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

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  Matplotlib error: Value Error: x and y must have same first dimension Abhishek <abhishek.mallela@gmail.com> - 2015-11-12 17:54 -0800
    Re: Matplotlib error: Value Error: x and y must have same first dimension Laura Creighton <lac@openend.se> - 2015-11-13 09:34 +0100
    Re: Matplotlib error: Value Error: x and y must have same first dimension Oscar Benjamin <oscar.j.benjamin@gmail.com> - 2015-11-13 14:04 +0000
    Re: Matplotlib error: Value Error: x and y must have same first dimension Laura Creighton <lac@openend.se> - 2015-11-13 16:43 +0100
    Re: Matplotlib error: Value Error: x and y must have same first dimension Abhishek Mallela <abhishek.mallela@gmail.com> - 2015-11-13 11:44 -0600

#98725 — 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?

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#98731

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.

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

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#98742

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

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#98747

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 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

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

Laura

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#98878

Thank you Laura and Oscar.

Abhishek

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