Hi All,
By way of introduction, I'm attempting to use Sage to document and
provide for easy use (via Sagenb) of my own Python codebase for
neuroscience data analysis, as well organise analysis and simulation
workflows using a few other Python and Matlab based neuroinformatics
tools. I'd like some general advice on the best strategies for
shuttling variables between Sage and Matlab (particularly from within
notebook cells using the Matlab interface), and some specific advice
on debugging the issue I describe below.
Prior to working with Sage, I used the scipy.io savemat function to
create .mat files, then switched over to Matlab to process them, and
then use loadmat to bring them back into Python. I'd like to use this
same strategy with Sage and make it fully automated, but I've run into
a problem passing a file name as a string into the Matlab "load"
function (the data import function). The way I started implementing it
is to pass the worksheet DATA directory path to my code and save
my .mat files there, then tell Matlab to load and process them, and
pull them back into Sage using loadmat.
In a notebook cell, manually putting the file path in works fine:
%matlab
load('/Users/myUserName/.sage/sage_notebook.sagenb/home/admin/9/data/
test1.mat')
doMyStuffInMatlab
However when I try this:
matlab("load('/Users/myUserName/.sage/sage_notebook.sagenb/home/admin/
9/data/test1.mat')")
or try to automate things by passing in strings like this:
matlab("load('%s')%PathToMatfileString)
The .mat file is not loaded and no Matlab error message is generated,
but a variable called sage0 of class 'Cell' that contains a string
'sage0' is generated in Matlab. Any suggestions on how to resolve
this? I've started digging into the matlab interface and expect
documentation, but any thoughts on where go from here would be greatly
appreciated.
For completeness... I'm running on Mac OS X 10.6.8, Matlab R2011A, and
Sage 4.7.2
Best,
Peter
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