How to create a numpy 2d array from database with null values

Question

I'm trying to work with 2d arrays that can be accessed by column names using python. The data come from a database and it may have different types and null values. NoneType is not allowed in the tuples so I tried to replace them by np.nan.

This piece of code works if there are no null values in the database. However, my final goal is to have a masked array, but I cannot even create an array.

import MySQLdb
import numpy

connection = MySQLdb.connect(host=server, user=user, passwd=password, db=db)
cursor = connection.cursor()
cursor.execute(query)
results = list(cursor.fetchall())

dt = [('cig', int), ('u_CIG', 'S10'), ('e_ICO', float), ('VCO', int)]

for index_r, row in enumerate(results):
    newrow = list(row)
    for index_c, col in enumerate(newrow):
        if col is None:
            newrow[index_c] = numpy.nan
    results[index_r] = tuple(newrow)
 x = numpy.array(results, dtype=dt)

The resulting error is:

x = numpy.array(results, dtype=dtypes)
ValueError: cannot convert float NaN to integer

After performing fetchall, results contain something like:

[(10L,
'*',
Decimal('3.47'),
180L),
(27L,
' ',
Decimal('7.21'),
None)]

Any idea of how can I solve this problem? Thank you!

Fred Foo · Accepted Answer · 2013-10-03 11:45:37Z

2

There is no integer representation of NaN. You can either switch to floating point, or construct the mask while filling the array:

>>> values = [1, 2, None, 4]
>>> arr = np.empty(len(values), dtype=np.int64)
>>> mask = np.zeros(len(values), dtype=np.bool)
>>> for i, v in enumerate(values):
...     if v is None:
...         mask[i] = True
...     else:
...         arr[i] = v
...         
>>> np.ma.array(arr, mask=mask)
masked_array(data = [1 2 -- 4],
             mask = [False False  True False],
       fill_value = 999999)

answered Oct 3, 2013 at 11:45

Fred Foo

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2 Comments

tetrarquis Over a year ago

But the problem comes using tuples. If you define a list of tuples it throws exceptions: e.g. values = [(1, 2), (None, 4)] arr = np.empty(len(values), dtype=[('c1', np.int64),('c2', np.int64)])

Fred Foo Over a year ago

@tetrarquis: then use np.empty((len(values), len(values[0])). What I posted is just an example, you'll have to adapt it to your use case.

Jblasco · Accepted Answer · 2013-10-04 08:56:31Z

0

Working on Larsmans example, I think what you want would be:

    import numpy as np
    import numpy.ma as ma

    values = [('<', 2, 3.5, 'as', 6), (None, None, 6.888893, 'bb', 9),
              ('a', 66, 77, 'sdfasdf', 45)]
    nrows = len(values)

    arr = ma.zeros(nrows, dtype=[('c1', 'S1'),('c2', np.int), ('c3', np.float), 
                                 ('c4', 'S8'), ('c5', np.int)])

    for i, row in enumerate(values):
        for j, cell in enumerate(values[i]):
            if values[i][j] is None:
                arr.mask[i][j] = True
            else:
                arr.data[i][j] = cell

    print arr

answered Oct 4, 2013 at 8:56

Jblasco

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