Re: [Pytables-users] Pytables-users Digest, Vol 86, Issue 8

[Pushkar R. P. <top...@gm...>]

Both loadtxt and genfromtxt read the entire data into memory which is not
desirable. Is there a way to achieve streaming writes?

Thanks,
Pushkar


On Wed, Jul 17, 2013 at 7:04 PM, Pushkar Raj Pande <top...@gm...>wrote:

> Thanks Antonio and Anthony. I will give this a try.
>
> -Pushkar
>
>
> On Wed, Jul 17, 2013 at 2:59 PM, <
> pyt...@li...> wrote:
>
>> Date: Wed, 17 Jul 2013 16:59:16 -0500
>> From: Anthony Scopatz <sc...@gm...>
>> Subject: Re: [Pytables-users] Pytables bulk loading data
>> To: Discussion list for PyTables
>>         <pyt...@li...>
>> Message-ID:
>>         <
>> CAP...@ma...>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Pushkar,
>>
>> I agree with Antonio.  You should load your data with NumPy functions and
>> then write back out to PyTables.  This is the fastest way to do things.
>>
>> Be Well
>> Anthony
>>
>>
>> On Wed, Jul 17, 2013 at 2:12 PM, Antonio Valentino <
>> ant...@ti...> wrote:
>>
>> > Hi Pushkar,
>> >
>> > Il 17/07/2013 19:28, Pushkar Raj Pande ha scritto:
>> > > Hi all,
>> > >
>> > > I am trying to figure out the best way to bulk load data into
>> pytables.
>> > > This question may have been already answered but I couldn't find what
>> I
>> > was
>> > > looking for.
>> > >
>> > > The source data is in form of csv which may require parsing, type
>> > checking
>> > > and setting default values if it doesn't conform to the type of the
>> > column.
>> > > There are over 100 columns in a record. Doing this in a loop in python
>> > for
>> > > each row of the record is very slow compared to just fetching the rows
>> > from
>> > > one pytable file and writing it to another. Difference is almost a
>> factor
>> > > of ~50.
>> > >
>> > > I believe if I load the data using a C procedure that does the parsing
>> > and
>> > > builds the records to write in pytables I can get close to the speed
>> of
>> > > just copying and writing the rows from 1 pytable to another. But may
>> be
>> > > there is something simple and better that already exists. Can someone
>> > > please advise? But if it is a C procedure that I should write can
>> someone
>> > > point me to some examples or snippets that I can refer to put this
>> > together.
>> > >
>> > > Thanks,
>> > > Pushkar
>> > >
>> >
>> > numpy has some tools for loading data from csv files like loadtxt [1],
>> > genfromtxt [2] and other variants.
>> >
>> > Non of them is OK for you?
>> >
>> > [1]
>> >
>> >
>> http://docs.scipy.org/doc/numpy/reference/generated/numpy.loadtxt.html#numpy.loadtxt
>> > [2]
>> >
>> >
>> http://docs.scipy.org/doc/numpy/reference/generated/numpy.genfromtxt.html#numpy.genfromtxt
>> >
>> >
>> > cheers
>> >
>> > --
>> > Antonio Valentino
>> >
>> >
>> >
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