reading scientific notation csv file with numpy

Question

I'm trying to load a file that represents a 2D matrix with numpy loadtxt

cov = np.loadtxt("cov.csv")

The first element is in scientific notation which causes a failure

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-80-0796abd8c0f7> in <module>()
----> 1 cov = np.loadtxt("cov.csv")

C:\home\Anaconda3\lib\site-packages\numpy\lib\npyio.py in loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin)
    858 
    859             # Convert each value according to its column and store
--> 860             items = [conv(val) for (conv, val) in zip(converters, vals)]
    861             # Then pack it according to the dtype's nesting
    862             items = pack_items(items, packing)

C:\home\Anaconda3\lib\site-packages\numpy\lib\npyio.py in <listcomp>(.0)
    858 
    859             # Convert each value according to its column and store
--> 860             items = [conv(val) for (conv, val) in zip(converters, vals)]
    861             # Then pack it according to the dtype's nesting
    862             items = pack_items(items, packing)

ValueError: could not convert string to float: b'5.0e-7,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0'

I couldn't find any documentation on how to make this work.

numpy version: 1.9.2 
python version: 3.4.3 |Anaconda 2.3.0 (32-bit)| (default, Mar  6 2015, 12:08:17) [MSC v.1600 32 bit (Intel)]

DSM · Accepted Answer · 2015-11-17 22:34:10Z

It's not scientific notation that's the problem; it's that the loadtxt default delimiter is any whitespace. You're reading a csv, so specify delimiter=",":

>>> np.loadtxt("cov.csv")
Traceback (most recent call last):
  File "<ipython-input-1-6fdfa7467ef5>", line 1, in <module>
    np.loadtxt("cov.csv")
  File "/usr/local/lib/python3.4/dist-packages/numpy/lib/npyio.py", line 928, in loadtxt
    items = [conv(val) for (conv, val) in zip(converters, vals)]
  File "/usr/local/lib/python3.4/dist-packages/numpy/lib/npyio.py", line 928, in <listcomp>
    items = [conv(val) for (conv, val) in zip(converters, vals)]
  File "/usr/local/lib/python3.4/dist-packages/numpy/lib/npyio.py", line 659, in floatconv
    return float(x)
ValueError: could not convert string to float: b'5.0e-7,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0'

>>> np.loadtxt("cov.csv", delimiter=",")
array([  5.00000000e-07,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00])

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