matplotlib-users Mailing List for matplotlib

El día 15 de marzo de 2012 05:14, questions anon
<que...@gm...> escribió:
> I think my error is from the np.genfromtxt because I just checked the size
> of my data and it appears in 1D rather than 2D.

This is unsurprising since your file has just one row of data. I
overlooked that because the weird error message drove all my attention
to it. You can reshape the resulting array to (691, 886). Still that
error message should not be there in any case.

>> I don't really understand what np.logical_or is or how to use it?
>> I have tried just calling it at the beginning of the script

np.logical_or computes the logical out of two boolean arrays. It's
called internally by countourf and that's triggering the exception:

AttributeError: logical_or

Which makes no sense at all because:
1. np is expected to be an alias for numpy and numpy *does* have an
attribute called logical_or.
2. In case np didn't have an attribute called logical_or (for whatever
reason) it would cause an exception but the error message should be
something like "AttributeError: 'module' object has no attribute
'logical_or'".

You where asked to call np.logical_or at the beginning of the script
in order to know if it triggers the exception in that context.

>> [...] but I still end up with the same error.

So the call at the beginning didn't trigger the error?

Regards

Goyo

On Thu, Mar 15, 2012 at 12:31 PM, Thøger Rivera-Thorsen <
tho...@gm...> wrote:

> Hello people,
>
> I am trying to do a surface plot of some data, with some line plots
> marking some lines of special interest - see attachment.
>
> It would be really nice if the surface plot would hide the lines that are
> "behind" the surface, but every single line piece is clearly visible, which
> makes the picture a good deal more messy than I'd like it to be. Is this a
> bug, and/or is there a way to fix it?
>

This is a common problem and is partly addressed here in the mplot3d FAQ:

http://matplotlib.sourceforge.net/mpl_toolkits/mplot3d/faq.html#my-3d-plot-doesn-t-look-right-at-certain-viewing-angles

For your particular situation, the surface plot is represented by a single
"z" value (z in the viewing coordinates, not the graph coordinates).
Depending on how your lines are being done, the group of lines may each be
represented by their own z values or there is a single z-value for all of
the lines (again, depending on how you are plotting).  For your kind of
scene, there are some work-arounds.  Specifically, I might try modifying
the surface object itself.  It is pretty much just a PolyCollection.  You
can get/set the edgecolors, specifically modifying the elements that
correspond to the lines you want to color.  Note that it is a bit tricky in
that you have to also modify the collection's "_edgecolors3d" attribute as
it is what stores the original colors (the colors that are displayed gets
shaded with user-interaction, so we have to store the original colors
there).

I hope this rambling makes some sense.  Let me know if you have questions.

Ben Root

Hello people,

I am trying to do a surface plot of some data, with some line plots 
marking some lines of special interest - see attachment.

It would be really nice if the surface plot would hide the lines that 
are "behind" the surface, but every single line piece is clearly 
visible, which makes the picture a good deal more messy than I'd like it 
to be. Is this a bug, and/or is there a way to fix it?

On Thu, Mar 15, 2012 at 6:01 AM, kususe <ku...@in...> wrote:

>
> Hi folks,
> I'd like to remove the black border which is created when I save the image,
> letting just the white background and the graph.
> Is there a solution??
> Thanks,
> K.
> --


Matplotlib provides a function that *almost* does this: `plt.axis('off')`
or `ax.set_axis_off()`, but these functions clear the white background as
well (along with the ticks, spines, and axis labels).

The following snippet clears only the spines and ticks:

    ax.xaxis.set_ticks([])
    ax.yaxis.set_ticks([])
    for spine in ax.spines.itervalues():
        spine.set_visible(False)

I've wrapped this up into a utility function:
https://github.com/tonysyu/mpltools/blob/master/mpltools/layout.py

-Tony

Hullo matplotlib list,

I've discovered (with pleasure!) that matplotlib has recently learned 
how to create Sankey diagrams.  Thank you Kevin and Yannick!

One of my less-technically inclined fellow graduate students is 
searching for his toolset of choice for generating these suckers, and is 
currently looking at Stan.  As I'm an open-source advocate I'd love to 
be able to say, "you can do this with X", where X in this case is 
clearly matplotlib.

Specifically, I've not heavily used matplotlib before, and from the 
given examples I see on matplotlib.sf.net, I'm not clear on exactly the 
capabilities of this recently-added code.  What my fellow grad student 
has opined would be nice for his uses would be boxes that are built into 
the flows, rather than just used as labels.  Something like:

"Page Load"
http://modernl.com/images/diagrams/web-traffic-sankey-diagram.png

"Input", "Gas Turbine", "HRSG", "Waste", "BP Turbine", "Output"
http://www.bucknell.edu/images/Depts/Facilities/sankeythumb.jpg

Is this currently possible, /without/ manually adjusting the graphic?

Thanks!

Kevin

Hello list;

I have some data that I would like to display a bit like it is done in 
this example:

      
http://matplotlib.sourceforge.net/mpl_toolkits/mplot3d/tutorial.html#d-plots-in-3d

Only, instead of the line plot in the z=0 plane, I would like to 
represent my data as a pcolormesh (and instead of the scatter I would 
like to do a line plot of the levels at chosen y-values, bu that is not 
the problem now).

However, when I try to do a ax.pcolormesh() - which should be inherited 
- it creates the object just fine, but when I write 'draw()', I get the 
error message:

             AttributeError: 'QuadMesh' object has no attribute 
'do_3d_projection'

Is there a different way to obtain what I wanbt - that is, an image plot 
with customizeable coordinate axes, in a given plane (here z=0) of the 
Axes3D?

Cheers;

Emil

Hello list;

I have some data that I would like to display a bit like it is done in 
this example:

http://matplotlib.sourceforge.net/mpl_toolkits/mplot3d/tutorial.html#d-plots-in-3d

Only, instead of the line plot in the z=0 plane, I would like to represent 
my data as a pcolormesh (and instead of the scatter I would like to do a 
line plot of the levels at chosen y-values, bu that is not the problem 
now).

However, when I try to do a ax.pcolormesh() - which should be inherited - 
it creates the object just fine, but when I write 'draw()', I get the 
error message:

             AttributeError: 'QuadMesh' object has no attribute 
'do_3d_projection'

Is there a different way to obtain what I wanbt - that is, an image plot 
with customizeable coordinate axes, in a given plane (here z=0) of the 
Axes3D?

Cheers;

Emil

Hello list;

I have some data that I would like to display a bit like it is done in 
this example:

http://matplotlib.sourceforge.net/mpl_toolkits/mplot3d/tutorial.html#d-plots-in-3d

Only, instead of the line plot in the z=0 plane, I would like to 
represent my data as a pcolormesh (and instead of the scatter I would 
like to do a line plot of the levels at chosen y-values, bu that is not 
the problem now).

However, when I try to do a ax.pcolormesh() - which should be inherited 
- it creates the object just fine, but when I write 'draw()', I get the 
error message:

             AttributeError: 'QuadMesh' object has no attribute 
'do_3d_projection'

Is there a different way to obtain what I wanbt - that is, an image plot 
with customizeable coordinate axes, in a given plane (here z=0) of the 
Axes3D?

Cheers;

Emil

Hi,

Am 14. November 2011 15:04 schrieb Friedrich Romstedt
<fri...@gm...>:
> 2011/11/14 Michael Droettboom <md...@st...>:
>> Thanks for all the time you've devoted to this.  It does look like possibly
>> some kind of compiler bug.  The font loads and renders fine on Linux, for
>> what it's worth (just as a data point).
>>
>> To confirm this theory: if you move NISC1803.ttf somewhere temporary, delete
>> ~/.matplotlibrc/fontList.cache and then import matplotlib, do you get the
>> crash?  That at least confirms that loading this font file triggers the bug
>> (wherever the bug may be).  Test with matplotlib 1.1.0 or git master so we
>> have a sense of the current behavior.
>
> Hi Mike,
>
> the following fonts on my system are offending:
>
> /Library/Fonts/NISC18030.ttf
> /Library/Fonts/AppleMyungjo.ttf
> /Library/Fonts/Gungseouche.ttf
>
> With these fonts made unfindable by matplotlib (:file:`*.ttf_`) it
> exits cleanly.
>
> I will provide with a patch to matplotlib for an rc setting
> "fonts.bus-error : ...", e.g. ``fonts.bus-error : NISC18030.ttf,
> AppleMyungjo.ttf, Gungseouche.ttf`` in the next days.

I just took the time to recompile the whole thingy, including
supporting libraries.  I used:

–  libfreetype-2.4.9
–  matplotlib-1.1.0
–  MACOSX_DEPLOYMENT_TARGET=10.5
–  The files noted in the citation above are in place (i.e.,
accessible as .ttf files)

My theory was that a compiler error triggers the error with the font
files in question.  Because recompiling ft2font.so with a different
MACOSX_DEPLOYMENT_TARGET made the crash disappear I supposed that
ft2font would trigger that compiler error.  It needed to be a compiler
error because that environment variable was the only change that made
the crash disappear.  Now it is the question if with more recent
software that error still persists.  I have found that this is not the
case.  I recompiled with the libraries noted above (all compiled from
source), and I can successfully import matplotlib.figure.  This import
previously provoked the crash.  So I believe that either I was wrong
in some respect, or the more recent software toolchain no longer
provokes the crash, because its code changed.  Since it works just
flawlessly on my system now, I see little need to implement the
mechanism for excluding font files from being loaded – if it is not
needed I will not code it.

Friedrich

P.S.: Of course I moved the font cache before, so that it is recreated
when importing matplotlib.figure for the first time.
P.P.S.: One more difference is that the current Python is not a
framework Python anymore, but a regular Python.

> It was clear from the beginning (well, from the point I got a handle
> on it), that loading the font makes the 2009 matplotlib crash.  The
> only question unanswered is where the codepath is that triggers this
> compiler bug (I think the compiler but hypothesis is not disproven and
> works well atm).  If the code path is in ft2font.cpp, we could (you
> could) reformulate ft2font.cpp in an equivalent way with the exception
> that it is not equivalent in crashing.  You might want to augment
> ft2font.cpp by printf() or something to see if the crash appears
> inside a call to libfreetype or if all those calls return cleanly.
>
> To my understanding, since recompiling ft2font.so without
> MACOSX_DEPLOYMENT_TARGET different from 10.6 helps, ft2font.cpp should
> be the culprit resp. victim.  The only alternative I'm seeing would be
> that it has to to do with the load mechanism of the dylib, but I deem
> this rather unlikely.  Well, unlikely is not the best word in this
> context, since all this things here were pretty unlikely.
>
> If the codepath is in libfreetype this would be an issue for their list. ...
>
> Friedrich

Hey,

last weekend I wrote a hook which can track figure creation. Basically
it takes care of creating the new figure and wraps it to track all
changes to it. Its a hack, and the code is not cleaned up or tested
much, but I like to do scripts that I run with many parameters to create
plots and it works well to allow me to open the figures in a way that I
can zoom, etc. and would allow editing (a bit) later on too. So while I
doubt the approach can be made something serious, and there are probably
things that don't work (right now 3D Axis can be done with a bit extra
but mouse zooming does not work inside a 3D Axis, though I think its
likely not difficult to change), I thought I would put it online because
I am not aware of any way to save matplotlib figures:

https://github.com/seberg/haunter-for-matplotlib-figures

Maybe someone finds it useful or interesting :)

Regards,

Sebastian Berg

Hi folks, 
I'd like to remove the black border which is created when I save the image,
letting just the white background and the graph. 
Is there a solution??
Thanks, 
K.
-- 
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On Wed, Mar 14, 2012 at 2:38 PM, kususe <ku...@in...> wrote:

>
> I got an error using the first subplot function because I have to specify
> 3
> parameters.
> If i do it, I get that "AxesSubplot' object is not iterable"
> I coded using 3 subplot functions, getting the same error.
>
> Thanks
> K.
>
>
Note that I wrote `subplots` with an "s", which is a different command than
`subplot`. (You're really having problems with "s"s today :)

BTW, would you mind interleaving or bottom-posting
replies<http://en.wikipedia.org/wiki/Posting_style#Placement_of_replies>.
It's a bit easier to follow the conversation that way.

-Tony


Yes, for sure I coded: 

                fig, axes = plt.subplot(3,1,1)
		ax1, ax2, ax3 = axes
		p1, = ax1.plot(self.data0,self.data1)
		....
		plt.subplot(3,1,2)
		p2, = ax2.plot(self.data0,self.data2)
		.......
                plt.subplot(3,1,3)
		p3, = ax3.plot(self.data0,self.data4)
		........
		for ax in axes:
	       		ax.set_xticks([])

but I got the error which said you. 
-- 
View this message in context: http://old.nabble.com/How-to-remove-x-axis-in-a-subplotted-graph-tp33500598p33507959.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

I think my error is from the np.genfromtxt because I just checked the size
of my data and it appears in 1D rather than 2D.
if I try taking out 'skip_header' I end up with this error:

Traceback (most recent call last):
  File "d:\BoMdata\plotrainfall.py", line 63, in <module>
    f=np.genfromtxt(inputfile, dtype=None, names=True)
  File "C:\Python27\lib\site-packages\numpy\lib\npyio.py", line 1560, in
genfromtxt
    raise ValueError(errmsg)
ValueError: Some errors were detected !
    Line #7 (got 886 columns instead of 2)
    Line #8 (got 886 columns instead of 2)
    Line #9 (got 886 columns instead of 2)
    Line #10 (got 886 columns instead of 2)
    Line #11 (got 886 columns instead of 2)
    Line #12 (got 886 columns instead of 2)
    Line #13 (got 886 columns instead of 2)

my data as opened in notepad looks like:

ncols         886
nrows         691
xllcorner     111.975
yllcorner     -44.525
cellsize      0.05
NODATA_value  -9999
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

how do I skip those first few rows but still end up with a 2D array?


On Thu, Mar 15, 2012 at 12:16 PM, questions anon
<que...@gm...>wrote:

> I don't really understand what np.logical_or is or how to use it?
> I have tried just calling it at the beginning of the script but I still
> end up with the same error.
>
>
> On Thu, Mar 15, 2012 at 10:59 AM, Pierre GM <pgm...@gm...> wrote:
>
>> That's your whole log? You're sure you're not redefining np in the
>> background, via a variable or another module?
>> Have you tried to call np.logical_or at the very beginning of your
>> script, or in a brand new environment (after importing numpy as np)?
>> It's definitely not a matplotlib pb, but where is it coming on your side,
>> that's the question...
>> On Mar 14, 2012 11:35 PM, "questions anon" <que...@gm...>
>> wrote:
>>
>>> Thanks for responding. It is 'sort of' good to know that it can't be
>>> explained as I just thought it was my incompetency!
>>> I tried the np rather than N but that made no differences.
>>> thanks again
>>>
>>>
>>> On Thu, Mar 15, 2012 at 7:48 AM, Benjamin Root <ben...@ou...> wrote:
>>>
>>>>
>>>>
>>>> On Tue, Mar 13, 2012 at 4:23 PM, questions anon <
>>>> que...@gm...> wrote:
>>>>
>>>>> also I have tried running it on a different computer and the same
>>>>> error occurred
>>>>>
>>>>>
>>>>> On Wed, Mar 14, 2012 at 8:22 AM, questions anon <
>>>>> que...@gm...> wrote:
>>>>>
>>>>>> thanks for looking into this Goyo.
>>>>>> The complete code:
>>>>>>
>>>>>>
>>>>>> import numpy as N
>>>>>> import matplotlib.pyplot as plt
>>>>>> from numpy import ma as MA
>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>> import os
>>>>>>
>>>>>> shapefile="E:/GIS_layers/DSE_REGIONS"
>>>>>> inputfile=r"d:/BoMdata/r19000117.txt"
>>>>>> outputfolder=r"d:/BoMdata/outputfolder"
>>>>>>
>>>>>> f=N.genfromtxt(inputfile, skip_header=6,  dtype=float, names=True)
>>>>>> print f[0:5]
>>>>>>
>>>>>>
>>>>>> map = Basemap(projection='merc',llcrnrlat=-45,urcrnrlat=-9,
>>>>>>
>>>>>> llcrnrlon=111.975,urcrnrlon=156.525,lat_ts=0,resolution='i')
>>>>>> map.drawcoastlines()
>>>>>> map.drawstates()
>>>>>> map.readshapefile(shapefile, 'DSE_REGIONS')
>>>>>>
>>>>>> xi=N.linspace(111.975, 156.275, 886)
>>>>>> yi=N.linspace(-44.525, -9.975, 691)
>>>>>> x,y=map(*N.meshgrid(xi,yi))
>>>>>> plt.title('rainfall')
>>>>>> CS = map.contourf(x,y, f, 15,cmap=plt.cm.jet)
>>>>>> l,b,w,h =0.1,0.1,0.8,0.8
>>>>>> cax = plt.axes([l+w+0.025, b, 0.025, h])
>>>>>> plt.colorbar(CS,cax=cax, drawedges=True)
>>>>>> plt.savefig((os.path.join(outputfolder, 'rainfall.png')))
>>>>>> plt.show()
>>>>>> plt.close()
>>>>>>
>>>>>>
>>>>>> and the complete error:
>>>>>>
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>>   File "d:/BoMdata/plotrainfall_v2.py", line 23, in <module>
>>>>>>
>>>>>>     CS = map.contourf(x,y, f, 15,cmap=plt.cm.jet)
>>>>>>   File
>>>>>> "C:\Python27\lib\site-packages\mpl_toolkits\basemap\__init__.py", line
>>>>>> 3072, in contourf
>>>>>>
>>>>>> np.logical_or(outsidemask,np.logical_or(ma.getmaskarray(data),xymask))
>>>>>> AttributeError: logical_or
>>>>>>
>>>>>> Any feedback/ideas will be greatly appreciated.
>>>>>>
>>>>>>
>>>>>>
>>>> Your error is very strange and it just simply should not be happening.
>>>> On a completely wild guess, could you try replacing "import numpy as N"
>>>> with "import numpy as np" and replace all instances of "N" with "np"?
>>>>
>>>> Ben Root
>>>>
>>>>
>>>
>>>
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