matplotlib-users

[Matplotlib-users] Bug when zooming on multiple lines separated by None

[Charleux L. <lud...@gm...>]

Hello,

I want to plot multiple lines using matplotlib.pyplot.plot using the None
separator: when i zoom or plot lines that go far away from the axis limits,
they their direction is changed. I encounter a bug shown by the folowing
code:

import matplotlib.pyplot as plt

# Single line
x = [0., 1., 1., 0., 0.]
y = [0., 0., 1., 1., 0.]

# Multiple lines separated by None
x2 = [0., 1., None ,1., 0.]
y2 = [0., 0., None, 1., 1.]

# Let's plot
fig = plt.figure(0)
plt.clf()
ax = fig.add_subplot(121)
plt.title('No zoom')
plt.xlim([-1, 2])
plt.ylim([-1, 2])
plt.plot(x,y, 'bo-', label = 'This is ok')
plt.plot(x2,y2, 'ro-', label = 'This is not ok')
plt.legend()
ax = fig.add_subplot(122)
plt.title('With zoom one a corner')
plt.xlim([-.05, .1])
plt.ylim([.95, 1.05])
plt.plot(x,y, 'bo-', label = 'This is ok')
plt.plot(x2,y2, 'ro-', label = 'This is not ok')
plt.legend()
plt.show()

I tried several approaches to solve the problem but never succeeded. I
don't wich to use 2D arrays or LineCollections because this solution is
faster and allows the declaration of all lines with a single label and
color. Has anyone any idea ?

Regards.

Re: [Matplotlib-users] Bug when zooming on multiple lines separated by None

[Phil E. <pel...@gm...>]

This works for me with 1.2 (not tested before that):


import matplotlib.pyplot as plt
import numpy as np


x = np.array([0, 1, None, 1, 0])
y = np.array([0, 1, None, 0, 1])

plt.plot(x, y)

plt.show()



I get two distinct lines crossing each other at (0.5, 0.5)


HTH,

Re: [Matplotlib-users] Bug when zooming on multiple lines separated by None

[Charleux L. <lud...@gm...>]

Hello Phil,

Your example does not trigger the bug because you don't zoom or specifiy
xlim/ylim so that some points are (far) out of the current axis. For
example, if you just add these lines to your code, you'll have it:

import matplotlib.pyplot as plt
import numpy as np
x = np.array([0, 1, None, 1, 0])
y = np.array([0, 1, None, 0, 1])
plt.plot(x, y)
# Add this or zoom in the upper left corner.
plt.xlim([0., 0.2])
plt.ylim([.9, 1.1])
plt.show()

Here I see an horizontal line where I should see a 45° tilted line. And the
nasty part of this bug is that it only affects lines declared with at least
one None in them where continuous lines seem unaffected as shown here:

import matplotlib.pyplot as plt
import numpy as np
x0 = np.array([0, 1])
y0 = np.array([0, 1])
x1 = np.array([1, 0])
y1 = np.array([0, 1])
plt.plot(x0, y0)
plt.plot(x1, y1)
# Add this
plt.xlim([0., 0.2])
plt.ylim([.9, 1.1])
plt.show()

I get a 45° line.

Ludovic

ps: I use matplotlib 1.1.1rc (stock version available on repositories) on
Xubuntu 12.04 (precise) 64-bit

2012/10/3 Phil Elson <pel...@gm...>

> This works for me with 1.2 (not tested before that):
>
>
> import matplotlib.pyplot as plt
> import numpy as np
>
>
> x = np.array([0, 1, None, 1, 0])
> y = np.array([0, 1, None, 0, 1])
>
> plt.plot(x, y)
>
> plt.show()
>
>
>
> I get two distinct lines crossing each other at (0.5, 0.5)
>
>
> HTH,
>



-- 

 *Ludovic Charleux*
Assistant Professor

*SYMME / Polytech' Annecy Chambery *
<http://www.polytech.univ-savoie.fr/index.php?id=symme_accueil&L=1> Domaine
Universitaire, BP 80439
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Re: [Matplotlib-users] Bug when zooming on multiple lines separated by None

[Eric F. <ef...@ha...>]

On 2012/10/03 4:24 AM, Charleux Ludovic wrote:
> Hello,
>
> I want to plot multiple lines using matplotlib.pyplot.plot using the
> None separator: when i zoom or plot lines that go far away from the axis
> limits, they their direction is changed. I encounter a bug shown by the
> folowing code:
>
> import matplotlib.pyplot as plt
>
> # Single line
> x = [0., 1., 1., 0., 0.]
> y = [0., 0., 1., 1., 0.]
>
> # Multiple lines separated by None
> x2 = [0., 1., None ,1., 0.]
> y2 = [0., 0., None, 1., 1.]

I'm surprised this works at all.  I don't think we have ever 
intentionally supported object arrays, which is what you get when you 
take np.array() of a list with a None in it.

If you want to use this method to make a set of line segments, use 
np.nan in place of None.

Eric

>
> # Let's plot
> fig = plt.figure(0)
> plt.clf()
> ax = fig.add_subplot(121)
> plt.title('No zoom')
> plt.xlim([-1, 2])
> plt.ylim([-1, 2])
> plt.plot(x,y, 'bo-', label = 'This is ok')
> plt.plot(x2,y2, 'ro-', label = 'This is not ok')
> plt.legend()
> ax = fig.add_subplot(122)
> plt.title('With zoom one a corner')
> plt.xlim([-.05, .1])
> plt.ylim([.95, 1.05])
> plt.plot(x,y, 'bo-', label = 'This is ok')
> plt.plot(x2,y2, 'ro-', label = 'This is not ok')
> plt.legend()
> plt.show()
>
> I tried several approaches to solve the problem but never succeeded. I
> don't wich to use 2D arrays or LineCollections because this solution is
> faster and allows the declaration of all lines with a single label and
> color. Has anyone any idea ?
>
> Regards.
>
>
>
>
> ------------------------------------------------------------------------------
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Re: [Matplotlib-users] Bug when zooming on multiple lines separated by None

[Phil E. <pel...@gm...>]

I don't get this on matplotlib/master (and therefore probably not on
1.2rc2).

I'm pretty sure masked array line plotting was fixed at some point this
release cycle (I cannot find the appropriate github issue to link to), so I
suggest this is a known bug with 1.1.1 and fixed in 1.2. Just to be clear,
I am using the TkAgg backend, and there is a remote possiblity that this
bug is backend dependent. Is there any chance you could test this with the
latest release candidate?

Many Thanks,




On 3 October 2012 17:47, Charleux Ludovic <lud...@gm...>wrote:

> Hello Phil,
>
> Your example does not trigger the bug because you don't zoom or specifiy
> xlim/ylim so that some points are (far) out of the current axis. For
> example, if you just add these lines to your code, you'll have it:
>
>
> import matplotlib.pyplot as plt
> import numpy as np
> x = np.array([0, 1, None, 1, 0])
> y = np.array([0, 1, None, 0, 1])
> plt.plot(x, y)
> # Add this or zoom in the upper left corner.
> plt.xlim([0., 0.2])
> plt.ylim([.9, 1.1])
> plt.show()
>
> Here I see an horizontal line where I should see a 45° tilted line. And
> the nasty part of this bug is that it only affects lines declared with at
> least one None in them where continuous lines seem unaffected as shown here:
>
>
> import matplotlib.pyplot as plt
> import numpy as np
> x0 = np.array([0, 1])
> y0 = np.array([0, 1])
> x1 = np.array([1, 0])
> y1 = np.array([0, 1])
> plt.plot(x0, y0)
> plt.plot(x1, y1)
> # Add this
> plt.xlim([0., 0.2])
> plt.ylim([.9, 1.1])
> plt.show()
>
> I get a 45° line.
>
> Ludovic
>
> ps: I use matplotlib 1.1.1rc (stock version available on repositories) on
> Xubuntu 12.04 (precise) 64-bit
>
>
> 2012/10/3 Phil Elson <pel...@gm...>
>
>> This works for me with 1.2 (not tested before that):
>>
>>
>> import matplotlib.pyplot as plt
>> import numpy as np
>>
>>
>> x = np.array([0, 1, None, 1, 0])
>> y = np.array([0, 1, None, 0, 1])
>>
>> plt.plot(x, y)
>>
>> plt.show()
>>
>>
>>
>> I get two distinct lines crossing each other at (0.5, 0.5)
>>
>>
>> HTH,
>>
>
>
>
> --
>
>  *Ludovic Charleux*
> Assistant Professor
>
> *SYMME / Polytech' Annecy Chambery *
>  <http://www.polytech.univ-savoie.fr/index.php?id=symme_accueil&L=1> Domaine
> Universitaire, BP 80439
> <http://maps.google.com/maps?q=Domaine+Universitaire%2C+BP+80439%2C+Annecy+le+vieux+cedex%2C+F74944%2C+France&hl=en>Annecy le vieux cedex, F74944 France
>   *Work:* 33 (0) 4 50 09 65 62
> *Fax:* 33 (0) 4 50 09 65 43
> *Email:* lud...@un...
>  *Professional Profile<http://fr.linkedin.com/pub/ludovic-charleux/22/611/997>
> *
>      See who we know in common<http://www.linkedin.com/e/wwk/79152451/?hs=false&tok=1JhCnH2Q-kS5g1> Want
> a signature like this?<http://www.linkedin.com/e/sig/79152451/?hs=false&tok=3gCpNtR8KkS5g1>
>

Re: [Matplotlib-users] Bug when zooming on multiple lines separated by None

[Benjamin R. <ben...@ou...>]

On Wed, Oct 3, 2012 at 1:02 PM, Phil Elson <pel...@gm...> wrote:

> I don't get this on matplotlib/master (and therefore probably not on
> 1.2rc2).
>
> I'm pretty sure masked array line plotting was fixed at some point this
> release cycle (I cannot find the appropriate github issue to link to), so I
> suggest this is a known bug with 1.1.1 and fixed in 1.2. Just to be clear,
> I am using the TkAgg backend, and there is a remote possiblity that this
> bug is backend dependent. Is there any chance you could test this with the
> latest release candidate?
>
> Many Thanks,
>
>
This issue may be dependent upon which version of Numpy one is using.  As
Eric pointed out, one should be getting an object array if you have a None
in the list.  On top of that, I wouldn't be surprised if the different
backends handled this object array differently.

As far as I am concerned, using None in the list is the bug and is not only
unsupported, but should be actively discouraged.  Use NaNs or masked arrays
instead.

(and to ward off the inevitable question, I would advise against explicitly
checking for object arrays because there are times when it is correct to
have such arrays, i.e., python decimal or datetime objects).

Cheers!
Ben Root

Re: [Matplotlib-users] Bug when zooming on multiple lines separated by None

[Charleux L. <lud...@gm...>]

Thanks for your multiple answers. I'll try the same manipulation with the
1.2 version as soon as possible. Concerning the debate between the use of
None and numpy.nan, I tryed both methods before posting and they both lead
to the same bug on my version. I'm using the None/numpy.nan trick to plot
finite element 2D meshes (Matplotlib  allows very neat vectorial plots) and
I often adjust xlim/ylim to magnify interesting zones and so this bug is
everywhere. I'm not totally sure but I think the bug was not present in the
1.0.x versions I tested before.

Regards.

Ludovic Charleux

2012/10/3 Benjamin Root <ben...@ou...>

>
>
> On Wed, Oct 3, 2012 at 1:02 PM, Phil Elson <pel...@gm...> wrote:
>
>> I don't get this on matplotlib/master (and therefore probably not on
>> 1.2rc2).
>>
>> I'm pretty sure masked array line plotting was fixed at some point this
>> release cycle (I cannot find the appropriate github issue to link to), so I
>> suggest this is a known bug with 1.1.1 and fixed in 1.2. Just to be clear,
>> I am using the TkAgg backend, and there is a remote possiblity that this
>> bug is backend dependent. Is there any chance you could test this with the
>> latest release candidate?
>>
>> Many Thanks,
>>
>>
> This issue may be dependent upon which version of Numpy one is using.  As
> Eric pointed out, one should be getting an object array if you have a None
> in the list.  On top of that, I wouldn't be surprised if the different
> backends handled this object array differently.
>
> As far as I am concerned, using None in the list is the bug and is not
> only unsupported, but should be actively discouraged.  Use NaNs or masked
> arrays instead.
>
> (and to ward off the inevitable question, I would advise against
> explicitly checking for object arrays because there are times when it is
> correct to have such arrays, i.e., python decimal or datetime objects).
>
> Cheers!
> Ben Root
>
>

Re: [Matplotlib-users] Bug when zooming on multiple lines separated by None

[Eric F. <ef...@ha...>]

On 2012/10/03 8:11 AM, Charleux Ludovic wrote:
> Thanks for your multiple answers. I'll try the same manipulation with
> the 1.2 version as soon as possible. Concerning the debate between the
> use of None and numpy.nan, I tryed both methods before posting and they
> both lead to the same bug on my version. I'm using the None/numpy.nan
> trick to plot finite element 2D meshes (Matplotlib  allows very neat
> vectorial plots) and I often adjust xlim/ylim to magnify interesting
> zones and so this bug is everywhere. I'm not totally sure but I think
> the bug was not present in the 1.0.x versions I tested before.

Please--there is *no* None trick. This is not a debate. Please do *not* 
use None.  Use np.nan or a masked array.  Unless you go into the lower 
levels of the api, mpl will convert a floating-point array with nans 
into a masked array for operations such as auto-scaling.

If you must use an object array (e.g., as Ben notes, if you are using 
datetime objects--it must be something for which there is a registered 
converter, because at the plotting level mpl works with floats), then 
make it a masked array if you need to put gaps in it.  If that does not 
work, then it is a bug in the conversion process.  Masked arrays should 
work for any input type supported by mpl.

Eric

>
> Regards.
>
> Ludovic Charleux
>
> 2012/10/3 Benjamin Root <ben...@ou... <mailto:ben...@ou...>>
>
>
>
>     On Wed, Oct 3, 2012 at 1:02 PM, Phil Elson <pel...@gm...
>     <mailto:pel...@gm...>> wrote:
>
>         I don't get this on matplotlib/master (and therefore probably
>         not on 1.2rc2).
>
>         I'm pretty sure masked array line plotting was fixed at some
>         point this release cycle (I cannot find the appropriate github
>         issue to link to), so I suggest this is a known bug with 1.1.1
>         and fixed in 1.2. Just to be clear, I am using the TkAgg
>         backend, and there is a remote possiblity that this bug is
>         backend dependent. Is there any chance you could test this with
>         the latest release candidate?
>
>         Many Thanks,
>
>
>     This issue may be dependent upon which version of Numpy one is
>     using.  As Eric pointed out, one should be getting an object array
>     if you have a None in the list.  On top of that, I wouldn't be
>     surprised if the different backends handled this object array
>     differently.
>
>     As far as I am concerned, using None in the list is the bug and is
>     not only unsupported, but should be actively discouraged.  Use NaNs
>     or masked arrays instead.
>
>     (and to ward off the inevitable question, I would advise against
>     explicitly checking for object arrays because there are times when
>     it is correct to have such arrays, i.e., python decimal or datetime
>     objects).
>
>     Cheers!
>     Ben Root
>
>
>
>
>
> ------------------------------------------------------------------------------
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> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
>
>
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