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

Torgil Svensson torgil.svensson@gmail....
Sun Jul 8 15:31:41 CDT 2007


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
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> >>
> >>
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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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