"AttributeError: sqrt" when calculating a simple standard deviation

Question

I found a very unusual error when trying to calculate the standard deviation of a two-dimensional numpy array. Basically, I do this:

np.std(myarray, axis=1) 

which gives the following error:

 /home/user/env/local/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc in std(a, axis, dtype, out, ddof, keepdims) 2588 2589 return _methods._std(a, axis=axis, dtype=dtype, out=out, ddof=ddof, -> 2590 keepdims=keepdims) 2591 2592 def var(a, axis=None, dtype=None, out=None, ddof=0, /home/user/env/local/lib/python2.7/site-packages/numpy/core/_methods.pyc in _std(a, axis, dtype, out, ddof, keepdims) 103 104 if isinstance(ret, mu.ndarray): --> 105 ret = um.sqrt(ret, out=ret) 106 else: 107 ret = um.sqrt(ret) AttributeError: sqrt 

In line 105, ret is defined as:

 array([0.0757800982464383, 0.6065241443345735, 0.3162436337971689, 0.025387106329804794, 0.023465650294750118, 0.01234409423996419, 0.03686346121524665, 0.456152653196993, 0.15598749370862977, 0.0041977155187445945, 0.018816207536006213, 0.018011541017004237, 0.01046808236307669, 0.0037176987848958156, 0.004346127061033225, 0.06885161954332783, 0.004758430435294487, 0.010064124660786879, 0.08732648466448349, 0.14957009536890314, 0.007277246755033778, 0.0043521569980290355, 0.010174973078043143, 0.33905025844712544, 0.7960121881423348], dtype=object) 

type(myarray): <type 'numpy.ndarray'>

 repr(myarray): array([[1.2258313, 1.2258313, 1.3756552, 1.1849703, 1.334794, 1.1849703, 1.1441092, 1.334794, 1.3075534, 1.2258313, 1.3756552, 0.95342433, 1.1441092, 1.0760075, 1.1168685, 1.1168685, 1.334794, 0.8036005, 0.46309182, 0.3405087], [1.3756552, 0.95342433, 1.1441092, 1.0760075, 1.1168685, 1.1168685, 1.334794, 0.8036005, 0.46309182, 0.3405087, 0.313268, 0.38136974, 0.27240697, 0.38136974, -1.8387468999999996, -0.50395286, -0.14982383, -0.46309182, -0.3405087, -0.19068487],... 

buy I see nothing wrong with this array. np.sum and np.mean work correctly.

What could be causing this error?

Answer 1

It seems that the problem is typing dtype as an object . Even if numpy allows this, it is usually a bad idea, as you lose most of the internal optimizations.

An exception is present only with the axis keyword:

 >>> import numpy as np >>> a = np.arange(10).reshape(5,2) >>> b = np.arange(10, dtype=object).reshape(5,2) >>> np.std(a) 2.8722813232690143 >>> np.std(a, axis=1) array([ 0.5, 0.5, 0.5, 0.5, 0.5]) >>> np.std(b) 2.8722813232690143 >>> np.std(b, axis=1) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.7/dist-packages/numpy/core/fromnumeric.py", line 2590, in std keepdims=keepdims) File "/usr/lib/python2.7/dist-packages/numpy/core/_methods.py", line 105, in _std ret = um.sqrt(ret, out=ret) AttributeError: sqrt