Introduction

This is the July 8, 2008 version of a manual for using the programs stack_analyze and pca_gui for analysis of spectromicroscopy data. The latter program uses Principal Component Analysis (PCA) and cluster analysis, as well as singular value decomposition for calculating image thicknesses based on known spectra. The ideas behind stack_analyze are described in one paper [1], and the program was written by Chris Jacobsen. The ideas behind pca_gui are described in another paper [2] with angle distance measurements added in a second paper [3]; the program was written by M. Lerotic and C. Jacobsen.

This manual describes normal operation of the programs. However, it does not describe the additional features of pca_gui that are available in the ``expert'' mode. To execute the program in ``expert'' mode, type

IDL> pca_gui,/expert

Both programs are available in pre-compiled versions that can be run under the IDL virtual machine. To use these, you must first install IDL from the Research Systems, Inc. web site. You can then download the programs stack_analyze and pca_gui and double-click on them to run them.