[Numpy-discussion] convert csv file into recarray without pre-specifying dtypes and variable names

Vincent Nijs v-nijs@kellogg.northwestern....
Sun Jul 8 16:36:12 CDT 2007


Torgil,

The function seems to work well and is slightly faster than your previous
version (about 1/6th faster).

Yes, I do have columns that start with, what looks like, int's and then turn
out to be floats. Something like below (col6).

    data = [['col1', 'col2', 'col3', 'col4', 'col5', 'col6'],
            ['1','3','1/97','1.12','2.11','0'],
            ['1','2','3/97','1.21','3.12','0'],
            ['2','1','2/97','1.12','2.11','0'],
            ['2','2','4/97','1.33','2.26','1.23'],
            ['2','2','5/97','1.73','2.42','1.26']]

I think what your function assumes is that the 1st element will be the
appropriate type. That may not hold if you have missing values or 'mixed
types'.

Best,

Vincent


On 7/8/07 3:31 PM, "Torgil Svensson" <torgil.svensson@gmail.com> wrote:

> Hi
> 
> I stumble on these types of problems from time to time so I'm
> interested in efficient solutions myself.
> 
> Do you have a column which starts with something suitable for int on
> the first row (without decimal separator) but has decimals further
> down?
> 
> This will be little tricky to support. One solution could be to yield
> StopIteration, calculate new type-conversion-functions and start over
> iterating over both the old data and the rest of the iterator.
> 
> It'd be great if you could try the load_gen_iter.py I've attached to
> my response to Tim.
> 
> Best Regards,
> 
> //Torgil
> 
> On 7/8/07, Vincent Nijs <v-nijs@kellogg.northwestern.edu> wrote:
>> I am not (yet) very familiar with much of the functionality introduced in
>> your script Torgil (izip, imap, etc.), but I really appreciate you taking
>> the time to look at this!
>> 
>> The program stopped with the following error:
>> 
>>   File "load_iter.py", line 48, in <genexpr>
>>     convert_row=lambda r: tuple(fn(x) for fn,x in
>> izip(conversion_functions,r))
>> ValueError: invalid literal for int() with base 10: '2174.875'
>> 
>> A lot of the data I use can have a column with a set of int¹s (e.g., 0¹s),
>> but then the rest of that same column could be floats. I guess finding the
>> right conversion function is the tricky part. I was thinking about sampling
>> each, say, 10th obs to test which function to use. Not sure how that would
>> work however.
>> 
>> If I ignore the option of an int (i.e., everything is a float, date, or
>> string) then your script is about twice as fast as mine!!
>> 
>> Question: If you do ignore the int's initially, once the rec array is in
>> memory, would there be a quick way to check if the floats could pass as
>> int's? This may seem like a backwards approach but it might be 'safer' if
>> you really want to preserve the int's.
>> 
>> Thanks again!
>> 
>> Vincent
>> 
>> 
>> On 7/8/07 5:52 AM, "Torgil Svensson" <torgil.svensson@gmail.com> wrote:
>> 
>>> Given that both your script and the mlab version preloads the whole
>>> file before calling numpy constructor I'm curious how that compares in
>>> speed to using numpy's fromiter function on your data. Using fromiter
>>> should improve on memory usage (~50% ?).
>>> 
>>> The drawback is for string columns where we don't longer know the
>>> width of the largest item. I made it fall-back to "object" in this
>>> case.
>>> 
>>> Attached is a fromiter version of your script. Possible speedups could
>>> be done by trying different approaches to the "convert_row" function,
>>> for example using "zip" or "enumerate" instead of "izip".
>>> 
>>> Best Regards,
>>> 
>>> //Torgil
>>> 
>>> 
>>> On 7/8/07, Vincent Nijs <v-nijs@kellogg.northwestern.edu> wrote:
>>>> Thanks for the reference John! csv2rec is about 30% faster than my code on
>>>> the same data.
>>>> 
>>>> If I read the code in csv2rec correctly it converts the data as it is being
>>>> read using the csv modules. My setup reads in the whole dataset into an
>>>> array of strings and then converts the columns as appropriate.
>>>> 
>>>> Best,
>>>> 
>>>> Vincent
>>>> 
>>>> 
>>>> On 7/6/07 8:53 PM, "John Hunter" <jdh2358@gmail.com> wrote:
>>>> 
>>>>> On 7/6/07, Vincent Nijs <v-nijs@kellogg.northwestern.edu> wrote:
>>>>>> I wrote the attached (small) program to read in a text/csv file with
>>>>>> different data types and convert it into a recarray without having to
>>>>>> pre-specify the dtypes or variables names. I am just too lazy to type-in
>>>>>> stuff like that :) The supported types are int, float, dates, and
>>>>>> strings.
>>>>>> 
>>>>>> I works pretty well but it is not (yet) as fast as I would like so I was
>>>>>> wonder if any of the numpy experts on this list might have some
>>>>>> suggestion
>>>>>> on how to speed it up. I need to read 500MB-1GB files so speed is
>>>>>> important
>>>>>> for me.
>>>>> 
>>>>> In matplotlib.mlab svn, there is a function csv2rec that does the
>>>>> same.  You may want to compare implementations in case we can
>>>>> fruitfully cross pollinate them.  In the examples directy, there is an
>>>>> example script examples/loadrec.py
>>>>> _______________________________________________
>>>>> Numpy-discussion mailing list
>>>>> Numpy-discussion@scipy.org
>>>>> http://projects.scipy.org/mailman/listinfo/numpy-discussion
>>>>> 
>>>> 
>>>> 
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>> 
>> --
>> Vincent R. Nijs
>> Assistant Professor of Marketing
>> Kellogg School of Management, Northwestern University
>> 2001 Sheridan Road, Evanston, IL 60208-2001
>> Phone: +1-847-491-4574 Fax: +1-847-491-2498
>> E-mail: v-nijs@kellogg.northwestern.edu
>> Skype: vincentnijs
>> 
>> 
>> 
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-- 
Vincent R. Nijs
Assistant Professor of Marketing
Kellogg School of Management, Northwestern University
2001 Sheridan Road, Evanston, IL 60208-2001
Phone: +1-847-491-4574 Fax: +1-847-491-2498
E-mail: v-nijs@kellogg.northwestern.edu
Skype: vincentnijs





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