Allen J. Hall

Materials Science & Engineering, Productivity, and Life

Work

Latex Hint: Use your computer leverage to output large amounts of data.

After a few weeks of doing cryogenic cathodoluminescence spectroscopy on some of my samples, I have gobs and gobs of spectra to look over, and the task is a bit daunting.  Oh sure, you can do so on the computer in many different ways, but often, I need to see my data on the page (old school) before I can really sort through it.  Sometimes even then there’s just too much of it and playing with the data in MatLab all together is critical.

Here’s what I came up with to help output my data very quickly into a printable document that included numerous graphs.  First, the primary goal of this quick method is to be quick- to get tons of graphics (of same proportions) into a doc for printing or perusing.  Second- it should be relatively minimal typing, if possible.  [We all know we can do it by hand 100x; while grad-student pay rate is low, there's gotta be a better way.]

1. Get a directory listing for all the items wanted to be included and dump this in a text file.  (ls *.pdf > filelist.tex)
2. Create a main.tex file which includes the code we’ll need to do this fast.  [You can reuse this file for other directories of graphics needed to be printed.]  My example uses the following:
\documentclass[%
,secnumarabic%
\usepackage[pdftex]{color,graphicx,rotating}
\setkeys{Gin}{width=0.85\columnwidth}

%Simple way to call images and add filenames to captions - for lots of data.
\newcommand{\dataimg}[1]{
\includegraphics[width=3in]{#1}
Filename: #1

}

\begin{document}
\title{CL Results\\
\textit{Internal document not for distribution.}}
\date{\today}
\author{Allen Hall}
\maketitle

\include{filenames}

\printfigures
\end{document}

The important code is the “\include{}” line and also the “\newcommand{\dataimg}…” section. This is what is going to do all the work for us.

3. Now, we need to take your filelist and add at the beginning of each line and end of each line the following:
\dataimg{

and at the end:

}

One way to do this simply is with a command line gawk command:


To see how this looks in compiled LaTeX output and another example, click “More”…

Filmetrics Rocks- iPod Touch 32g!!

Boston rocked: I’m writing this on a new iPod Touch! Filmetrics was running a drawing for those who brought samples to test! Big thankyou’s go out to Filmetrics and AVS. I will write more about the conference in a series of posts coming soon. I’m hoping everyone had a great week while I was gone.

AVS-Boston next week!

The society formerly known as the American Vacuum Society (AVS) is holding their international conference in Boston, MA next week! And I’ll be there! [Exciting!] If you are going to be there, drop me a line on the blog and we can snag a coffee or beer together.

The programs and cards sent out may have a familiar image!

My AFM image of the CuInSe2 Bicrystals I grow in our lab won second place in the Art-Zone competition last year! It was great fun! [Thanks goes to AVS for being a fantastic organization!]

Wish me luck with my talk!!

Part III: Matlab Function for Xpert XRD Reciprocal Space Mapping

A series of MATLAB functions will follow. Some of these “.m” files call each other, so ensure you have all of them before you start.

The purpose of this file is to load in all the .x00 files in a directory of Omega-Omega-2-Theta slices for reciprocal space mapping of a sample. “OmegAxis” determines the scale for the Omega axis (y) for reciprocal space mapping. [again, this is not yet in Q-space, that will come at a later date]

The first function loads data into your workspace for a directory of .x00 files that have a common base filename. The user needs to supply the first index number and last index number for loading the files. The program then attempts to load “filenameIndex.x00″ in a linear fashion for all .x00 files of that filename indexed in the cd’d directory. [Change directory to the working directory needed before starting this function.]

Part II: Matlab XRD- reciprocal space maps from XPert XRD files (.x00)

A series of MATLAB functions will follow. Some of these “.m” files call each other, so ensure you have all of them before you start.

The purpose of this file is to load in all the .x00 files in a directory of Omega-Omega-2-Theta slices for reciprocal space mapping of a sample. Please note that as of this writing, the data has not yet been converted to Q-space.

The first function loads data into your workspace for a directory of .x00 files that have a common base filename. The user needs to supply the first index number and last index number for loading the files. The program then attempts to load “filenameIndex.x00″ in a linear fashion for all .x00 files of that filename indexed in the cd’d directory. [Change directory to the working directory needed before starting this function.]

Intro to Multipart Post: Reciprocal Space Mapping (XRD) for XPert in MATLAB

There will be a number of posts following this one that will attempt to recreate reciprocal space mapping in MATLAB. The functions that will be posted in the coming days read in .x00 files from the Philips XPert XRD system and try to recreate the slices of Omega Omega-2Theta scans produced for reciprocal space mapping.

Currently I haven’t changed the data into Q-space, so they will be reported in Omega -v- Omega2Theta space.

An example call to the function is:

DisplayQSpace1('',9,184);

Example output of the function(s):

Part I: MATLAB Functions for Philips XPert XRD Files

I decided here and there to publish various MATLAB functions I’ve written for my own work. There’s just one caveat- each one of these is a serious work in progress. In fact, they may not progress much more than what is disclosed here since they get the job done for me.

But, I felt that this likely would help a few people who are trying to do the same type of thing, and I’d rather ease those who come after me, and give them a slight step ahead if possible.

For those of you with old version of the Philips XPert XRD software (specifically those who can’t output in XRDML files), I offer a crude import function for simple scans.

Painful to work with- Science Direct

One thing I find extremely helpful in my research, is the ability to download citations for articles my co-workers send. I like to import them into BibDesk and auto-file the journal articles by first-author. Unfortunately, not everyone has Bibtex export abilities. This isn’t too bad, as BibDesk imports most major citation files. One thing that I do abhorr, is when a major company decides not to offer a citation download option! Science Direct is the fellow who gets my wrath this evening. It’s so bad I’ve been looking for other companies who keep track of journals that have downloads for the ones that Science Direct publishes!

I wonder if you pay their absurd journal prices, if you get citation downloads…

For more on Absurd Journal pricing, see: Knuth and “Trapped…”

A Quick Introduction...

I'm a graduate student (PhD Candidate) at the University of Illinois at Urbana-Champaign.

I've studied and researched in two fields of Materials Science and Engineering (Polymers and Semiconductors). My interests are as diverse as my musical tastes and I usually have my hand in some crazy project during my free time.