matplotlib-users Mailing List for matplotlib

On Fri, Aug 7, 2009 at 7:27 PM, John Hunter<jd...@gm...> wrote:
> On Thu, Aug 6, 2009 at 8:48 PM, Patrick Rynhart<pry...@gm...> wrote:
>> Dear all,
>>
>> We are using Python 2.5, matplotlib and NumPy on Windows to assist
>> with the teaching for an undergraduate paper.  On a small number of
>> installations, an error attempting to load some required DLL's is
>> being reported (on approx 3 machines out of approximately 60).  There
>> doesn't appear to be any pattern with this - we can seen it on one
>> install of Windows Server 2008 and also on various versions of Windows
>> XP (Professional and Home).
>>
>> Symptoms are, after a "from pylab import *", the following traceback:
>>
>> Traceback (most recent call last):
>>  File "C:\Documents and
>> Settings\Jo\workspace\test\src\root\nested\__init__.py", line 2, in
>> <module>
>>    from pylab import *
>>  File "C:\Python25\Lib\site-packages\pylab.py", line 1, in <module>
>>    from matplotlib.pylab import *
>>  File "C:\Python25\Lib\site-packages\matplotlib\pylab.py", line 206,
>> in <module>
>>    from matplotlib import mpl  # pulls in most modules
>>  File "C:\Python25\Lib\site-packages\matplotlib\mpl.py", line 1, in <module>
>>    from matplotlib import artist
>>  File "C:\Python25\Lib\site-packages\matplotlib\artist.py", line 4, in <module>
>>    from transforms import Bbox, IdentityTransform, TransformedBbox,
>> TransformedPath
>>  File "C:\Python25\Lib\site-packages\matplotlib\transforms.py", line
>> 34, in <module>
>>    from matplotlib._path import affine_transform
>> ImportError: DLL load failed: The specified module could not be found.
>
> We have seen this problem several times  before, and have labored hard
> to banish it, but it always has a way of coming back to haunt us.  I
> am aware of a bug in python2.6 which causes mingw to build broken
> win32 binaries, but am not aware of such  a problem w/ python2.5,
> which you appear to be using.  We often use a program called
> dependency walker to track these problems down:
>
>  http://www.dependencywalker.com/
>
> Open the problematic file (it should be
> C:\Python25\Lib\site-packages\matplotlib\_path.pyd) and report any
> errors you find here; it should tell you which DLLs are missing.
> Search the good and the bad boxes for these DLL filenames and see if
> it is a difference in the boxes, eg do the good boxes have the DLL and
> the bad boxes not, and if so maybe you can figure out why (different
> version in the OS patch level?).  I am really interested to know the
> difference in the boxes because it may give us the critical clue as to
> why some users report this problem and others do not see it.
>
> Also, on one of the bad boxes, could you try the new 0.99 release and
> let me know if you have the same issue?
>
> I build the python2.5 installers with mingw; Christoph builds the
> python2.6 installers with Visual Studio precisely because mingw is
> broken on python2.6.  If we can't banish this bug on 2.5 w/ mingw, I
> may have to lean on his generosity and ask him to make a python2.5
> installer with Visual Studio as well.
>
> JDH
>
> PS: rereading your email, I see you are using 0.98.3.  The first time
> I read it, when I wrote the response above, I thought you were using
> 0.98.5.3 -- the .3 at the end tricked me.  The latter is fairly
> recent, and came out 10 months after 0.98.3, and we did several things
> to fix exactly this dll problem in interim.  At a minimum, you need to
> be testing and installing 0.98.5.3.  This is a very stable, bug fix
> release, suitable for use in the classroom.  I can't guarantee you
> won't hit the same problem, but at least you will be using a version
> that *shouldn't* have it, though I am still interested in the results
> of the dependency walker tests above, because I have wasted so much
> time trying to fix these win32 installers.
>

Dear John,

Many thanks for your detailed post with regard to how to troubleshoot
this issue.  The use of dependency walker allowed me to determine that
affected systems were missing the Visual C/C++ shared runtime
libraries - in particular, MSVCP71.DLL (the version of the runtime
shipped with Microsoft Visual C++ .NET 2003) was missing on these
systems.

According to http://support.microsoft.com/default.aspx/kb/326922,
installing the .NET 1.1 framework should - as a side-effect - also
install this DLL.  However, on Windows Server 2008 (the only box that
I have direct access to in a faulted state) this DLL didn't seem to
install when I installed the .NET 1.1 framework.

(Aside: This could be because Explorer in Vista/2K8 appears to hide
system files exceptionally well.  Even after playing with the Windows
Desktop Search syntax I couldn't get a match.  Dropping to a cmd
prompt and listing %systemroot%\system32 also didn't provide a match
for the DLL.)

On one of the student Windows XP machines, I copied the above DLL from
a working XP SP3 install to "C:\Python25\Lib\site-packages\matplotlib"
and confirmed that matplotlib then works correctly.  Attempting the
same trick on Server 2K8 didn't work, but this is probably to be
expected (given that it's a major version change of Windows NT).
Also, I don't think that M$ permit redistribution of the runtime by
just copying a DLL across, so I have asked students to try installing
the .NET framework 1.1.

Thanks again for your help.  Do you think that testing for the version
of the Visual C redistributable is required during an install of
matplotlib (and/or possibly at runtime).

Thanks again for your assistance - this has been most appreciated.

Regards,

Patrick

-- 
Dr Patrick Rynhart
Linux Systems Administrator / Team Leader
IT Support Group
School of Engineering and Advanced Technology
AgHort A Room 3.61
Massey University (Turitea Campus)
NEW ZEALAND
Phone +64 6 356 9099 extn 2444

Hi,

I just installed matplotlib 0.99.0 and I see that this problem is  
still there.
The command plot(a,ls='steps') is equivalent to plot(a,ls='steps-pre')  
and both cause the first value of the array to NOT be plotted.  This  
is REALLY not what should happen when one plots an array with several  
values.  It is fine if there is a custom option to make that behavior  
(like 'steps-pre'), but the default for ls='steps' or step(x,y) must  
be to have the first flat level at the level of the first entry (what  
the 'steps-post' does).

The docstring now correctly describes the behavior, so that is good,  
but please please make the default "steps" be "steps-post".

Thanks,

-- Paul

On Jul 19, 2009, at 9:35 AM, John Hunter wrote:

> On Fri, Jul 17, 2009 at 5:15 PM, Paul Ray<Pau...@nr...>  
> wrote:
>>
>>
>> Ryan Krauss-2 wrote:
>>>
>>> RTFM:
>>>
>>> plot(t,y, drawstyle='steps-post')
>>>
>>>
>>
>> Actually, 'steps-pre' (which is the default) and 'steps-post' seem  
>> to have
>> swapped definitions.
>> Here is what the docs say:
>>    *where*: [ 'pre' | 'post' | 'mid'  ]
>>      If 'pre', the interval from x[i] to x[i+1] has level y[i]
>>      If 'post', that interval has level y[i+1]
>>      If 'mid', the jumps in *y* occur half-way between the
>>      *x*-values.
>>
>> In fact both the default behavior and what you get with steps-pre  
>> are what
>> SHOULD happen with steps-post.  And steps-post (as you point out)  
>> does what
>> should be the default behavior and that of steps-pre.
>>
>> I have filed a bug report on this, since it is very important that  
>> this work
>> as expected.  As the original poster pointed out, this used to work
>> correctly but recently seems to have gotten broken.
>
>
>
> I am looking first at the behavior of plot with the drawstyle property
> set -- let's make sure this is correct before turning to the steps
> command, which just uses plot with the drawstyle set -- here is my
> test code
>
> import numpy as np
> import matplotlib.pyplot as plt
>
> fig = plt.figure()
> ax = fig.add_subplot(111)
>
> a = np.array([1,2,3,4,5])
>
> styles = 'default' , 'steps' , 'steps-pre' , 'steps-mid' , 'steps- 
> post'
> styles = 'steps' , 'steps-pre'
> for ls in styles:
>    ax.plot(a, ls=ls, label=ls, lw=2)
>
> ax.legend(loc='upper left')
>
> plt.show()
>
>
> pre causes the step to rise on the x[i], post causes it to rise on
> x[i+1] and mid in the middle.  This seems like the correct behavior.
> So it does look like the docstring for  'step' is incorrect, and I've
> changed it to read
>
>
>        *where*: [ 'pre' | 'post' | 'mid'  ]
>          If 'pre', the interval from x[i] to x[i+1] has level y[i+1]
>
>          If 'post', that interval has level y[i]
>
>          If 'mid', the jumps in *y* occur half-way between the
>
>
> JDH

Jouni K. Seppänen wrote:
> "Werner F. Bruhin" <wer...@fr...> writes:
>
>   
>> I trying to create a Pareto diagram and would like that the percentage
>> marker is center aligned on the bars,
>>     
>
> Perhaps the easiest solution is to use bar(...,align='center').
>   
Thanks, that does the trick for me, after getting rid of some hack for 
the bar labels.

Werner

Werner F. Bruhin wrote:
> The other problem I have is that the xtick_labels are cut off at the 
> bottom when the frame is resized below a certain size.  How can I 
> prevent this?

I don't think MPL yet has a system for making things fit, so you need to 
change the size/position of your axes object:

axes.set_position(pos, which='both')

"""
     Set the axes position with:

     pos = [left, bottom, width, height]
"""

these are in "figure units" which are relative to figure size, from 0 to 
1. Unfortunately, what this means is that the amount of space for the 
axis labels varies with the size of the figure, as you've discovered.


The default for a single axes in a figure is:

(0.125,  0.1,  0.9,  0.9)

so you might try something like:

axes.set_position((0.125,  0.15,  0.9,  0.85) )

what is best depends on what size you want your figure to look good at.

-Chris


-- 
Christopher Barker, Ph.D.
Oceanographer

Emergency Response Division
NOAA/NOS/OR&R            (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

"Werner F. Bruhin" <wer...@fr...> writes:

> I trying to create a Pareto diagram and would like that the percentage
> marker is center aligned on the bars,

Perhaps the easiest solution is to use bar(...,align='center').

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

Please, take your time and post a "standalone" code that reproduces
your problem so that others can actually test. Also, please describe
what results you have and why they are wrong.

On Tue, Aug 25, 2009 at 4:08 AM, Daniel
Platz<mai...@go...> wrote:
> fig1.colorbar(pc1,ax=ax1,orientation='horizontal',pad=0.025,ticks=temp,format=r"$%2.1f\%%$")
>     cb1.ax.set_xticklabels(temp,fontsize=10,family='serif')

The set_xticklabels command actually overrides the format setting you
specified in the colorbar call, which might be the reason that the
script does not work as you intended. But, it is hard to tell without
the runnable code.

-JJ

You made my day!

Long life to The "close()"

All my ram and swap file was sucked every time a run my script to generate
260 png images...almost killing my ubuntu!

On Tue, May 26, 2009 at 2:23 PM, John Hunter <jd...@gm...> wrote:

> On Tue, May 26, 2009 at 7:39 AM, Michael Droettboom <md...@st...>
> wrote:
> > Does it help if you add a call to "plt.clf()" to the bottom of the loop?
> >
> > The pyplot interface keeps a reference around to every figure created
> > until they are destroyed so that it can be obtained again by number
> > (this is functionality inspired by matlab).  Alternatively, you can use
> > the object-oriented interface to create the figure, which does not have
> > this behavior, e.g., replace
> >
> >   fig = plt.figure()
> >
> > with
> >
> >   from matplotlib import figure
> >   fig = figure.Figure()
> >
> > If all this doesn't help, let me know and I'll look further.
> >
> > Cheers,
> > Mike
> >
> > iCy-fLaME wrote:
> >> I was trying to use matplotlib to plot a series of 2D images, but
> >> python was using up a large amount of RAM very quickly. I don't know
> >> matplotlib that well, so the chance are I am missing something, would
> >> appreciate it if anyone can point me to the right direction.
> >>
> >> I am using:
> >> Python 2.4.3 (#1, Jan 21 2009, 01:11:33)
> >> [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2
> >>
> >> Example code to run in interpreter mode:
> >>
> >> ########################################
> >> from numpy import zeros
> >>
> >> x = 1651
> >> y = 452
> >> page = zeros((x, y)).astype('float')
> >>
> >> import matplotlib
> >> matplotlib.use('Agg')
> >> import matplotlib.pyplot as plt
> >>
> >> for i in range(1000):
> >>       fig = plt.figure()
> >>       ax = fig.add_subplot(111)
> >>       cax = ax.imshow(page, cmap=plt.cm.spectral_r, extent=(-44, 176,
> -30,
> >> 30), interpolation = 'bicubic', vmin = -0.003, vmax = 0.003)
> >>       title = "Time = %(i)0.3es)" % {'i':i}
> >>       ax.set_title(title,fontsize=14)
> >>
> >>       fig.colorbar(cax, ticks=[-2e-3, -1e-3, 0, 1e-3, 2e-3],
> >> orientation='horizontal')
> >>
> >>       fig.savefig('_tmp.' + str(i) + ".png", dpi=300)
>
>
> This code creates 1000 different figures -- either reuse the same
> figure and clear it as Michael suggests
>
>  fig = plt.figure(1)  # by putting 1 here you reuse the same fig
>  fig.clf()  # and clear it
>
> or close the figure in the loop
>
>  fig = plt.figure()
>  # draw and save here
>  plt.close(fig)
>
> JDH
>
>
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I trying to create a Pareto diagram and would like that the percentage 
marker is center aligned on the bars, i.e. the blue point should be 
center aligned on the bar instead of to be aligned on the left edge in 
the following image.



The other problem I have is that the xtick_labels are cut off at the 
bottom when the frame is resized below a certain size.  How can I 
prevent this?

Thanks for any tips on these problems.
Werner

Auré Gourrier <aur...@ya...> writes:

> The patches hide the contourf correctly, as expected, but not the
> contour lines...

Sounds like a zorder problem:

http://matplotlib.sourceforge.net/examples/pylab_examples/zorder_demo.html

> Below are the code lines.

Since several details were edited out, the code sample is not runnable,
so I couldn't try it out myself. I think it's probably the zorder,
though.

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

We are pleased to announce the release of APLpy 0.9.4, which includes
bug fixes, improvements, and new features.

APLpy is a python module that makes it easy to interactively produce
publication-quality plots of astronomical images in FITS format. More
details are available at http://aplpy.sourceforge.net/

The main change with this release is that APLpy now requires
matplotlib 0.99. More information on the changes in this version is
available in the release notes available from the APLpy homepage.

>From the front page you can sign up to the mailing list and/or the
Twitter feed to be kept up-to-date on future releases.

Cheers,

Eli Bressert and Thomas Robitaille

Can't figure this out: I create a figure, add some axes, define data to be plotted as a contourf + contour on top and then add some patches to hide some regions of my plot.
The patches hide the contourf correctly, as expected, but not the contour lines...
Could someone telle me whether I'm doing something wrong ?
Below are the code lines.
I'm using python 2.4, matplotlib 0.91.2

Thanks in advance,

Aure


#----------
    pylab.clf()

    fig = pylab.figure(figsize=(7.,3.8),dpi=100,facecolor='white')

    axes1 = fig.add_axes((.....),label='axes1')
    axes2 = fig.add_axes((.....),label='axes2')            
    axes3 = fig.add_axes((.....),label='axes3')            

    #define contour data
    contourstep = 0.05
    contourx  = np.arange(0.01,2.5+contourstep,contourstep)
    contoury = np.arange(0.01,4.+contourstep,contourstep)
    contourxy1 = np.ones((len(contoury),len(contourx)))
    contourxy2 = np.ones((len(contoury),len(contourx)))
    x = np.arange(0.,6.,0.01)
    for j in range(contourxy1.shape[0]):
        for k in range(contourxy1.shape[1]):
            newval1=...
            newval2=...
            contourxy1[j,k] = newval1
            contourxy2[j,k] = newval2
                
    #add contour
    levels = np.arange(0.0,0.85,0.05)
    cf1 = axes1.contourf(-contourx,contoury,contourxy2,levels,cmap=bone_r,extend = 'max')   #cmap=mpl.cm.gray_r)
    cf2 = axes2.contourf(contourx,contoury,contourxy1,levels,cmap=bone_r,extend = 'max')   #cmap=mpl.cm.gray_r)
    levels2 = np.arange(0.,.45,0.05)
    axes1.contour(-contourx,contoury,contourxy2,levels2,colors='gray')
    axes2.contour(contourx,contoury,contourxy1,levels2,colors='gray')

    #add patches
    axes1.add_patch(mpl.patches.Polygon([(-1.,1),(-2.,1.),(-2.,2.)],
                                        edgecolor='k',
                                        facecolor='w',
                                        ))
    axes1.add_patch(mpl.patches.Polygon([(-1.,1.),(0.,0.),(0.,1.)],
                                        edgecolor='k',
                                        facecolor='w',
                                        ))
    axes2.add_patch(mpl.patches.Polygon([(0.,1.),(2.,1.),(2.,2.),(0.,2.)],
                                        edgecolor='k',
                                        facecolor='w',
                                        ))

    pylab.savefig(outputfilename)
#----------



      

The solution I came up with without delving into the code is to add the 
following two lines to lines.py:286, so that self._transformed_path gets 
assigned a value if it is None before it is accessed:
if self._transformed_path is None:
            self._transform_path()

Worked like a charm. Thank you very much!
I really appreciate the sample code and teaching by example.


Jouni K. Seppänen wrote:
> 
> "Ravi A." <rav...@gm...> writes:
> 
>> I am using boxplot and i wanted to mark current value or any special
>> value
>> on the box plot. How do i achieve this? Something like below.
> 
> Just "plot" the special value, with hold=True if you have set the hold
> default to false. One small issue is that plot autoscales the view
> tightly, which looks bad with the boxes, so you may want to nudge it a
> bit:
> 
> from pylab import *
> boxplot(random((10,10)))
> plot(arange(1,11), random(10), 'rx', ms=5, mew=2, hold=True)
> a,b = xlim()
> xlim(a-.5,b+.5)
> show()
> 
> -- 
> Jouni K. Seppänen
> http://www.iki.fi/jks
> 
> 
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-- 
View this message in context: http://www.nabble.com/showing-current-value-on-boxplot-tp25115648p25130265.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Jae-Joon Lee wrote:
> On Fri, Aug 21, 2009 at 10:01 AM, Scott
> Sinclair<sco...@gm...> wrote:
>>> I just realized that I did not give the correct plot object when creating
>>> the colorbar. Now it works perfectly to pass arguments by set_xticklabels().
>>>
>>> However, another question just arose. To format the numbers on the tick
>>> labels I tried to pass a format string when creating the colorbar with the
>>> format parameter. But it has no effect. The same when I give a
>>> FormatStrFormatter object. I also tried to use
>>> cb.ax.axis.set_major_formatter(). The effect of this was. That it sets the
>>> labels to the range between 0 and 1. Is there a solution for this problem
>>> besides entering the tick labels manually?
> 
> The tick locator and tick formatter needs to be passed during the
> colorbar creation. Otherwise,
> it gets very tricky to deal with. This is because the data coordinate
> of the colorbar axes is not directly associated with the ticklabels.
> 
> If passing the formatter during the colorbar creation has no effect,
> this should be filed as a bug. Please post a small standalone example
> that reproduces your problem. Also, please report your version of
> matplotlib. If you're using older version, I recommend you to test it
> with newer version.
> 
> Just in case, my quick test worked fine.
> 
> imshow([[1,2],[2,3]])
> cb=colorbar(format=r"$%2.1f\%%$")
> 
> -JJ
> 

I just tried this but it did not work for me. The code that I am using 
looks like this

     ax1 = fig1.add_subplot(3,len(fname)/2,i+1,frameon=False)
     temp = np.linspace(data1_amp.min(),data1_amp.max(),3)
     pc1 = ax1.imshow(data1_amp,cmap=nat,vmin=temp[0],vmax=temp[-1])
     ax1.set_xlim((0,250))
     ax1.set_ylim((0,256))
     ax1.set_xticks([])
     ax1.set_yticks([])
     ax1.set_xticklabels('')
     ax1.set_yticklabels('')
     if i==0:
         ax1.set_ylabel('Amplitude 
[mV]',family='serif',size=10,weight='bold')
     ax1.set_title(title[i],family='serif',fontsize=10,weight='bold')
     cb1 = 
fig1.colorbar(pc1,ax=ax1,orientation='horizontal',pad=0.025,ticks=temp,format=r"$%2.1f\%%$")
     cb1.ax.set_xticklabels(temp,fontsize=10,family='serif')
     setp(cb1.ax.get_xticklines(),visible=False)
     plt.draw()
     a    = ax1.get_position().get_points()
     b    = cb1.ax.get_position().get_points()
     temp = [a[0,0], b[0,1], (a[1,0]-a[0,0]), (b[1,1]-b[0,1])]
     cb1.ax.set_position(temp)

I am using matplotlib 0.98.5.2. If anyone has an idea I would be very 
glad if you can post here.

Thanks in advance

Daniel

"Ravi A." <rav...@gm...> writes:

> I am using boxplot and i wanted to mark current value or any special value
> on the box plot. How do i achieve this? Something like below.

Just "plot" the special value, with hold=True if you have set the hold
default to false. One small issue is that plot autoscales the view
tightly, which looks bad with the boxes, so you may want to nudge it a
bit:

from pylab import *
boxplot(random((10,10)))
plot(arange(1,11), random(10), 'rx', ms=5, mew=2, hold=True)
a,b = xlim()
xlim(a-.5,b+.5)
show()

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