matplotlib-users — Discussion related to using matplotlib

Re: [Matplotlib-users] problems making grayscale lines

[Jonathan S. <js...@cf...>]

D'oh! Caught my mistake.  I was thinking of the grayscale backwards.
color = '1.0' is white not black!  Got it working now.

Jon
-- 
______________________________________________________________
Jonathan D. Slavin              Harvard-Smithsonian CfA
js...@cf...         60 Garden Street, MS 83
phone: (617) 496-7981           Cambridge, MA 02138-1516
 cell: (781) 363-0035           USA
______________________________________________________________

Re: [Matplotlib-users] Black and white mode

[Tony Yu <ts...@gm...>]

On Tue, Oct 2, 2012 at 11:04 AM, Benjamin Root <ben...@ou...> wrote:

>
>
> On Tue, Oct 2, 2012 at 8:31 AM, William Furnass <wi...@th...>wrote:
>
>> Did anything ever come of the MPL black and white mode mentioned in
>> the following?  I rarely want to produce colour plots and having an
>> inbuilt mechanism for cycling through line styles that can be
>> activated with a keyword argument would be very handy.
>>
>>
>> http://www.mail-archive.com/mat...@li.../msg00367.html
>>
>> Cheers,
>>
>> Will
>>
>>
> Perhap's Tony Yu's mpltools might be the closest we have gotten to this
> goal.  There has been a number of technical hurdles that I have not had the
> time or resources to iron out.  Hopefully, it will be helpful to you.
>
> http://tonysyu.github.com/mpltools/getting_started.html
>
> Cheers!
> Ben Root
>

Thanks for the advertisement Ben ;)

Will: If you're just interested in grayscale plotting, here's a direct link
to the example:


http://tonysyu.github.com/mpltools/auto_examples/style/plot_grayscale.html

The discussion that you link to talks specifically about line styles. In
the past there's been discussion of adding a linestyle cycle rc param, but
I don't think there's been progress on that front.

BTW, Ben: are you still thinking about some sort of hierarchical
configuration management? I think it'd make a great MEP, if you find the
time.

Best,
-Tony

Re: [Matplotlib-users] Black and white mode

[Benjamin R. <ben...@ou...>]

On Tue, Oct 2, 2012 at 8:31 AM, William Furnass <wi...@th...> wrote:

> Did anything ever come of the MPL black and white mode mentioned in
> the following?  I rarely want to produce colour plots and having an
> inbuilt mechanism for cycling through line styles that can be
> activated with a keyword argument would be very handy.
>
>
> http://www.mail-archive.com/mat...@li.../msg00367.html
>
> Cheers,
>
> Will
>
>
Perhap's Tony Yu's mpltools might be the closest we have gotten to this
goal.  There has been a number of technical hurdles that I have not had the
time or resources to iron out.  Hopefully, it will be helpful to you.

http://tonysyu.github.com/mpltools/getting_started.html

Cheers!
Ben Root

Re: [Matplotlib-users] X Window System error

[Mic <mic...@gm...>]

Hi Eric,
I have a dataset which contains about 4600 values.

Is it possible to display 4600 values with a bar char and labels?

Thank you in advance.



On Tue, Oct 2, 2012 at 4:04 PM, Eric Firing <ef...@ha...> wrote:

> On 2012/10/01 7:28 PM, Mic wrote:
> > Hi,
> >
> > I have got the following error with the following code:
> > /$ python mpl.py/
> > /Traceback (most recent call last):/
> > /  File
> > "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
> > line 398, in expose_event/
> > /    self._render_figure(self._pixmap, w, h)/
> > /  File
> >
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
> > line 75, in _render_figure/
> > /    FigureCanvasAgg.draw(self)/
> > /  File
> > "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
> > line 416, in draw/
> > /    self.renderer = self.get_renderer()/
> > /  File
> > "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
> > line 435, in get_renderer/
> > /    self.renderer = RendererAgg(w, h, self.figure.dpi)/
> > /  File
> > "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
> > line 72, in __init__/
> > /    self._renderer = _RendererAgg(int(width), int(height), dpi,
> > debug=False)/
> > /ValueError: width and height must each be below 32768/
> > /The program 'mpl.py' received an X Window System error./
> > /This probably reflects a bug in the program./
> > /The error was 'BadAlloc (insufficient resources for operation)'./
> > /  (Details: serial 486 error_code 11 request_code 53 minor_code 0)/
> > /  (Note to programmers: normally, X errors are reported asynchronously;/
> > /   that is, you will receive the error a while after causing it./
> > /   To debug your program, run it with the --sync command line/
> > /   option to change this behavior. You can then get a meaningful/
> > /   backtrace from your debugger if you break on the gdk_x_error()
> > function.)/
> >
> > With the following code:
> > /import random /
> > /import matplotlib.pyplot as plt /
> > //
> > /coverages = [random.randint(1,10)*2] * 4605 /
> > /contig_names = ['AAB0008r'] * len(coverages) /
> > /# Set the figure size /
> > /#fig = plt.figure(1, [20, 2]) /
> > /fig = plt.figure(figsize=(int(len(coverages)*0.1), 4)) /
> > //
> > /ax = fig.add_subplot(111) /
> > //
> > /# Set the x-axis limit /
> > /#ax.set_xlim(-1,100) /
> > /ax.set_xlim(0,len(coverages)) /
> > /#ax.set_ylim(0,3) /
> > /ax.yaxis.grid(True, linestyle='-', which='major', color='grey',
> > alpha=0.5) /
> > //
> > /ind = range(len(coverages)) /
> > /rects = ax.bar(ind, coverages, width=0.1, align='center',
> > color='thistle') /
> > /ax.set_xticks(ind) /
> > /#ax.set_xticklabels(contig_names)/
> > /#ax.tick_params(axis='both', which='major', labelsize=10)/
> > /#ax.tick_params(axis='both', which='minor', labelsize=8)/
> > /
> > /
> > /
> > /
> > /#function to auto-rotate the x axis labels/
> > /fig.autofmt_xdate()/
> > /plt.setp(ax.get_xticklabels(), fontsize=8, rotation='vertical')/
> > /plt.show()/
> >
> > How is it possible to get big charts?
>
> It looks like you are trying to make a figure that is 460 inches by 4
> inches.  How do you expect to display or print it?  I think displaying
> it is out of the question, so you would need to use a non-interactive
> backend.  I don't know whether ps or pdf can handle those sorts of
> dimensions.
>
> Eric
>
> >
> > Thank you in advance.
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Don't let slow site performance ruin your business. Deploy New Relic APM
> > Deploy New Relic app performance management and know exactly
> > what is happening inside your Ruby, Python, PHP, Java, and .NET app
> > Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> > http://p.sf.net/sfu/newrelic-dev2dev
> >
> >
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
>
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
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Re: [Matplotlib-users] imlim in ax.imshow

[Damon M. <dam...@gm...>]

On Tue, Oct 2, 2012 at 2:19 PM, Benjamin Root <ben...@ou...> wrote:
>
>
> On Mon, Oct 1, 2012 at 7:20 PM, Michael Aye <kmi...@gm...> wrote:
>>
>> Hi!
>>
>> I see that the function ax.imshow takes the parameter 'imlim' but in
>> the source (status: EPD 7.3-2) it is not being used?
>> So what is it for?
>>
>> Best regards,
>> Michael
>>
>>
>
> Confirmed.  I don't see imlim anywhere except in the imshow() signature.  I
> have no recollection of this parameter, so it might be from before my time.
>
> Ben Root

Is there some functionality you were looking for or were you just
exploring the codebase?

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] imlim in ax.imshow

[Benjamin R. <ben...@ou...>]

On Mon, Oct 1, 2012 at 7:20 PM, Michael Aye <kmi...@gm...> wrote:

> Hi!
>
> I see that the function ax.imshow takes the parameter 'imlim' but in
> the source (status: EPD 7.3-2) it is not being used?
> So what is it for?
>
> Best regards,
> Michael
>
>
>
Confirmed.  I don't see imlim anywhere except in the imshow() signature.  I
have no recollection of this parameter, so it might be from before my time.

Ben Root

Re: [Matplotlib-users] static linking

[Damon M. <dam...@gm...>]

On Sun, Sep 30, 2012 at 8:30 AM, Nelle Varoquaux
<nel...@gm...> wrote:
> When you build a shared library yourself, you always need to set the
> variable LD_LIBRARY_PATH.

This is not true. In fact, it is actively
discouraged<http://xahlee.info/UnixResource_dir/_/ldpath.html>.

The way to resolve it is to correctly pass the -I and -L compiler
flags when linking. As Rita has discovered, pkg-config does this for
you for some packages.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

[Matplotlib-users] Black and white mode

[William F. <wi...@th...>]

Did anything ever come of the MPL black and white mode mentioned in
the following?  I rarely want to produce colour plots and having an
inbuilt mechanism for cycling through line styles that can be
activated with a keyword argument would be very handy.

http://www.mail-archive.com/mat...@li.../msg00367.html

Cheers,

Will

Re: [Matplotlib-users] X Window System error

[Eric F. <ef...@ha...>]

On 2012/10/01 7:28 PM, Mic wrote:
> Hi,
>
> I have got the following error with the following code:
> /$ python mpl.py/
> /Traceback (most recent call last):/
> /  File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
> line 398, in expose_event/
> /    self._render_figure(self._pixmap, w, h)/
> /  File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
> line 75, in _render_figure/
> /    FigureCanvasAgg.draw(self)/
> /  File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
> line 416, in draw/
> /    self.renderer = self.get_renderer()/
> /  File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
> line 435, in get_renderer/
> /    self.renderer = RendererAgg(w, h, self.figure.dpi)/
> /  File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
> line 72, in __init__/
> /    self._renderer = _RendererAgg(int(width), int(height), dpi,
> debug=False)/
> /ValueError: width and height must each be below 32768/
> /The program 'mpl.py' received an X Window System error./
> /This probably reflects a bug in the program./
> /The error was 'BadAlloc (insufficient resources for operation)'./
> /  (Details: serial 486 error_code 11 request_code 53 minor_code 0)/
> /  (Note to programmers: normally, X errors are reported asynchronously;/
> /   that is, you will receive the error a while after causing it./
> /   To debug your program, run it with the --sync command line/
> /   option to change this behavior. You can then get a meaningful/
> /   backtrace from your debugger if you break on the gdk_x_error()
> function.)/
>
> With the following code:
> /import random /
> /import matplotlib.pyplot as plt /
> //
> /coverages = [random.randint(1,10)*2] * 4605 /
> /contig_names = ['AAB0008r'] * len(coverages) /
> /# Set the figure size /
> /#fig = plt.figure(1, [20, 2]) /
> /fig = plt.figure(figsize=(int(len(coverages)*0.1), 4)) /
> //
> /ax = fig.add_subplot(111) /
> //
> /# Set the x-axis limit /
> /#ax.set_xlim(-1,100) /
> /ax.set_xlim(0,len(coverages)) /
> /#ax.set_ylim(0,3) /
> /ax.yaxis.grid(True, linestyle='-', which='major', color='grey',
> alpha=0.5) /
> //
> /ind = range(len(coverages)) /
> /rects = ax.bar(ind, coverages, width=0.1, align='center',
> color='thistle') /
> /ax.set_xticks(ind) /
> /#ax.set_xticklabels(contig_names)/
> /#ax.tick_params(axis='both', which='major', labelsize=10)/
> /#ax.tick_params(axis='both', which='minor', labelsize=8)/
> /
> /
> /
> /
> /#function to auto-rotate the x axis labels/
> /fig.autofmt_xdate()/
> /plt.setp(ax.get_xticklabels(), fontsize=8, rotation='vertical')/
> /plt.show()/
>
> How is it possible to get big charts?

It looks like you are trying to make a figure that is 460 inches by 4 
inches.  How do you expect to display or print it?  I think displaying 
it is out of the question, so you would need to use a non-interactive 
backend.  I don't know whether ps or pdf can handle those sorts of 
dimensions.

Eric

>
> Thank you in advance.
>
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

[Matplotlib-users] X Window System error

[Mic <mic...@gm...>]

Hi,

I have got the following error with the following code:
*$ python mpl.py*
*Traceback (most recent call last):*
*  File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
line 398, in expose_event*
*    self._render_figure(self._pixmap, w, h)*
*  File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
line 75, in _render_figure*
*    FigureCanvasAgg.draw(self)*
*  File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
line 416, in draw*
*    self.renderer = self.get_renderer()*
*  File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
line 435, in get_renderer*
*    self.renderer = RendererAgg(w, h, self.figure.dpi)*
*  File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
line 72, in __init__*
*    self._renderer = _RendererAgg(int(width), int(height), dpi,
debug=False)*
*ValueError: width and height must each be below 32768*
*The program 'mpl.py' received an X Window System error.*
*This probably reflects a bug in the program.*
*The error was 'BadAlloc (insufficient resources for operation)'.*
*  (Details: serial 486 error_code 11 request_code 53 minor_code 0)*
*  (Note to programmers: normally, X errors are reported asynchronously;*
*   that is, you will receive the error a while after causing it.*
*   To debug your program, run it with the --sync command line*
*   option to change this behavior. You can then get a meaningful*
*   backtrace from your debugger if you break on the gdk_x_error()
function.)*

With the following code:
*import random

                                          *
*import matplotlib.pyplot as plt

                                          *
*

                                          *
*coverages = [random.randint(1,10)*2] * 4605

                                          *
*contig_names = ['AAB0008r'] * len(coverages)

                                         *
*# Set the figure size

                                          *
*#fig = plt.figure(1, [20, 2])

                                          *
*fig = plt.figure(figsize=(int(len(coverages)*0.1), 4))

                                         *
*

                                          *
*ax = fig.add_subplot(111)

                                          *
*

                                          *
*# Set the x-axis limit

                                         *
*#ax.set_xlim(-1,100)

                                         *
*ax.set_xlim(0,len(coverages))

                                          *
*#ax.set_ylim(0,3)

                                          *
*ax.yaxis.grid(True, linestyle='-', which='major', color='grey', alpha=0.5)

                                         *
*

                                          *
*ind = range(len(coverages))

                                          *
*rects = ax.bar(ind, coverages, width=0.1, align='center', color='thistle')

                                         *
*ax.set_xticks(ind)

                                         *
*#ax.set_xticklabels(contig_names)*
*#ax.tick_params(axis='both', which='major', labelsize=10)*
*#ax.tick_params(axis='both', which='minor', labelsize=8)*
*
*
*
*
*#function to auto-rotate the x axis labels*
*fig.autofmt_xdate()*
*plt.setp(ax.get_xticklabels(), fontsize=8, rotation='vertical')*
*plt.show()*

How is it possible to get big charts?

Thank you in advance.

Re: [Matplotlib-users] Qt4/PySide memory leak

[Christoph G. <cg...@uc...>]

On 9/24/2012 5:50 PM, Christoph Gohlke wrote:
> On 9/24/2012 3:32 PM, David Honcik wrote:
>> I've run into a large memory leak using Matplotlib with PySide and the
>> Qt4 back end.  I'm using :
>> Python 3.2
>> Numpy 1.6.2
>> Pyside 1.1.1 (qt474)
>> Matplotlib 1.2 (first the Capetown Group port to Python 3, then 1.2 RC2)
>> on Windows XP 32 bit
>> I've tried using the Python 2.7 branch of all of the above and don't see
>> the problem.  I don't see the problem with the Tk back end.  I don't see
>> the problem with the Qt4 back end and PyQt4.  Only with the above
>> mentioned versions and using the Qt4 back end with PySide.
>> The following script will reproduce the problem :
>> --------------------
>> import matplotlib
>> matplotlib.use('Qt4Agg')
>> matplotlib.rcParams['backend.qt4']='PySide'
>> import pylab
>> arrayX = []
>> arrayY = []
>> for nIndex in range(0, 100):
>> arrayX.append(nIndex)
>> arrayY.append(nIndex)
>> Figure = matplotlib.pyplot.figure(1)
>> Axes = Figure.add_axes([ 0.05, 0.05, 0.95, 0.95])
>> Axes.plot(arrayX,
>> arrayY,
>> color      = "blue",
>> marker     = "o",
>>             markersize = 5.0)
>> Axes.set_xlim(arrayX[0], arrayX[len(arrayX) - 1])
>> Axes.set_ylim(arrayY[0], arrayY[len(arrayY) - 1])
>> matplotlib.pyplot.show()
>> --------------------
>> I run the above, grab the lower right sizing handle on the plot window
>> and start resizing the window.  Watching the python process in task
>> manager, each resize leaks a noticeable amount of memory.  A few minutes
>> of this will get process memory up to ~2.5 GB. At that point it crashes.
>> I'm new here, am I in the right place?
>>
>
> I can reproduce this exactly, also with pyside 1.1.2 and an empty plot.
> Looks like QtGui.QImage is leaking.
>
> import matplotlib
> matplotlib.use('Qt4Agg')
> matplotlib.rcParams['backend.qt4']='PySide'
> from matplotlib import pyplot
> pyplot.plot()
> pyplot.show()
>
> --
> Christoph
>
>

As a workaround, until PySide is fixed, use the attached patch, which 
forcibly decreases the reference count of the string buffer after use.

Christoph

Re: [Matplotlib-users] static linking

[Rita <rmo...@gm...>]

Figured it out.

The real trick is to set the PKG_CONFIG_PATH properly. No need for
LD_LIBRARY_PATH

On Sun, Sep 30, 2012 at 9:52 AM, Rita <rmo...@gm...> wrote:

> Nelly,
> I would like to compile libpng into matplotlib if possible, ie static.
> Seems like thats not possible and I would like to would LD_LIBRARY_PATH as
> much as possible. I much prefer -Wl, rpath or LD_PRELOAD.
>
> Jouni,
> for the pkg-config can I use the one with my OS, /usr/bin/pkg-config? and
> also libpng comes with its own variation of pkg-config (not named that).
> How can I include that? do I set PKG_CONFIG_PATH ?
>
>
>
>
>
> On Sun, Sep 30, 2012 at 3:30 AM, Nelle Varoquaux <
> nel...@gm...> wrote:
>
>>
>> On 30 Sep 2012 06:11, "Jouni K. Seppänen" <jk...@ik...> wrote:
>> >
>> > Rita <rmo...@gm...> writes:
>> >
>> > > i have a micro distribution setup. I am building python, numpy, scipy
>> from
>> > > scratch. I am building matplotlib from scratch also.
>> > >
>> > > I am doing a simple, /apps/bin/python setup.py build.
>> > >
>> > > I also compiled libpng and cairo in a location.
>>
>> When you build a shared library yourself, you always need to set the
>> variable LD_LIBRARY_PATH. This is independant from the compilation. At
>> runtime, the program merely tries to load the library if it has not been
>> loaded previously.
>>
>> Usually, to avoid setting manually the path to the library, one adds this
>> to its bashrc/zshrc.
>>
>> I hope this helps.
>> Cheers,
>> N.
>>
>> >
>> > Have you set up pkg-config for your build of libpng? If you can't do
>> > that for some reason, you can edit basedirlist in setup.cfg.
>> >
>> > --
>> > Jouni K. Seppänen
>> > http://www.iki.fi/jks
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Everyone hates slow websites. So do we.
>> > Make your web apps faster with AppDynamics
>> > Download AppDynamics Lite for free today:
>> > http://ad.doubleclick.net/clk;258768047;13503038;j?
>> > http://info.appdynamics.com/FreeJavaPerformanceDownload.html
>> > _______________________________________________
>> > Matplotlib-users mailing list
>> > Mat...@li...
>> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://ad.doubleclick.net/clk;258768047;13503038;j?
>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
>
> --
> --- Get your facts first, then you can distort them as you please.--
>



-- 
--- Get your facts first, then you can distort them as you please.--

[Matplotlib-users] imlim in ax.imshow

[Michael A. <kmi...@gm...>]

Hi!

I see that the function ax.imshow takes the parameter 'imlim' but in 
the source (status: EPD 7.3-2) it is not being used?
So what is it for?

Best regards,
Michael

Re: [Matplotlib-users] static linking

[Rita <rmo...@gm...>]

Nelly,
I would like to compile libpng into matplotlib if possible, ie static.
Seems like thats not possible and I would like to would LD_LIBRARY_PATH as
much as possible. I much prefer -Wl, rpath or LD_PRELOAD.

Jouni,
for the pkg-config can I use the one with my OS, /usr/bin/pkg-config? and
also libpng comes with its own variation of pkg-config (not named that).
How can I include that? do I set PKG_CONFIG_PATH ?





On Sun, Sep 30, 2012 at 3:30 AM, Nelle Varoquaux
<nel...@gm...>wrote:

>
> On 30 Sep 2012 06:11, "Jouni K. Seppänen" <jk...@ik...> wrote:
> >
> > Rita <rmo...@gm...> writes:
> >
> > > i have a micro distribution setup. I am building python, numpy, scipy
> from
> > > scratch. I am building matplotlib from scratch also.
> > >
> > > I am doing a simple, /apps/bin/python setup.py build.
> > >
> > > I also compiled libpng and cairo in a location.
>
> When you build a shared library yourself, you always need to set the
> variable LD_LIBRARY_PATH. This is independant from the compilation. At
> runtime, the program merely tries to load the library if it has not been
> loaded previously.
>
> Usually, to avoid setting manually the path to the library, one adds this
> to its bashrc/zshrc.
>
> I hope this helps.
> Cheers,
> N.
>
> >
> > Have you set up pkg-config for your build of libpng? If you can't do
> > that for some reason, you can edit basedirlist in setup.cfg.
> >
> > --
> > Jouni K. Seppänen
> > http://www.iki.fi/jks
> >
> >
> >
> ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://ad.doubleclick.net/clk;258768047;13503038;j?
> > http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://ad.doubleclick.net/clk;258768047;13503038;j?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>


-- 
--- Get your facts first, then you can distort them as you please.--

Re: [Matplotlib-users] static linking

[Nelle V. <nel...@gm...>]

On 30 Sep 2012 06:11, "Jouni K. Seppänen" <jk...@ik...> wrote:
>
> Rita <rmo...@gm...> writes:
>
> > i have a micro distribution setup. I am building python, numpy, scipy
from
> > scratch. I am building matplotlib from scratch also.
> >
> > I am doing a simple, /apps/bin/python setup.py build.
> >
> > I also compiled libpng and cairo in a location.

When you build a shared library yourself, you always need to set the
variable LD_LIBRARY_PATH. This is independant from the compilation. At
runtime, the program merely tries to load the library if it has not been
loaded previously.

Usually, to avoid setting manually the path to the library, one adds this
to its bashrc/zshrc.

I hope this helps.
Cheers,
N.

>
> Have you set up pkg-config for your build of libpng? If you can't do
> that for some reason, you can edit basedirlist in setup.cfg.
>
> --
> Jouni K. Seppänen
> http://www.iki.fi/jks
>
>
>
------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://ad.doubleclick.net/clk;258768047;13503038;j?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Re: [Matplotlib-users] static linking

[Jouni K. S. <jk...@ik...>]

Rita <rmo...@gm...> writes:

> i have a micro distribution setup. I am building python, numpy, scipy from
> scratch. I am building matplotlib from scratch also.
>
> I am doing a simple, /apps/bin/python setup.py build.
>
> I also compiled libpng and cairo in a location.

Have you set up pkg-config for your build of libpng? If you can't do
that for some reason, you can edit basedirlist in setup.cfg.

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

Re: [Matplotlib-users] static linking

[Rita <rmo...@gm...>]

i have a micro distribution setup. I am building python, numpy, scipy from
scratch. I am building matplotlib from scratch also.

I am doing a simple, /apps/bin/python setup.py build.

I also compiled libpng and cairo in a location.




On Fri, Sep 28, 2012 at 10:49 PM, Eric Firing <ef...@ha...> wrote:

> On 2012/09/28 3:40 PM, Rita wrote:
> > Whenever I use matplot lib its asking me for libpng and when I do
> > LD_LIBRARY_PATH it works. Is there a way I can compile matplotlib so I
> > can avoid doing an export LD_LIBRARY_PATH ?
>
> Normally one doesn't need it, so I don't know why you do need it.  You
> might get a useful response from someone who knows more about linking
> than I do if you provide some information about your platform and about
> how you are presently building matplotlib.
>
> Eric
>
>
>
> ------------------------------------------------------------------------------
> How fast is your code?
> 3 out of 4 devs don\\\'t know how their code performs in production.
> Find out how slow your code is with AppDynamics Lite.
> http://ad.doubleclick.net/clk;262219672;13503038;z?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>



-- 
--- Get your facts first, then you can distort them as you please.--

Re: [Matplotlib-users] static linking

[Eric F. <ef...@ha...>]

On 2012/09/28 3:40 PM, Rita wrote:
> Whenever I use matplot lib its asking me for libpng and when I do
> LD_LIBRARY_PATH it works. Is there a way I can compile matplotlib so I
> can avoid doing an export LD_LIBRARY_PATH ?

Normally one doesn't need it, so I don't know why you do need it.  You 
might get a useful response from someone who knows more about linking 
than I do if you provide some information about your platform and about 
how you are presently building matplotlib.

Eric

[Matplotlib-users] static linking

[Rita <rmo...@gm...>]

Whenever I use matplot lib its asking me for libpng and when I do
LD_LIBRARY_PATH it works. Is there a way I can compile matplotlib so I can
avoid doing an export LD_LIBRARY_PATH ?




-- 
--- Get your facts first, then you can distort them as you please.--

Re: [Matplotlib-users] example of pareto chart

[Paul T. <pau...@gm...>]

On 9/26/12 12:31 PM, Benjamin Root wrote:
>
>
> On Wed, Sep 26, 2012 at 12:10 PM, Paul Tremblay 
> <pau...@gm... <mailto:pau...@gm...>> wrote:
>
>     Thanks. I know when doing 8/9 in python 2.x you get 0. With python
>     3 you get a decimal (Hooray, Python 3!).
>
>     I ran the script I submitted with python 3. Do I need to change
>     the defects and totals from integers to floats to make my chart
>     work universally?
>
>     P.
>
>
Here is my latest version of the Pareto chart. If the developers feel it 
is worthy, then they can include it in the gallery. Otherwise, it will 
have to remain in these threads, useful when, needing such a chart, 
someone searches the web and ends up here.

import matplotlib.pyplot as plt
import numpy as np

# the data to plot
defects = [32.0, 22.0, 15.0, 5.0, 2.0]
labels = ['vertical', 'horizontal', 'behind', 'left area', 'other']
the_sum = sum(defects) # ie, 32 + 22 + 15 + 5 + 2
the_cumsum = np.cumsum(defects) #  32, 32 + 22, 32 + 22 + 15, 32 + 22 + 
15 + 5, 32 + 22, + 15 + 5 + 2
percent = (np.divide(the_cumsum, the_sum)) * 100
ind = np.arange(len(defects))  # the x locations for the groups
width = .98 # with do of the bars, where a width of 1 indidcates no 
space between bars
x = ind + .5 * width # find the middle of the bar
fig = plt.figure() # create a figure
ax1 = fig.add_subplot(111) # and a subplot
ax2 = ax1.twinx() # create a duplicate y axis
rects1 = ax1.bar(ind, defects, width=width) # draw the chart
line, = ax2.plot(x, percent) # draw the  line
ax1.set_ylim(ymax=the_sum) # without these limits, graphs will not work
ax2.set_ylim(0, 100)
ax1.set_xticks(x) # set ticks for middle of bars
ax1.set_xticklabels(labels) # create the labels for the bars
ax1.set_ylabel('Defects') # create the left y axis label
ax2.set_ylabel('Percentage') # create the right y axis label
plt.show()

Re: [Matplotlib-users] default data sets for matplotlib?

[Paul T. <pau...@gm...>]

On 9/26/12 10:15 AM, Michael Droettboom wrote:
> On 09/26/2012 09:33 AM, Benjamin Root wrote:
>>
>>
>> On Wed, Sep 26, 2012 at 9:10 AM, Michael Droettboom <md...@st... 
>> <mailto:md...@st...>> wrote:
>>
>>     On 09/26/2012 12:28 AM, jos...@gm...
>>     <mailto:jos...@gm...> wrote:
>>     > On Wed, Sep 26, 2012 at 12:05 AM, Paul Tremblay
>>     <pau...@gm... <mailto:pau...@gm...>> wrote:
>>     >> In R, there are many default data sets one can use to both
>>     illustrate code
>>     >> and explore the scripting language. Instead of having to fake
>>     data, one can
>>     >> pull from meaningful data sets, created in the real world. For
>>     example, this
>>     >> one liner actually produces a plot:
>>     >>
>>     >> plot(mtcars$hp~mtcars$mpg)
>>     >>
>>     >> where mtcars refers to a built-in data set taken from Motor
>>     Trend Magazine.
>>     >> I don't believe matplotlib has anything similar. I have
>>     started to download
>>     >> some of the R data sets and store them as pickles for my own
>>     use. Does
>>     >> anyone else have any interest in creating a repository for
>>     these data sets
>>     >> or otherwise sharing them in some way?
>>     > Vincent converted several R datasets back to csv, that can be
>>     easily
>>     > loaded from the web with, for example, pandas.
>>     > http://vincentarelbundock.github.com/Rdatasets/
>>     > The collection is a bit random.
>>     >
>>     > statsmodels has some datasets that we use for examples and tests
>>     > http://statsmodels.sourceforge.net/devel/datasets/index.html
>>     > We were always a bit slow with adding datasets because we were too
>>     > cautious about licensing issues. But R seems to get away with
>>     > considering most datasets to be public domain.
>>     > We keep adding datasets to statsmodels as we need them for new
>>     models.
>>     >
>>     > The machine learning packages like sklearn have packaged the
>>     typical
>>     > machine learning datasets.
>>     >
>>     > If you are interested, you could join up with statsmodels or with
>>     > Vincent to expand on what's available.
>>     >
>>     It seems to me like contributing to (rather than duplicating) the
>>     work
>>     of one of these projects would be a great idea.  It would also be
>>     nice
>>     to add functionality in matplotlib to make it easier to download
>>     these
>>     things as a one-off -- obviously not exactly the same syntax as
>>     with R,
>>     but ideally with a single function call.
>>
>>     Mike
>>
>>
>> We did have such a thing. matplotlib.cbook.get_sample_data().  I 
>> think we got rid of it for 1.2.0?
> It was removed because the server side was a moving target and would 
> constantly break.  It was based on pulling files out of the svn (and 
> later git) repository, and sourceforge and github have had a habit of 
> changing the urls used to do so.  All of the data that was there was 
> moved into the main repository and is now installed alongside 
> matplotlib, so get_sample_data() still works.
>
> See this PR: https://github.com/matplotlib/matplotlib/pull/498
>
> I should have mentioned it earlier, that we do have a very small set 
> of standard data sets included there -- but these other projects 
> linked to above are much better and more extensive.  If we can rely on 
> them to have static urls over time, I think they are much better 
> options than anything matplotlib has had in the past.
>
> Mike
Drawing on other posts, it is conceivable to download both the R sets 
and the stats models sets and include them in 
site-packages/matplotlib/mpl-data/sample_data/? I understand that 
pulling data sets not in this directory creates problems because of 
moving URLs, but why even try to do a web pull when the data can exists 
in a reliable place?

I suppose one might raise reasonable objections to my suggestion, but at 
any rate, it doesn't seem I can add anything else to either project, 
since they both seem complete. I see only a small though significant 
problem with the R data sets in that it leaves out the header of the 
first column because of the structure of R data frames. Python needs 
this header.

Paul

Re: [Matplotlib-users] error reading netcdf file

[Michael R. <raw...@ya...>]

>________________________________
> From: Benjamin Root <ben...@ou...>
>To: Michael Rawlins <raw...@ya...> 
>Cc: Matplotlib Users <mat...@li...> 
>Sent: Thursday, September 27, 2012 2:29 PM
>Subject: Re: [Matplotlib-users] error reading netcdf file
> 
>
>Michael,
>
>The .missing_value attribute is not used anymore (It is ._FillValue now).  Anyway, if your data had any value that matched ._FillValue, then, by default, netCDF4 will give you a masked array anyway.  You will only need to set the mask if the fill value doesn't exist or if it is different from what you were expecting.
>
>Ben Root
>
>
>

Thanks Ben. I'll play around with ._FillValue and masked arrays. Glad to have everything working again with this new OS.

Mike

Re: [Matplotlib-users] error reading netcdf file

[Benjamin R. <ben...@ou...>]

Michael,

The .missing_value attribute is not used anymore (It is ._FillValue now).
Anyway, if your data had any value that matched ._FillValue, then, by
default, netCDF4 will give you a masked array anyway.  You will only need
to set the mask if the fill value doesn't exist or if it is different from
what you were expecting.

Ben Root

[Matplotlib-users] Possible bug (or unclear docs) with quiver

[Sergio <ser...@gm...>]

Hi,

trying to create a velocity plot for a 2d ode and superimposing it onto
a trajectory, I am encountering some issues with quiver.

Let ns1(x,t) be a vector function defining the ode, ready to be integrated with
scipy odeint and actually invariant with t. Here, x is a 1d state array with 2
entries.

I get the velocity field by first creating vectors of interesting points on the
two axis, say xg and yg. Then I make a grid with

xxg, yyg = np.meshgrid(xg, yg)

and I finally compute the velocity components as

vel = np.asarray(map(lambda x1, x2: ns1((x1,x2),0), xxg.flat, yyg.flat))
u=vel[:,0]
v=vel[:,1]

Now, I try to superimpose a trajectory with the velocity plot.
However, after having plotted the integrated trajectory, I cannot call

plt.quiver(xxg, yyg, u, v)

because the u and v components have very different ranges.

Trying to normalize as

plt.quiver(xxg, yyg, u/xrange, v/yrange)

looks (almost) right, but it is not nice to have to precompute the ranges.

I was expecting

plt.quiver(xxg, yyg, u, v, angles='xy')

to do the job automatically, but this is not the case.
For points with null x coordinate my arrows always have null length,
while this was not the case with the previous test.

any clue?

Re: [Matplotlib-users] error reading netcdf file

[Michael R. <raw...@ya...>]

----- Original Message -----
> From: Michael Rawlins <raw...@ya...>
> To: Jeff Whitaker <jef...@no...>; Benjamin Root <ben...@ou...>; Matplotlib Users <mat...@li...>
> Cc: 
> Sent: Wednesday, September 26, 2012 6:23 PM
> Subject: Re: [Matplotlib-users] error reading netcdf file
> 
> 
> 
>> ________________________________
>>  From: Jeff Whitaker <jef...@no...>
>> To: Benjamin Root <ben...@ou...>; Michael Rawlins 
> <ra...@ge...>; Matplotlib Users 
> <mat...@li...> 
>> Sent: Wednesday, September 26, 2012 5:10 PM
>> Subject: Re: [Matplotlib-users] error reading netcdf file
>> 
>> 
>> Michael:  You can't change an attribute in a read-only dataset.  It 
> should never have worked.
>> 
>> -Jeff
>> 
>> 
> 
> 
> Thanks Jeff and Ben.
> 
> Below is a complete version of one such program I use. I was give the program by 
> a colleague and I do not know who wrote that code.  My previous post showed only 
> as far as the missing data statement.
> 


<snip>

I've gotten my script to work by setting the missing value another way. I'm showing lines commented out as well.

#data.missing_value=-9.99
#try:
#    mval=data.missing_value
#    print " using specified missing value =",mval
#except:
    mval=-9.99
#    print " faking missing value=",mval
# make a masked array: using missing value(s) in mval
maskdat=ma.masked_values(slice,mval)


If I understand correctly, in previous versions the value of -9.99 was passed through the data.missing_value into mval. A mistake in coding that did not result in an error.  I will implement the change. Tomorrow I'll check that this solution is backward compatible.

Mike