[SciPy-User] loading mat file in scipy

Robin robince@gmail....
Tue Oct 20 11:25:07 CDT 2009


I think these kind of heavily nested structures are just very slow to
load with scipy.io.loadmat.

I noticed this previously with a similarly structured file (but this
is only 1MB so much more convenient for testing) which I provided.

http://www.robince.net/robince/structs_cells.mat
http://mail.scipy.org/pipermail/scipy-user/2009-April/020860.html

Make sure you are using a recent version of scipy. I think there was
some performance fixes that improved it - with current scipy SVN on a
macbook pro structs_cells.mat takes about 28s to load
(structs_as_record doesn't seem to make a difference). This is already
some improvement (40s in April, 4 minutes prior to that). On Matlab it
takes about 1.4s.

Cheers

Robin

On Tue, Oct 20, 2009 at 4:35 PM, Robert Kern <robert.kern@gmail.com> wrote:
> On Tue, Oct 20, 2009 at 10:33, Alireza Alemi-Neissi <alemi@sissa.it> wrote:
>> Dear All,
>>
>> I do not know if it is the right place to ask this question. If not,
>> please let me know where I can post it.
>> This the problem:
>>
>> I have recently tried to use scipy.io.loadmat() to load a mat file to
>> python.
>> The mat file is a complicated nested structure in matlab. It turned out
>> that it takes a long time (around 5 min) to load this data the size of
>> which is around 120MB.
>> On the other hand it take only a couple of seconds to load it in Matlab.
>> What is wrong with loadmat in scipy?
>
> Without seeing the file, I have no idea.
>
> --
> Robert Kern
>
> "I have come to believe that the whole world is an enigma, a harmless
> enigma that is made terrible by our own mad attempt to interpret it as
> though it had an underlying truth."
>  -- Umberto Eco
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