[Numpy-discussion] convert csv file into recarray without pre-specifying dtypes and variable names
torgil.svensson at gmail.com
Thu Jul 19 06:30:25 EDT 2007
1. Your code is fast due to that you convert whole at once columns in
numpy. The first step with the lists is also very fast (python
implements lists as arrays). I like your version, I think it's as fast
as it gets in pure python and has to keep only two versions of the
data at once in memory (since the string versions can be garbage
If memory really is an issue, you have the nice "load_spec" version
and can always convert the files once by iterating over the file twice
like the attached script does.
4. Okay, that makes sense. I was confused by the fact that your
generated function had the same name as the builtin iter() operator.
On 7/19/07, Vincent Nijs <v-nijs at kellogg.northwestern.edu> wrote:
> Hi Torgil,
> 1. I got an email from Tim about this issue:
> "I finally got around to doing some more quantitative comparisons between
> your code and the more complicated version that I proposed. The idea behind
> my code was to minimize memory usage -- I figured that keeping the memory
> usage low would make up for any inefficiencies in the conversion process
> since it's been my experience that memory bandwidth dominates a lot of
> numeric problems as problem sized get reasonably large. I was mostly wrong.
> While it's true that for very large file sizes I can get my code to
> outperform yours, in most instances it lags behind. And the range where it
> does better is a fairly small range right before the machine dies with a
> memory error. So my conclusion is that the extra hoops my code goes through
> to avoid allocating extra memory isn't worth it for you to bother with."
> The approach in my code is simple and robust to most data issues I could
> come-up with. It actually will do an appropriate conversion if there are
> missing values or int's and float in the same column. It will select an
> appropriate string length as well. It may not be the most memory efficient
> setup but given Tim's comments it is a pretty decent solution for the types
> of data I have access to.
> 2. Fixed the spelling error :)
> 3. I guess that is the same thing. I am not very familiar with zip, izip,
> map etc. just yet :) Thanks for the tip!
> 4. I called the function generated using exec, iter(). I need that function
> to transform the data using the types provided by the user.
> On 7/18/07 7:57 PM, "Torgil Svensson" <torgil.svensson at gmail.com> wrote:
> > Nice,
> > I haven't gone through all details. That's a nice new "missing"
> > feature, maybe all instances where we can't find a conversion should
> > be "nan". A few comments:
> > 1. The "load_search" functions contains all memory/performance
> > overhead that we wanted to avoid with the fromiter function. Does this
> > mean that you no longer have large text-files that change sting
> > representation in the columns (aka "0" floats) ?
> > 2. ident=" "*4
> > This has the same spelling error as in my first compile try .. it was
> > meant to be "indent"
> > 3. types = list((i,j) for i, j in zip(varnm, types2))
> > Isn't this the same as "types = zip(varnm, types2)" ?
> > 4. return N.fromiter(iter(reader),dtype = types)
> > Isn't "reader" an iterator already? What does the "iter()" operator do
> > in this case?
> > Best regards,
> > //Torgil
> > On 7/18/07, Vincent Nijs <v-nijs at kellogg.northwestern.edu> wrote:
> >> I combined some of the very useful comments/code from Tim and Torgil
> >> came-up with the attached program to read csv files and convert the data
> >> into a recarray. I couldn't use all of their suggestions because,
> frankly, I
> >> didn't understand all of them :)
> >> The program use variable names if provided in the csv-file and can
> >> auto-detect data types. However, I also wanted to make it easy to
> >> data types and/or variables names if so desired. Examples are at the
> >> of the file. Comments are very welcome.
> >> Thanks,
> >> Vincent
> >> _______________________________________________
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> >> Numpy-discussion at scipy.org
> > _______________________________________________
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> > Numpy-discussion at scipy.org
> 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 at kellogg.northwestern.edu
> Skype: vincentnijs
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