matplotlib-users Mailing List for matplotlib (Page 4)

On 22 September 2012 16:57, Jae-Joon Lee wrote:
> I recommend you to use OffsetImage. Here is an example of how one can
> use OffsetImage.
>
> http://matplotlib.org/examples/pylab_examples/demo_annotation_box.html
>
> And attached is the modified version of the original script.

Thank you JJ, I wasn't aware of OffsetImage. It works perfectly now,
thanks again.

Andrea.

"Imagination Is The Only Weapon In The War Against Reality."
http://xoomer.alice.it/infinity77/

Here is my example of a Pareto chart.

For an explanation of a Pareto chart:

http://en.wikipedia.org/wiki/Pareto_chart

Could I get this chart added to the matplolib gallery?


Thanks

Paul


import matplotlib.pyplot as plt
import numpy as np


def update_ax2(axx):
   ax2.set_ylim(0, 100)
   ax2.figure.canvas.draw()


# the data to plot
defects = [32, 22, 15, 5, 2]
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
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
# create the callback to automatically update the y axis
ax1.callbacks.connect("ylim_changed", update_ax2)
# create an upper limit for the y axis.
# The upper limit is the sum of all the numbers
ax1.set_ylim(ymax=the_sum)
rects1 = ax1.bar(ind, defects, width=width) # draw the chart
line, = ax1.plot(x, the_cumsum) # draw the  line
ax1.set_xticks(ind+ .5 * width) # 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()

On Sat, Sep 22, 2012 at 12:40 PM, Eric Firing <ef...@ha...> wrote:
> On 2012/09/22 3:03 AM, reckoner wrote:
>> Hi,
>>
>> I have a plot that includes arrows drawn by the quiver command. I would
>> like to create animation using Func Animation, but I don't know how to
>> update the quiver arrows. I can update everything else on the plot and
>> animates fine.
>>
>> Does anybody know how to update the quiver arrows in an animation? I
>> know the quiver arrows have a XY property, but changing that doesn't
>> update the plot.
>
> You cannot update the arrow positions without making a new Quiver
> instance, so to animate with varying positions, you will need to delete
> the previous Quiver instance and make a new one for each frame.

Given this, it might be best to use ArtistAnimation then, which should
handle turning on and off artists that you provide as a list of list
of artists.

Ryan

-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Hi Everyone,

I am considering the best practices for producing high-quality plots for
publication.  I would like to be able to use colour and and transparency
for screen viewing, but also want to ensure that the graphs print well.

The typical problem I run into is using colors for data curves.  When  
printed
on laser printers, these curves become halftone grayscale which appear  
very
"blurry" compared with the pure black curves.

I would like to develop a set of practises that will allow me to specify
two types of colors - those for data that should be rendered in true  
black
(but perhaps with varying line-thickneses corresponding to the original
darkness) when printed, and those for shading, axis frames etc. in the
background where blurry halftones are acceptable.

Has this topic been discussed anywhere?  I know of several threads  
discussing
general conversion to grayscale, but nothing discussion the issues of  
blurry
halftones when printing.

Thanks,
Michael.

Refs:
http://thread.gmane.org/gmane.comp.python.matplotlib.general/5479/focus=5484
http://thread.gmane.org/gmane.comp.python.matplotlib.general/28576/focus=28578

On 2012/09/23 9:27 AM, Benjamin Root wrote:
>
>
> On Sunday, September 23, 2012, Giovanni Plantageneto wrote:
>
>     Hi everybody,
>     sorry, I guess the question is trivial, but I confess my matplotlib
>     and python ignorance.
>
>     I'm running some code written by someone else, and apparently some
>     bits of the code are not compliant with newer versions of matplotlib.
>     So, how can I rewrite the following, which give AttributError?
>
>      > self.ax.get_figure().axes = []
>
>     and
>
>      > self.ax.get_figure().axes = [self.ax <http://self.ax>]
>
>     Thanks a lot.
>
>
> Without context, it would be hard to say.  What was the exception
> message?  I bet it was a NoneType object being returned by get_figure(),
> which would mean that the Axes object was created without a figure,
> which is rarely done.

It looks to me like the code was trying to delete all axes but one from 
the figure.  This probably worked when Figure.axes was a plain list, but 
for quite some time it has been a read-only list generated from an 
AxesStack instance.

The code will need rewriting based on an understanding of what it is 
trying to do, and how mpl works now.  There is no shortcut.  For this 
particular problem, you might be able to do something like this:

fig = self.ax.get_figure()
axlist = fig.axes
for ax in axlist:
     if not ax == self.ax:
         fig.delaxes(ax)

Eric

>
> Also, it looks like the code was trying to manage the hierarchy of
> objects itself (maybe the code was trying to detach an axes from one
> figure and transfer to another?  Lots of bookkeeping code like this is
> not needed, but you may still have other issues lurking.
>
> Ben Root
>
>
>
> ------------------------------------------------------------------------------
> 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
>

On 2012/09/23 9:45 AM, Giovanni Plantageneto wrote:
> One of the suggestions I got works:
>
>> Maybe this:
>
>> self.ax.get_figure().clf()
>> self.ax.get_figure().add_axes(self.ax)

This seems a bit dangerous, because logically, even if does not 
presently do so, the clf() call could remove the figure reference from 
self.ax.  If you want to go this route, then:

fig = self.ax.get_figure()
fig.clf()
fig.add_axes(self.ax)

Eric

>
>> But it looks really weird to me.
>
> If I understand it correctly, from matplotlib version 1.1.1 (?)
> statements as "self.ax.get_figure().axes = []" are not possible any
> more as axes are not lists anymore. Don't take my word for it, though.
>
> Thanks for the support.
>
>
> 2012/9/23 Giovanni Plantageneto <g.p...@gm...>:
>> Hi everybody,
>> sorry, I guess the question is trivial, but I confess my matplotlib
>> and python ignorance.
>>
>> I'm running some code written by someone else, and apparently some
>> bits of the code are not compliant with newer versions of matplotlib.
>> So, how can I rewrite the following, which give AttributError?
>>
>>> self.ax.get_figure().axes = []
>>
>> and
>>
>>> self.ax.get_figure().axes = [self.ax]
>>
>> Thanks a lot.
>
> ------------------------------------------------------------------------------
> 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
>

One of the suggestions I got works:

>Maybe this:

>self.ax.get_figure().clf()
>self.ax.get_figure().add_axes(self.ax)

>But it looks really weird to me.

If I understand it correctly, from matplotlib version 1.1.1 (?)
statements as "self.ax.get_figure().axes = []" are not possible any
more as axes are not lists anymore. Don't take my word for it, though.

Thanks for the support.


2012/9/23 Giovanni Plantageneto <g.p...@gm...>:
> Hi everybody,
> sorry, I guess the question is trivial, but I confess my matplotlib
> and python ignorance.
>
> I'm running some code written by someone else, and apparently some
> bits of the code are not compliant with newer versions of matplotlib.
> So, how can I rewrite the following, which give AttributError?
>
>> self.ax.get_figure().axes = []
>
> and
>
>> self.ax.get_figure().axes = [self.ax]
>
> Thanks a lot.

On Sunday, September 23, 2012, Giovanni Plantageneto wrote:

> Hi everybody,
> sorry, I guess the question is trivial, but I confess my matplotlib
> and python ignorance.
>
> I'm running some code written by someone else, and apparently some
> bits of the code are not compliant with newer versions of matplotlib.
> So, how can I rewrite the following, which give AttributError?
>
> > self.ax.get_figure().axes = []
>
> and
>
> > self.ax.get_figure().axes = [self.ax]
>
> Thanks a lot.
>
>
Without context, it would be hard to say.  What was the exception message?
 I bet it was a NoneType object being returned by get_figure(), which would
mean that the Axes object was created without a figure, which is rarely
done.

Also, it looks like the code was trying to manage the hierarchy of objects
itself (maybe the code was trying to detach an axes from one figure and
transfer to another?  Lots of bookkeeping code like this is not needed, but
you may still have other issues lurking.

Ben Root

Hi everybody,
sorry, I guess the question is trivial, but I confess my matplotlib
and python ignorance.

I'm running some code written by someone else, and apparently some
bits of the code are not compliant with newer versions of matplotlib.
So, how can I rewrite the following, which give AttributError?

> self.ax.get_figure().axes = []

and

> self.ax.get_figure().axes = [self.ax]

Thanks a lot.

Hey Ben,

Here is the code I am using to generate this plot, in addition to an
example input. It's basicaIlly a list of lists, where each inner list is a
time series. Plotting a 3D time series as a 3D surface rectangle is
probably a pretty common problem. It would be awesome if I didn't have to
switch to using rpy + ggplot or even worse, mlabwrap. Thank for any ideas
that anyone has!

def ThreeDSurfacePlot(list_of_lists):
    plt.clf()
    fig = plt.figure()
    list_of_lists = Smooth(list_of_lists)
    xs = numpy.arange(0,list_of_lists.shape[1],1)
    zs = numpy.arange(0,len(list_of_lists),1)
    ax = p3.Axes3D(fig)
    X = numpy.meshgrid(xs,zs)[0]
    Y = numpy.meshgrid(xs,zs)[1]
    Z = list_of_lists
    ax.plot_surface(X, Y, Z, cmap=cm.jet, cstride=1, rstride=1)
    ax.set_xlabel("Sequence Elements")
    ax.set_ylabel("Trial")
    ax.set_zlabel("Inter-Key-Interval")
    ax.set_xscale

    # Set up x ticks


    tick_locs_x = range(20)
    tick_lbls_x = ['d', 'j', 'k', 'f', 'j', 'd', 'f', 'k', 'd', 'f', 'k',
'j', 'd', 'f', 'k', 'f', 'j', 'd', 'k', 'j']
    plt.xticks(tick_locs_x, tick_lbls_x)

    # Set up y (or z?) ticks


    tick_locs_y = range(len(list_of_lists))
    tick_lbls_y = []

    for day in range(len(data["keylog"])):
        day_trial_ctr = 0
        for trial in range(len(data["keylog"][day])):
            if len(data["keylog"][day][trial]) == 20:
                if day_trial_ctr % 20 == 0:
                    tick_lbls_y.append("Day:" + str(day) + ", Trial: " +
str(day_trial_ctr))
                else:
                    tick_lbls_y.append("")

                    day_trial_ctr += 1

    plt.yticks(tick_locs_y, tick_lbls_y, fontsize=10)

    ax.auto_scale_xyz([0,20],[0,50],[0,1])
    ax.view_init(20,45)

    ax.axis('tight')
    plt.savefig(subject + "_3d_surface.png")

    if show: plt.show()

>>> print accurateseries[:3]
[[ 0.5         0.5         0.49699092  0.5         0.68226504  0.48422813
   0.42276716  0.46813011  0.42340088  0.40479589  0.41090202  0.31301808
   0.30782294  0.27784109  0.36982799  0.48932219  0.38784313  0.33056998
   0.40356588  0.32964206]
 [ 0.5         0.57195497  0.30683708  0.46926498  0.44043994  0.46917915
   0.32043695  0.41017413  0.40825605  0.28631306  0.40151811  0.31961489
   0.35328102  0.22550416  0.36752486  0.55106211  0.39073801  0.38961005
   0.36436582  0.34787703]
 [ 0.4480989   0.49201202  0.25450802  0.39503598  0.32998705  0.33187294
   0.35646415  0.36470699  0.3162992   0.28596401  0.39307094  0.4239881
   0.32525587  0.30294204  0.38540196  0.296211    0.35584903  0.31555796
   0.35734415  0.36554003]]


On Thu, Sep 20, 2012 at 7:46 PM, Benjamin Root <ben...@ou...> wrote:

>
>
> On Thursday, September 20, 2012, Brian J Mingus wrote:
>
>> Hi all,
>>
>> I have managed to create a 3d plot with uneven aspect ratio via
>> auto_scale_xyz but I haven't yet figured out how to fix the grid. If you
>> could give me a pointer I would appreciate it.
>>
>> http://imagebin.org/index.php?mode=image&id=229196
>>
>> Thanks,
>>
>>
> Brian,
>
> Just today, I submitted a PR that involved extensive fixes to autoscaling
> in mplot3d.  I don't have the PR number on me, but it should be easy to
> find on the github page.  While I don't think it will fix much for you, I
> would be interested to know if it breaks your code.
>
> As for your issues, it is hard to help out without a code sample to see
> how you got to where you are.  Did you happen to use my experimental
> daspect branch?
>
> Cheers!
> Ben Root
>
>>
>>


-- 
Brian Mingus
Graduate student
Computational Cognitive Neuroscience Lab
University of Colorado at Boulder
http://grey.colorado.edu/mingus
1-720-587-9482

On 2012/09/22 3:03 AM, reckoner wrote:
> Hi,
>
> I have a plot that includes arrows drawn by the quiver command. I would
> like to create animation using Func Animation, but I don't know how to
> update the quiver arrows. I can update everything else on the plot and
> animates fine.
>
> Does anybody know how to update the quiver arrows in an animation? I
> know the quiver arrows have a XY property, but changing that doesn't
> update the plot.

You cannot update the arrow positions without making a new Quiver 
instance, so to animate with varying positions, you will need to delete 
the previous Quiver instance and make a new one for each frame.

Eric

>
> Thanks!

I recommend you to use OffsetImage. Here is an example of how one can
use OffsetImage.

http://matplotlib.org/examples/pylab_examples/demo_annotation_box.html

And attached is the modified version of the original script.

Regards,

-JJ

Hi,

I have a plot that includes arrows drawn by the quiver command. I would 
like to create animation using Func Animation, but I don't know how to 
update the quiver arrows. I can update everything else on the plot and 
animates fine.

Does anybody know how to update the quiver arrows in an animation? I 
know the quiver arrows have a XY property, but changing that doesn't 
update the plot.

Thanks!

Here's the uname -a output:

Darwin Pico.local 12.0.0 Darwin Kernel Version 12.0.0: Sun Jun 24 23:00:16
PDT 2012; root:xnu-2050.7.9~1/RELEASE_X86_64 x86_64

I just modified the script that was here:
http://matplotlib.org/faq/installing_faq.html#building-and-installing-from-source-on-osx-with-epd

I don't actually have EPD, but it didn't look like there was anything
really EPD specific in that script so I used it.

Thanks,

-Ranjit


On Fri, Sep 21, 2012 at 5:59 PM, <
mat...@li...> wrote:

> Send Matplotlib-users mailing list submissions to
>         mat...@li...
>
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Matplotlib-users digest..."
>
>
> Today's Topics:
>
>    1. Re: install problem on OSX 10.8 (Benjamin Root)
>    2. Fwd:  install problem on OSX 10.8 (Benjamin Root)
>    3. Re: Image as marker and axes "equal" aspect ratio (Andrea Gavana)
>    4. Re: install problem on OSX 10.8 (Damon McDougall)
>    5. Re: netcdf4-python build (Michael Rawlins)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Sep 2012 14:53:26 -0400
> From: Benjamin Root <ben...@ou...>
> Subject: Re: [Matplotlib-users] install problem on OSX 10.8
> To: Ranjit Chacko <ra...@ge...>
> Cc: mat...@li...
> Message-ID:
>         <
> CAN...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Fri, Sep 21, 2012 at 2:19 PM, Ranjit Chacko <ra...@ge...>
> wrote:
>
> > I'm having some trouble compiling matplotlib, and I'm not sure how to fix
> > it. Does anyone have any advice on how to proceed given the following
> > traceback?
> >
> > Thanks,
> >
> > -Ranjit
> >
> >
> Which version of matplotlib?  How are you building it (i.e., what set of
> directions are you following)?
>
> Ben Root
> -------------- next part --------------
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> ------------------------------
>
> Message: 2
> Date: Fri, 21 Sep 2012 15:01:59 -0400
> From: Benjamin Root <ben...@ou...>
> Subject: [Matplotlib-users] Fwd:  install problem on OSX 10.8
> To: Matplotlib Users <mat...@li...>
> Message-ID:
>         <CANNq6FkLV83c8szb-Yjh=
> 3Qy...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Note: please use "Reply-All" to make sure the mailing list continues to get
> this thread.
>
> Could you do a "uname -a" at the command-line and give us that output?  I
> was not aware that Apple shipped any 32-bit machines anymore.
>
> Ben Root
>
> ---------- Forwarded message ----------
> From: Ranjit Chacko <ra...@ge...>
> Date: Fri, Sep 21, 2012 at 2:55 PM
> Subject: Re: [Matplotlib-users] install problem on OSX 10.8
> To: Benjamin Root <ben...@ou...>
>
>
> I'm just cloned the repo from master yesterday, and I tried running the
> following script:
> NAME=matplotlib
> VERSION=v1.1.x
> PREFIX=$HOME
> cd matplotlib
> export LDFLAGS="-Os -arch i386 -L/usr/X11/lib"
> export CFLAGS="-Os -arch i386  -I/usr/X11/include
> -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng12"
> export PKG_CONFIG_PATH="/usr/X11/lib/pkgconfig"
> export ARCHFLAGS="-arch i386"
> python setup.py build
> # use --prefix if you don't want it installed in the default location:
> python setup.py install #--prefix=$PREFIX
> cd ..
>
> Thanks,
>
> -Ranjit
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
>

>________________________________
> From: Damon McDougall <dam...@gm...>
>To: Michael Rawlins <raw...@ya...> 
>Cc: "mat...@li..." <mat...@li...> 
>Sent: Friday, September 21, 2012 2:50 PM
>Subject: Re: [Matplotlib-users] netcdf4-python build
> 
>
>
>
>From what I remember dealing with the netcdf c library, you have to explicitly set a compile flag to enable hdf5 support. That was a while ago, though. I'm not sure if things have changed.
>
>
>Hope this helps.
>
>
>
>
>I did not do a source compile. 
>
>I've reinstalled libhdf5-serial-1.8.4 package and now have the right HDF5 library files. Successfully built and installed netCDF4-1.0.  My script loads in module but a read/write issue is present. This is code that worked on previous system. Error:
>
>  File "test.py", line 96, in <module>
>    data.missing_value=-9.99
>  File "netCDF4.pyx", line 2570, in netCDF4.Variable.__setattr__ (netCDF4.c:28242)
>  File "netCDF4.pyx", line 2392, in netCDF4.Variable.setncattr (netCDF4.c:26309)
>  File "netCDF4.pyx", line 1013, in netCDF4._set_att (netCDF4.c:12699)
>AttributeError: NetCDF: Write to read only
>
>
>The statement in the code triggers the error.
>
>data.missing_value=-9.99 .
>
>MR
>

On Friday, September 21, 2012, Benjamin Root wrote:

> Note: please use "Reply-All" to make sure the mailing list continues to
> get this thread.
>
> Could you do a "uname -a" at the command-line and give us that output?  I
> was not aware that Apple shipped any 32-bit machines anymore.
>
> Ben Root
>
> ---------- Forwarded message ----------
> From: Ranjit Chacko <ra...@ge... <javascript:_e({}, 'cvml',
> 'ra...@ge...');>>
> Date: Fri, Sep 21, 2012 at 2:55 PM
> Subject: Re: [Matplotlib-users] install problem on OSX 10.8
> To: Benjamin Root <ben...@ou... <javascript:_e({}, 'cvml',
> 'ben...@ou...');>>
>
>
> I'm just cloned the repo from master yesterday, and I tried running the
> following script:
> NAME=matplotlib
> VERSION=v1.1.x
> PREFIX=$HOME
> cd matplotlib
> export LDFLAGS="-Os -arch i386 -L/usr/X11/lib"
> export CFLAGS="-Os -arch i386  -I/usr/X11/include
> -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng12"
> export PKG_CONFIG_PATH="/usr/X11/lib/pkgconfig"
> export ARCHFLAGS="-arch i386"
> python setup.py build
> # use --prefix if you don't want it installed in the default location:
> python setup.py install #--prefix=$PREFIX
> cd ..
>
> Thanks,
>
> -Ranjit
>
>
I'm not sure 10.8 supports 32-bit machines at all. Apple even dropped
support for some 64-bit machines in the 10.8 release.


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

Hi Eric, All,

On 21 September 2012 15:46, Moore, Eric (NIH/NIDDK) [F] wrote:
>> -----Original Message-----
>> From: Andrea Gavana [mailto:and...@gm...]
>> Sent: Wednesday, September 19, 2012 11:09 AM
>> To: mat...@li...
>> Subject: [Matplotlib-users] Image as marker and axes "equal" aspect
>> ratio
>>
>> Hi All,
>>
>>     I am currently trying to plot 4 points (but they will be more, in
>> an animated sequence later), and I am trying to use an image as a point
>> marker. I am using the axes transData transform to get the point
>> coordinates from the data world to the display world.
>>
>> Everything seems to be working OK (i.e., the images are placed
>> correctly close to the plot points); however, as soon as I try to force
>> the axes into an "equal" aspect ratio with this command:
>>
>> ax.set_aspect('equal')
>>
>> Then all the calculations are messed up and the images end up very far
>> from the plot points. I have tried also the approach mentioned in this
>> StackOverflow post:
>>
>> http://stackoverflow.com/questions/2318288/how-to-use-custom-marker-
>> with-plot
>>
>> But I get the same wrong answer when I set the "equal" aspect ratio for
>> the axes.
>>
>> I am attaching a small sample application which demonstrates the
>> problem, a small  "smiley.png" image needed to run the script and two
>> plots generated by my script, one with the "equal" aspect ratio and the
>> other without.
>>
>> I appreciate any suggestion, as I feel I am missing something
>> important...
>>
> The source of the problem is that the transformation you are using has not been updated to account for your set_aspect call.  I played around a little bit, but I'm not sure how to force mpl to update the transform.  Perhaps someone else can comment.  This is a very fragile way to do things anyway because figimage places the image in screen coordinates and you really would like to place it relative to the axis.

Thank you for your answer and for taking the time to play with the
sample I posted. I know that using figimage is not exactly the best
way to go, but I can only think of two other approaches:

1) Use imshow: from the documentation, it appears to me that you can't
place an image wherever you want, and I was unable to find any example
on how to use imshow to place multiple images in a specific place
inside the axes;

2) Use scatter: again, from the docs it seems that scatter supports
symbols, mathtext, paths and regular polygons, but no images...

I may of course be wrong about the above statements, and again I
welcome any suggestion you may have.

Thank you.

Andrea.

"Imagination Is The Only Weapon In The War Against Reality."
http://xoomer.alice.it/infinity77/

Note: please use "Reply-All" to make sure the mailing list continues to get
this thread.

Could you do a "uname -a" at the command-line and give us that output?  I
was not aware that Apple shipped any 32-bit machines anymore.

Ben Root

---------- Forwarded message ----------
From: Ranjit Chacko <ra...@ge...>
Date: Fri, Sep 21, 2012 at 2:55 PM
Subject: Re: [Matplotlib-users] install problem on OSX 10.8
To: Benjamin Root <ben...@ou...>


I'm just cloned the repo from master yesterday, and I tried running the
following script:
NAME=matplotlib
VERSION=v1.1.x
PREFIX=$HOME
cd matplotlib
export LDFLAGS="-Os -arch i386 -L/usr/X11/lib"
export CFLAGS="-Os -arch i386  -I/usr/X11/include
-I/usr/X11/include/freetype2 -I/usr/X11/include/libpng12"
export PKG_CONFIG_PATH="/usr/X11/lib/pkgconfig"
export ARCHFLAGS="-arch i386"
python setup.py build
# use --prefix if you don't want it installed in the default location:
python setup.py install #--prefix=$PREFIX
cd ..

Thanks,

-Ranjit

On Fri, Sep 21, 2012 at 2:19 PM, Ranjit Chacko <ra...@ge...> wrote:

> I'm having some trouble compiling matplotlib, and I'm not sure how to fix
> it. Does anyone have any advice on how to proceed given the following
> traceback?
>
> Thanks,
>
> -Ranjit
>
>
Which version of matplotlib?  How are you building it (i.e., what set of
directions are you following)?

Ben Root

On Friday, September 21, 2012, Michael Rawlins wrote:

>
> After the build, I determined that 'install' was also needed.
>
> > python setup.py install
>
> completed with no errors.  OK, finally built and installed. But now my
> matplotlib script gives this error:
>
> Traceback (most recent call last):
>   File "map_PrcpBias_Northeast.py", line 21, in <module>
>     from netCDF4 import Dataset as NetCDFFile
> ImportError: /usr/local/lib/python2.7/dist-packages/netCDF4.so: undefined
> symbol: nc_inq_var_endian
>
>
> So, checking shared library dependencies:
>
> > ldd /usr/local/lib/python2.7/dist-packages/netCDF4.so
>
>     linux-gate.so.1 =>  (0xb776a000)
>     libnetcdf.so.7 => /usr/local/lib/libnetcdf.so.7 (0xb7604000)
>     libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xb75d3000)
>     libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb742d000)
>     libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7401000)
>     /lib/ld-linux.so.2 (0xb776b000)
>
> and
>
> > ldd /usr/local/lib/libnetcdf.so.7
>
>     linux-gate.so.1 =>  (0xb7765000)
>     libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7663000)
>     libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb74be000)
>     /lib/ld-linux.so.2 (0xb7766000)
>
> no libhdf5 there. Can this be fixed?
>
> MR
>
>
>
>
>From what I remember dealing with the netcdf c library, you have to
explicitly set a compile flag to enable hdf5 support. That was a while ago,
though. I'm not sure if things have changed.

Hope this helps.


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

I'm having some trouble compiling matplotlib, and I'm not sure how to fix
it. Does anyone have any advice on how to proceed given the following
traceback?

Thanks,

-Ranjit

building 'matplotlib.ft2font' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Os -I/usr/X11/include
-I/usr/X11/include/freetype2 -I/usr/X11/include/libpng12 -arch i386
-DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1
-I/usr/local/include -I/usr/include -I/usr/X11/include
-I/opt/getaround/lib/python2.7/site-packages/numpy/core/include
-I/usr/local/include -I/usr/include -I/usr/X11/include -I.
-I/usr/local/include/freetype2 -I/usr/include/freetype2
-I/usr/X11/include/freetype2
-I/opt/getaround/lib/python2.7/site-packages/numpy/core/include/freetype2
-I/usr/local/include/freetype2 -I/usr/include/freetype2
-I/usr/X11/include/freetype2 -I./freetype2
-I/opt/getaround/include/python2.7 -c src/ft2font.cpp -o
build/temp.macosx-10.4-i386-2.7/src/ft2font.o
src/ft2font.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’:
src/ft2font.cpp:854:   instantiated from here
src/ft2font.cpp:854: error: explicit instantiation of
‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition
available
src/ft2font.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’:
src/ft2font.cpp:854:   instantiated from here
src/ft2font.cpp:854: error: explicit instantiation of
‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition
available
src/ft2font.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’:
src/ft2font.cpp:854:   instantiated from here
src/ft2font.cpp:854: error: explicit instantiation of
‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition
available
src/ft2font.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’:
src/ft2font.cpp:854:   instantiated from here
src/ft2font.cpp:854: error: explicit instantiation of
‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition
available
src/ft2font.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’:
src/ft2font.cpp:854:   instantiated from here
src/ft2font.cpp:854: error: explicit instantiation of
‘std::basic_ostream<_CharT, _Traits>&
std::operator<<(std::basic_ostream<_CharT, _Traits>&, const
std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits =
std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition
available
error: command 'gcc' failed with exit status 1

On Wed, Sep 19, 2012 at 9:14 AM, Fabien Lafont <laf...@gm...>wrote:

> Actually I want to try to plot something like this picture:
>
> http://physics.aps.org/assets/d88621a594e78eea
>
> With a color for inside and another for outside.
>
>
Probably not to the level of control one may wish to have, but one can
achieve shading effects assuming a light source.  plot_surface() can assume
a light source for you, or you could provide one IIRC.  This isn't very
well documented (in fact, it is downright non-existent!).

The most simple way of getting something like what you want is to set
shade=True and not use a colormap.  This shades the surface according to
the normal vector to the surface.

One can also provide a "lightsource".  I just noticed this is not
documented.  One can specify a "lightsource" kwarg to plot_surface (note
that shade must be set to True, a cmap must be provided, and oddly enough,
facecolors has to be not None (this might be a bug)), and a colorbar won't
work (seem to throw an exception...).  By default (i.e., lightsource=None),
a matplotlib.color.LightSource object with azdeg=135 and altdeg=55 is used
to shade based on the data and colormap.  You can provide your own light
source to achieve the effect you would like by positioning it properly
(don't ask me how, I never played with that part).

I know this was kind of vague, but I hope it is at least somewhat
illuminating.

Cheers!
Ben Root

After the build, I determined that 'install' was also needed.

> python setup.py install

completed with no errors.  OK, finally built and installed. But now my matplotlib script gives this error:

Traceback (most recent call last):
  File "map_PrcpBias_Northeast.py", line 21, in <module>
    from netCDF4 import Dataset as NetCDFFile 
ImportError: /usr/local/lib/python2.7/dist-packages/netCDF4.so: undefined symbol: nc_inq_var_endian


So, checking shared library dependencies:

> ldd /usr/local/lib/python2.7/dist-packages/netCDF4.so

    linux-gate.so.1 =>  (0xb776a000)
    libnetcdf.so.7 => /usr/local/lib/libnetcdf.so.7 (0xb7604000)
    libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xb75d3000)
    libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb742d000)
    libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7401000)
    /lib/ld-linux.so.2 (0xb776b000)

and

> ldd /usr/local/lib/libnetcdf.so.7

    linux-gate.so.1 =>  (0xb7765000)
    libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7663000)
    libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb74be000)
    /lib/ld-linux.so.2 (0xb7766000)

no libhdf5 there. Can this be fixed?

MR

> -----Original Message-----
> From: Andrea Gavana [mailto:and...@gm...]
> Sent: Wednesday, September 19, 2012 11:09 AM
> To: mat...@li...
> Subject: [Matplotlib-users] Image as marker and axes "equal" aspect
> ratio
> 
> Hi All,
> 
>     I am currently trying to plot 4 points (but they will be more, in
> an animated sequence later), and I am trying to use an image as a point
> marker. I am using the axes transData transform to get the point
> coordinates from the data world to the display world.
> 
> Everything seems to be working OK (i.e., the images are placed
> correctly close to the plot points); however, as soon as I try to force
> the axes into an "equal" aspect ratio with this command:
> 
> ax.set_aspect('equal')
> 
> Then all the calculations are messed up and the images end up very far
> from the plot points. I have tried also the approach mentioned in this
> StackOverflow post:
> 
> http://stackoverflow.com/questions/2318288/how-to-use-custom-marker-
> with-plot
> 
> But I get the same wrong answer when I set the "equal" aspect ratio for
> the axes.
> 
> I am attaching a small sample application which demonstrates the
> problem, a small  "smiley.png" image needed to run the script and two
> plots generated by my script, one with the "equal" aspect ratio and the
> other without.
> 
> I appreciate any suggestion, as I feel I am missing something
> important...
> 
> Thank you in advance.
> 
> 
> Andrea.
> 
> "Imagination Is The Only Weapon In The War Against Reality."
> http://xoomer.alice.it/infinity77/
> 
> # ------------------------------------------------------------- # def
> ask_mailing_list_support(email):
> 
>     if mention_platform_and_version() and include_sample_app():
>         send_message(email)
>     else:
>         install_malware()
>         erase_hard_drives()
> # ------------------------------------------------------------- #

Andrea, 

The source of the problem is that the transformation you are using has not been updated to account for your set_aspect call.  I played around a little bit, but I'm not sure how to force mpl to update the transform.  Perhaps someone else can comment.  This is a very fragile way to do things anyway because figimage places the image in screen coordinates and you really would like to place it relative to the axis.

Eric 

On Thursday, September 20, 2012, Brian J Mingus wrote:

> Hi all,
>
> I have managed to create a 3d plot with uneven aspect ratio via
> auto_scale_xyz but I haven't yet figured out how to fix the grid. If you
> could give me a pointer I would appreciate it.
>
> http://imagebin.org/index.php?mode=image&id=229196
>
> Thanks,
>
>
Brian,

Just today, I submitted a PR that involved extensive fixes to autoscaling
in mplot3d.  I don't have the PR number on me, but it should be easy to
find on the github page.  While I don't think it will fix much for you, I
would be interested to know if it breaks your code.

As for your issues, it is hard to help out without a code sample to see how
you got to where you are.  Did you happen to use my experimental daspect
branch?

Cheers!
Ben Root

>
>