Object Too Deep for Desired Array - scipy.integrate.odeint

Question

I've just started with Python yesterday, and I'm getting an error using scipy.integrate.odeint.

I've defined a function

def SIR(x, t, beta, gamma, mu, M):

which takes the numpy.array objects x, t, and M; and the scalar floats beta, gamma, and mu.

M is (60,60) in size, but I don't think this matters.

x and t are both nonsingleton, with x.shape being (180,) and t.shape being (5000,). I've tried giving them a singleton dimension, such that they have shapes (180,1) and (5000,1) respectively, but I still get the same error :

In [1]: run measles_age.py
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/IPython/utils/py3compat.py in execfile(fname, *where)
    173             else:
    174                 filename = fname
--> 175             __builtin__.execfile(filename, *where)

/Users/qcaudron/Documents/SIR/measles_age.py in <module>()
    111 
    112 
--> 113         x = integrate.odeint(SIR, x0, t, args=(beta, gamma, mu, M));
    114 
    115 #       plot(t, x);


/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/scipy/integrate/odepack.py in odeint(func, y0, t, args, Dfun, col_deriv, full_output, ml, mu, rtol, atol, tcrit, h0, hmax, hmin, ixpr, mxstep, mxhnil, mxordn, mxords, printmessg)
    141     output = _odepack.odeint(func, y0, t, args, Dfun, col_deriv, ml, mu,
    142                              full_output, rtol, atol, tcrit, h0, hmax, hmin,
--> 143                              ixpr, mxstep, mxhnil, mxordn, mxords)
    144     if output[-1] < 0:
    145         print _msgs[output[-1]]

I get this error even when SIR just returns x, and if I strip all arguments apart from x and t from it :

def SIR(x, t):
    return x;

As you can see, the line causing the error is

x = integrate.odeint(SIR, x0, t, args=(beta, gamma, mu, M));

EDIT :

I've been asked to add the full code for the SIR method. Because it's relatively long, I've dropped the full .py script in a pastebin : http://pastebin.com/RphJbCHN

Thanks again.

Welcome to python! Most of those semicolons are unnecessary in your code. — askewchan
– askewchan, Commented Mar 29, 2013 at 19:20
Thanks. I'm aware they're unnecessary - I just think things looks cleaner with them :) Thanks for the edit above. — Quentin
– Quentin, Commented Mar 29, 2013 at 19:22
From the documentation, SIR should return dx/dt at t. Is that what SIR does? — askewchan
– askewchan, Commented Mar 29, 2013 at 19:28
Yes, in the full code, it does. Where it returns x immediately, it's not really relevant - the equation we're solving could well be dx/dt = x, in which case, yes, it's returning the correct calculation. I'm not sure why an "object is too deep for desired array" error is being returned. — Quentin
– Quentin, Commented Mar 29, 2013 at 19:38
The source is in fortran. Have you tried using integrate.ode? — askewchan
– askewchan, Commented Mar 29, 2013 at 19:45

Warren Weckesser · Accepted Answer · 2016-05-10 18:02:54Z

3

I can reproduce your error in several ways.

The error occurs immediately if either the y0 argument or the t argument to odeint is not a 1-D array. In the code example posted on pastebin (referred to in a comment), t is reshaped like this:

t = np.arange(0, 520, 1);
t = t.reshape(len(t),1);

Delete the line that reshapes t. t must be a 1-D array, not a 2-D array with shape (len(t), 1).

For example...

In [177]: def SIR(x, t):
   .....:     return x
   .....:

This works...

In [178]: x0 = [0.1, 0.2]

In [179]: odeint(SIR, x0, t=[0, 0.5, 1])
Out[179]: 
array([[ 0.1       ,  0.2       ],
       [ 0.16487213,  0.32974426],
       [ 0.27182822,  0.54365643]])

This results in the error:

In [180]: x0 = [[0.1, 0.2]]  # wrong shape

In [181]: odeint(SIR, x0, t=[0, 0.5, 1])
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-181-a37878f92395> in <module>()
----> 1 odeint(SIR, x0, t=[0, 0.5, 1])

/home/warren/anaconda/lib/python2.7/site-packages/scipy/integrate/odepack.pyc in odeint(func, y0, t, args, Dfun, col_deriv, full_output, ml, mu, rtol, atol, tcrit, h0, hmax, hmin, ixpr, mxstep, mxhnil, mxordn, mxords, printmessg)
    142     output = _odepack.odeint(func, y0, t, args, Dfun, col_deriv, ml, mu,
    143                              full_output, rtol, atol, tcrit, h0, hmax, hmin,
--> 144                              ixpr, mxstep, mxhnil, mxordn, mxords)
    145     if output[-1] < 0:
    146         print _msgs[output[-1]]

ValueError: object too deep for desired array

Check that the initial condition that you give to odeint (the second argument) is a 1-D numpy array (not a 2-D array with shape (1, 180) or (180, 1)).

I also get the 'object too deep...' error if SIR returns an array with the wrong shape. It must return a 1-D array, with the same shape as its first argument. Make sure it is truly 1-D, and not 2-D with shape (1, 180) or (180, 1).

edited May 10, 2016 at 18:02

answered Mar 29, 2013 at 20:30

Warren Weckesser

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4 Comments

Quentin Over a year ago

Thank you - however, I've checked this. SIR returns a numpy array (180,) in size, and the y0 argument to odeint is also (180,) in shape.

Warren Weckesser Over a year ago

@Quentin: If you can, please add your code for SIR to the question, along with a self-contained way of running it, so we can reproduce the error you get.

Warren Weckesser Over a year ago

I updated my answer with a comment about t being 1-D. Don't reshape it to be a 2-D array.

Quentin Over a year ago

Thank you so much, Warren. I don't know how I missed that. I fixed this, and it seems to run.

MattDMo · Accepted Answer · 2013-03-29 19:25:30Z

-1

From the tutorial it looks like the first argument to integrate.odeint() needs to be a function to operate on (in your case) x0 and t. Since your SIR() function only takes one argument, the operation is failing. It's possible that the size and/or shape of the results returned from SIR() are important in relation to the rest of the arguments.

answered Mar 29, 2013 at 19:25

MattDMo

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1 Comment

Quentin Over a year ago

Sorry, perhaps I wasn't clear. I stripped it to just that to see if the problem was the SIR function. It wasn't. I got the same error as when SIR took five arguments : def SIR(x, t, beta, gamma, mu): return x; and was called using x = integrate.odeint(SIR, x0, t, args=(beta, gamma, mu));

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