[SciPy-user] common storage between matlab and python
Tue May 6 11:46:28 CDT 2008
Have you considered mlabwrap (a scikits project)? It allows bridged
calls into the matlab runtime (bridging sclaars, strings, numpy
arrays, etc.; I don't remember if it bridges structs). Although it's,
in some ways, a half-way solution, it would allow the issue to remain
more transparent to matlab users at the expense of a bit of overhead
for the python users.
On Tue, May 6, 2008 at 1:42 AM, Roger Herikstad
> Thanks alot! I was looking at hdf5 as an alternative, and by your
> description I think it might suit my needs. I've been considering
> using PyTables for a while, but never had the initiative to do so, but
> I guess this is it... My one concern is to make this as invisible to
> pure matlab users as possible. For the time being, we are using both
> languages, and I was hoping there was a way for both python and matlab
> to coexist. I'll look into it.. Thanks again!
> ~ Roger
> On Tue, May 6, 2008 at 2:10 PM, Albert Strasheim <firstname.lastname@example.org> wrote:
> > Hello,
> > On Tue, May 6, 2008 at 5:26 AM, Roger Herikstad
> > <email@example.com> wrote:
> > > Hi list,
> > > Does anyone know of a matlab i/o interface beyond that of
> > > scipy.io.loadmat /savemat? I know these routines will handle scalars
> > > and vector, but what about matlab structures? My problem is that we
> > > have a substantial amount of code written in matlab that makes use of
> > > matlab's object oriented programming, storing the results of various
> > > calculations in objects. What I would like to do is to interface with
> > > these objects in python, that is read them from disk, do some
> > > calculations, and write them back in a format consistent with what the
> > > matlab object expects. So, for instance for the matlab object obj, the
> > > data is stored as obj.data.field1, obj.data.field2, etc. Is there a
> > > way for me to read the matlab file, do something to field1 and field2,
> > > in python, then store the modified fields back into the structure for
> > > matlab to read? Thanks!
> > If you don't find a solution specific to MATLAB, I'd recommend using HDF5.
> > Using HDF5 allows me to move my "objects" seamlessly between MATLAB,
> > Python and Java.
> > You'll have to write a bit of MATLAB code to take a struct and inspect
> > it using setfield, getfield and fieldnames, and then use hdf5write to
> > write it to disk.
> > obj might be stored in the HDF5 file obj.h5, with a "data" group, and
> > two datasets ("field1" and "field2").
> > Then you can load it up in PyTables, which should give you an
> > interface very similar to what you have in MATLAB. I think
> > obj.data.field1 might just work thanks to the magic that is PyTables
> > (where field1 could be a returned as a NumPy array).
> > Hope this helps.
> > Cheers,
> > Albert
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