This file is to get you started using the PMI Toolbox. Additional (albeit still sketchy) documentation can be in the Doc directory of the toolbox, along with some sample code.
The toolbox source is available on-line at http://www.nmr.mgh.harvard.edu/~jstott/PMI/. Copies of the program documentation are available there as well.
After downloading the toolbox, unpack it to a convenient location (I
like either "~/matlab/PMI2" or with the other matlab
toolboxes). The PMI toolbox is distributed as a gzip-ed tar file. To
unpack it under Unix, type
gunzip -c PMI2.tgz | tar xvf -
which will create a PMI2 directory inside the current directory and
install the toolbox there.
Under Windows, use "WinZip" or one of its clones.
The actual location of the directory containing the toolbox is unimportant; the configuration described below handles all thte necessary details.
Under Unix systems, the time-domain forward problem and a small number of other key routines have been re-written in C for extra accuracy and efficiency (a parallel set of Matlab routines are also available, should you choose not to use the C routines). This code must be compiled before it can be used. The source code can be found in the "*/MEX" directories throughout the toolbox; there is a Makefile in each directory, as well as one in the root directory of the Toolbox. To build the compiled files, edit the compiler flags and the paths in the top-level Makefile to match your own system and type "make".
Note: the time-domain C code uses routines from the GNU Scientific Library (GSL) to handle the numerical integration. The GSL must be installed somewhere in your system for the PMI code to compile correctly.
Under Windows systems, I have not figured out how to get the GSL to build. Given a working copy of the GSL though, (check the URL above, there may be a pre-compiled version available by now), it should be straight-forward to build the time-domain MEX code under windows as well, although I have yet to verify this.
Before you can use the toolbox routines, you must tell Matlab where
to find them. This is done by calling pmipath (found inside the PMI
Toolbox directory), which sets up all the appropriate paths. pmipath
takes a single argument, which is the base directory of the toolbox.
On my computer, I type
% pmipath('/homes/monte/1/home/jstott/matlab/PMI2');
to configure the paths. Since this is rather cumbersome to type every
time, I recommend putting the call to pmipath in your startup.m file,
which will set up the path automatically every time you start Matlab.
You are now ready to begin using the PMI toolbox. Look in "PMI2/Doc" for additional sample code and toolbox documentation.