matplotlib-users Mailing List for matplotlib

On 2012/07/30 1:17 AM, Jeffrey Spencer wrote:
> I'd agree as then it would work as pcolormesh or imshow does which when
> passed in the same norm will only set vmin or vmax that wasn't
> previously set.
>
> Assume this would be a really easy fix but I can have a look at
> submitting a patch if someone else isn't going to do so just let me know.

I will take care of it, thanks.

Eric

>
> Cheers,
> Jeff
>
> On Mon, Jul 30, 2012 at 2:31 AM, Eric Firing <ef...@ha...
> <mailto:ef...@ha...>> wrote:
>
>     On 2012/07/29 5:13 AM, Jeffrey Spencer wrote:
>
>         Eric,
>
>         Normalize appears to be working correctly and as you stated
>         above but
>         when passed into contourf appears to have inconsistent results not
>         following the docstring by allowing the value to change.
>
>         Quick examples:
>
>         X, Y = meshgrid(arange(20),arange(20)__)
>         Z = arange(20*20)
>         Z = Z.reshape(20,20)
>         norm = colors.Normalize(vmin=200,__vmax=None)
>         print norm.vmin
>         fig = figure(10)
>         ax = fig.add_subplot(111)
>         surf = ax.contourf(X,Y,Z, 100, cmap=matplotlib.cm.jet, norm = norm)
>
>         This vmin has no effect where if you pass in:
>
>         X, Y = meshgrid(arange(20),arange(20)__)
>         Z = arange(20*20)
>         Z = Z.reshape(20,20)
>         norm = colors.Normalize(vmin=200,__vmax=Z.max())
>         print norm.vmin
>         fig = figure(10)
>         ax = fig.add_subplot(111)
>         surf = ax.contourf(X,Y,Z, 100, cmap=matplotlib.cm.jet, norm = norm)
>
>         it has the desired effect.
>
>         Let me know if this is correct or I'm missing something here.
>
>         Cheers,
>         Jeff
>
>
>     You are correct.  Contour and contourf are respecting vmin, vmax
>     that have been set in the norm only if both have been set, so that
>     it is fully scaled.  I think that changing this to respect a single
>     preset vmin or vmax would be reasonable.
>
>     Eric
>
>

I also got the dimensions of the arrays and was wandering if the problem
might be there

shape data = (101, 512) 
shape v = (512, 512) 
shape tdata = (101, 1) 
shape x = (512,)



Benjamin Root-2 wrote:
> 
> On Sun, Jul 1, 2012 at 12:50 PM, surfcast23 <sur...@gm...> wrote:
> 
>>
>> Hi,
>>   I am translating a Matlab code to python and get the following error
>> when
>> the codes reaches the plotting section
>>
>> Warning (from warnings module):
>>   File "C:\Documents and Settings\My Documents\PHYSICS\Wave-eqn.py", line
>> 40
>>     w = (D*v)
>> RuntimeWarning: overflow encountered in multiply
>> Traceback (most recent call last):
>>   File "C:\Documents and Settings\My Documents\PHYSICS\Wave-eqn\.py",
>> line
>> 50, in <module>
>>     ax.plot_wireframe(x,tdata,data, rstride=10, cstride=10)
>>   File "C:\Python32\lib\site-packages\mpl_toolkits\mplot3d\axes3d.py",
>> line
>> 906, in plot_wireframe
>>     tylines = [tY[i] for i in cii]
>>   File "C:\Python32\lib\site-packages\mpl_toolkits\mplot3d\axes3d.py",
>> line
>> 906, in <listcomp>
>>     tylines = [tY[i] for i in cii]
>> IndexError: index out of bounds
>>
>> My code
>>
>> import numpy as np
>> from numpy import *
>> from math import  pi
>> from scipy.linalg import toeplitz
>> from scipy.special import cotdg
>> from mpl_toolkits.mplot3d import axes3d
>> import matplotlib.pyplot as plt
>>
>>
>>
>> N = 512
>> h = 2*np.pi/N
>> x = h*(np.arange(N) + 1)
>> t = 0
>> dt = h / 4
>> a = .1
>> tmax = 15;
>> tplot = .15;
>> nplots = int(round((tmax/tplot)));
>> plotgap = int(around(tplot/dt));
>> c = a + np.sin(x - 1)**2
>> v = np.exp(-100 * (x - 1)**2)
>> vold = np.exp(-100 * (x - a*dt - 1)**2)
>>
>> #i = np.arange(1, N)
>> #column = np.hstack([0, .5 * (-1**i) * cotdg(i * h/2)])
>> #D = toeplitz(column, -column)
>>
>> column = ((0.5*(-1)**arange(1,N+1))*cotdg(arange(1,N+1))*(h/2));
>> D = toeplitz(column,-column);print(D.shape);
>>
>> k = np.zeros(((nplots,N))); print(v.shape);print(k.shape);
>> data = np.concatenate((v.reshape((512,1)).transpose(), k))#data =
>> np.concatenate((v, k),axis = 1);
>> #data = np.vstack([v,k]);
>> tdata = t;
>>
>> for i in range(1,nplots+1):
>>     for n in range(1,plotgap+1):
>>         t = t+dt
>>         w = (D*v)
>>         vnew = vold-2*dt*c*w
>>         vold = v
>>         v = vnew
>>     data[i,:] = v[0,:]
>>     tdata = vstack([tdata, t])
>>
>> fig = plt.figure()
>> ax = fig.add_subplot(111, projection='3d')
>> #X, Y, Z = axes3d.get_test_data(0.05)
>> ax.plot_wireframe(x,tdata,data, rstride=10, cstride=10)
>>
>> plt.show()
>>
>> I looked at the error line and it seems as if the y axes is where the
>> problem is, but I am not seeing why and would appreciate any help. Thank
>> you!
>>
> 
> numpy arrays are indexed starting at 0, not 1.  So when you populate your
> "data" array with "data[i,:] = v[0,:]", and "i" only goes from 1 to
> nplots,
> data[0,:] is left completely uninitialized (unless it is being done by
> some
> of your pre-for-loop code, which is confusing to understand.)
> 
> What I can tell you is that the error isn't in plot_wireframe() as much as
> the error exist with the inputs to plot_wireframe().  Perhaps the shapes
> aren't right or something.  I will try and look at your code closer
> tomorrow and see if I can figure it out, but I suggest double-checking
> those arrays.
> 
> Cheers!
> Ben Root
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
> 

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Hi Ben,

  I was working on some other things and have finally gotten a chance to get
back to this. I changed the for loops to

for i in range(nplots):
    for n in range(plotgap):
        t = t+dt
        w = (D*v)
        vnew = vold-2*dt*c*w
        vold = v
        v = vnew
    data[i,:] = v[0,:]
    tdata = vstack([tdata, t])    

But I still get the same error as in my original post.

Khary


surfcast23 wrote:
> 
> I will try initializing starting at 0
> 
> Benjamin Root-2 wrote:
>> 
>> On Sun, Jul 1, 2012 at 12:50 PM, surfcast23 <sur...@gm...> wrote:
>> 
>>>
>>> Hi,
>>>   I am translating a Matlab code to python and get the following error
>>> when
>>> the codes reaches the plotting section
>>>
>>> Warning (from warnings module):
>>>   File "C:\Documents and Settings\My Documents\PHYSICS\Wave-eqn.py",
>>> line
>>> 40
>>>     w = (D*v)
>>> RuntimeWarning: overflow encountered in multiply
>>> Traceback (most recent call last):
>>>   File "C:\Documents and Settings\My Documents\PHYSICS\Wave-eqn\.py",
>>> line
>>> 50, in <module>
>>>     ax.plot_wireframe(x,tdata,data, rstride=10, cstride=10)
>>>   File "C:\Python32\lib\site-packages\mpl_toolkits\mplot3d\axes3d.py",
>>> line
>>> 906, in plot_wireframe
>>>     tylines = [tY[i] for i in cii]
>>>   File "C:\Python32\lib\site-packages\mpl_toolkits\mplot3d\axes3d.py",
>>> line
>>> 906, in <listcomp>
>>>     tylines = [tY[i] for i in cii]
>>> IndexError: index out of bounds
>>>
>>> My code
>>>
>>> import numpy as np
>>> from numpy import *
>>> from math import  pi
>>> from scipy.linalg import toeplitz
>>> from scipy.special import cotdg
>>> from mpl_toolkits.mplot3d import axes3d
>>> import matplotlib.pyplot as plt
>>>
>>>
>>>
>>> N = 512
>>> h = 2*np.pi/N
>>> x = h*(np.arange(N) + 1)
>>> t = 0
>>> dt = h / 4
>>> a = .1
>>> tmax = 15;
>>> tplot = .15;
>>> nplots = int(round((tmax/tplot)));
>>> plotgap = int(around(tplot/dt));
>>> c = a + np.sin(x - 1)**2
>>> v = np.exp(-100 * (x - 1)**2)
>>> vold = np.exp(-100 * (x - a*dt - 1)**2)
>>>
>>> #i = np.arange(1, N)
>>> #column = np.hstack([0, .5 * (-1**i) * cotdg(i * h/2)])
>>> #D = toeplitz(column, -column)
>>>
>>> column = ((0.5*(-1)**arange(1,N+1))*cotdg(arange(1,N+1))*(h/2));
>>> D = toeplitz(column,-column);print(D.shape);
>>>
>>> k = np.zeros(((nplots,N))); print(v.shape);print(k.shape);
>>> data = np.concatenate((v.reshape((512,1)).transpose(), k))#data =
>>> np.concatenate((v, k),axis = 1);
>>> #data = np.vstack([v,k]);
>>> tdata = t;
>>>
>>> for i in range(1,nplots+1):
>>>     for n in range(1,plotgap+1):
>>>         t = t+dt
>>>         w = (D*v)
>>>         vnew = vold-2*dt*c*w
>>>         vold = v
>>>         v = vnew
>>>     data[i,:] = v[0,:]
>>>     tdata = vstack([tdata, t])
>>>
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111, projection='3d')
>>> #X, Y, Z = axes3d.get_test_data(0.05)
>>> ax.plot_wireframe(x,tdata,data, rstride=10, cstride=10)
>>>
>>> plt.show()
>>>
>>> I looked at the error line and it seems as if the y axes is where the
>>> problem is, but I am not seeing why and would appreciate any help. Thank
>>> you!
>>>
>> 
>> numpy arrays are indexed starting at 0, not 1.  So when you populate your
>> "data" array with "data[i,:] = v[0,:]", and "i" only goes from 1 to
>> nplots,
>> data[0,:] is left completely uninitialized (unless it is being done by
>> some
>> of your pre-for-loop code, which is confusing to understand.)
>> 
>> What I can tell you is that the error isn't in plot_wireframe() as much
>> as
>> the error exist with the inputs to plot_wireframe().  Perhaps the shapes
>> aren't right or something.  I will try and look at your code closer
>> tomorrow and see if I can figure it out, but I suggest double-checking
>> those arrays.
>> 
>> Cheers!
>> Ben Root
>> 
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and 
>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> 
>> 
> 
> 

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2012/7/31 Benjamin Root <ben...@ou...>:
>
>
> On Sun, Jul 29, 2012 at 7:39 PM, Vlastimil Brom <vla...@gm...>
> wrote:
>>
>> 2012/7/30 Benjamin Root <ben...@ou...>:
>> >
>> >
>> > On Sunday, July 29, 2012, Vlastimil Brom wrote:
>> >>
>> >> Hi all,
>> >> I'd like to ask about the possibility to eventually reuse the gui of
>> >> pylab for showing and manipulating the plots in the custom application
>> >> (written in wxpython).
>> >> [...]
>> >> Thanks in advance for any hints
>> >>   regards
>> >>  Vlastimil Brom
>> >
>> >
>> > Absolutely! It is one of the things mpl does best. Do a search in the
>> > online
>> > documentation for "embedding codex".
>> >
>> > I hope that helps!
>> >
>> > Ben Root
>>
>> Thanks for the quick response and a useful hint!
>>
>> I apparently didn't search for the right terms before...
>> I turns out, that
>>
>> http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_wx2.html
>> shows exactly, what I need.
>>
>> By the way is there a place to propose a small correction of the example
>> code?
>> namely
>>         self.SetBackgroundColour(wx.NamedColor("WHITE"))
>>
>> causes an error in wxpython 2.9, which removed the "...Color" aliases
>> and only knows "...Colour"
>> hence:
>>
>>         self.SetBackgroundColour(wx.NamedColour("WHITE"))
>>
>> works in wxpython 2.9 and should be backwards compatible too.
>>
>> Thanks again,
>>     vbr
>>
>
> Thanks for catching that mistake.  Unfortunately, we don't do a good enough
> job of keeping up to date on changes in various backends.  The best way to
> make sure that gets fixed is to send us a pull request on github.  At the
> very least, post an issue report on it.
>
> Ben
>
Thanks, I created an issue:
https://github.com/matplotlib/matplotlib/issues/1048
about this and also tried to send the pull requests about the four
"wx.NamedColor" occurrences I could find.
Unfortunately, I haven't any experiences with code management tools
and github infrastructure, I didn't mess something up.

Regards,
  vbr

On Sun, Jul 29, 2012 at 7:39 PM, Vlastimil Brom <vla...@gm...>wrote:

> 2012/7/30 Benjamin Root <ben...@ou...>:
> >
> >
> > On Sunday, July 29, 2012, Vlastimil Brom wrote:
> >>
> >> Hi all,
> >> I'd like to ask about the possibility to eventually reuse the gui of
> >> pylab for showing and manipulating the plots in the custom application
> >> (written in wxpython).
> >> [...]
> >> Thanks in advance for any hints
> >>   regards
> >>  Vlastimil Brom
> >
> >
> > Absolutely! It is one of the things mpl does best. Do a search in the
> online
> > documentation for "embedding codex".
> >
> > I hope that helps!
> >
> > Ben Root
>
> Thanks for the quick response and a useful hint!
>
> I apparently didn't search for the right terms before...
> I turns out, that
>
> http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_wx2.html
> shows exactly, what I need.
>
> By the way is there a place to propose a small correction of the example
> code?
> namely
>         self.SetBackgroundColour(wx.NamedColor("WHITE"))
>
> causes an error in wxpython 2.9, which removed the "...Color" aliases
> and only knows "...Colour"
> hence:
>
>         self.SetBackgroundColour(wx.NamedColour("WHITE"))
>
> works in wxpython 2.9 and should be backwards compatible too.
>
> Thanks again,
>     vbr
>
>
Thanks for catching that mistake.  Unfortunately, we don't do a good enough
job of keeping up to date on changes in various backends.  The best way to
make sure that gets fixed is to send us a pull request on github.  At the
very least, post an issue report on it.

Ben