matplotlib-users Mailing List for matplotlib

2010/8/17 Stephen T. <obs...@ho...>:
> http://passingcuriosity.com/2009/installing-pil-on-mac-os-x-leopard/

That's a good thing to know when people run into /opt/ trouble of this
kind ... Thanks

> So I had in mind to try this with the matplotlib installation, but for some
> reason the make command did not fail in error this time... as before, I had
> typed in my bash shell:
> export PREFIX=~/dev
> make -f make.osx fetch deps mpl_install
> and I am not sure why but those previous error messages never came up. So in
> the end I just included the new matplotlib directory in my python path (in
> .bash_profile):
> export PYTHONPATH:~/dev/lib/python2.6/site-packages:$PYTHONPATH

You surely mean export PYTHONPATH= ... (with an equality sign)?

> and it appears to be working ok.

*sigh* mysteries of Mac OS X compilations ...

Am I right with guessing that you do not want to dig into this?

Friedrich

Hi Tony,
My mpl version is 0.98.5.2. I saved the figure using GUI. I just tried
saving with savefig function. In that case, the size of the figure is
exactly what i gave in figsize arguement. You question helped me. Thank you.

Thanks,
Bala

On Tue, Aug 17, 2010 at 5:50 PM, Tony S Yu <ts...@gm...> wrote:

>
> On Aug 17, 2010, at 11:02 AM, Bala subramanian wrote:
>
> > Friends,
> >
> > I am trying to make a figure for publication. I am making a double column
> figure of 7inch as per journal guidelines. The figure comes out nicely but
> the final size of the figure that is saved is not what i have given in
> 'figsize'. It is 10inch X 5.38 inch. How can i make mpl to create the figure
> of exact size and resolution?
> >
> > fig=plt.figure(figsize=(7,4))
> > fig.subplots_adjust(wspace=0.1,hspace=0.1)
> > ax1=fig.add_subplot(221)
> > ax2=fig.add_subplot(222,sharex=ax1,sharey=ax1)
> > ax3=fig.add_subplot(223,sharex=ax1,sharey=ax1)
> > ax4=fig.add_subplot(224,sharex=ax1,sharey=ax1)
> >
> > Thanks,
> > Bala
>
> That's strange. I don't see any problems with the figure size on my system.
> This may seem like a silly question, but do you have the same sizing issue
> for the following code:
>
> import matplotlib.pyplot as plt
> fig=plt.figure(figsize=(7,4))
> fig.subplots_adjust(wspace=0.1,hspace=0.1)
> ax1=fig.add_subplot(221)
> ax2=fig.add_subplot(222,sharex=ax1,sharey=ax1)
> ax3=fig.add_subplot(223,sharex=ax1,sharey=ax1)
> ax4=fig.add_subplot(224,sharex=ax1,sharey=ax1)
> plt.savefig('test.pdf')
> # works fine on my system with png, pdf, and eps
>
> I just want to make sure you aren't altering the figure in any other way
> before you save.
>
> Are you using savefig or are you saving from a GUI window? Are you on a
> current version of matplotlib (if yes, you might be interested in
> `plt.subplots` to create your axes)? What image format are you using?
>
> -Tony
>
>
>

On Aug 17, 2010, at 11:02 AM, Bala subramanian wrote:

> Friends,
> 
> I am trying to make a figure for publication. I am making a double column figure of 7inch as per journal guidelines. The figure comes out nicely but the final size of the figure that is saved is not what i have given in 'figsize'. It is 10inch X 5.38 inch. How can i make mpl to create the figure of exact size and resolution?
> 
> fig=plt.figure(figsize=(7,4))
> fig.subplots_adjust(wspace=0.1,hspace=0.1)
> ax1=fig.add_subplot(221)
> ax2=fig.add_subplot(222,sharex=ax1,sharey=ax1)
> ax3=fig.add_subplot(223,sharex=ax1,sharey=ax1)
> ax4=fig.add_subplot(224,sharex=ax1,sharey=ax1)
> 
> Thanks,
> Bala

That's strange. I don't see any problems with the figure size on my system. This may seem like a silly question, but do you have the same sizing issue for the following code:

import matplotlib.pyplot as plt
fig=plt.figure(figsize=(7,4))
fig.subplots_adjust(wspace=0.1,hspace=0.1)
ax1=fig.add_subplot(221)
ax2=fig.add_subplot(222,sharex=ax1,sharey=ax1)
ax3=fig.add_subplot(223,sharex=ax1,sharey=ax1)
ax4=fig.add_subplot(224,sharex=ax1,sharey=ax1)
plt.savefig('test.pdf')
# works fine on my system with png, pdf, and eps

I just want to make sure you aren't altering the figure in any other way before you save.

Are you using savefig or are you saving from a GUI window? Are you on a current version of matplotlib (if yes, you might be interested in `plt.subplots` to create your axes)? What image format are you using?

-Tony

Hello everyone.

If I try to use LaTeX for text processing (i.e. text.usetex : True in my matplotlibrc), I get a cryptic LaTeX error which didn't use to be there before. I get the same problem when using matplotlib-0.98.5 which I compiled from source, and matplotlib-1.0.0 from macports. My python version is 2.6.5 (from macports) and I am running Mac OS X 10.6.4.

The error messages are pretty much the same no matter what I plot, and everything works fine if text.usetex : False.

Regards
Paul.

Friends,

I am trying to make a figure for publication. I am making a double column
figure of 7inch as per journal guidelines. The figure comes out nicely but
the final size of the figure that is saved is not what i have given in
'figsize'. It is 10inch X 5.38 inch. How can i make mpl to create the figure
of exact size and resolution?

fig=plt.figure(figsize=(7,4))
fig.subplots_adjust(wspace=0.1,hspace=0.1)
ax1=fig.add_subplot(221)
ax2=fig.add_subplot(222,sharex=ax1,sharey=ax1)
ax3=fig.add_subplot(223,sharex=ax1,sharey=ax1)
ax4=fig.add_subplot(224,sharex=ax1,sharey=ax1)

Thanks,
Bala

On Mon, Aug 16, 2010 at 6:13 PM, Jae-Joon Lee <lee...@gm...> wrote:
> Using the set_powerlimits method didn't help?

I couldn't get set_powerlimits or set_scientific to change anything in
my colorbar scaling.  If I used setOffset(False) then there was no
scaling; an improvement, but not ideal.

>
> As far as I know, the current implementation does not allow a custom
> scale factor.
> But if the scale factor is power of 10 (10, 100, 1000, ...), I believe
> using set_powerlimits method (as in my previous example, or some
> variation) is good enough.

Unfortunately in my simple example (and in my real world case), the
scale factor is some number (i.e. 5) times a power of 10.

Am I missing something?  I'm running matplotlib version 1.0.0.

Thanks,
Jeremy



import numpy
import matplotlib.pyplot as pyplot

a = 5000
b = 5002

M = (b-a)*numpy.random.random((5,5))+a

fig = pyplot.figure()
pc = pyplot.pcolor(M)

cbar = fig.colorbar(pc)
cbar.formatter.set_scientific(False)
cbar.formatter.set_powerlimits((0,2))
# cbar.formatter.set_useOffset(False)

cbar.update_ticks()

Hi Friedrich,
Thanks for your help. Just thought I would follow up to say that it appears to be working now. I am not sure what was different this time and last - my libxml file still points to the one with the architecture shown below, but I had come across this post about changing the targeted architecture called for gcc manually:
http://passingcuriosity.com/2009/installing-pil-on-mac-os-x-leopard/
So I had in mind to try this with the matplotlib installation, but for some reason the make command did not fail in error this time... as before, I had typed in my bash shell:
export PREFIX=~/devmake -f make.osx fetch deps mpl_install
and I am not sure why but those previous error messages never came up. So in the end I just included the new matplotlib directory in my python path (in .bash_profile):export PYTHONPATH:~/dev/lib/python2.6/site-packages:$PYTHONPATH and it appears to be working ok.
So sorry for all the trouble, but thanks for your time!
All the best,Stephen

From: obs...@ho...
To: fri...@gm...
CC: mat...@li...
Subject: RE: [Matplotlib-users] installation of matplotlib on OS X 10.5 with python.org Python 2.6
Date: Fri, 6 Aug 2010 13:06:20 -0700








Hi Friedrich,Thanks again for your response. I've been away traveling (with no internet connection) and just returned... hope you can help me troubleshoot this last bit (hopefully last bit)!> This is important. I recently had a similar issue (sort of). I think> the macports library is 32-bit only, and I know that at least for> building Python the build performs 64-bit only by default (this was my> issue) on a 64bit system. Of course, in case you want to make a 64bit> build against a 32bit library the error would be sensible.> > To check this, try to run:> $ file /opt/local/lib/libxml2.2.dylib> > When I run it on the Apple supplied file it gives:> > /usr/lib/libxml2.dylib: Mach-O universal binary with 3 architectures> /usr/lib/libxml2.dylib (for architecture x86_64):	Mach-O 64-bit> dynamically linked shared library x86_64> /usr/lib/libxml2.dylib (for architecture i386):	Mach-O dynamically> linked shared library i386> /usr/lib/libxml2.dylib (for architecture ppc7400):	Mach-O dynamically> linked shared library ppcmine gives only:/opt/local/lib/libxml2.2.dylib: Mach-O dynamically linked shared library i386Is this the problem?Thanks so much!Stephen
 		 	   		  

Would anyone be so kind as to show me how to modify setupext.py such that
the install actually works?  I'm surprised this hasn't come up already,
actually, as there definitely are a lot of bugs in trying to set it up now.

At the very list, it seems that ConfigParser is constructing an empty list,
and the matplotlib setup hasn't caught that error.  If anyone who has
successfully built on Cygwin could kindly send me their modified setupext.py
and also what packages they have installed, that'd be greatly appreciated.

On Mon, Aug 16, 2010 at 6:25 PM, Michiel de Hoon <mjl...@ya...>wrote:

> Matplotlib works well with Cygwin (I am using it with the gtkcairo
> backend), but installing it can be a hassle. You'll have to fix errors such
> as the ones you're seeing by modifying setup.py or setupext.py.
> --Michiel.
>
> --- On *Mon, 8/16/10, Adam Gustafson <am...@st...>* wrote:
>
>
> From: Adam Gustafson <am...@st...>
> Subject: [Matplotlib-users] Cygwin and matplotlib
> To: mat...@li...
> Date: Monday, August 16, 2010, 7:23 PM
>
>
> Could someone please kindly let me know if matplotlib is compatible with
> Cygwin?  I installed all the necessary dependencies, yet I cannot get
> matplotlib to compile correctly.  At the build step, this is what I get:
>
> $ python setup.py build
> basedirlist is: ['/usr/local', '/usr']
>
> ============================================================================
> BUILDING MATPLOTLIB
>             matplotlib: 1.0.0
>                 python: 2.6.5 (r265:79063, Jun 12 2010, 17:07:01)  [GCC
>                         4.3.4 20090804 (release) 1]
>               platform: cygwin
>
> REQUIRED DEPENDENCIES
>                  numpy: 1.4.1
>              freetype2: found, but unknown version (no pkg-config)
>                         * WARNING: Could not find 'freetype2' headers in
> any
>                         * of '/usr/include', '.', '/usr/include/freetype2',
>                         * './freetype2'.
>
> OPTIONAL BACKEND DEPENDENCIES
>                 libpng: found, but unknown version (no pkg-config)
>                         * Could not find 'libpng' headers in any of
>                         * '/usr/include', '.'
> cygwin warning:
>   MS-DOS style path detected: C:/Cygwin/usr/share/tcl8.4/tclConfig.sh
>   Preferred POSIX equivalent is: /usr/share/tcl8.4/tclConfig.sh
>   CYGWIN environment variable option "nodosfilewarning" turns off this
> warning.
>   Consult the user's guide for more details about POSIX paths:
>     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
> Traceback (most recent call last):
>   File "setup.py", line 162, in <module>
>     if check_for_tk() or (options['build_tkagg'] is True):
>   File "/home/Adam/installs/matplotlib-1.0.0/setupext.py", line 816, in
> check_for_tk
>     explanation = add_tk_flags(module)
>   File "/home/Adam/installs/matplotlib-1.0.0/setupext.py", line 1080, in
> add_tk_flags
>     result = parse_tcl_config(tcl_lib_dir, tk_lib_dir)
>   File "/home/Adam/installs/matplotlib-1.0.0/setupext.py", line 938, in
> parse_tcl_config
>     tk_lib = tk_vars.get("default", "TK_LIB_SPEC")[1:-1].split()[0][2:]
> IndexError: list index out of range
>
>
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On Mon, Aug 16, 2010 at 5:20 PM, Graham Taylor <ess...@ho...>wrote:

>  I'm trying to display several rectangles (from matplotlib.patches) in 3D.
> I thought it would be possible to use the add_collection3d method similar to
> the demo on the examples page:
> http://matplotlib.sourceforge.net/mpl_toolkits/mplot3d/tutorial.html
>
> However, when I call this method on a PatchCollection, I get an error at
> line 295 in art3d.py.
> It expects the collection to have offsets, but offsets is None (by default)
> when I create the collection.
>
> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mpl_toolkits/mplot3d/art3d.pyc
> in set_3d_properties(self, zs, zdir)
>     293
>     294     def set_3d_properties(self, zs, zdir):
> --> 295         xs, ys = zip(*self.get_offsets())
>     296         self._offsets3d = juggle_axes(xs, ys, zs, zdir)
>     297         self._facecolor3d = self.get_facecolor()
>
> ValueError: need more than 0 values to unpack
>
> I am relatively new to Matplotlib, so I don't know if this is a bug or it
> is just my own misunderstanding.
>
>
> Here's a simple example where I try it on a single rectangle and it fails
> with the above error message.
>
> # ----start example
>
> from mpl_toolkits.mplot3d import Axes3D
> from matplotlib.collections import PolyCollection,PatchCollection
> from matplotlib.colors import colorConverter
> import matplotlib.pyplot as plt
> from matplotlib.patches import Rectangle
> import numpy as np
>
> fig = plt.figure()
> ax = fig.gca(projection='3d')
>
>
> rec = Rectangle((5,2),2,2)
> recs = [rec]
> col = PatchCollection(recs)
> ax.add_collection3d(col, zs=[0.6], zdir='z')
>
> # ----end example
>
>
> Graham
>
>
Graham,

Good catch, it is a bug.  It is similar to one I encountered recently but
have not gotten a response for.

The issue is that Patch3DCollection seems to be assuming that .set_offset()
has been called on the original PatchCollection object, thereby setting the
internal offsets.  And, even if you do manually call .set_offsets(), the
rest of the mplot3d code assumes that Patch3DCollection has
.set_sort_zpos(), but it doesn't.

Offsets seem to be hardly used in 2d plotting, and the Patch3DCollection
object code appears to have not been kept up to date with the rest of
matplotlib and mplot3d. Can anyone shed some insight into this?

Ben Root

Matplotlib works well with Cygwin (I am using it with the gtkcairo backend), but installing it can be a hassle. You'll have to fix errors such as the ones you're seeing by modifying setup.py or setupext.py.
--Michiel.

--- On Mon, 8/16/10, Adam Gustafson <am...@st...> wrote:

From: Adam Gustafson <am...@st...>
Subject: [Matplotlib-users] Cygwin and matplotlib
To: mat...@li...
Date: Monday, August 16, 2010, 7:23 PM

Could someone please kindly let me know if matplotlib is compatible with Cygwin?  I installed all the necessary dependencies, yet I cannot get matplotlib to compile correctly.  At the build step, this is what I get:



$ python setup.py build
basedirlist is: ['/usr/local', '/usr']
============================================================================
BUILDING MATPLOTLIB
            matplotlib: 1.0.0


                python: 2.6.5 (r265:79063, Jun 12 2010, 17:07:01)  [GCC
                        4.3.4 20090804 (release) 1]
              platform: cygwin

REQUIRED DEPENDENCIES
                 numpy: 1.4.1


             freetype2: found, but unknown version (no pkg-config)
                        * WARNING: Could not find 'freetype2' headers in any
                        * of '/usr/include', '.', '/usr/include/freetype2',


                        * './freetype2'.

OPTIONAL BACKEND DEPENDENCIES
                libpng: found, but unknown version (no pkg-config)
                        * Could not find 'libpng' headers in any of


                        * '/usr/include', '.'
cygwin warning:
  MS-DOS style path detected: C:/Cygwin/usr/share/tcl8.4/tclConfig.sh
  Preferred POSIX equivalent is: /usr/share/tcl8.4/tclConfig.sh


  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames


Traceback (most recent call last):
  File "setup.py", line 162, in <module>
    if check_for_tk() or (options['build_tkagg'] is True):
  File "/home/Adam/installs/matplotlib-1.0.0/setupext.py", line 816, in check_for_tk


    explanation = add_tk_flags(module)
  File "/home/Adam/installs/matplotlib-1.0.0/setupext.py", line 1080, in add_tk_flags
    result = parse_tcl_config(tcl_lib_dir, tk_lib_dir)
  File "/home/Adam/installs/matplotlib-1.0.0/setupext.py", line 938, in parse_tcl_config


    tk_lib = tk_vars.get("default", "TK_LIB_SPEC")[1:-1].split()[0][2:]
IndexError: list index out of range



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Using the set_powerlimits method didn't help?

As far as I know, the current implementation does not allow a custom
scale factor.
But if the scale factor is power of 10 (10, 100, 1000, ...), I believe
using set_powerlimits method (as in my previous example, or some
variation) is good enough.

Let me know if it does not work or you have any other problem.
Regards,

-JJ


On Tue, Aug 17, 2010 at 3:17 AM, Jeremy Conlin <jlc...@gm...> wrote:
> On Sun, Aug 15, 2010 at 10:49 PM, Jae-Joon Lee <lee...@gm...> wrote:
>> On Fri, Aug 13, 2010 at 3:34 AM, Jeremy Conlin <jlc...@gm...> wrote:
>>> I have a problem with the scaling of the numbers on a colorbar.  The
>>> problem occurs when the numbers used as colorbar labels need to be
>>> scaled (i.e. by 1E3).  The colorbar correctly puts the scaling value
>>> on the top of the colorbar, but instead of of multiplying by a scale
>>> factor, addition is used instead.  See the attached script and figure
>>> for example.  In the example, it looks like the color scale goes from
>>> 0 to 2*5E3.  At least, that's what I thought when I first looked at
>>> it.  Instead it means 5000 to 5002.
>>>
>>> Is there anyway I can scale the colorbar labels by *multiplying* them
>>> by a scaling factor instead of *adding* a scaling factor?  That seems
>>> more intuitive to me and those I work with.
>>>
>>
>> Given the value range of 5000-5002, I doubt how using the scaling
>> factor improve your plot.
>>
>> To disable the use of offset (+5000),
>>
>> cb = fig.colorbar(pc)
>>
>> # do not use offset
>> cb.formatter.set_useOffset(False)
>>
>> cb.update_ticks()
>>
>> If you do want to use scaling factor,
>>
>> # to use scaling factor
>> cb.formatter.set_scientific(True)
>> cb.formatter.set_powerlimits((0,0))
>>
>> cb.update_ticks()
>>
>> This will only work with matplotlib v1.0.
>> In older versions, try to replace "update_ticks" with
>> "update_bruteforce" (but I'm not sure if this will work)
>>
>> IHTH,
>>
>
> Thanks for your suggestions.  I recognize that a range of 5000–5002 is
> not much; it was used simply to illustrate my point.
>
> I was able to turn the scaling off with set_useOffset(False).  Is
> there anyway to scale by multiplying instead of adding?
>
> Thanks,
> Jeremy
>