Matplotlib error: Value Error: x and y must have same first dimension
Abhishek
abhishek.mallela at gmail.com
Thu Nov 12 20:54:28 EST 2015
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?
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