[SciPy-user] Reading in data as arrays, quickly and easily?

Sebastian Haase haase at msg.ucsf.edu
Mon Jul 12 12:19:50 CDT 2004


On Saturday 10 July 2004 10:29 am, Eric Jonas wrote:
> > I assume you talk about Numeric, but in case you are open for numarray I
> > use numarray's memmap quite successfully on files even larger than 1 GB
> > (Linux; I think the effective limit for Windows might be lower ). It
> > works for all datatypes and for byteswapped data too. You can skip any
> > amount of bytes by having your mem-"slice" start at any offset you want.
> > I actually  map the first part into a record-array so that I can read the
> > parts of the "header"-information I'm interested in.
>
> Well, I had been focusing on numarray, because everything I read seems
> to suggest that it's the wave of the future, although at the same time
> no one really seems to be using it much yet. May I ask how much larger
> than 1 GB?  I'm dealing with between 1-20 GB EEG files, and for some
> reason I don't thinK I'll be able to afford 64-bit hardware in the near
> future : )

I'm also interested in maybe 20 GB (3D,time) image data. But that will require 
us to buy 64 hardware, I think. 
E.g. on (32bit) Linux the maximum address space for a user application is 2 GB 
- and I have been told to now expect much more than half of that being 
available for memmap. In other words, the largest file I was able to read was 
maybe about 1.3 GB.

>
> What I really want is to read in some fairly complex records, do endian
> swapping, alignment, etc. all in C. I'm mostly interested in spectral
> analysis, so the hope was that I'd be able to read in 32kB chunks at a
> time for my periodograms.
>
> Also, I looked through the numarray docs again, and still couldn't find
> anything about memory mapping -- any pointers? What command(s) have you
> been using to pull this off?

The the source code file '/numarray/Lib/memmap.py' contains 200 lines of 
comments/documentation just at the beginning of that file - I don't know why 
that didn't make it into the official documention.


Regards,
Sebastian Haase



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