matplotlib-users Mailing List for matplotlib

Hello,
When I plot using the errorbar() routine, I get beautiful plots,
complete with error bars. Then, when I want to perform manipulations
on the data after the fact, I use
lines = axes.get_lines()
to get at the lines
lines[n].get_xdata() and set_xdata()
to edit the data etc...
The problem is when I do errobar() I get not only the data lines, but
also a bunch of small lines for drawing the error bars, and it's very
difficult to sort them all out to get at the data of the plot.
My question is, is there an easy/bulletproof way to tell if a given
line from get_lines() is an error bar or the actual data?
Thanks!
Jack

Suresh Pillai wrote:
> I guess I didn't read the following carefully:
> 
> "... The aspect ratio of the figure window is that of the array
> ... Because of how matshow() tries to
> set the figure aspect ratio to be the one of the array, ..."
> 
> which would explain the behaviour below.
> 
> Why the restrictions? Seems one would want to put colorbars, etc in the 
> same figure and so why not behave like imshow() which it calls to make the 
> output. And why the new figure (so no possibility of subplots or 
> overlays)? Just curious ... I guess I will use imshow() directly and 
> modify the axes as suggested before to get the output looking like 
> matshow()
> 
Suresh,
I think the general answer to your questions is "historical accident". 
Matshow was contributed a long time ago, and has been updated only 
minimally to take into account changes made elsewhere. There was even a 
suggestion that it might not be needed any more, but I think that it can 
continue to be useful and is worth updating to be an axes method, etc. 
This is on my growing mental list of things to do, and is probably one 
of the easier ones.
Eric
> Cheers,
> Suresh
> 
> On Thu, 8 Mar 2007, Suresh Pillai wrote:
> 
>> If one inserts a colorbar after using matshow, then the matrix plot's aspect 
>> ratio is incorrect altered. Here are 2 cases to compare
>>
>> import pylab
>> matrix = pylab.rand(30,30)
>>
>> 1) matshow() before colorbar()
>>
>> pylab.matshow(matrix)
>> pylab.colorbar()
>> pylab.show()
>>
>> The matrix plot is squished in the x-direction while not in the y thus losing 
>> its proper aspect ratio (equal by default).
>>
>> 2) imshow() before colorbar()
>>
>> pylab.imshow(matrix)
>> pylab.colorbar()
>> pylab.show()
>>
>> Everthing is okay in this case.
>>
>>
>> Thanks,
>> Suresh
>>
>>
> 
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Suresh Pillai <sto...@ya...> writes:
> I discovered the same problem, so I went looking and found the mailing 
> list properly archived at nabble.com:
Another useful mailing list archive is gmane.org:
http://dir.gmane.org/gmane.comp.python.matplotlib.general
http://dir.gmane.org/gmane.comp.python.matplotlib.devel
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Jeff Peery <jef...@ya...> writes:
> hello, I have an application I'm working on, and I need to remove
> figtext() without using a figure.clear(). how can I do this? thanks.
When you call figtext, save the return value, and then call
set_visible(False) on it to hide it, or delete it from the figure's
texts list:
ft=fig.figtext(x, y, text)
# ...
ft.set_visible(False); draw()
# or:
fig.texts.remove(ft); draw()
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

set markerfacecolor (a.k.a. mfc) = 'None' (make sure you include the 
quotes).
-Andrew
John T Whelan wrote:
> Dear matplotlib gurus,
>
> When I use
>
> plot(t,x,'rx',t,y,'bs');
>
> in matlab, it produces blue boxes for y, i.e., squares with a blue
> border and a transparent interior, so that if one of them lies on top
> of a red x, I can see the red x inside the blue box. The same
> construction in matplotlib produces blue squares: squares with a black
> border and a blue interior. I can change the color of the interior
> with the markerfacecolor or mfc argument, e.g.,
>
> plot(t,x,'rx');
> plot(t,y,'bs',mec='b',mfc='w');
>
> but that produces an opaque white interior which renders invisible any
> red x it covers up.
>
> I can change the transparency of a line with the alpha argument, but
> there seems to be no corresponding markerfacealpha.
>
> Is there a way in matplotlib to get a square marker with a blue border
> and a transparent interior?
>
> 				Thanks,
> 

Dear matplotlib gurus,
When I use
plot(t,x,'rx',t,y,'bs');
in matlab, it produces blue boxes for y, i.e., squares with a blue
border and a transparent interior, so that if one of them lies on top
of a red x, I can see the red x inside the blue box. The same
construction in matplotlib produces blue squares: squares with a black
border and a blue interior. I can change the color of the interior
with the markerfacecolor or mfc argument, e.g.,
plot(t,x,'rx');
plot(t,y,'bs',mec='b',mfc='w');
but that produces an opaque white interior which renders invisible any
red x it covers up.
I can change the transparency of a line with the alpha argument, but
there seems to be no corresponding markerfacealpha.
Is there a way in matplotlib to get a square marker with a blue border
and a transparent interior?
 				Thanks,
-- 
======================================================================
Office: 0.17 (Golm) Dr. John T. Whelan
Phone: +49 331 567 7117 MPI for Gravitational Physics
FAX: +49 331 567 7298 (Albert-Einstein Institute)
http://www.aei.mpg.de/~whelan/ D-14424 Potsdam
joh...@li... joh...@ae...
======================================================================

I guess I didn't read the following carefully:
"... The aspect ratio of the figure window is that of the array
 ... Because of how matshow() tries to
 set the figure aspect ratio to be the one of the array, ..."
which would explain the behaviour below.
Why the restrictions? Seems one would want to put colorbars, etc in the 
same figure and so why not behave like imshow() which it calls to make the 
output. And why the new figure (so no possibility of subplots or 
overlays)? Just curious ... I guess I will use imshow() directly and 
modify the axes as suggested before to get the output looking like 
matshow()
Cheers,
Suresh
On Thu, 8 Mar 2007, Suresh Pillai wrote:
> If one inserts a colorbar after using matshow, then the matrix plot's aspect 
> ratio is incorrect altered. Here are 2 cases to compare
>
> import pylab
> matrix = pylab.rand(30,30)
>
> 1) matshow() before colorbar()
>
> pylab.matshow(matrix)
> pylab.colorbar()
> pylab.show()
>
> The matrix plot is squished in the x-direction while not in the y thus losing 
> its proper aspect ratio (equal by default).
>
> 2) imshow() before colorbar()
>
> pylab.imshow(matrix)
> pylab.colorbar()
> pylab.show()
>
> Everthing is okay in this case.
>
>
> Thanks,
> Suresh
>
>

We are looking for someone to fill a position at the Space Telescope 
Science Institute (in Baltimore, MD) to work on Python tools for 
astronomical data processing and analysis. Details can be found at:
http://www.stsci.edu/institute/brc/hr/co/external/Req559.html

I discovered the same problem, so I went looking and found the mailing 
list properly archived at nabble.com:
http://www.nabble.com/Creating-a-non-linear-colormap.-t3362841.html
Cheers,
Suresh
On Fri, 9 Mar 2007, Ken McIvor wrote:
> On Mar 9, 2007, at 5:11 AM, Uwe Schmitt wrote:
>>
>> Thanks, but I can not access this article from the mailing lists
>> archive.
>> On sourceforge the newest posting is from 23th feb.
>
> I'm not sure what the problem with SourceForge is. I'll forward you
> that email off-list.
>
> Ken
>
>
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>

Thank you, I think thatthis will solve my problem :)
I didn't know this class existed.
Matthieu
2007年3月9日, John Hunter <jd...@gm...>:
>
> On 3/9/07, Matthieu Brucher <mat...@gm...> wrote:
>
> > What I have is a set of points in a numpy.array - for instance size
> (2000,
> > 2) -. What I have as well is a nump.array of size (2000, 3). How can I
> make
> > plot understand that each line of the set points must be painted with
> the
> > corresponding line in the colour array ?
>
> You'll probably want to use a regular poly collection, as in the
> example below. Your array of facecolors can pretty much be whatever
> you want:
>
> from pylab import figure, nx, show, cm
> from matplotlib.collections import RegularPolyCollection
>
>
> fig = figure()
> ax = fig.add_subplot(111)
>
> offsets = nx.mlab.rand(20,2)
> facecolors = [cm.jet(x) for x in nx.mlab.rand(20)]
> black = (0,0,0,1)
>
> collection = RegularPolyCollection(
> fig.dpi,
> numsides=5, # a pentagon
> rotation=0,
> sizes=(50,),
> facecolors = facecolors,
> edgecolors = (black,),
> linewidths = (1,),
> offsets = offsets,
> transOffset = ax.transData,
> )
>
> ax.add_collection(collection)
>
> show()
>
>
>
>
>
>
>
> > Matthieu
> >
> >
> -------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of IT
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> your
> > opinions on IT & business topics through brief surveys-and earn cash
> >
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> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
> >
>

On 3/9/07, Matthieu Brucher <mat...@gm...> wrote:
> What I have is a set of points in a numpy.array - for instance size (2000,
> 2) -. What I have as well is a nump.array of size (2000, 3). How can I make
> plot understand that each line of the set points must be painted with the
> corresponding line in the colour array ?
You'll probably want to use a regular poly collection, as in the
example below. Your array of facecolors can pretty much be whatever
you want:
from pylab import figure, nx, show, cm
from matplotlib.collections import RegularPolyCollection
fig = figure()
ax = fig.add_subplot(111)
offsets = nx.mlab.rand(20,2)
facecolors = [cm.jet(x) for x in nx.mlab.rand(20)]
black = (0,0,0,1)
collection = RegularPolyCollection(
 fig.dpi,
 numsides=5, # a pentagon
 rotation=0,
 sizes=(50,),
 facecolors = facecolors,
 edgecolors = (black,),
 linewidths = (1,),
 offsets = offsets,
 transOffset = ax.transData,
 )
ax.add_collection(collection)
show()
> Matthieu
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
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>
>

>
> Complete examples always help ince we have no way of knowing what the
> points data structures look like, but I'll hazard a gues. The x and y
> arguments to "plot" need to be sequences. Ie, something like
>
> plot([0.5], [0.5], 'ro')
>
> It can be inefficient to plot many separate points this way -- if you
> have a lot of points, use a
> matplotlib.collections.RegularPolyCollection or scatter.
>
Thank you for your answer :)
OK, I'll try to wrap them :|. The best solution would indeed be to paint
them all at once, but I didn't manage to do that, even when I looked in the
scatter_demo2 example :(
What I have is a set of points in a numpy.array - for instance size (2000,
2) -. What I have as well is a nump.array of size (2000, 3). How can I make
plot understand that each line of the set points must be painted with the
corresponding line in the colour array ?
Matthieu

On 3/9/07, Fernando Perez <fpe...@gm...> wrote:
> (or matlab for that matter) in my life, I was rather surprised by the
> behavior and (mis)understood it as a bug.
>
> I've always gotten by just fine in pylab without even knowing what
> hold did, and simply clearing the figure by hand when needed or just
> making a new one.
Just to add a few data points -- the default "hold" state can be set
in your rc file. It is a property of the current figure and the
current axes. In you example, when you set fold before creating the
third figure, the setting applued to the current figure (figure 2) but
not the next figure.
JDH

On 3/9/07, Uwe Schmitt <usc...@mi...> wrote:
> I would like to display an image using pylab
> without automatic scaling to the default size of the plot window.
>
> How can I achieve this ?
If you want displayed image to just be a pixel dump of the actual
image use figimage
http://matplotlib.sf.net/examples/figimage_demo.py
JDH

On 3/9/07, Matthieu Brucher <mat...@gm...> wrote:
> Hi,
>
> I'm trying to plot a set of points, each point having a different color.
> For the moment, I'm trying to do something like that :
>
> for indice in range(0, points.shape[0]):
> pl.plot(points[indice, 0], points[indice, 1], 'o', c =
> colours[indice,:], hold = True)
>
> where points is a numpy array of point and colours is a numpy array of
> dimension (points.shape[0], 3)
>
> With Matlab, something like this would function, but not in matplotlib, it
> tells me :
> ValueError: need more than 0 values to unpack
Complete examples always help ince we have no way of knowing what the
points data structures look like, but I'll hazard a gues. The x and y
arguments to "plot" need to be sequences. Ie, something like
 plot([0.5], [0.5], 'ro')
It can be inefficient to plot many separate points this way -- if you
have a lot of points, use a
matplotlib.collections.RegularPolyCollection or scatter.
JDH

On Mar 9, 2007, at 5:11 AM, Uwe Schmitt wrote:
>
> Thanks, but I can not access this article from the mailing lists 
> archive.
> On sourceforge the newest posting is from 23th feb.
I'm not sure what the problem with SourceForge is. I'll forward you 
that email off-list.
Ken

Hi, All
Is it possible to draw any graphical primitives in the plot area using
its scale?
Let say, I want to plot a filled circle there. Where do I have to look on?
Thanks in advance,
Alexey

Ken McIvor wrote:
> Uwe,
>
> I don't know the answer to your question, but yesterday Rob Hetland 
> sent out and email entitled "Creating a non-linear colormap." that 
> includes example code. That might help you get started.
>
> Ken
>
Thanks, but I can not access this article from the mailing lists archive.
On sourceforge the newest posting is from 23th feb.
Greetings, Uwe

Hi,
I'm trying to plot a set of points, each point having a different color.
For the moment, I'm trying to do something like that :
 for indice in range(0, points.shape[0]):
 pl.plot(points[indice, 0], points[indice, 1], 'o', c =
colours[indice,:], hold = True)
where points is a numpy array of point and colours is a numpy array of
dimension (points.shape[0], 3)
With Matlab, something like this would function, but not in matplotlib, it
tells me :
ValueError: need more than 0 values to unpack
I am missing something ?
Matthieu

Hello,
I would like to display an image using pylab
without automatic scaling to the default size of the plot window.
How can I achieve this ?
Greetings, Uwe

Hi Simon,
On 3/8/07, Simon Wood <sgw...@gm...> wrote:
> On 3/8/07, Fernando Perez <fpe...@gm...> wrote:
> > Hi all,
> >
> > today at work we ran into some odd behavior, all of which seems to be
> > triggered by calling hold(). I'm using a fresh SVN build from this
> > afternoon.
> >
> > Here's the first example demonstrating the problem, it's best to run
> > this in a fresh pylab shell or from the command line, since I suspect
> > internal state matters (when it shouldn't):
> >
> > import pylab as P
> >
> > x = P.arange(10)
> > y = x+1
> >
> > P.figure()
> > P.plot(x,label='one')
> > P.plot(y,label='two')
> > P.legend()
> > P.title('Two plots ok')
> >
> > P.figure()
> > P.hold(True)
> > P.plot(x,label='one')
> > P.plot(y,label='two')
> > P.legend()
> > P.title('Two plots ok - HOLD called')
> > P.hold(False)
> >
> > P.figure()
> > P.plot(x,label='one')
> > P.plot(y,label='two')
> > P.legend()
> > P.title('One plot MISSING!')
> >
> > P.show()
> >
> > #### EOF
> >
>
> I do not think this is a bug. The default value for the hold function is
> True. When you originally plotted x and y the hold state was already set to
> True. So, actually your first case and second case are the same. However,
> right before your third figure you set P.hold(False) . You then plot x
> followed by y. So, yes I would expect to see only one line in the final
> figure. This is exactly like Matlab (perhaps with the exception that the
> default state of hold is False in Matlab). Perhaps that is what is confusing
> you and your colleague. In Matlab the default state of hold is False,
> however in Matplotlib is looks like the default state of hold is True.
Many thanks for your clear explanation. Since I had never used hold
(or matlab for that matter) in my life, I was rather surprised by the
behavior and (mis)understood it as a bug.
I've always gotten by just fine in pylab without even knowing what
hold did, and simply clearing the figure by hand when needed or just
making a new one.
Sorry for the noise.
Regards,
f

On 3/8/07, Fernando Perez <fpe...@gm...> wrote:
>
> Hi all,
>
> today at work we ran into some odd behavior, all of which seems to be
> triggered by calling hold(). I'm using a fresh SVN build from this
> afternoon.
>
> Here's the first example demonstrating the problem, it's best to run
> this in a fresh pylab shell or from the command line, since I suspect
> internal state matters (when it shouldn't):
>
> import pylab as P
>
> x = P.arange(10)
> y = x+1
>
> P.figure()
> P.plot(x,label='one')
> P.plot(y,label='two')
> P.legend()
> P.title('Two plots ok')
>
> P.figure()
> P.hold(True)
> P.plot(x,label='one')
> P.plot(y,label='two')
> P.legend()
> P.title('Two plots ok - HOLD called')
> P.hold(False)
>
> P.figure()
> P.plot(x,label='one')
> P.plot(y,label='two')
> P.legend()
> P.title('One plot MISSING!')
>
> P.show()
>
> #### EOF
>
I do not think this is a bug. The default value for the hold function is
True. When you originally plotted x and y the hold state was already set to
True. So, actually your first case and second case are the same. However,
right before your third figure you set P.hold(False) . You then plot x
followed by y. So, yes I would expect to see only one line in the final
figure. This is exactly like Matlab (perhaps with the exception that the
default state of hold is False in Matlab). Perhaps that is what is confusing
you and your colleague. In Matlab the default state of hold is False,
however in Matplotlib is looks like the default state of hold is True.
-Simon

Hi all,
today at work we ran into some odd behavior, all of which seems to be
triggered by calling hold(). I'm using a fresh SVN build from this
afternoon.
Here's the first example demonstrating the problem, it's best to run
this in a fresh pylab shell or from the command line, since I suspect
internal state matters (when it shouldn't):
import pylab as P
x = P.arange(10)
y = x+1
P.figure()
P.plot(x,label='one')
P.plot(y,label='two')
P.legend()
P.title('Two plots ok')
P.figure()
P.hold(True)
P.plot(x,label='one')
P.plot(y,label='two')
P.legend()
P.title('Two plots ok - HOLD called')
P.hold(False)
P.figure()
P.plot(x,label='one')
P.plot(y,label='two')
P.legend()
P.title('One plot MISSING!')
P.show()
#### EOF
And here's the second manifestation of the problem, where the colorbar
gets all messed up:
import numpy as N
import pylab as P
a = N.random.rand(64,64)
P.figure()
P.imshow(a)
P.colorbar()
P.title('Colorbar OK')
# If the hold() calls are commented out, the problem disappears
P.figure()
P.hold(True)
P.plot(range(10))
P.hold(False)
P.figure()
P.imshow(a)
P.colorbar()
P.title('Colorbar BROKEN!')
P.show()
#### EOF
It looks like making calls to hold() messes up internal state in pylab
somehow. I've never used hold() myself before, but my officemate did,
coming from matlab, and started seeing bizarre behavior. These are
little self-contained examples showing the problem.
Cheers,
f