[Numpy-discussion] How to start at line # x when using numpy.memmap

Jeremy Conlin jlconlin@gmail....
Fri Aug 19 10:09:26 CDT 2011


On Fri, Aug 19, 2011 at 8:01 AM, Brent Pedersen <bpederse@gmail.com> wrote:
> On Fri, Aug 19, 2011 at 7:29 AM, Jeremy Conlin <jlconlin@gmail.com> wrote:
>> On Fri, Aug 19, 2011 at 7:19 AM, Pauli Virtanen <pav@iki.fi> wrote:
>>> Fri, 19 Aug 2011 07:00:31 -0600, Jeremy Conlin wrote:
>>>> I would like to use numpy's memmap on some data files I have. The first
>>>> 12 or so lines of the files contain text (header information) and the
>>>> remainder has the numerical data. Is there a way I can tell memmap to
>>>> skip a specified number of lines instead of a number of bytes?
>>>
>>> First use standard Python I/O functions to determine the number of
>>> bytes to skip at the beginning and the number of data items. Then pass
>>> in `offset` and `shape` parameters to numpy.memmap.
>>
>> Thanks for that suggestion. However, I'm unfamiliar with the I/O
>> functions you are referring to. Can you point me to do the
>> documentation?
>>
>> Thanks again,
>> Jeremy
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>>
>
> this might get you started:
>
>
> import numpy as np
>
> # make some fake data with 12 header lines.
> with open('test.mm', 'w') as fhw:
>    print >> fhw, "\n".join('header' for i in range(12))
>    np.arange(100, dtype=np.uint).tofile(fhw)
>
> # use normal python io to determine of offset after 12 lines.
> with open('test.mm') as fhr:
>    for i in range(12): fhr.readline()
>    offset = fhr.tell()
>
> # use the offset in your call to np.memmap.
> a = np.memmap('test.mm', mode='r', dtype=np.uint, offset=offset)

Thanks, that looks good. I tried it, but it doesn't get the correct
data. I really don't understand what is going on. A simple code and
sample data is attached if anyone has a chance to look at it.

Thanks,
Jeremy
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