This directory contains my R packages for interferogram analysis and related tasks

This directory contains my R packages for interferogram analysis and related tasks. Windows binaries are named pkgname_x.x.x.zip. Source packages are provided as both .zip and tar.gz files. The unpacked copies are identical. The main package is zernike. The package lppuw implements some linear programming model algorithms for phase unwrapping and is strictly optional.

This version of zernike contains two PSI analysis demos. For users interested in running them here are step by step instructions for getting started in Windows. If you happen to be a Linux user the process is similar, except you will have to locate a suitable binary in rpm form or build R and the required supplemental packages from source.

1) You need R, version 2.6.0 or later and the optional supplemantal package rgl. If you don't already have R go to http://www.r-project.org and click on the CRAN link to find a download mirror. Download the windows binary of the R setup program. You can also download a windows binary of the supplemental package there, or you can install it later. If you download now, save it in a convenient place and don't unzip it.

2) Download the windows binary of zernike from this directory.

3)Install R and let it put a shortcut on the desktop. If you want to create a folder to store R data files edit the shortcut's properties to point to it.

4) Start R. If you didn't download rgl you can do so now by selecting the menu item "Packages, Install Packages...". Pick a download mirror if prompted, and select rgl from the list of available packages. If you did already download rgl use the menu item "Packages, Install package(s) from local zip files..." and browse to wherever you saved them to install. You'll also use this dialog to install zernike_x.x.x.zip.

5) It's optional but a good idea to turn off output buffering. Select the menu item Misc and uncheck Buffered Output.

6) In the R console window the prompt is "> " with an unblinking cursor. That's where you enter the following command to run the first demo:

demo(psiest, package=”zernike”)

Also included is a “sliding window” demonstration analysis of sets of 6 frames from the 12 frame, 2 cycle sequence of PSI data. To run it type:

demo(winfit, package=”zernike”)

7) That's it! The demos are fully automated and once started run without user intervention, although you may be prompted to hit ENTER to display graphs.

8) You can exit R by typing q(). Save the workspace or not when prompted.

PSI data are courtesy of Vladimir Galogaza. Steve Koehler provided valuable programming advice. Basic image file I/O was adapted from code in package “biOps” developed by Matias Bordes and Walter Alini.