matplotlib-users Mailing List for matplotlib (Page 3)

Ah, yes.  That is all true.  I'm not sure what options there may be in 
that case.

Mike

On 05/27/2011 10:56 AM, Simon Jesenko wrote:
> Setting 'pdf.fonttype'=3 had no effect, embedded fonts are of fonttype=1
> nonetheless. I guess that pdf.fonttype parameter is used only when
> matplotlib uses it's own engine to render latex, and not when
> text.usetex=true is used.
>
> Cairo backend is not support when text.usetex=true (only Agg, pdf and ps
> according to documentation)
>
> On 05/27/2011 03:53 PM, Michael Droettboom wrote:
>> Have you tried setting the rcParams "pdf.fonttype" to 3?  That should
>> subset the fonts.
>>
>> Also, the Cairo backend supports font subsetting.
>>
>> Mike
>>
>> On 05/27/2011 07:00 AM, Simon Jesenko wrote:
>>> Hi,
>>>
>>> I have a problem with large file-sizes of plots saved to pdf, when using
>>> rcParams['text.usetex']=True
>>>
>>> Files are very large (~150kb for simple line plot with some mathematical
>>> latex expressions) as all fonts are fully embedded into pdf. When
>>> resulting pdf is postprocessed (e.g. as is
>>> http://zeppethefake.blogspot.com/2008/05/embedding-fonts-in-pdf-with-ghostscript.html),
>>> so that only subset of fonts is embedded, file size is reduced
>>> drastically(e.g. from 150kb to 15kb).
>>>
>>> Is there a way to enable embedding of subset of fonts in matplotlib?
>>>
>>> I am using matplotlib version 0.99.3.
>>>
>>> Did anyone else experience similar problems/found solution?
>>>
>>> Thank you for info/assistance!
>>> Simon
>>>
>>> ------------------------------------------------------------------------------
>>> vRanger cuts backup time in half-while increasing security.
>>> With the market-leading solution for virtual backup and recovery,
>>> you get blazing-fast, flexible, and affordable data protection.
>>> Download your free trial now.
>>> http://p.sf.net/sfu/quest-d2dcopy1
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> ------------------------------------------------------------------------------
>> vRanger cuts backup time in half-while increasing security.
>> With the market-leading solution for virtual backup and recovery,
>> you get blazing-fast, flexible, and affordable data protection.
>> Download your free trial now.
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>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
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> _______________________________________________
> Matplotlib-users mailing list
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Setting 'pdf.fonttype'=3 had no effect, embedded fonts are of fonttype=1 
nonetheless. I guess that pdf.fonttype parameter is used only when 
matplotlib uses it's own engine to render latex, and not when 
text.usetex=true is used.

Cairo backend is not support when text.usetex=true (only Agg, pdf and ps 
according to documentation)

On 05/27/2011 03:53 PM, Michael Droettboom wrote:
> Have you tried setting the rcParams "pdf.fonttype" to 3?  That should
> subset the fonts.
>
> Also, the Cairo backend supports font subsetting.
>
> Mike
>
> On 05/27/2011 07:00 AM, Simon Jesenko wrote:
>> Hi,
>>
>> I have a problem with large file-sizes of plots saved to pdf, when using
>> rcParams['text.usetex']=True
>>
>> Files are very large (~150kb for simple line plot with some mathematical
>> latex expressions) as all fonts are fully embedded into pdf. When
>> resulting pdf is postprocessed (e.g. as is
>> http://zeppethefake.blogspot.com/2008/05/embedding-fonts-in-pdf-with-ghostscript.html),
>> so that only subset of fonts is embedded, file size is reduced
>> drastically(e.g. from 150kb to 15kb).
>>
>> Is there a way to enable embedding of subset of fonts in matplotlib?
>>
>> I am using matplotlib version 0.99.3.
>>
>> Did anyone else experience similar problems/found solution?
>>
>> Thank you for info/assistance!
>> Simon
>>
>> ------------------------------------------------------------------------------
>> vRanger cuts backup time in half-while increasing security.
>> With the market-leading solution for virtual backup and recovery,
>> you get blazing-fast, flexible, and affordable data protection.
>> Download your free trial now.
>> http://p.sf.net/sfu/quest-d2dcopy1
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Have you tried setting the rcParams "pdf.fonttype" to 3?  That should 
subset the fonts.

Also, the Cairo backend supports font subsetting.

Mike

On 05/27/2011 07:00 AM, Simon Jesenko wrote:
> Hi,
>
> I have a problem with large file-sizes of plots saved to pdf, when using
> rcParams['text.usetex']=True
>
> Files are very large (~150kb for simple line plot with some mathematical
> latex expressions) as all fonts are fully embedded into pdf. When
> resulting pdf is postprocessed (e.g. as is
> http://zeppethefake.blogspot.com/2008/05/embedding-fonts-in-pdf-with-ghostscript.html),
> so that only subset of fonts is embedded, file size is reduced
> drastically(e.g. from 150kb to 15kb).
>
> Is there a way to enable embedding of subset of fonts in matplotlib?
>
> I am using matplotlib version 0.99.3.
>
> Did anyone else experience similar problems/found solution?
>
> Thank you for info/assistance!
> Simon
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hi,

I have a problem with large file-sizes of plots saved to pdf, when using
rcParams['text.usetex']=True

Files are very large (~150kb for simple line plot with some mathematical 
latex expressions) as all fonts are fully embedded into pdf. When 
resulting pdf is postprocessed (e.g. as is 
http://zeppethefake.blogspot.com/2008/05/embedding-fonts-in-pdf-with-ghostscript.html), 
so that only subset of fonts is embedded, file size is reduced 
drastically(e.g. from 150kb to 15kb).

Is there a way to enable embedding of subset of fonts in matplotlib?

I am using matplotlib version 0.99.3.

Did anyone else experience similar problems/found solution?

Thank you for info/assistance!
Simon

Hi All,

I have a pcolor plot with 101 rows, and I was using this:

...
ODEPTH = np.linspace(0, 10, 101)
...
odepthl = [str(x) for x in ODEPTH]
ax.yaxis.set_ticks(np.arange(ODEPTH.size)+0.5)
ax.yaxis.set_ticklabels(odepthl)
...

To set the ticks centered on each row. Now I'm interested on having
the ticks on fewer locations, for example on integers. I tried:

...
ODEPTH = np.linspace(0, 10, 101)
...
odepthax =  np.linspace(0, 10, 11)
odepthl = [str(x) for x in odepthax]
ax.yaxis.set_ticks(np.arange(odepthax.size)+0.5)
ax.yaxis.set_ticklabels(odepthl)
...

But I'm only getting the desired labels (integers from 0 to 10), but
the location is the one from the ten previous ticks (from 0 to 1,
spaced by 0.1). I've been googling, reviewing the doc and playing with
it, but I cannot achieve it. Any clue?

Regards,
Sergi

Apologies for cross-posting - if you are not using ubuntu, don't read ahead.

  If you are using ipython combined with '-wthread' (for mayavi's mlab) or   
'-pylab' (for matplotlib), there is currently a bug in Ubunty 11.04 (natty) 
with ipython 0.10.1, which prevents the correct thread handling:
  e.g. with mayavi's mlab, it is necessary to use 'show()' to interact with 
the window, which is not very practical (and is blocking). And for '-pylab', 
the GTK and wx (Aggg) backend do not work...

  The bug is known and already corrected in ipython 0.10.2:
https://github.com/ipython/ipython/issues/185

  So the remaining issue is to get the new version as an update in ubuntu 
11.04/natty !
=> this is why I'm writing this email, so that other people concerned can vote 
for the bug and, if maintainers read this, if they can push this as stable-
release-update (SRU)...

  The bug to vote for is @:
https://bugs.launchpad.net/bugs/777420

  Incidentally, it is easy to install ipython 0.10.2 'manually', as it is 
already available for ubuntu oneiric (11.10):

wget http://launchpadlibrarian.net/70857487/ipython_0.10.2-1_all.deb
sudo dpkg -i ipython_0.10.2-1_all.deb


		Vincent
-- 
Vincent Favre-Nicolin

CEA / INAC                              http://inac.cea.fr
Université Joseph Fourier        http://www.ujf-grenoble.fr

http://vincefn.net
ObjCryst & Fox : http://objcryst.sourceforge.net

Hi,

firstly, I do not fully understand why you have chosen such a complicated
solution to a rather simple problem. If the data in your file really is like
the example then you could simply put the file 'ch1.csv' into the same
directory as your Python script.

I have slightly modified it (I don't like the "from" import statements too
much) and commented your lines.

#from matplotlib import mlab

#from pylab import figure, show

#import matplotlib.cbook as cbook

import pylab



#datafile = cbook.get_sample_data('ch1.csv', asfileobj=False)

datafile = 'ch1.csv'

print 'loading', datafile

#a = mlab.csv2rec(datafile)

a = pylab.loadtxt(datafile, comments='#', delimiter=';')

a.sort()

print a.dtype



fig = pylab.figure()

ax = fig.add_subplot(111)

#ax.plot(a.date, a.adj_close, '-')

#fig.autofmt_xdate()

ax.plot(a, 'o')

fig.show()



I hope it helps, let me know wether you need a different approach!
2011/5/25 Karthikraja Velmurugan <vel...@gm...>

>  Hello friends,
>
>
>
> I am a newbee to matplotlib and I am trying to plot (scatter plot) some
> values. The data is quite big and I have them in a CSV file. For a starter I
> thought I will use *loadrec.py* example to see if I am able to import the
> data from the CSV file. The loadrec.py goes like this:
>
>
>
> from matplotlib import mlab
>
> from pylab import figure, show
>
> import matplotlib.cbook as cbook
>
>
>
> datafile = cbook.get_sample_data('msft.csv', asfileobj=False)
>
> print 'loading', datafile
>
> a = mlab.csv2rec(datafile)
>
> a.sort()
>
> print a.dtype
>
>
>
> fig = figure()
>
> ax = fig.add_subplot(111)
>
> ax.plot(a.date, a.adj_close, '-')
>
> fig.autofmt_xdate()
>
>  I believe, for the CSV file to be accessed, it has to be placed in the *
> sample_data* folder (for windows). So I placed my csv file in the
> sample_data folder and ran the script.
>
>
>
> The output was
>
>
>
> *Traceback (most recent call last):*
>
> *  File "C:\Python26\loadrec.py", line 5, in <module>*
>
> *    datafile = cbook.get_sample_data('ch1.csv', asfileobj=False)*
>
> *  File "C:\Python26\Lib\site-packages\matplotlib\cbook.py", line 662, in
> get_sample_data*
>
> *    return myserver.get_sample_data(fname, asfileobj=asfileobj)*
>
> *  File "C:\Python26\Lib\site-packages\matplotlib\cbook.py", line 620, in
> get_sample_data*
>
> *    raise KeyError(msg)*
>
> *KeyError: 'file ch1.csv not in cache; received HTTP Error 404: Not Found
> when trying to retrieve'*
>
>
>
> The data in my CSV file looks like this
>
>
>
> 0.9963
>
> 0
>
> 0.499
>
> 0.9901
>
> 0.0025
>
> 0
>
> 1
>
> 0.0017
>
> 1
>
> 0.0173
>
> 0.9837
>
> If anyone can understand the problem please give me your suggestions. I
> will be very thankful if any of you can show me exactly how to scatter plot
> this kind of data.
>
>
>
> *Karthikraja Velmurugan, *
>
> *Graduate research assistant, *
>
> *Dept of Biomedical Informatics, *
>
> *Arizona State University, *
>
> *248-421-7394*
>
>
>
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Hi!

I am wondering if there is a bug in:
mpl_toolkits.axes_grid1.AxesGrid

I am trying to run this example (I am of course working on something else, but I am trying to build a minimal example of my problem):
http://matplotlib.sourceforge.net/examples/axes_grid/demo_axes_grid.html
This would be a very compact and nice way of showing my results, and I am beginning to love it. There is one thing, though. Given the code attached at the end of this message, the two versions produce figures that look identical. To my mind, however, it doesn't exactly seem that the colorbars are "shared" in any real sense. 

Try commenting out the 2-3 lines marked # Version 1 and # Version 2. I attach two plots of what I get: same-looking plots with wildly varying colorbar numbers. I'd like to get the numbers to be the same.

TL;DR: In version 1 I am scaling the data for one of the contour plots by a factor 1000, and would expect that plot to look quite different from the others.

Cheers
Paul.


# CODE:
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import AxesGrid


def get_demo_image():
    import numpy as np
    from matplotlib.cbook import get_sample_data
    f = get_sample_data("axes_grid/bivariate_normal.npy", asfileobj=False)
    z = np.load(f)
    # z is a numpy array of 15x15
    return z, (-3,4,-4,3)

def demo_grid_with_single_cbar(fig):
    """
    A grid of 2x2 images with a single colobar
    """
    grid = AxesGrid(fig, 132, # similar to subplot(132)
                    nrows_ncols = (2, 2),
                    axes_pad = 0.0,
                    share_all=True,
                    label_mode = "L",
                    cbar_location = "top",
                    cbar_mode="single")

    Z, extent = get_demo_image()

    # Version 1
    #for i in range(3):
        #im = grid[i].imshow(Z, extent=extent, interpolation="nearest")
    #im = grid[3].imshow(1000 * Z, extent=extent, interpolation="nearest")
    # Version 2
    for i in range(4):
        im = grid[i].imshow(Z, extent=extent, interpolation="nearest")

    # The rest is the same
    grid.cbar_axes[0].colorbar(im)

    # This affects all axes as share_all = True.
    grid.axes_llc.set_xticks([-2, 0, 2])
    grid.axes_llc.set_yticks([-2, 0, 2])


if 1:
    F = plt.figure(1, (5.5, 2.5))

    F.subplots_adjust(left=0.05, right=0.98)

    demo_grid_with_single_cbar(F)

    plt.savefig('cbars')
    #plt.draw()
    #plt.show()

Hello friends, 

 

I am a newbee to matplotlib and I am trying to plot (scatter plot) some
values. The data is quite big and I have them in a CSV file. For a starter I
thought I will use loadrec.py example to see if I am able to import the data
from the CSV file. The loadrec.py goes like this: 

 

from matplotlib import mlab

from pylab import figure, show

import matplotlib.cbook as cbook

 

datafile = cbook.get_sample_data('msft.csv', asfileobj=False)

print 'loading', datafile

a = mlab.csv2rec(datafile)

a.sort()

print a.dtype

 

fig = figure()

ax = fig.add_subplot(111)

ax.plot(a.date, a.adj_close, '-')

fig.autofmt_xdate()

 I believe, for the CSV file to be accessed, it has to be placed in the
sample_data folder (for windows). So I placed my csv file in the sample_data
folder and ran the script. 

 

The output was 

 

Traceback (most recent call last):

  File "C:\Python26\loadrec.py", line 5, in <module>

    datafile = cbook.get_sample_data('ch1.csv', asfileobj=False)

  File "C:\Python26\Lib\site-packages\matplotlib\cbook.py", line 662, in
get_sample_data

    return myserver.get_sample_data(fname, asfileobj=asfileobj)

  File "C:\Python26\Lib\site-packages\matplotlib\cbook.py", line 620, in
get_sample_data

    raise KeyError(msg)

KeyError: 'file ch1.csv not in cache; received HTTP Error 404: Not Found
when trying to retrieve'

 

The data in my CSV file looks like this 

 


0.9963


0


0.499


0.9901


0.0025


0


1


0.0017


1


0.0173


0.9837

	

If anyone can understand the problem please give me your suggestions. I will
be very thankful if any of you can show me exactly how to scatter plot this
kind of data.  

 

Karthikraja Velmurugan, 

Graduate research assistant, 

Dept of Biomedical Informatics, 

Arizona State University, 

248-421-7394

 

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello,

I would like to stack subplots in a figure with a couple of basic
x,y-line plots with the subplot frames removed.
But possible overlap of subplots is limited, because the drawn data
lines are clipped on the border, if you'd lets say manually reset the
ylims and decrease it below the highest data y-values.
I know it is possible with any kind of text or data annotation, but do
not find a way to let the data lines cross the frame border.

I hope I made myself halfway clear - pls. don't hesitate to ask if not.
Does one of you possibly have a solution or is it maybe plain
impossible?
Thanks!

Cheers,
Nix
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You probably have "ps.useafm" set, right?  Unfortunately, the stock 
Postscript AFM fonts do not have a blackboard style.  Setting ps.useafm 
to False will use Truetype fonts, and it should work.

Cheers,
Mike

On 05/24/2011 10:50 AM, Oscar Benjamin wrote:
> Hello,
>
> I'm getting an error using latex mathbb and exporting to eps. The 
> following script demonstrates:
>
> from pylab import figure, show
> fig = figure()
> ax = fig.add_subplot(1, 1, 1)
> ax.set_title(r'$\mathbb{R}$')
> fig.savefig('mathbb.eps')
>
> On Windows the above gives me a long traceback ending with:
> IOError: [Errno 2] No such file or directory: 
> 'q:\\tools\\Python26\\lib\\site-packages\\matplotlib\\mpl-data\\fonts\\afm\\bb.afm'
>
> It works fine if using \mathbf instead of \mathbb or when saving to 
> pdf etc.
>
> I thought I had this working on Linux, does anyone know if this is a 
> problem to do with my installation, or maybe an unsupported feature.
>
> Thanks,
> Oscar.
>
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>    


-- 
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA

Hello,

I'm getting an error using latex mathbb and exporting to eps. The following
script demonstrates:

from pylab import figure, show
fig = figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title(r'$\mathbb{R}$')
fig.savefig('mathbb.eps')

On Windows the above gives me a long traceback ending with:
IOError: [Errno 2] No such file or directory:
'q:\\tools\\Python26\\lib\\site-packages\\matplotlib\\mpl-data\\fonts\\afm\\bb.afm'

It works fine if using \mathbf instead of \mathbb or when saving to pdf etc.

I thought I had this working on Linux, does anyone know if this is a problem
to do with my installation, or maybe an unsupported feature.

Thanks,
Oscar.

2011/5/24 Marco Trapanese <mar...@gm...>:
> I draw something with the plot command.
> Now I want to "update" the entire plot, saving the current axes settings.

I think you might use this one:

http://github.com/friedrichromstedt/matplotlayers/

Friedrich

Hello,

I draw something with the plot command.
Now I want to "update" the entire plot, saving the current axes settings.

That is I'd like to clear and plot again.

I tried clf, cla, hold=false but I need to setup again my (multiple) axes.
Because I need to go quite fast I'm looking for a more elegant method.

May you suggest something?
Thanks
Marco

try: x,y=np.loadtxt(f3,unpack=True)

without the str().



On Fri, May 20, 2011 at 11:20 PM, uxv2g <am...@co...> wrote:
>
>  So, I installed EPD python for mac. From the terminal I go into a directory
> where the file I'd like to read exists. In a python program I create a 2
> column data array and below I open it as "f3". The line in bold is that
> referenced in the error. fwiw I'm just trying to do an easy x,y plot and
> this is my first python attempt.
> ....
>        f3=open(sys.argv[1]+ext, 'r')
>
>        import matplotlib.pyplot as plt
>        import numpy as np
>
>        x,y=np.loadtxt(str(f3),unpack=True)
>
>        plotfile='sys.argv[1].png'
>        plt.plot(x,y)
>        plt.xtitle('step number')
>        plt.ytitle('energy')
>        plt.grid("off")
>        plt.output(plotfile,'png medium transparent picsize 600 400')
>        f3.close()
> ....
> ***error below&***
> File "SCFscript.py", line 40, in <module>
>    x,y=np.loadtxt(str(f3),unpack=True)
>  File
> "/Library/Frameworks/Python.framework/Versions/7.0/lib/python2.7/site-packages/numpy/lib/npyio.py",
> line 635, in loadtxt
>    fh = open(fname, 'U')
> IOError: [Errno 2] No such file or directory: "<open file 'gq_1014.log.hy',
> mode 'r' at 0x2a93e8>"
>
> *****
> The file exists, I checked. Where is it looking? In the python framework
> directory above? Shouldn't it be opening the file from the current
> directory? Am I missing something here?
>
> Thanks for any help!!
>
>
> --
> View this message in context: http://old.nabble.com/numpy.loadtxt-is-not-finding-an-existing-file.-What%27s-up--tp31668985p31668985.html
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Hi all,

I'm trying to set up a callback for when the limits of an interactive
axes object, with an image plot, has its limits changed.  The callback
itself is somewhat expensive, and the zooming procedure seems to
figure sequential events for each axis -- x and y -- that is changed.
This results in doubling up on the work that is done.

Is there a way to either suppress until the display itself is updated,
or to connect to a single event that gets called when both axes are
changed?

Thanks!

-Matt

Hello everyone,

I have been using Matplotlib for a while and I have to make a Volumetric
slice plot.  I created 2d images by using imshow() but couldnt find anything
to create 3d image with those 2d ones.

I hope we (Matplotlib user's) have a solution for this.

Thanks alot

On Sat, May 21, 2011 at 10:38 AM, welsberr <wel...@ba...> wrote:

>
>
> Daniel Mader-2 wrote:
> >
> > Hello,
> >
> > I have a problem with the 3D plotting of PolyCollections with
> > python-matplotlib-1.0.0 (on openSUSE 11.3 x86_64):
> >
> > instead of being correctly stacked as in the example
> > http://matplotlib.sourceforge.net/examples/mplot3d/polys3d_demo.html,
> > the plots are weirdly overlapping. The example works OK for me [...]
> >
> >
>
> The example does not work OK for me. I used it as a basis to plot some of
> my
> data, and at first I thought all was well. Two examples of my data plots
> and
> a plot showing the problem directly from the demo code are up at
>
>
> http://austringer.net/wp/index.php/2011/05/20/plotting-a-dolphin-biosonar-click-train/
>
> I tried using the manually-closed polygon workaround in my script without
> noticeable improvement.
>
>
The example had two separate issues.  One was the layering issue, the second
is some sort of odd polygon-closing issue.  Your problem for your example
(actually, there are two, but I will get to the second one later) is only
the layering issue.  This can not be addressed by the manually closing the
polygons, as that was only trying to deal with the odd bug (which I still
have not solved).


> I then went back to the demo code, and I can reproduce the error just based
> on it.
>
> The last two plots show the problem. For my data plot, the first polygon
> (red) is plotted over the second polygon (blue). The problem is worse at
> various other angles, where up to a third of the polygons are plotted out
> of
> order. The plot from the demo code shows the blue polygon overlaid on the
> yellow polygon, when it should be the other way around.
>
>
This is a fundamental issue with the design of how mplot3d works with
matplotlib.  Because matplotlib is strictly a 2-D plotting library with
layering.  Therefore, mplot3d reduces the 3D data into an array of 2D
coordinates, and a single 'Z' value that is passed to the layering feature.
That single Z value represents the depth of all of the components of the 3D
polygons.  Because of this dimension reduction is intrinsic to how
matplotlib works, this can never be completely resolved until matplotlib
itself supports 3D data (which will likely have to wait until some new
features come into numpy).

Therefore, mplot3d is only suggested to be used for "simple" 3D plots, and
more advanced 3D plots can be achieved with more advanced tools such as
mayavi.  That being said...


> For the plot with more polygons, more ranges of viewing angle show the
> problem. I had to do a bit of searching to find the, admittedly odd,
> viewing
> angle that showed the problem in the demo code. I also changed both "alpha"
> specifications in the demo code to "1.0" so that transparency wasn't an
> issue in viewing, but the problem can be replicated in the unmodified demo
> script.
>
>
There are ways to "mitigate" the issue.  For example, in the demo code
"polys3d_demo.py", we see that multiple polygons are added to a single
collection.  Instead, you can create multiple collections with a single
polygon in them.  This way, each polygon will have a better Z-value to
better represent more realistic sorting.  In addition, there is a
set_zsort() function for Poly3DCollection that accepts a value of "average",
"min" and "max".  By default, a Poly3DCollection uses the average depth
value of the vertices as the representative depth, but in some cases, the
minimum or the maximum might be better.  Note that your PolyCollection
object gets turned into a Poly3DCollection after calling add_collection3d(),
so you can call set_zsort() after adding the collection to the 3d axes.



> Software versions:
> Python 2.6.2 (Windows)
> Matplotlib 0.99.3
>
>
As for the second issue I noticed.  In your figures, the axes labels were
completely "askew" when you labeled your axes with longer names.  This was a
bug that only recently was fixed.  I believe I got it in for v1.0.1, but I
could be wrong.  The fix is most definitely in the master branch of
matplotlib on the github repository.  I am also currently working on making
the axes3d objects act a lot more like traditional axes objects, but this
will take some time.

I do like your plots, and I hope this information can help you produce a
better looking figure.  (maybe you could even be able to sneak it in for
your publication during the revision process?)  If you can get the figure
looking well enough, I might even be able to combine it with the new
animation module and produce an animated plot of a dolphin chirp?

I hope this information helps, and thank you for using matplotlib!
Ben Root

Daniel Mader-2 wrote:
> 
> Hello,
> 
> I have a problem with the 3D plotting of PolyCollections with
> python-matplotlib-1.0.0 (on openSUSE 11.3 x86_64):
> 
> instead of being correctly stacked as in the example
> http://matplotlib.sourceforge.net/examples/mplot3d/polys3d_demo.html,
> the plots are weirdly overlapping. The example works OK for me [...]
> 
> 

The example does not work OK for me. I used it as a basis to plot some of my
data, and at first I thought all was well. Two examples of my data plots and
a plot showing the problem directly from the demo code are up at

http://austringer.net/wp/index.php/2011/05/20/plotting-a-dolphin-biosonar-click-train/

I tried using the manually-closed polygon workaround in my script without
noticeable improvement.

I then went back to the demo code, and I can reproduce the error just based
on it. 

The last two plots show the problem. For my data plot, the first polygon
(red) is plotted over the second polygon (blue). The problem is worse at
various other angles, where up to a third of the polygons are plotted out of
order. The plot from the demo code shows the blue polygon overlaid on the
yellow polygon, when it should be the other way around.

For the plot with more polygons, more ranges of viewing angle show the
problem. I had to do a bit of searching to find the, admittedly odd, viewing
angle that showed the problem in the demo code. I also changed both "alpha"
specifications in the demo code to "1.0" so that transparency wasn't an
issue in viewing, but the problem can be replicated in the unmodified demo
script.

Software versions:
Python 2.6.2 (Windows)
Matplotlib 0.99.3

Wesley R. Elsberry
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Sent from the matplotlib - users mailing list archive at Nabble.com.

 So, I installed EPD python for mac. From the terminal I go into a directory
where the file I'd like to read exists. In a python program I create a 2
column data array and below I open it as "f3". The line in bold is that
referenced in the error. fwiw I'm just trying to do an easy x,y plot and
this is my first python attempt.
....
        f3=open(sys.argv[1]+ext, 'r')

        import matplotlib.pyplot as plt
        import numpy as np
      
        x,y=np.loadtxt(str(f3),unpack=True)

        plotfile='sys.argv[1].png'
        plt.plot(x,y)
        plt.xtitle('step number')
        plt.ytitle('energy')
        plt.grid("off")
        plt.output(plotfile,'png medium transparent picsize 600 400')
        f3.close()
....
***error below&***
File "SCFscript.py", line 40, in <module>
    x,y=np.loadtxt(str(f3),unpack=True)
  File
"/Library/Frameworks/Python.framework/Versions/7.0/lib/python2.7/site-packages/numpy/lib/npyio.py",
line 635, in loadtxt
    fh = open(fname, 'U')
IOError: [Errno 2] No such file or directory: "<open file 'gq_1014.log.hy',
mode 'r' at 0x2a93e8>"

*****
The file exists, I checked. Where is it looking? In the python framework
directory above? Shouldn't it be opening the file from the current
directory? Am I missing something here? 

Thanks for any help!!


-- 
View this message in context: http://old.nabble.com/numpy.loadtxt-is-not-finding-an-existing-file.-What%27s-up--tp31668985p31668985.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

On Thu, May 19, 2011 at 10:37 PM, Steve Ward <pla...@gm...> wrote:

> >From running the code below, I see only 8 subticks between the major
> ticks.  But the documentation
> <
> http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.set_xscale
> >
> says there should be 10.  I'm using matplotlib version 0.99.3.
>
> #----------------------------
> import matplotlib.pyplot as plt
> import numpy as np
> y = range(1, 4)
> x = np.power(10, y)
> plt.gca().set_xscale('log', basex=10, subsx=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
> plt.gca().plot(x, y)
> plt.show()
> #----------------------------
>
> However, even if 10 are being drawn, I think there would only be 9
> subticks between the major ticks because the first subtick is on a
> major tick.  Am I wrong?
>
>
> Steve
>
>
You are mostly correct.  The documentation, however, is very wrong.  The
first visible subtick would be for 20.  Therefore, there will only be 8
visible subticks.  The suggestion of doing [0, 1, 2, 3, ...] for subsx has
two problems.  First, the subtick at 0 will never show up!  Second, the
subtick for 1 is also a major tick.  While this isn't technically wrong,
(maybe the major ticks get turned off or something...), it is a poor example
and I will fix it.

Thank you for pointing it out.

Ben Root

I have this error. I am running 2.6.5 Python and compiled myself the SVN 
maybe two weeks ago. The issue came when I tried to compile a version of 
2.6.6 using the tcmalloc library. I compiled my own version of Python 
but had some issues with external packages. I removed 2.6.6 for now. 
Then I get this error which also occurs in Ipython upon startup. This 
also was one of the only errors with the 2.6.6 install which makes me 
think it could have not been with the install.

I was having issues with linking packages such as wxPython2.8 for 
matplotlib with the usr/local/lib archives. Would I have to compile 
wxPython myself if I wanted it to go with my compiled version of 2.6.6. 
This was my next step but just gave up for now. Anyone knows or has 
compiled there own Python. Please let me know. Especially 2.6 when you 
already have 2.6 on the system.

Error below:

import AuditoryModelT
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "AuditoryModelT.py", line 1, in <module>
     from gammaFilterBank import computeCF, makeFilters, outBank
   File "gammaFilterBank.py", line 3, in <module>
     from matplotlib.pyplot import plot, clf, show, cla, xlim, xscale, 
imshow, ylabel, xlabel, figure, savefig, close,  bar,  title,  xticks, 
yticks, axes, axis
   File "/usr/local/lib/python2.6/dist-packages/matplotlib/pyplot.py", 
line 95, in <module>
     new_figure_manager, draw_if_interactive, show = pylab_setup()
   File 
"/usr/local/lib/python2.6/dist-packages/matplotlib/backends/__init__.py", line 
25, in pylab_setup
     globals(),locals(),[backend_name])
   File 
"/usr/local/lib/python2.6/dist-packages/matplotlib/backends/backend_wxagg.py", 
line 23, in <module>
     import backend_wx    # already uses wxversion.ensureMinimal('2.8')
   File 
"/usr/local/lib/python2.6/dist-packages/matplotlib/backends/backend_wx.py", 
line 65, in <module>
     raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython >=2.8
 >>>

-- 
________________________
Jeffrey Spencer
jef...@gm...

http://clscomp.com.br/cool01.11.php?SID=981

http://clscomp.com.br/cool01.11.php?SID=685

>From running the code below, I see only 8 subticks between the major
ticks.  But the documentation
<http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.set_xscale>
says there should be 10.  I'm using matplotlib version 0.99.3.

#----------------------------
import matplotlib.pyplot as plt
import numpy as np
y = range(1, 4)
x = np.power(10, y)
plt.gca().set_xscale('log', basex=10, subsx=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
plt.gca().plot(x, y)
plt.show()
#----------------------------

However, even if 10 are being drawn, I think there would only be 9
subticks between the major ticks because the first subtick is on a
major tick.  Am I wrong?


Steve