RIPS (Rapid Identification of Points for SIMS) Tutorial
Example of sample surface image.
Introduction
This page provides access, and a short tutorial on how to use the
image registration software. The software was developed to make the
process of finding and identifying points to analyze in complicated
samples much quicker.
Quick, Simple Instructions
This is the simplest, step-by-step way to use this suit of programs
(also in the
'Overview'
section of the manual). There are more options (see the pod
attached with each file) and longer descriptions (see the manual) if
you have further questions.
Acquire images to map to SIMS stage.
Open up Inkscape and import images. Put every image in a separate
layer for each (if you have only one image, don't worry about the
layers). Leave Inkscape open.
Double click
on correlator.html and
fill that form out, while tagging those locations on your images
in Inkscape. Using the upper-left corner of rectangles, and make
certain that the tags are in the same layer as the image you are
tagging.
When finished, save your Inkscape file in the same (or sub-directory) as the perl files and close Inkscape.
Click on the 'Output .txt file' button in correlator.html . A
window will pop-up with your data. Save that window (unless you
are in IE, click File->Save As) as 'yoursamplename.txt' in the
same directory as the .svg file you just made.
Transfer the new .hpl file to the Sun workstation. Load the
file, double check the locations, and run your analysis.
Software and Documentation
Written software is as follows separately or all together:
correlator.html A
JavaScript-powered html page. It outputs a tabbed list that is used with
a .svg of tagged images by svg_generator.pl.
(version: 11/06/08 17:55)
run_quick.pl[pod]
which runs svg_generator.pl, fit_function.pl, and remove_rectangles.pl, and removes all the intermediate files.
(version: 11/06/08 19:42)
svg_generator.pl[pod]
This program takes an .svg with imported images that have been
tagged, and a .txt file from correlator.html and sets up a
nicely-formatted SVG file ready for fit_function.pl.
(version: 11/10/08 13:26)
startdialog.pl[pod]
This sets up an SVG file, which needs images to be added (and tagged) before it
is ready for fit_function.pl.
(version: 11/06/08 20:35)
fit_function.pl[pod]
which adjusts layers so points identified (by rectangles) fit on top of each
other. Requires the Perl module Math::MatrixReal (see below on setting up a version of Perl with this).
(version: 11/06/08 18:06)
remove_rectangles.pl[pod]
which removes all rectangle elements from a SVG file.
(version: 11/06/08 18:21)
svg2hpl.pl[pod] which
converts a SVG file to a holder file which the ims-1270 software
can read, and optionally a tab-delimited text file.
(version: 11/06/08 20:41)
txt2hpl.pl[pod]
which converts a tab-delimited text file into a holder file.
(version: 11/06/08 20:42)
hpl2txt.pl[pod]
which converts a holder file into a tab-delimited text file.
(version: 11/06/08 20:43)
A more manual-like documentation was written
in LaTeX
[PDF]
[html]
(LaTeX file version: 12/19/08 20:39).
Installation Requirements
In order to use these you must have:
A Perl interpreter and
Math::MatrixReal. If you are in Windows XP, the easiest way to get
Perl working is:
Copy
Math::MatrixReal into the
directory C:\Perl\site\lib\Math (file only works
with ActivePerl v.5.10).
An SVG editor that acts
like Inkscape. If you are
in Windows XP, here is a mirror
of Inkscape 0.46.
If you use correlator.html you need a browser with JavaScript
. It works best with Internet
Explorer. Firefox
and Opera work. Safari and
Google Chrome (as of testing) don't work so well.
If you plan on moving the .hpl file to the SUN, we suggest you use
a SCP program
to move it there.
Linux, Solaris,
Mac OS X have SCP programs accessible through the command-line. If
you use Windows, you can use WinSCP
(copy v.4.17 here).
Copyright Compliance for Binary Packages
Please note that Perl and Math::MatrixReal use
GPL v1.
Inkscape and WinSCP
use GPL v2.
See Also
These are links to files and books that are in the See Also section
of the Perl files but could not be linked from there.
