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#### Matplotlib error: Value Error: x and y must have same first dimension

I am trying to run some Python code for the last few hours. How can I achieve the effect of "dot divide" from Matlab, in the following code? I am having trouble working with list comprehension and numpy arrays and getting the following error:

Traceback (most recent call last):
File "Thurs.py", line 128, in <module>
plt.plot(np.array(range(1,N/2+2)), Splot[alpha][iii,val]/utot[iii,val],color=cmap(iii/50))

ValueError: x and y must have same first dimension

Code:

import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from scipy.integrate import odeint

N = 2
K00 = np.logspace(3,5,101,10)
len1 = len(K00)
Qvec = np.logspace(-2,2,2,10)
S10vec = np.logspace(2,6,2,10)
len2 = len(Qvec)
y0 = [0]*(3*N/2+3)
Kplot = np.zeros((len1,len2))
Pplot = np.zeros((len1,len2))
S = [np.zeros((len1,len2)) for kkkk in range(N/2+1)]
KS = [np.zeros((len1,len2)) for kkkk in range(N/2)]
PS = [np.zeros((len1,len2)) for kkkk in range(N/2)]
Splot = [np.zeros((len1,len2)) for kkkk in range(N/2+1)]
KSplot = [np.zeros((len1,len2)) for kkkk in range(N/2)]
PSplot = [np.zeros((len1,len2)) for kkkk in range(N/2)]

for val in range(0,len2):
for series in range(0,len1):
K0 = K00[series]
Q = Qvec[val]
S10 = S10vec[val]
r1 = 0.0001
r2 = 0.001
a = 0.001
d = 0.001
k = 0.999
P0 = 1
tfvec = [1e7, 1e10]
tf = tfvec[val]
time = np.linspace(0,tf,1001)

def f(y,t):
for alpha in range(0,(N/2+1)):
S[alpha] = y[alpha]
for beta in range((N/2)+1,N+1):
KS[beta-N/2-1] = y[beta]
for gamma in range(N+1,3*N/2+1):
PS[gamma-N-1] = y[gamma]
K = y[3*N/2+1]
P = y[3*N/2+2]

ydot = np.zeros((3*N/2+3,1))
B = range((N/2)+1,N+1)
G = range(N+1,3*N/2+1)
runsumPS = 0
runsum1 = 0
runsumKS = 0
runsum2 = 0

for m in range(0,N/2):
runsumPS = runsumPS + PS[m]
runsum1 = runsum1 + S[m+1]
runsumKS = runsumKS + KS[m]
runsum2 = runsum2 + S[m]
ydot[B[m]] = a*K*S[m]-(d+k+r1)*KS[m]

for i in range(0,N/2-1):
ydot[G[i]] = a*P*S[i+1]-(d+k+r1)*PS[i]

for p in range(1,N/2):
ydot[p] = -S[p]*(r1+a*K+a*P)+k*KS[p-1]+d*(PS[p-1]+KS[p])

ydot[0] = Q-(r1+a*K)*S[0]+d*KS[0]+k*runsumPS
ydot[N/2] = k*KS[N/2-1]-(r2+a*P)*S[N/2]+d*PS[N/2-1]
ydot[G[N/2-1]] = a*P*S[N/2]-(d+k+r2)*PS[N/2-1]
ydot[3*N/2+1] = (d+k+r1)*runsumKS-a*K*runsum2
ydot[3*N/2+2] = (d+k+r1)*(runsumPS-PS[N/2-1])- \
a*P*runsum1+(d+k+r2)*PS[N/2-1]

ydot_new = []
for j in range(0,3*N/2+3):
ydot_new.extend(ydot[j])
return ydot_new

y0[0] = S10
for i in range(1,3*N/2+1):
y0[i] = 0
y0[3*N/2+1] = K0
y0[3*N/2+2] = P0

soln = odeint(f,y0,time, mxstep = 5000)
for alpha in range(0,(N/2+1)):
S[alpha] = soln[:,alpha]
for beta in range((N/2)+1,N+1):
KS[beta-N/2-1] = soln[:,beta]
for gamma in range(N+1,3*N/2+1):
PS[gamma-N-1] = soln[:,gamma]

for alpha in range(0,(N/2+1)):
Splot[alpha][series,val] = soln[len(time)-1,alpha]
for beta in range((N/2)+1,N+1):
KSplot[beta-N/2-1][series,val] = soln[len(time)-1,beta]
for gamma in range(N+1,3*N/2+1):
PSplot[gamma-N-1][series,val] = soln[len(time)-1,gamma]

u1 = 0
u2 = 0
u3 = 0

for alpha in range(0,(N/2+1)):
u1 = u1 + Splot[alpha]
for beta in range((N/2)+1,N+1):
u2 = u2 + KSplot[beta-N/2-1]
for gamma in range(N+1,3*N/2+1):
u3 = u3 + PSplot[gamma-N-1]

K = soln[:,3*N/2+1]
P = soln[:,3*N/2+2]
Kplot[series] = soln[len1-1,3*N/2+1]
Pplot[series] = soln[len1-1,3*N/2+2]
utot = u1+u2+u3

plt.figure(val)
cmap = mpl.cm.autumn
for iii in range(0,100,50):
for alpha in range(0,(N/2+1)):
plt.plot(np.array(range(1,N/2+2)), Splot[alpha][iii,val]/utot[iii,val],color=cmap(iii/50))
plt.xlabel('i')
plt.ylabel(r'$\frac{S_i}{S_{tot}}$ (nM)')
plt.title('N = 20: Behavior at [S](0) = 10^' + str(log10(Qvec[val]) + 4) + '(nM)', fontsize=20)
plt.show()

At the very least, can I extract the values that I need just for the plot?

 0
Abhishek
11/13/2015 1:54:28 AM
comp.lang.python 77058 articles. 6 followers.

4 Replies
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In a message of Thu, 12 Nov 2015 17:54:28 -0800, Abhishek writes:
>I am trying to run some Python code for the last few hours. How can I ach=
ieve the effect of "dot divide" from Matlab, in the following code? I am h=
aving trouble working with list comprehension and numpy arrays and getting=
the following error:
>
>    Traceback (most recent call last):
>      File "Thurs.py", line 128, in <module>
>        plt.plot(np.array(range(1,N/2+2)), Splot[alpha][iii,val]/utot[iii=
,val],color=3Dcmap(iii/50))
>
>    ValueError: x and y must have same first dimension

Splot is a list.  matplotlib wants 2 numpy arrays.  You have to cast
it with np.array() too.

no guarantees that the rest of the code works -- it is not plotting for
me -- but that gets rid of that error at any rate.

Laura

 0
Laura
11/13/2015 8:34:23 AM
On 13 November 2015 at 08:34, Laura Creighton <lac@openend.se> wrote:
> In a message of Thu, 12 Nov 2015 17:54:28 -0800, Abhishek writes:
>>I am trying to run some Python code for the last few hours. How can I achieve the effect of "dot divide" from Matlab, in the following code? I am having trouble working with list comprehension and numpy arrays and getting the following error:
>>
>>    Traceback (most recent call last):
>>      File "Thurs.py", line 128, in <module>
>>        plt.plot(np.array(range(1,N/2+2)), Splot[alpha][iii,val]/utot[iii,val],color=cmap(iii/50))
>>
>>    ValueError: x and y must have same first dimension
>
> Splot is a list.  matplotlib wants 2 numpy arrays.  You have to cast
> it with np.array() too.

Actually the plot command is perfectly happy converting lists or lists
of lists etc. to arrays (by calling np.array internally) so you don't
need to convert any of your inputs. By the way: np.arange(1, N/2+2)
would be the usual way to create a numpy array that is a range.

The error here comes because (after both arguments are converted to
arrays) they have incompatible sizes. In other words:

len(range(1,N/2+2)) != len(Splot[alpha][iii,val]/utot[iii,val])

I'm not sure what the solution is as the code is too complex for me to
spend time trying to guess what it's trying to do.

--
Oscar

 0
Oscar
11/13/2015 2:04:01 PM
In a message of Fri, 13 Nov 2015 14:04:01 +0000, Oscar Benjamin writes:
>On 13 November 2015 at 08:34, Laura Creighton <lac@openend.se> wrote:
>> In a message of Thu, 12 Nov 2015 17:54:28 -0800, Abhishek writes:
>>>I am trying to run some Python code for the last few hours. How can I a=
chieve the effect of "dot divide" from Matlab, in the following code? I am=
having trouble working with list comprehension and numpy arrays and getti=
ng the following error:
>>>
>>>    Traceback (most recent call last):
>>>      File "Thurs.py", line 128, in <module>
>>>        plt.plot(np.array(range(1,N/2+2)), Splot[alpha][iii,val]/utot[i=
ii,val],color=3Dcmap(iii/50))
>>>
>>>    ValueError: x and y must have same first dimension
>>
>> Splot is a list.  matplotlib wants 2 numpy arrays.  You have to cast
>> it with np.array() too.
>
>Actually the plot command is perfectly happy converting lists or lists
>of lists etc. to arrays (by calling np.array internally) so you don't
>need to convert any of your inputs. By the way: np.arange(1, N/2+2)
>would be the usual way to create a numpy array that is a range.
>
>The error here comes because (after both arguments are converted to
>arrays) they have incompatible sizes. In other words:
>
>    len(range(1,N/2+2)) !=3D len(Splot[alpha][iii,val]/utot[iii,val])
>
>I'm not sure what the solution is as the code is too complex for me to
>spend time trying to guess what it's trying to do.
>
>--
>Oscar

I am sorry for the bad information.  Thank you Oscar.

Laura

 0
Laura
11/13/2015 3:43:54 PM
Thank you Laura and Oscar.

Abhishek

 0
Abhishek
11/13/2015 5:44:04 PM

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