Thread: [Matplotlib-users] IndexError: index out of bounds

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!
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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

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

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

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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