所需阵列的对象太深-scipy.integrate.odeint [英] Object Too Deep for Desired Array - scipy.integrate.odeint

问题描述

我昨天刚开始使用Python，使用scipy.integrate.odeint时出现错误.

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

我已经定义了一个函数

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

接受numpy.array个对象x，t和M；标量浮点数beta，gamma和mu.

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

M的大小为(60,60)，但我认为这无关紧要.

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

x和t都是非单例的，其中x.shape是(180,)和t.shape是(5000,).我尝试给他们一个单例尺寸，以使它们分别具有形状(180,1)和(5000,1)，但是我仍然遇到相同的错误:

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]]

即使SIR仅返回x，并且如果我从中剥离x和t的所有参数，我也会收到此错误:

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;

如您所见，导致错误的行是

As you can see, the line causing the error is

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

已要求我为SIR方法添加完整的代码.由于时间相对较长，因此将完整的.py脚本放入了pastebin中: http://pastebin.com/RphJbCHN

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

再次感谢.

推荐答案

我可以通过多种方式重现您的错误.

I can reproduce your error in several ways.

如果odeint的y0自变量或t自变量不是一维数组，则会立即发生错误.在发布在pastebin上的代码示例(在注释中引用)中，t的格式如下:

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);

删除重塑t的线. t必须是一维数组，而不是形状为(len(t)，1)的二维数组.

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

例如...

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

这有效...

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]])

这会导致错误:

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

检查您赋予odeint的初始条件(第二个参数)是否为 1-D numpy数组(而不是形状为(1，180)或(的2-D数组180，1)).

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)).

如果SIR 返回具有错误形状的数组，我也会收到对象太深..."错误.它必须返回一个 1-D 数组，其形状与第一个参数相同.确保它是真正的一维，而不是形状为(1，180)或(180，1)的2D.

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).

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