758, in 
 refresh
 dmin, dmax = self.viewlim_to_dt()
   File c:\python26\lib\site-packages\matplotlib\dates.py, line 530,
 in viewlim_to_dt
 return num2date(vmin, self.tz), num2date(vmax, self.tz)
   File c:\python26\lib\site-packages\matplotlib\dates.py, line 289,
 in num2date
 if not cbook.iterable(x): return _from_ordinalf(x, tz)
   File c:\python26\lib\site-packages\matplotlib\dates.py, line 203,
 in _from_ordinalf
 dt = datetime.datetime.fromordinal(ix)
 ValueError: ordinal must be = 1

 Adding a 0  the current date stops getting the exception, but the
 range seems wildly messed up. (2011 - 2014).

I can't figure out what's going on here, the calls in the stack trace
seem unrelated to Y data.
As a quick and dirty workaround you can set the first and last Y
values to 0 --won't work well if you use markers.

Goyo

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Re: [Matplotlib-users] Is there a way to create a plot and call show() so as not to use the main Qt loop?

[Goyo]

2012/11/4 Brickle Macho bricklema...@gmail.com:
 [...] When I show() a plot form within a Qt application I get the
 following message printed on the console:

 QCoreApplication::exec: The event loop is already running

 I think I understand the error, obviously the application I calling form
 control the even loop.  I suppose I need to somehow supply a parent
 window to pylab plot or the show() function.   Is there a way to create
 a plot and show so as not to use the main loop?

Do not use show() in a GUI application.
If you have a FigureCanvas instance embedded in your app, call its
draw() method.
If you use pyplot.figure() to create a matplotlib window from your
app, call pyplot.draw().

Goyo

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Re: [Matplotlib-users] using draw_if_interactive in library plots?

[Goyo]

2012/11/14 Skipper Seabold jsseab...@gmail.com:
 Hi All,

 Hoping someone can help me get a definitive answer to this question.
 Is draw_if_interactive bad to have in library plotting code?

I think the only issue here is the overhead of importing the whole
pyplot stuff and checking every now and then for interactive mode in
code which is not mainly designed for interactive use.

Something that I often do is writing non interactive plotting
functions or methods and then wrappers for interactive use which call
draw_if_interactive ant do other fancy things.

Goyo


 Based on this thread [1], we've been working under the assumption that
 calling draw_if_interactive in plotting code is bad. Though I'm
 skeptical that this is the takeaway that we should have. I also asked
 this question on the IPython mailing list [2] since the recommendation
 comes from their type of usage, but I'm still not clear.

 I'll repeat the gist of the question here.

 We have plotting functions that are designed to update a given axes. I
 often work in interactive mode, and I'd like it if these functions
 updated my axes in the way that I expect (and an R user doing plotting
 in Python would expect). But now I'm forced to litter my user scripts
 with draw_if_interactive after I call a function I expect to update a
 plot - say updating a scatter plot with a regression line. Would be
 harmful to just include these draw_if_interactive calls in our plot
 functions. To be clear, I never have to call show or draw because I'm
 working in interactive mode, so the recommendation to just call show()
 at the end of a script is not what I want.

 My understanding of the pitfalls is 1) there's a performance hit to
 calling draw instead of just making one call. This is moot because
 we're only calling draw_if_interactive - so we assume the user is
 working interactively and actually wants to do the drawing and doesn't
 care about the performance hit. And 2) we are assuming that the user
 has imported and is using pyplot and there are possible side effects.
 A user wouldn't be using pyplot in a GUI or in some sort of embedded
 plotting framework. However, my intuition says that if this is the
 case, draw_if_interactive won't do anything because interactive will
 be False in these cases.

 Can someone please help clear this up? Thanks,

 Skipper


 [1] 
 https://groups.google.com/forum/#!msg/pystatsmodels/biNlCvJPNNY/BT7bQJmOa1cJ
 [2] 
 http://python.6.n6.nabble.com/IPython-User-using-matplotlib-draw-if-interactive-in-library-code-td4991275.html

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Re: [Matplotlib-users] Legend Marker Color Bug

[Goyo]

2012/8/30 Sterling Smith smit...@fusion.gat.com:

 Thank you for taking the time to consider my question.  I'm sorry that I 
 didn't pose my question correctly.  I should have said: 'Consider the 
 _results_ of the following script:'  I originally tried to attach the results 
 I obtained, which showed no change in color for the markers in the legend, 
 while the line connecting the markers in the legend did change color.

Actualy your question is correctly posted but I misread it. Calling
set_color changes only the line color, not the markers. This is
expected and documented behavoir. There are separate methods for the
markers:

line[0].set_markerfacecolor
line[0].set_markeredgecolor

See 
http://matplotlib.sourceforge.net/api/artist_api.html#matplotlib.lines.Line2D

Regards

Goyo

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Re: [Matplotlib-users] Legend Marker Color Bug

[Goyo]

2012/8/28 Sterling Smith smit...@fusion.gat.com:
 List,

 Consider the following script:

 import pylab
 pylab.plot(pylab.linspace(0,1,100),label='Test',marker='o',ls='')
 pylab.plot(pylab.linspace(0,1,100),label='Test2',marker='o',ls='-')
 leg=pylab.legend(loc='best')
 line=leg.get_lines()
 line[0].set_color('black')
 line[1].set_color('black')
 pylab.draw()

 I am attaching the results I see with the TkAgg baackend.  I am using version 
 1.1.0.

 I would expect the markers to change colors also.  However, I can't seem to 
 find the markers recorded in the legend object to be able to change them.  Is 
 this a bug or a feature (resetting the color could lead to inconsistencies 
 between legend and plot)?


I think it's a design issue, there's no connection kept between plot
lines and the legend. You can change colors in the plot an then call
legend again instead.

Cheers

Goyo

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Re: [Matplotlib-users] space between bar and y-axis: works with 2 bars not with 3

[Goyo]

2012/8/17 mgurling magurl...@gmail.com:
 I've attached 2.py and 3.py which differ only in how many bars are graphed.
 The nudge variable was intended to move the left-most bar away from
 the y-axis.

Better use xlim to move the y-axis away from the bar:

a = [20, 35]
nudge = 0.2
ind = np.arange(2) + nudge
width = 0.30
bar(ind, a, width)
xlim(left=0)

Goyo

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Re: [Matplotlib-users] FancyBBox set_width

[Goyo]

2012/8/19 Peter Combs pcombs+...@gmail.com:
 Hi all,
 I'm trying to have a Text object with a fancy box, as in this example:
 http://matplotlib.sourceforge.net/mpl_examples/pylab_examples/fancybox_demo2.py
 .  However, the key difference is that I want to have the box (in my case,
 I'm interested in an RArrow) be a specified width (in units of the plot),
 rather than just fitting it to the text I've given (crude ascii art below).
 The following seems not to work:


 ax = gca()
 txtobj = ax.text(0, -.1 * yrange, 'text',
  bbox=dict(boxstyle='rarrow'))
 txtobj.get_bbox_patch().set_
 width(SIZE_IM_INTERESTED_IN)
 draw_if_interactive()

 It seems like draw()ing the text object will reset the size of the BBox...
 Any idea how to fix this? At the moment, I'm experimenting with continually
 drawing, polling the get_width() method, and when it's too small, adding in
 spaces around the text field, but that seems both not to work reliably, and
 be an incredibly boneheaded way to go about it.

Not ideal but better:

from pyplot import *
subplot(111)
text(0.1, 0.3, 'XXX', alpha=0, bbox=dict(boxstyle='rarrow'))
text(0.1, 0.3, 'short')
text(0.1, 0.6, 'XXX', alpha=0, bbox=dict(boxstyle='rarrow'))
text(0.1, 0.6, 'looong')
show()

Goyo

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Re: [Matplotlib-users] Matplotlib window not showing anymore

[Goyo]

2012/6/19 Mogliii mogl...@gmx.net:
 Hi,

 Kubuntu 12.04 with python 2.7 and matplotlib 1.1.1

 Suddenly the matplotlib window does not open anymore. I tried from
 konsole with pyton, ipython and also from eclipse with pydev. Last time
 I know it worked was maybe 5 days ago, haven't tried since then.

 In ipython --pylab it looks like this:

 In [1]: plt.plot(np.arange(5))
 Out[1]: [matplotlib.lines.Line2D at 0x2804fd0]

 In [2]: plt.show()

 In [3]:

 but no widow opens.

Make sure an interactive backend is in use:

plt.get_backend()


 I think it normally shouldn't give the object ID.

Yes, it should.

Goyo

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Re: [Matplotlib-users] Matplotlib window not showing anymore

[Goyo]

2012/6/19 Goyo goyod...@gmail.com:
 I think it normally shouldn't give the object ID.

 Yes, it should.


Sorry, not an object ID but a string representation of the returned object.

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Re: [Matplotlib-users] where did my plots go?

[Goyo]

2012/6/19 Andre' Walker-Loud walksl...@gmail.com:
 But my plots still vanish as soon as the script is done :

That's to be expected. You can make the script not to end until the
user ask for  it explicitly:

raw_input('Press Enter when you are done')

Goyo

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Re: [Matplotlib-users] suppress plotting window

[Goyo]

2012/6/8 Maximilian Fabricius mfabric...@gmail.com:
 Hi all,

 it seems that whenever I plot something, a window opens.

 from matplotlib import pylab
 import numpy
 pylab.plot(numpy.random.normal(size=100))

 Now, I have code that is supposed to produce diagnostic plots as PDFs. Only
 when I pass a command line option the script should actually open a
 window and also display
 the results on the screen.

 I am pretty sure that in earlier times the window would only open when
 I call pylab.show().

 It may well be that I messed too much with my matplotlibrc, if you
 could just point me in the right direction ...

 I use matplotlib 1.0.1 on a Mac with the MacOSX backend.

From 
http://matplotlib.sourceforge.net/faq/usage_faq.html#non-interactive-example:

--
import matplotlib.pyplot as plt
plt.ioff()
plt.plot([1.6, 2.7])

Nothing happened–or at least nothing has shown up on the screen
(unless you are using macosx backend, which is anomalous).
--


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Re: [Matplotlib-users] where did my plots go?

[Goyo]

2012/6/19 Benjamin Root ben.r...@ou.edu:


 On Tue, Jun 19, 2012 at 2:40 PM, Andre' Walker-Loud walksl...@gmail.com
 wrote:

 Hi Goyo,

  2012/6/19 Andre' Walker-Loud walksl...@gmail.com:
  But my plots still vanish as soon as the script is done :
 
  That's to be expected. You can make the script not to end until the
  user ask for  it explicitly:
 
  raw_input('Press Enter when you are done')

 If this is expected - it is a new feature.

 My understanding was that changing

 interactive  : True

 in the matplotlibrc file, then the plots would not vanish until explicitly
 closed by the user.

 Is my understanding incorrect?


 Thanks,

 Andre


 That is correct.  If you have a call to show(), then the script should not
 finish on their own until the windows are closed -- regardless of whether or
 not interactive is True or False.  The interactive setting should only
 dictate whether or not the script execution pauses or not at the call to
 show().

Then the script is supposed to keep itself alive, after executing the
last statment, until the plot windows are closed? Does not work that
way for me (tkagg, qt4agg and gtk*) and I wouldn't expect that.

BTW this may be better than using raw_input:

import matplotlib.pyplot as plt
plt.ion()
plt.plot([1.6, 2.7])  # The plot windows shows up.
# Do stuff, even user interaction, more plots, etc.
# ...
# Wait until all plot windows are closed.
plt.ioff()
plt.show()

Goyo

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Re: [Matplotlib-users] Scatter legend woes.

[Goyo]

2012/6/13 Mike Kaufman mck...@gmail.com:
 On 6/13/12 3:23 PM, Steven Boada wrote:
 Whoops, I forgot to change the subject. Sorry list.

 List,

 I'm making a scatter plot using a for loop. Here's a simple example..

 for i in range(10):
       x=rand()
       y=rand()
       scatter(x,y,label='point')

 legend()
 show()


 When you do this, you get a legend entry for every single point. In this
 case, I get 9 entries in my legend.

 Is there a way to only get a single entry?

Maybe you can adapt this to your use case:

for i in range(10):
 x=rand()
 y=rand()
 collection = scatter(x,y,label='point')

legend((collection,), ('Label',))
show()

Goyo

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Re: [Matplotlib-users] dates for x-axis

[Goyo]

El día 19 de abril de 2012 05:31, questions anon
questions.a...@gmail.com escribió:
 Thank you, I was able to get it to work but only if I imported datetime
 within the loop, otherwise I ended up with the
 AttributeError: type object 'datetime.datetime' has no attribute 'datetime'
 and if I added 'import datetime' at the top of my script it had an error
 where I loop through combining each month
     stop_month = datetime(2011, 03, 01)
 TypeError: 'module' object is not callable

If you can write a standalone, minimal executable script which
reproduces the problem I'll take a look. Send it as an attachement and
add sample data files if necessary.

Goyo

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Re: [Matplotlib-users] dates for x-axis

[Goyo]

El día 12 de abril de 2012 03:46, questions anon
questions.a...@gmail.com escribió:

 I am not sure how to recognise that x-axis are dates like 20110101,
 20110102, 20110103 etc.

Use datetime objects instead of strings.

Goyo

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Re: [Matplotlib-users] open ascii grid data and plot

[Goyo]

El día 21 de marzo de 2012 01:03, questions anon

 f=np.genfromtxt(inputfile, skip_header=6, dtype=None, names=True)

I don't think you should be using dtype=None if you wand a 2D array.
Also the names=True thing makes no sense to me since there isn't a row
with field names. Try just this and I guess you'll get a 2D array:

f=np.genfromtxt(inputfile, skip_header=6)

Goyo

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Re: [Matplotlib-users] open ascii grid data and plot

[Goyo]

El día 15 de marzo de 2012 05:14, questions anon
questions.a...@gmail.com escribió:
 I think my error is from the np.genfromtxt because I just checked the size
 of my data and it appears in 1D rather than 2D.

This is unsurprising since your file has just one row of data. I
overlooked that because the weird error message drove all my attention
to it. You can reshape the resulting array to (691, 886). Still that
error message should not be there in any case.

 I don't really understand what np.logical_or is or how to use it?
 I have tried just calling it at the beginning of the script

np.logical_or computes the logical out of two boolean arrays. It's
called internally by countourf and that's triggering the exception:

AttributeError: logical_or

Which makes no sense at all because:
1. np is expected to be an alias for numpy and numpy *does* have an
attribute called logical_or.
2. In case np didn't have an attribute called logical_or (for whatever
reason) it would cause an exception but the error message should be
something like AttributeError: 'module' object has no attribute
'logical_or'.

You where asked to call np.logical_or at the beginning of the script
in order to know if it triggers the exception in that context.

 [...] but I still end up with the same error.

So the call at the beginning didn't trigger the error?

Regards

Goyo

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Re: [Matplotlib-users] open ascii grid data and plot

[Goyo]

El día 12 de marzo de 2012 23:25, questions anon
questions.a...@gmail.com escribió:
[...]

 Is this how the data should look when it has been imported from an ascii to
 a numpy array?

I can't see anything obiously wrong in your code or your data --I did
not dive too deep into it though. What is weird is the traceback:

Traceback (most recent call last):
  File d:\plotrainfall.py, line 40, in module
CS = map.contourf(x,y, f, 15,cmap=plt.cm.jet)
  File C:\Python27\lib\site-packages\mpl_toolkits\basemap\__init__.py,
line 3072, in contourf
np.logical_or(outsidemask,np.logical_or(ma.getmaskarray(data),xymask))
AttributeError: logical_or

Is that the complete traceback?

Goyo

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Re: [Matplotlib-users] where is line after remove?

[Goyo]

El día 13 de marzo de 2012 00:25, Federico Ariza
ariza.feder...@gmail.com escribió:
 [...]
 I want to turn visibility on and off for lines.
 I can not use the visible property, using it the autolimits relim keeps
 considering the lines as being there.
 As consequence the limits are wrong (if we think only on the visible lines).

I faced this some time ago and my workaround was writing my own
(simplified) version of relim, if memory serves. But this may not fit
your needs here. Maybe a better solution is modify relim upstream so
it can take visibility into account (maybe using a new keyword). Just
a quick thought.

 So I resorted to remove the line from its axes by line.remove()

 The question is:
 If I do not want to use another variable to keep track of this line, how can
 I find it again from the figure instance (or somewhere else)?
 get_children gets me nowhere or maybe?

I don't think matplotlib keeps a reference to a line object after you
remove it from the axes. If I'm right and you want to follow that path
you'll need to track it yourself.

Regards

Goyo

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Re: [Matplotlib-users] python nltk plots are not showing up

[Goyo]

El día 12 de marzo de 2012 17:05, Gias Uddin gia...@gmail.com escribió:
 I have posted the following message in StackOverflow about my problem with
 graph plotting using python nltk using Matplotlib and numpy.
 Advices will be tremendously helpful. Thanks in advance.

 http://stackoverflow.com/questions/9661909/python-nltk-plots-are-not-showing-up

This usually happens when you're using a non interactive backend.
What's the output of plt.get_backend()?

Goyo

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Re: [Matplotlib-users] Set various parameters of a plot window.

[Goyo]

El día 11 de marzo de 2012 11:31, gsal salger...@gmail.com escribió:

 I am not quite sure what you are asking, but, can you simply just add your
 own attribute to the window objects?  Python is friendly that way, you know?
 It's dynamic.

There are some dialogs not accesible using the mpl api. The save
dialogs seem to be the standard ones for the underlying toolkit so
reading the toolkit docs may help. Then there are the subplot params
configuration dialogs.

Goyo

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Re: [Matplotlib-users] Non-interactive plotting to window?

[Goyo]

2011/12/15 John Thorstensen john.thorsten...@dartmouth.edu:

 So my question:  Is there a simple way of getting matplotlib to display a
 plot in a window and then surrender control to the main program, without
 destroying the plot?  Something like a method to kill mainloop would be
 ideal.

Just make sure you use interactive mode and get rid of the show calls:

import matplotlib.pyplot as plt
plt.ion()  # set interactive mode
plt.plot(foo)  # plot something
bar()  # do stuff while the plot is visible
plt.close()  # if you want to close the plot window from the script

This works in mpl 1.1.0 al least with tkagg, gtkagg and qt4agg backends.

Goyo

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Re: [Matplotlib-users] missing library animation from enthought distribution

[Goyo]

2011/11/22 Robert Kern robert.k...@gmail.com:

 To get matplotlib 1.1.0 right now, you will have to build it yourself from
 sources.

Matplotlib packages for Precise also seem to work well in Oneiric.

Goyo

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Re: [Matplotlib-users] I have a problem with installation of python(x, y).

[Goyo]

2011/11/15 Jun Tanaka tna...@gmail.com:
 Dear All,
 I have a problem with installation of python(x,y). When I try, it says
 python 2.6.2 msi was not found If anyone knows how to resolve this issue,
 please help me. My OS is windows 7 64bit.
  If this mailing lists does not help pyhton(x,y) issue, please lead me to a
 right place.

Try the python(x,y) discussion group
http://groups.google.com/group/pythonxy

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Re: [Matplotlib-users] Inexact drawing of points

[Goyo]

2011/11/7 Anton Daitche a.dait...@googlemail.com:

 Do you remember the name of the thread? I would like to understand the
 details on this.

I can't find it right now but I guess Michael's answer helps you.

 I also would like to find out if i can force the renderer to do exact
 drawing (at some computational cost).

Do you mean using an interactive backend? You can try gtkcairo and wx.
I think they have their own issues though.

Goyo

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Re: [Matplotlib-users] Inexact drawing of points

[Goyo]

2011/11/2 Anton Daitche a.dait...@googlemail.com:
 Hallo,
 i am observing inexact drawing of point in matplotlib.

As I remember from an earlier discussion on this, it's assumed that
these small deviations are tolerable in the agg renderer. This makes
the interactive backends more responsive at expenses of accuracy.

I can see the same deviations using the tkagg backend with mpl 1.1.0
but if I save as pdf using the save button I get an accurate rendering
(see attachment).

Best regards

Goyo


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Re: [Matplotlib-users] Forcing the size of a figure

[Goyo]

Maybe you need to call fig.canvas.draw() to get the figura actually resized.


2011/8/12, Benjamin Root ben.r...@ou.edu:
 On Fri, Aug 12, 2011 at 10:04 AM, David Just just.da...@mayo.edu wrote:

  Now that I’m pre-building all my enlarged interpolated images to scroll
 through,  I’m having trouble forcing the figure/FigureCanvas to be the
 size
 I want.

 I’m trying:
 fig.set_size_inches(768 / 72.0, 768 / 72.0),  but it ends up the same size
 as the default plot.

 Thanks,
 Dave



 Dave,

 Don't know if that is a bug or not (never tried that function).  Typically,
 I just use the figsize kwarg in the figure constructor.  Is it possible to
 do it from there, or are you looking to adjust the figure size *after* the
 figure has been displayed already?

 Ben Root


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Re: [Matplotlib-users] Autoscaling after removing lines.

[Goyo]

Seems like Axes.relim is what I was looking for. It does not take
collections into account but I don't need that for now.

2011/8/1, Goyo goyod...@gmail.com:
 Hy all,

 I recently had a pretty hard time trying to figure out how to properly
 autoscale a plot after removing a line (see attached script). Finally
 I found at [1] that I have to explicitly refresh the axes dataLim
 before autoscaling.

 In [1] John Hunter says that computing the proper dataLim can be
 complicated if there are several types of artists in the axes, like
 polygons and collections an that [it] would be useful to have an Axes
 method like auto_datalim to for the datalim to readjust to all the
 current data.

 My question is whether such a function has been implemented. Besides
 any suggestions about how to deal with this are welcome. I just need
 to adjust to lines right now but this may change in the future.

 Best regards

 Goyo

 [1] http://old.nabble.com/Removing-a-line-from-a-plot-td7249600.html


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[Matplotlib-users] Autoscaling after removing lines.

[Goyo]

Hy all,

I recently had a pretty hard time trying to figure out how to properly
autoscale a plot after removing a line (see attached script). Finally
I found at [1] that I have to explicitly refresh the axes dataLim
before autoscaling.

In [1] John Hunter says that computing the proper dataLim can be
complicated if there are several types of artists in the axes, like
polygons and collections an that [it] would be useful to have an Axes
method like auto_datalim to for the datalim to readjust to all the
current data.

My question is whether such a function has been implemented. Besides
any suggestions about how to deal with this are welcome. I just need
to adjust to lines right now but this may change in the future.

Best regards

Goyo

[1] http://old.nabble.com/Removing-a-line-from-a-plot-td7249600.html


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Description: Binary data
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Re: [Matplotlib-users] Basemap river plotting

[Goyo]

2011/6/16 stefanie lue...@googlemail.com:
 Hello!

 I'm plotting the river danube and some other stuff around it. Is there
 an easy way to extract several rectangles around the river and plot this
 rectangles next to each other? My aim is to print the whole river on a
 paper. My idea is to cut a rectangle every 100km, turn it straight (but
 marking North) and put all rectangles next/under each other. Or should I
 plot everything and continue with an image library?

You can add several maps to the print composer, then make each map
show the region you want.

Goyo

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Re: [Matplotlib-users] Text outside the graphs box

[Goyo]

2011/5/15 Johannes Radinger jradin...@gmx.at:
 How is the space between the axis and the outer margins of a figure defined?
 How much space is between the upper most plot and the upper end of the figure?
 This is the space e.g for the titles etc. but can this be space be increased?

Use subplots_adjust.

Goyo

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Re: [Matplotlib-users] Possible bug / odd behaviour in GridSpec?

[Goyo]

2011/5/12 David Andrews irbda...@gmail.com:
 Hi,

 I've come across something I don't entirely understand in the
 behaviour of gridspec.  It's not obvious from the code  docs for this
 module, but is it only supposed to be able to deal with 'square'
 layouts, e.g. 3x3, 4x4 etc?

 Taking some code from an example on the gridspec page ...

 import matplotlib.pylab as plt
 import matplotlib.gridspec as gridspec
 #gs = gridspec.GridSpec(3, 3) # OK
 gs = gridspec.GridSpec(6, 3) # Will cause an error later on
 ax1 = plt.subplot(gs[0, :])
 ax2 = plt.subplot(gs[1,:-1])
 ax3 = plt.subplot(gs[1:,-1])
 ax4 = plt.subplot(gs[-1,0])
 ax5 = plt.subplot(gs[-1,-2])
 plt.show()

 ... will fail if that line is uncommented, giving an index error.

Works for me.
Ubuntu 11.04 Natty, stock python 2.7.1 and matplotlib 1.0.1 from
https://launchpad.net/~valavanisalex/+archive/matplotlib.

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Re: [Matplotlib-users] Asymmetrical arrangements of subplots

[Goyo]

2011/5/5 Sebastian Krieger sebastian.krie...@usp.br:
 Dear all,

 I have a small question about subplot. I want to avoid creating plot axes
 manually using pylab.axes, to create an asymmetrical arrangement of subplots
 like the following code in Matlab:

 figure
 subplot(2,2,1:2)
 text(.5,.5,'subplot(2,2,1:2)',...
 'FontSize',14,'HorizontalAlignment','center')
 subplot(2,2,3)
 text(.5,.5,'subplot(2,2,3)',...
 'FontSize',14,'HorizontalAlignment','center')
 subplot(2,2,4)
 text(.5,.5,'subplot(2,2,4)',...
 'FontSize',14,'HorizontalAlignment','center')

 Reference: http://www.mathworks.com/help/techdoc/ref/subplot.html

 Is it possible in matplotlib?

Easier done than explained:

import matplotlib.pyplot as plt
plt.subplot(121)
plt.subplot(222)
plt.subplot(224)
plt.show()

Goyo

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Re: [Matplotlib-users] Subplot x-tick labels overlap with each other and with titles

[Goyo]

2011/5/5 Chris Rodgers chris.rodg...@berkeley.edu:
 1) Is this the intended behavior of matplotlib, or is there something
 wrong with my installation?

This is by design, hspace and vspace are proportional to the size of
each subplot. Also the number of ticks does not depend on the subplot
or labels size (using the default locator). So you have to fine tune
if things don't fit together. Of course you can write custom
subplot-like functions which take care of this the way you find more
convenient.

I wonder how other plotting packages deal with this.

Goyo

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Re: [Matplotlib-users] Date format the x-axis of a barh() plot?

[Goyo]

2011/4/23 jfortiv jfor...@gmail.com:

 Hi,

 This actually did not work for me.  Can you show me the full code that you
 used to successfully produce the time-format x-axis labels?

See attached files.

Goyo


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Re: [Matplotlib-users] Try to have none-overlapping labels in one axe using matshow

[Goyo]

2011/4/23 _olivier_ olir...@gmail.com:
 [...]

 I have got a matrix 6x500 (so one size is much biggger than the other one)
 and I try to expand the shorter axe so that the labels on it are well
 displayed (not overlapped.

Use the aspect kwarg in matshow.

Goyo

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Re: [Matplotlib-users] Linecollection, labels

[Goyo]

2011/4/13 Tim Åberg qw...@hotmail.com:

 Due to that my first question a couple of day back was a mess i thougth i
 could clear things up.

 Is there any way to label the lines using linecollection. In plot there is
 label, example;
 plot(x,y,label = Hello)

 But are there any way to do the same thing with linecollection?
 If not, is there any eother asy way of creating labels on a line?

You can customize the legend by hand.
http://matplotlib.sourceforge.net/users/legend_guide.html

Goyo

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Re: [Matplotlib-users] Error when plotting negative values on log scale

[Goyo]

2011/3/10 Søren Nielsen soren.skou.niel...@gmail.com:

 Is there a way I can get around this without having to search through my
 data and remove points that are negative or NaN or INF when the yscale needs
 to be log? That would also show an incorrect curve since a line would be
 drawn across the points that were removed.. It should rather be gaps in the
 line.

You can use masked arrays. Masked values don't get plotted. Sample
code (not tested):

import numpy.ma as ma  # masked arrays module
...
mdata = ma.masked_array(data)
mdata[mdata = 0] = ma.masked
plot(mdata)

Goyo

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Re: [Matplotlib-users] Axes formatting

[Goyo]

2011/3/11 Luciano Fleischfresser l_...@yahoo.com:
 [...]
 I have to confess that object-oriented programming seems very
 counter-intuitive to me.
 Hopefully it will come more naturally soon.

This has nothing to do with OOP, you just need to know what
command/function/method does what you want. It happens that in
matplotlib plots are autoscaled by default but not tightly. You can
change this behavoir using autoscale. There is a functional version
pyplot.autoscale but for scripting is usually better the
axes.autoscale version because it make explicit in your code which
axes is affected. For interactive plotting, the functional version may
be more convenient.


 Along the same lines of my original query, this one I think is more obscure,
 so here it goes:

 Same script, just another .csv file with the same format. This time around,
 the plot comes up
 with UTC times for the labels on the x-axis. The first one came with the
 dates.

 Does anybody know how to tell matplotlib to always put dates?

Matplotlib automatically choose a formatter for labels, based on the
interval to plot and the like. If you don't like it, use your own.
Maybe this:

import matplotlib.dates as mdates
formatter = mdates.DateFormatter('%d-%b-%y-%H:%M:%S')
axes.xaxis.set_major_formatter(formatter)

Goyo

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Re: [Matplotlib-users] pyplot.figure() memory leak?

[Goyo]

2011/3/8 Paul Anton Letnes paul.anton.let...@gmail.com:
 Hi!

 This simple loop:
 import time
 import pylab
 for i in range(100):
 ...     time.sleep(0.1)
 ...     pylab.figure()
 ...
 will have python use more and more memory. While this is not technically a 
 memory leak, it becomes one in practice, if I want to create a large number 
 of figure objects. How can I free the memory used by one or all figure 
 objects?

Your code creating many objects is not a memory leak. You can reuse
figures or dispose of them calling pylab.close(). See docstrings for
pylab.close and pylab.clf.

Goyo

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Re: [Matplotlib-users] Text box adaptable

[Goyo]

2011/3/7 Andrea Crotti andrea.crott...@gmail.com:
 [...]
 t = matplotlib.text.Text(0, 0, very long string)
 t.get_bbox_patch()

 to get the size and then do the rest.

 but this still returns None, probably because at this point there's
 probably something still missing, right?

 And when I get the resulting size, how do I make my axes big enough
 anyway?

As Ben explained you need to draw first. So the usual path is:
1. Draw
2. Figure out the size of potentially problematic things (labels,
titles...) and the space you need.
3. Adjust subplots or whatever needs adjustment to fit.
4. Draw again.

Sort of weird but it works and I think it's widely used.

Goyo

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Re: [Matplotlib-users] Best way to modify plot / subplot

[Goyo]

David, the preferred way to custom plots seems to be passing an Axes
instance to the plotting function. Some tricks allow use of
pylab/pyplot style:

def custom_plot(x, y, axes=None):
...
if axes is None: axes = pyplot.gca()
axes.plot(x, y)


What you don't get this way is the axes.custom_plot(x, y) sintax,
which requires subclassing Axes. But doing this is not common and not
straighforward if you want it to work well with pyplot.subplot() and
the like.

Maybe monkey patching would work but well, you know... I never tried it anyway.

Goyo

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Re: [Matplotlib-users] Histogram with single series - colour coding different ranges?

[Goyo]

2011/2/22 Benjamin Root ben.r...@ou.edu:

 Admittedly, this isn't using matplotlib's hist() function because it only
 allows for one color per dataset.  However, you can use numpy's histogram
 function to get the bins and counts yourself, and then use bar() to make the
 bars.  bar() will allow you to color the bars individually.

Pylab hist() returns a list of patches so you can also change their properties.

Goyo

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Re: [Matplotlib-users] Setting the ticks on an axis

[Goyo]

2011/2/20 Curiouslearn curiousle...@gmail.com:
 Thomas and Goyo,

 Thanks for the answers. I am fine with them being coverted to ints. In
 fact, my ax.set_ylim(bottom=0, top=6000) contains ints and I don't
 understand why they are converted to floats. I was thinking that there
 is perhaps another (more correct) way to set tick values.

You can use locators, but set_yticks is good enough for simple cases.
http://matplotlib.sourceforge.net/api/ticker_api.html

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Re: [Matplotlib-users] Setting the ticks on an axis

[Goyo]

2011/2/19 Thomas Lecocq thlec...@msn.com:

 To avoid having the warning, you can explicitly provide ints :

  ax.set_yticks(range(int(ax.get_ylim()[0]), int(ax.get_ylim()[1]), 400))

 I don't know any easier method of setting the ticks... Let's wait for the
 user community input !

If you don't want your floats converted to ints then use numpy arrange
or linespace.

Goyo

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Re: [Matplotlib-users] There is no plot in the PNG file. The PDF file is fine.

[Goyo]

2011/2/9 Curiouslearn curiousle...@gmail.com

 Can you please see the code below and let me know why the png figure
 comes out empty (it only contains the x-axis, does not contain the
 scatterplot). The pdf file has no such problems.

Seems like mpl is getting confused because of the rect argument of
add_axes. Note that bottom is 0.3 and height is 0.9 so bottom + heigt
 1. Maybe different backends differs handling the overflow.

Does this change in line 12 fix your issue?:

ax1 = fig1.add_axes([0.1, 0.3, 0.8, 0.6])

Goyo



 I have tried saving another usual line plot in .png format and I had
 no problems. Does this have to do with scatter plot and .png format?

 Thank you.

 The code

 import matplotlib.pyplot as plt
 import numpy

 differences = numpy.random.uniform(-2,2,190)

 bin_values = numpy.arange(-2,2.6,0.1)
 hist, bins = numpy.histogram(differences, bins = bin_values)

 fig1 = plt.figure()
 fig1.set_figwidth(6)
 fig1.set_figheight(3)
 ax1 = fig1.add_axes([0.1, 0.3, 0.8, 0.9])
 ax1.patch.set_facecolor('Linen')

 for left, hist_val in zip(bins[:-1], hist):
    xvec = [left]*hist_val
    yvec = 0.05*numpy.arange(hist_val) + 0.1
    if len(xvec)  0:
        ax1.scatter(xvec,yvec)

 ax1.axvline(1.3, ymax=0.6, color='DarkGreen')

 # The frame of the axes is referred to as
 # spines in matplotlib
 for i in ax1.spines.iteritems():
    if i[0] in ['top','right', 'left']:
        i[1].set_visible(False)
    print i


 # Ticks only in bottom
 ax1.xaxis.set_ticks_position('bottom')
 ax1.yaxis.set_ticks_position('none')
 ax1.set_ylim(bottom=0,top=1.5)



 fig1.savefig('trial_figure.png', facecolor='Linen')
 fig1.savefig('trial_figure.pdf', facecolor='Linen')

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Re: [Matplotlib-users] Bug in boxplot/mlab.prctile

[Goyo]

2011/1/1 OKB (not okblacke) brenb...@brenbarn.net:
        I noticed that the boxplot function incorrectly calculates the
 location of the median line in each box.  As a simple example, plotting
 the dataset [1, 2, 3, 4] incorrectly plots the median line at 3.

It seems to work fine in matplotlib 1.0.0:

u...@host:~$ python
Python 2.6.6 (r266:84292, Sep 15 2010, 16:22:56)
[GCC 4.4.5] on linux2
Type help, copyright, credits or license for more information.
 import matplotlib as mpl
 mpl.__version__
'1.0.0'
 import matplotlib.pyplot as plt
 import matplotlib.mlab as mlab
 plt.ion()
 plt.boxplot([1, 2, 3, 4])
{'medians': [matplotlib.lines.Line2D object at 0x3ad6250], 'fliers':
[matplotlib.lines.Line2D object at 0x3ad6610,
matplotlib.lines.Line2D object at 0x3ad69d0], 'whiskers':
[matplotlib.lines.Line2D object at 0x3acff50,
matplotlib.lines.Line2D object at 0x3ad4310], 'boxes':
[matplotlib.lines.Line2D object at 0x3ad4e50], 'caps':
[matplotlib.lines.Line2D object at 0x3ad46d0,
matplotlib.lines.Line2D object at 0x3ad4a90]}
 plt.grid()
 plt.boxplot([1, 2, 3, 4])
{'medians': [matplotlib.lines.Line2D object at 0x3dfbad0], 'fliers':
[matplotlib.lines.Line2D object at 0x3dfbe90,
matplotlib.lines.Line2D object at 0x3dff290], 'whiskers':
[matplotlib.lines.Line2D object at 0x3df8810,
matplotlib.lines.Line2D object at 0x3df8b90], 'boxes':
[matplotlib.lines.Line2D object at 0x3dfb710], 'caps':
[matplotlib.lines.Line2D object at 0x3df8f50,
matplotlib.lines.Line2D object at 0x3dfb350]}
 plt.grid()
 # See attached image.
...
 mlab.prctile([1, 2, 3, 4])
array([ 1.  ,  1.75,  2.5 ,  3.25,  4.  ])

Goyo


        It also seems that the quartile calculations for the box are a
 little peculiar.  I have seen some discussion in old mailing list
 postings about mlab.prctile and its ways of calculating percentiles,
 which are different than those of some other software.

        I'm aware that there is legitimate disagreement about the best
 way to calculate the quartiles.  However, it seems to me that mlab's way
 is still not any of these possibly-correct ways, because it uses int()
 or nparray.astype(int) to coerce the percentile result to an integer
 index.  This TRUNCATES the floating-point result.  No accepted quantile-
 calculating method that I'm aware of does this; they all ROUND instead
 of truncating (if they want to coerce to an integer index at all, in
 order to produce a quantile value that is an element of the data set),
 or in some cases they round uniformly up for the lower quartile and
 down for the upper.  You can see a summary of different methods at
 http://www.amstat.org/publications/jse/v14n3/langford.html ; the method
 used by mlab does not appear to agree with any of these.

        I would suggest that mlab.prctile be fixed to conform to some one
 or other of these methods, rather than adding to the proliferation of
 approaches to quantile-calculation.  Is there any motivation for always
 truncating to integer (other that it's quicker to type :-)?

        Also, regardless of these quartile issues, there is, as far as I'm
 aware, no one who denies that the median of a (sorted) data set with an
 even number of values is the mean of the middle two values.  Since numpy
 is already a dependency for matplotlib, boxplot shouldn't use
 mlab.prctile at all to decide where to plot the median line -- just use
 numpy.median.

 Thanks,
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Re: [Matplotlib-users] starting with pplots

[Goyo]

2010/12/19 Pawel pawe...@gmail.com:
 Hi,

 I am a new user of matplotlib so maybe my question is elementary, but
 have not been able to find an answer to my problem in the archive.

 I would like to make a 2D plot of colored points of 3D data (clusters).
 My data looks like this:

 11837.2120    -0.0858    2.
 23975.2120    -0.0672    2.
 37609.2120    -0.0306    2.
 53263.9800    -0.0690    2.
 72106.6760    0.2708     1.
 92674.6760    -0.0129    3.
 116758.676    -0.1245    3.
 ...

 So I need to plot the first and second column as points on the x-y axis
 and color the points according to the numbers in the third column (which
 are integers ranging from 1 to5).

 I'd appreciate any help. I realize something so typical should be
 somewhere in the documentation but I was not able to find it.

Try this:

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
x, y, z = np.loadtxt('data.txt', unpack=True)
cmap = ListedColormap(['b', 'g', 'r', 'c', 'm'])
plt.scatter(x, y, c=z, cmap=cmap, vmin=1, vmax=5)
plt.show()

You'll need to use a single space as column delimiter in your data
file or deal with more loadtxt arguments.

If your z data were color specifications you could just use
plt.scatter(x, y, c=z) as stated in the scatter docstring. Converting
arbitrary data to color specifications is the non trivial issue here.
You can write your own code to do this or use colormaps.


Goyo

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Re: [Matplotlib-users] unable to point pick 2nd axis after upgrade to mpl 1.0

[Goyo]

2010/12/9 C M cmpyt...@gmail.com:

 I have created a runnable sample app that demonstrates the problem

 Here is a much simpler 10 line sample that doesn't require wxPython and
 demonstrates the problem:  you can't pick the red line.  This seems like a
 bug in mpl 1.0.

Confirmed using tkagg, mpl 1.0.0 and Ubuntu 10.10. I do not know much
about the semantics of the pick event but it I don't think it should
discriminate between lines in the same canvas si I guess it's a bug.

Goyo

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Re: [Matplotlib-users] Limit legend to visible data

[Goyo]

2010/12/3 Justin McCann jne...@gmail.com:
 On Wed, Dec 1, 2010 at 11:58 AM, Justin McCann jne...@gmail.com wrote:
 This seems to do the trick, but might be a bit too clever. I'm not
 sure if get_children() (or findobjs) is the right call to retrieve all
 the plot elements.

If you are just looking for line2D instances then use ax.get_lines().

Goyo

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Re: [Matplotlib-users] Scatter Plot with different colors

[Goyo]

2010/10/10 Alessio Civ viandant...@gmail.com:


 Please, can someone help me? I've been digging the documentation, but I
 can't find a way to do this.

¿Didn't you get my message on oct-5? I didn't send it to the list by mistake:

--%
Make your variables numpy arrays and slice them using values in z:

x = np.array([1, 2, 3, 4])
y = np.array([2, 3, 4, 5])
z = np.array([0, 1, 0, 1])

x0 = x[z == 0]
y0 = y[z == 1]
x1 = x[z == 0]
y1 = y[z == 1]

plt.scatter(x0, y0, c='b')
plt.scatter(x1, y1, c='r')

--%

See the attached example, you can run it as a script or import it as a
module and use the function multi_scatter in your code.

Goyo


multi_scatter.py
Description: Binary data
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Re: [Matplotlib-users] Comet

[Goyo]

Hi David,

El sáb, 06-02-2010 a las 10:21 -0800, David Arnold escribió:
 Hi Eric,
 
 Matlab has two commands, comet and comet3, that animate the path. They are 
 used as in the following Matlab code:
 
 t=linspace(0,2*pi,2000);
 x=-sin(t);
 y=cos(t);
 comet(x,y)

You can just write the function:

import matplotlib.pyplot as plt

def comet(x, y, fmt='', step=1, **kwargs):
l, = plt.plot(x, y, fmt, **kwargs)
num_points = len(x)
for i in xrange(1, num_points + 1, step):
l.set_data(x[:i], y[:i])
plt.draw()
l.set_data(x, y)
plt.draw()

I think this could be better done using animation features of
matplotlib, but I never used them and I think they varies across
toolkits. Search the docs for animation examples anyway.

Goyo

 
 What then happens is the path is drawn live, as in my python code below.
 
 This is especially useful when teaching parametric equations in calculus. A 
 typical question in that section might be: find a parametrization for the 
 unit circle that starts at (0,1) and moves around the circle one time in the 
 counterclockwise direction. In this situation, the following is not helpful:
 
 t=linspace(0,2*pi,2000);
 x=-sin(t);
 y=cos(t);
 plot(x,y)
 
 Because the student just sees sees the finished path. The comet command, on 
 the other hand, allows the student to see that path as it is traced out in 
 real time.
 
 David.
 
 On Feb 6, 2010, at 9:09 AM, Eric Firing wrote:
 
  David Arnold wrote:
  All,
  I am still wondering why there is no comet command in matplotlib. I was 
  successful with the following:
  import matplotlib.pyplot as plt
  import numpy as np
  len=200
  t=np.linspace(0,2*np.pi,len)
  x=np.cos(t)
  y=np.sin(t)
  xd=[x[0]]
  yd=[y[0]]
  l,=plt.plot(xd,yd)
  plt.axis([-1,1,-1,1])
  for i in np.arange(1,len):
 xd.append(x[i])
 yd.append(y[i])
 l.set_xdata(xd)
 l.set_ydata(yd)
 plt.draw()
 
  plt.show()
  But it seems that a comet function added to the matplotlib library would 
  greatly simplify things for students using the interactive pylab in 
  ipython.
  
  I don't understand--what's the point of the example?  What is comet, and 
  how does it simplify anything?
  
  Eric
  
 
 
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Re: [Matplotlib-users] ginput then show causes segfault

[Goyo]

El sáb, 21-02-2009 a las 16:26 -0800, Daniel Soto escribió:
 i'd like to plot some data, get user input, and then plot the original  
 data and user input.  when i try to show() the data i get a segfault  
 after about ten seconds.
 
 any clue what i'm doing wrong?  using mac os x 10.5 with enthought  
 distribution.
 
 thanks,
 drs
 
 #!/usr/bin/env python
 
 import pylab
 
 x = pylab.arange(0,10,0.1)
 y = pylab.sin(x)
 
 # plot and get user input, then close fig
 pylab.plot(x,y)
 points = pylab.ginput(2)
 points = pylab.array(points)
 pylab.close()
 
 # replot with chosen points
 pylab.plot(x,y)
 pylab.plot(points[:,0],points[:,1],'ko')
 pylab.show()
 # wait for it, wait for it...now segfault

Your code works for me in Ubuntu 8.10, mpl 0.98.5.2 (Debian package!)
and GTKAgg backend.

Goyo


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Re: [Matplotlib-users] Issues with time display

[Goyo]

Hi clolern2,

 - for some reason a TZ has been inserted

Datetime values are stored as numbers. Timezone info is added when that numbers 
are converted again into datetimes for labelling.

 - graphs have white space buffers on either side of the X-axix

You can use axes.xlim in order to adjust it.

 - points on X-axis are separated by the hour, instead of values in datetime
 object

Matplotlib automagically chooses a format depending on the scale but you
can specify a format:

import matplotlib.dates as mdates
...
xaxis.set_major_formatter(mdates.DateFormatter('%Y-%b-%d %H:%M'))

Goyo

El mié, 11-02-2009 a las 09:38 -0800, collern2 escribió:
 Hi,
 
 I've managed to take the contents of my CSV file and display it with
 matplotlib. I'm having some issues with the way my X-axis is being
 displayed.
 
 For the X-axis, I pass in a list that filled with datetime objects, an
 example of one element on the list:
 
 datetime.datetime(2007, 12, 17, 20, 28, 15),
 
 Issues (please see the attached cpu.png:
 
 - for some reason a TZ has been inserted
 - graphs have white space buffers on either side of the X-axix
 - points on X-axis are separated by the hour, instead of values in datetime
 object
 
 I have tried many variations of plotdate, etc. If someone could please point
 me in the right direction.
 
 Thanks
 
 =
 Code http://www.nabble.com/file/p21958283/cpu.png 
 =
 
 #!/usr/bin/env python
 
 import csv
 import sys
 import matplotlib.pyplot as plt
 import datetime
 
 new_list = []
 time = []
 cpu = []
 
 fileReader = csv.reader(open(sample.csv, rb))
 for row in fileReader:
 new_list.append(row)
 
 # Converts papatimes time format into dattime
 def time_split(current_line):
 # splits papastats datetime format in useable python list
 dt = datetime.datetime.strptime(current_line[0],%Y/%m/%d %H:%M:%S)
 time.append(dt)
 
 def cpu_calc(current_line):
 cpu.append(current_line[11].rstrip(%))
 
 #Iterate over list of CSV values
 for i in new_list[1:]:
 time_split(i)
 cpu_calc(i)
 
 plt.plot(time, cpu, 'b-')
 #plt.plot_date(time, cpu, fmt='b-', xdate=False, ydate=False, tz=None)
 
 plt.xlabel('Time')
 plt.ylabel('CPU %')
 plt.title('Daily CPU Usage')
 plt.grid(True)
 plt.grid(alpha=0.2, color='black', linestyle='-', linewidth=0.1)
 plt.show()
 


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Re: [Matplotlib-users] How do I debug under PythonWin or IDLE?

[Goyo]

El jue, 08-01-2009 a las 12:09 -0600, de...@verizon.net escribió:
 I am sure this is a well know issue, so please feel free to just give a 
 link if the answer and solution are long.  I have a newly installed 
 matplotlib installations running on Windows XP using Python 2.5.4.  When 
 I execute a simple 4 line example (copied directly from the PyPlot 
 tutorial) in either PythonWin or IDLE, , it works fine and I terminate 
 by right clicking on the generated figure and doing a Close.  However, 
 when I rerun the code from the IDE (makes no difference if I use 
 PythonWin or IDLE) the figure hangs and eventually I get an abnormal 
 exit and crash out of the IDE (in PythonWin there is a dialogue box that 
 says “Runtime Error” in pythonwin.exe.  This makes debugging in an IDE 
 very clumsy, because I need to exit and restart it every time I run 
 python code.
 
 The test code is simply:
 
 import matplotlib.pyplot as plt
 plt.plot([1,2,3])
 plt.ylabel('Some Numbers')
 plt.show()
 
 
 Thanks in advance,
 
 David Lees

Interactive mode works for me in an IDLE shell:

import matplotlib.pyplot as plt
plt.ion()
plt.plot([1,2,3])
plt.ylabel('Some Numbers')
plt.show()  # You don't have to call show() in interactive mode though

Goyo


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Re: [Matplotlib-users] How do I debug under PythonWin or IDLE?

[Goyo]

El dom, 11-01-2009 a las 16:48 +0100, Goyo escribió:
 El jue, 08-01-2009 a las 12:09 -0600, de...@verizon.net escribió:
  I am sure this is a well know issue, so please feel free to just give a 
  link if the answer and solution are long.  I have a newly installed 
  matplotlib installations running on Windows XP using Python 2.5.4.  When 
  I execute a simple 4 line example (copied directly from the PyPlot 
  tutorial) in either PythonWin or IDLE, , it works fine and I terminate 
  by right clicking on the generated figure and doing a Close.  However, 
  when I rerun the code from the IDE (makes no difference if I use 
  PythonWin or IDLE) the figure hangs and eventually I get an abnormal 
  exit and crash out of the IDE (in PythonWin there is a dialogue box that 
  says “Runtime Error” in pythonwin.exe.  This makes debugging in an IDE 
  very clumsy, because I need to exit and restart it every time I run 
  python code.
  
  The test code is simply:
  
  import matplotlib.pyplot as plt
  plt.plot([1,2,3])
  plt.ylabel('Some Numbers')
  plt.show()
  
  
  Thanks in advance,
  
  David Lees
 
 Interactive mode works for me in an IDLE shell:
 
 import matplotlib.pyplot as plt
 plt.ion()
 plt.plot([1,2,3])
 plt.ylabel('Some Numbers')
 plt.show()  # You don't have to call show() in interactive mode though
 
 Goyo

I'm using the TKAgg backend, I guess there will be problems with other
interactive backends.

Goyo


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Re: [Matplotlib-users] Can't create graphs

[Goyo]

Make sure yu're using a backend with a user interface.

http://matplotlib.sourceforge.net/faq/installing_faq.html#what-is-a-backend

El mié, 19-11-2008 a las 10:49 -0500, Ron Brennan escribió:
 Hello,
 
 I am completely new to Matplotlib.  I can't seem to get my script (a
 copy and paste from a Histogram example) to generate a graph. When I
 run my script, the command prompt returns.
 
 Is there something I am missing?
 
 # 
 # histogram.py 
 # 
 import numpy as np
 import matplotlib.mlab as mlab
 import matplotlib.pyplot as plt
 
 mu, sigma = 100, 15
 x = mu + sigma*np.random.randn(1)
 
 # the histogram of the data
 n, bins, patches = plt.hist(x, 50, normed=1, facecolor='green',
 alpha=0.75)
 
 # add a 'best fit' line
 y = mlab.normpdf( bins, mu, sigma)
 l = plt.plot(bins, y, 'r--', linewidth=1)
 
 plt.xlabel('Smarts')
 plt.ylabel('Probability')
 plt.title(r'$\mathrm{Histogram\ of\ IQ:}\ \mu=100,\ \sigma=15$')
 plt.axis([40, 160, 0, 0.03])
 plt.grid(True)
 
 plt.show()
 
 Calling with:
 python histogram.py
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Re: [Matplotlib-users] Calling xlim makes x tick labels format get lost

[Goyo]

El dom, 12-10-2008 a las 13:22 -1000, Eric Firing escribió: 
 Goyo wrote:
  Hi all,
  
  I'm plotting time series and using a custom format for x tick labels
  because I want to see both date and time. But calling xlim makes the
  default format return -- only dates or only times, it depends on the
  displayed interval.
  
  I can get my preferred format back by calling set_major_formatter again,
  but this is inconvenient for interactive use.
  
  I wonder if there is a better way for changing x limits while keeping
  tick labels format unchanged.
  
  I'm using matplotlib 0.98.3
  
  Thanks
  
  Goyo
  
  
  Sample code -- you need a combination of python shell and matplotlib GUI
  which allows for interactive use in order to get this working as
  expected:
  
  
  
  from matplotlib import pyplot
  from matplotlib import dates
  from datetime import datetime, timedelta
  from numpy import random
  
  pyplot.ion()
  
  # create data
  dstart = datetime(2008, 1, 1, 0, 0)
  dend = datetime(2008, 1, 5, 23, 50)
  delta = timedelta(minutes=10)
  x = dates.drange(dstart, dend, delta)
  y = random.random_sample(len(x))
  
  # plot data
  pyplot.plot(x, y)
  
  # format x tick labels
  axis = pyplot.gca()
  fig = pyplot.gcf()
  axis.xaxis.set_major_formatter(dates.DateFormatter('%Y-%b-%d %H:%M'))
  fig.autofmt_xdate()
  
  # draw the figure
  pyplot.draw()
  
  --
  
  Look at the tick labels, they show both date and time even if you zoom
  and pan using the GUI.
  
  Now if I want to look at the second day:
  
  dstart = datetime(2008, 1, 1, 0, 0)
  dend = datetime(2008, 1, 1, 23, 50)
  pyplot.xlim(dstart, dend)
  
  And the format has changed.
 
 I don't see this problem using ipython -pylab with mpl from svn on 
 linux, gtkagg backend.  What version, backend, and platform are you using?

matplotlib 0.98.3-3ubuntu1~ppa1 from Benjamin Drung's ppa
(http://ppa.launchpad.net/bdrung/ubuntu) on Ubuntu Hardy.

It was the standard python shell and TKAgg, but I get the same result
with ipython -pylab and GTKAgg. Indeed the format change can be
documented:

print axis.xaxis.get_major_formatter()
pyplot.xlim(dstart, dend)
print axis.xaxis.get_major_formatter()

The first print:
matplotlib.dates.DateFormatter instance at 0xb6e2462c
and the second:
matplotlib.dates.AutoDateFormatter instance at 0x884dc4c

I did some debugging and realized that xaxis.units is None after
plotting, so xlim triggers a call to xaxis.set_units which sets the
default formatter (and units, whatever it means).

If I set my formatter again, xaxis.units is not None anymore but still
xaxis._update_axisinfo sets the default formatter.

Anyway I worked around this by writing my own version of xlim which
first saves the formatter, then sets xlim and sets the saved formatter
again.

Goyo


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[Matplotlib-users] Calling xlim makes x tick labels format get lost

[Goyo]

Hi all,

I'm plotting time series and using a custom format for x tick labels
because I want to see both date and time. But calling xlim makes the
default format return -- only dates or only times, it depends on the
displayed interval.

I can get my preferred format back by calling set_major_formatter again,
but this is inconvenient for interactive use.

I wonder if there is a better way for changing x limits while keeping
tick labels format unchanged.

I'm using matplotlib 0.98.3

Thanks

Goyo


Sample code -- you need a combination of python shell and matplotlib GUI
which allows for interactive use in order to get this working as
expected:



from matplotlib import pyplot
from matplotlib import dates
from datetime import datetime, timedelta
from numpy import random

pyplot.ion()

# create data
dstart = datetime(2008, 1, 1, 0, 0)
dend = datetime(2008, 1, 5, 23, 50)
delta = timedelta(minutes=10)
x = dates.drange(dstart, dend, delta)
y = random.random_sample(len(x))

# plot data
pyplot.plot(x, y)

# format x tick labels
axis = pyplot.gca()
fig = pyplot.gcf()
axis.xaxis.set_major_formatter(dates.DateFormatter('%Y-%b-%d %H:%M'))
fig.autofmt_xdate()

# draw the figure
pyplot.draw()

--

Look at the tick labels, they show both date and time even if you zoom
and pan using the GUI.

Now if I want to look at the second day:

dstart = datetime(2008, 1, 1, 0, 0)
dend = datetime(2008, 1, 1, 23, 50)
pyplot.xlim(dstart, dend)

And the format has changed.


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Re: [Matplotlib-users] GTKAgg throwing an exception

[Goyo]

I can't make much sense of this. You don't plot anything and don't use
canvas.

This code works:

import matplotlib
matplotlib.use('GTKAgg')
from matplotlib import pyplot
pyplot.plot([0, 1, 2, 3], [0, 1, 2, 3])
fig = pyplot.gcf()
fig.savefig('test.jpg')

But I don't know how to set the dpi value this way. I tried to use the
OO API but no success.

Goyo

El dom, 12-10-2008 a las 23:45 +0200, Jesper Larsen escribió:
 Hi matplotlib-users,
 
 I decided to try to make some plots that I have previously made in png
 format using the Agg backend in jpeg format using the GTKAgg backend
 (which I guess is the one I should use for this). Unfortunately my
 script exits with an error. I have therefore created a simple test
 script (test.py) that illustrates the problem (at least on my
 computer):
 
 import matplotlib
 from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as
 FigureCanvas
 
 fig = matplotlib.figure.Figure(dpi=100)
 canvas = FigureCanvas(fig)
 fig.savefig('test.jpg')
 
 When I run it I get:
 
 $ python test.py
 /usr/lib/python2.5/site-packages/matplotlib/backends/backend_gtk.py:357:
 GtkWarning: gtk_widget_realize: assertion `GTK_WIDGET_ANCHORED
 (widget) || GTK_IS_INVISIBLE (widget)' failed
   gtk.DrawingArea.realize(self)
 /usr/lib/python2.5/site-packages/matplotlib/backends/backend_gtk.py:360:
 GtkWarning: gdk_pixmap_new: assertion `(drawable != NULL) || (depth !=
 -1)' failed
   pixmap = gdk.Pixmap (self.window, width, height)
 Traceback (most recent call last):
   File test.py, line 6, in module
 fig.savefig('test.jpg')
   File /usr/lib/python2.5/site-packages/matplotlib/figure.py, line
 964, in savefig
 self.canvas.print_figure(*args, **kwargs)
   File /usr/lib/python2.5/site-packages/matplotlib/backend_bases.py,
 line 1310, in print_figure
 **kwargs)
   File /usr/lib/python2.5/site-packages/matplotlib/backends/backend_gtk.py,
 line 347, in print_jpeg
 return self._print_image(filename, 'jpeg')
   File /usr/lib/python2.5/site-packages/matplotlib/backends/backend_gtk.py,
 line 360, in _print_image
 pixmap = gdk.Pixmap (self.window, width, height)
 RuntimeError: could not create GdkPixmap object
 
 I am using matplotlib 0.98.3, pygtk 2.14.0. My system is a Linux Ubuntu:
 
 $ uname -a
 Linux blanket out #1 SMP Wed Aug 20 18:39:13 UTC 2008 i686 GNU/Linux
 
 Does anyone know what is wrong?
 
 Best regards,
 Jesper
 
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Re: [Matplotlib-users] GTKAgg throwing an exception

[Goyo]

El lun, 13-10-2008 a las 00:41 +0200, Goyo escribió:

 But I don't know how to set the dpi value this way. I tried to use the
 OO API but no success.

Well yes...

import matplotlib
matplotlib.use('GTKAgg')
from matplotlib import pyplot
fig = pyplot.figure(dpi=100)
ax = fig.add_subplot('111')
ax.plot([1, 2, 3], [1, 2, 3])
fig.savefig('test.jpg')

But changing the dpi value has no effect so maybe I'm missing something.

Goyo


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Re: [Matplotlib-users] plotting scattered data from array

[Goyo]

El jue, 25-09-2008 a las 22:19 +0200, Oz Nahum escribió:
 ¿What's the meaning of that data arrange? I can't make any sense of
 plotting a 2D scatter from a 3D array.
 
 when I wrote:
 head = [[0,0,10],
 [1,0,13],
 [2,0,11],
 [3,0,12],
 [1,2,11]]
 
 my meaning was to represent point of intereset with x, y coordinates
 and the 3rd number was height for example. 
 I felt like I couldn't access the individual points easily, because
 their are located in on big list...
 So I wanted to have the list broken into rows, and the each row
 represents a value on the y axis... like this:
 head = [
 [[0,0,10], [0,0,13]],
 [[2,0,11], [3,0,12]],
]

Mm... maybe this is better for your eyes but not for processing, I
think.

   
 But that's redundant I think now, after looking into the function
 zip. 
 Maybe I could write head in the following way:
   
   #   j = 0 1
 head = [
 [[0,10], [1,13]], # i =0
 [[0,11], [1,12]], # i =1
]

The same. Parsing a data file usually yields a sequence of rows
(records), data processing functions usually expects columns of
homogeneous data and convert from records to columns and back is pretty
straightforward using zip. If you want to use a different representation
for your data you'll need to handle more complex structures and
conversions. Do it if you think it pays (sometimes it does).

 But actually after understanding what zip does, I think I don't need
 it anyway...
 Talking about this: can you give me an example of another use of zip ?
 not just zip(*head)
 
 I did help(zip) but I could partially understand what it does. I
 learned more by doing:
 x,y,z = zip(*head)
 and then printing x,y,z individually.

There is no other use I can think of. If you think of the arguments
passed to zip as rows, it returns the columns. If the arguments are
columns, zip returns rows. How you name things depends on how you think
of your data. There is no other use I can think of.

zip expects each row (if they are rows) to be passed as an argument so
you usually need that * thing to unpack them. When you call zip(*x), x
being a sequence or array-like, you are actually passing each element of
x as an argument to zip.

Try this:

numbers = [1, 2, 3, 4, 5]
english = ['one', 'two', 'three', 'four', 'five']
spanish = ['uno', 'dos', 'tres', 'cuatro', 'cinco']
x = [numbers, english, spanish]
zip(numbers, english, spanish)
zip(x)
zip(*x)

You can learn about unpacking and zipping sequences reading the Python
Tutorial or another similar resource (maybe Dive into Python dives into
it, not sure but a useful reading anyway).

Goyo


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Re: [Matplotlib-users] plotting scattered data from array

[Goyo]

Try something like this:

import pylab as pl

head = ((0,0,10),
(1,0,13),
(2,0,11),
(3,0,12),
(1,2,11))

x, y, z = zip(*head)
xi, yi = pl.arange(0, 4, 0.1), pl.arange(0, 3, 0.1)
g = pl.griddata(x, y, z, xi, yi)
pl.scatter(x, y)
pl.contour(xi, yi, g)

Level values are automatically chosen in this example but you can
provide the number of values or a sequence of them.

Note that no extrapolation is done outside convex hull defined by input
data.

Goyo

El sáb, 20-09-2008 a las 11:13 +0200, Oz Nahum escribió:
 I'm trying again to understand how to plot scattered data from array into
contour graph.
I looked at
http://www.scipy.org/Cookbook/Matplotlib/Gridding_irregularly_spaced_data
and I understand I have to grid my data. However, in most samples the plot
is of a function.
Let's say I want to plot some geological data, suppose water table head, 
 and
I have the following 3D aray
x yhead
head =  ((0,0,10),
(1,0,13),
(2,0,11),
(3,0,12),
(1,2,11))
matplotlib has lot's of restrictions about how I can plot and interpolate
the data, which causes a lot of confusion in my side...
I'll be happy if someone could supply me a clue of how to plot contours of
data which comes in arrays or raster format and not an equation.
Thanks,
Oz
 
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Re: [Matplotlib-users] Lines drawn across NaN data

[Goyo]

Tanks, Michael. Maybe I'll try to build from SVN this weekend.

Goyo

El jue, 18-09-2008 a las 09:31 -0400, Michael Droettboom escribió:
 Proper NaN handling has been a long and winding road. 
 
 This particuar bug you're running into was fixed about a week *after* 
 the 0.98.3 release.  Here's the patch:
 
 http://matplotlib.svn.sourceforge.net/viewvc/matplotlib?view=revrevision=6018
 
 So SVN trunk currently works.  The patch against 0.98.3 is non-trivial 
 -- there were actually many changes throughout the code to make all this 
 work, so there isn't an easy workaround, and in any case requires a 
 recompile.
 
 If you can build from SVN, that's what I would suggest -- otherwise wait 
 for the 0.98.4 release (I don't believe we have an ETA on that, yet).
 
 Cheers,
 Mike
 
 Goyo wrote:
  I'm having trouble plotting data with NaN values. My plot has lines and
  markers and usually both are skipped for NaN values. But when I have
  more than 127 data a line is drawn from the last non-NaN to the next.
 
  I read somewhere about a similar issue (maybe here? sorry I can't find
  it just now), it seems like it has to do with some optimization
  performed for large datasets and the use if lineto instead of moveto or
  something like that. It was supposed to be fixed in 0.98.2 but I'm using
  0.98.3 from Benjamin Drung's PPA (http://ppa.launchpad.net/bdrung).
 
  This code shows the difference between plotting 127 and 128 data (look
  at the left of each figure):
 
  import pylab as pl
  x = pl.random(128)
  x[4:7] = pl.NaN
  y = x[:-1]
  pl.figure(1)
  pl.plot(x, '-o')
  pl.grid(True)
  pl.figure(2)
  pl.plot(y, '-o')
  pl.grid(True)
  pl.show()
 
  Is this a known issue? Is there any workaround?
 
  Thanks
 
  Goyo
 
 
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[Matplotlib-users] Lines drawn across NaN data

[Goyo]

I'm having trouble plotting data with NaN values. My plot has lines and
markers and usually both are skipped for NaN values. But when I have
more than 127 data a line is drawn from the last non-NaN to the next.

I read somewhere about a similar issue (maybe here? sorry I can't find
it just now), it seems like it has to do with some optimization
performed for large datasets and the use if lineto instead of moveto or
something like that. It was supposed to be fixed in 0.98.2 but I'm using
0.98.3 from Benjamin Drung's PPA (http://ppa.launchpad.net/bdrung).

This code shows the difference between plotting 127 and 128 data (look
at the left of each figure):

import pylab as pl
x = pl.random(128)
x[4:7] = pl.NaN
y = x[:-1]
pl.figure(1)
pl.plot(x, '-o')
pl.grid(True)
pl.figure(2)
pl.plot(y, '-o')
pl.grid(True)
pl.show()

Is this a known issue? Is there any workaround?

Thanks

Goyo


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