I had the pleasure of briefly meeting and listening to Dr. Gregg Zank (CTO- Dow Corning) this evening.  Some very interesting work going on at Dow Corning!  In particular, his discussion of a waterless powdered shampoo product for third world countries was quite amazing.  It’s wonderful to imagine a waterless shampoo, let alone one that is distributed as a dry product in single use packets!  Very interesting. It reminded me of another interesting humanitarian project that I’ve talked about before…

That attention to the developing world, and changing lives right now reminded me of my old post about Prof. Silver’s adaptive lenses.  I think that one of the greatest things that scientists can do is to positively influence lives.  We are in a unique position to do so in very large ways [think about all the amazing inventions you've used today alone].  It means so much when it enables others to benefit themselves also, by improving education, working hours of the day, personal and family health.  Remembering the fluid that Prof. Silver’s adaptive lenses use, I realized that this may also be a Dow Corning product, and I was correct!  Dow Corning has now partnered with The Center For Vision in the Developing World!  Fantastic news, and great to hear a company like Dow Corning is involved in such a great project!  Here is the project webpage: Child Vision and their press-release: Child Vision Partners with Dow Corning.  Their goal is to make smaller lighter adaptive glasses that can be used by young children to help their education.

So, my hat is off to Dow Corning this evening, for helping to improve the lives of others around the world.

Essentially you enter the vectors for the two planes of interest, then hit calculate, and all the unique angle solutions for the crystal space you chose (one gui for each crystal space right now- no interest in complicating it by combining at this time) gets output in the command window.

I populate some orientation matrices based upon the vectors you give. Then, from matrix calculations, using tetragonal and crystal symmetry operations, we determine all the symmetric orientations. Then, a simple subspace() command gives us the angles of greatest rise (dihedral angle) between the symmetric orientations. The calculations for these operations can be found in my Thesis (if it ever gets published), but can also be found in: V. Randle and O. Engler. Texture Analysis: Macrotexture, Microtexture & Orientation Mapping. CRC Press, 2000.

Please note- it’s your job to check if these are correct, I make no warranties about this stuff. It should work, but feel free to go in and edit everything to your liking. If you use my code, don’t worry too much about citing me (if you do, I appreciate it, but I often leave out others who have contributed also).

These are very simple, but hopefully they’ll help a bit for those working in cubic and tetragonal spaces.

Here’s the cubic symmetry angle calculator:
Vector Angle Calculator Cubic Symmetries

Here’s the tetragonal symmetry angle calculator:
Vector Angle Calculator Tetragonal Symmetries

I hope they work for you- please let me know if you have problems, if I have time I’ll try and help.

I do do manual backups, and in particular have a drive mirrored using rsync in osX so that it’s bootable (old computers and poor grad-students tend to make for older hard-drives). However, I wanted something a bit faster and easier to use. I wanted an automatic (or semiautomatic) backup of critical writings or data.

After digging here and there and playing around over the past of the past few weeks, I’ve figured it out. Since I didn’t see a very good writeup about how to accomplish this, I thought I’d share what I’ve done.

The first key is how to launch something when a USBkey is mounted in OsX 10.5.x+. To accomplish this, I setup a launch daemon process by editing the proper plist for launchd. However, shortly after the manual edit, I found Lignon, which is a great little GUI for the launchd processes, and I suggest you use it instead. The older (and free) 2.1.1 worked just fine for me [sourceforge] and a newer version is available on the Mac App store. [Feel free to edit the plist if you know what you're doing, the GUI does just that.]

If you are making your own plist, save it to something easily identifiable in your user account Library under LaunchAgents (~/Library/LaunchAgents):

In Lingon (at least the old version) this will look something like this:

If you look carefully, you’ll notice that this launch agent will launch at any drive mounting. When it does, it will attempt to execute a script (in this case named “AutoWorkBackup.sh”). A little trick I’ve used to only launch on the proper drive mount, is to save the script on the actual drive. So, the launch agent will launch the script, if it successfully mounts the usbkey. It’s a little fail-safe in case of a similarly labeled drive is mounted. However, it is worth noting at this point, that the script will successfully launch on any other drive also mounting (with the backup key currently mounted). If I have time (probably won’t) I may look into possible solutions for this. The only problem I’ve found running the script in this manner is that it appears the launch agent is paused and relaunched after 10seconds if the usbkey mount is slow. Launchd appears a bit fast on the draw for the drive mount process.

Finally, we need the script to do the actual dirty work. I use a mix of bash script and applescript to get the job done. I originally only used a bash script and auto-launching rsyncing. It worked quite well, but left me afraid to mount or unmount the key. So, I decided a user dialog would be better. However, I’m tempted to go back to the automatic method as it really was quite fast and I only mounted my key if I knew a backup was expected. In the interest of speed, I’ll assume you can chop out code in the bash script to make your own automatic rsyncing like my first successful script.

Here’s the code I use that launches an applescript dialog asking if a backup is wanted:

#!/bin/bash
/sw/bin/growlnotify -I /Users/allenhall/ShellScripts/LaCieKey.icns -t "Backup USB Key" -m "Backup Key Detected."
x=`/usr/bin/osascript <<EOT
tell application "Finder"
activate
display dialog "Would you like to start a backup?" buttons {"Backup", "No"} default button "Backup" giving up after 15
set myReply to button returned of result as text
end tell
EOT`
# the previous wraps a dialog inside a Finder tell clause to allow for user interaction - the result is returned as text
# test if we got the result properly
# echo $x
# note- trick to prevent error thrown- wrap $x in "" for the conditional
if [ "$x" = 'Backup' ]
then
# test for if statement
# echo 'I will back up!'
# Notify us that we are starting backups
/sw/bin/growlnotify -s -I /Users/allenhall/ShellScripts/LaCieKey.icns -t "Backup USB Key" -m "RSYNC Backup Has Begun."
# actual backup script
/sw/bin/rsync -r -X -A -a -S -v -x -p --exclude-from=/Users/allenhall/backup_excludes.txt $* /Users/allenhall/TEXWork /Volumes/AHallThesisBackup/
# notify us that we completed our backups
/sw/bin/growlnotify -s -I /Users/allenhall/ShellScripts/LaCieKey.icns -t "Backup USB Key" -m "RSYNC Backup Is Complete."
fi


The above script uses a trick to “tell application Finder” to display a dialog. This enables user interaction via an applescript code in a shell script. Useful little trick. Note the above shell script also uses growlnotify the command line part of Growl for notifying the user of tasks started and completed. I’m sorry the code is a bit jumbled above- looks like I’ll have to look for a code plugin for WordPress! Here is the code as ascii text: AutoWorkBackup. Please note that you can also add extra folders in the “actual backup script” portion – just watch the rules of rsync when you do. Of course all the above has to be changed to match your computer and your important folders, etc. [I assume you aren't dorking with launch agents and rsync without knowing a bit about it- or at least won't hold me responsible. ]

I hope you find this useful! Drop me a line if you end up using it, or if you’ve made some cute and useful changes! Here’s wishing you a healthy, productive, and prosperous new 2011!

The code I use utilizes the excellent XRDMLread.m function (available at this link) and then uses the meshgrid and regrid functions to translate the data into a standard gridded data in reciprocal space. Since I’m regridding the data, there is the unavoidable need to interpolate data to find representative signal levels at new coordinate points. So, it’s important to remember this with my code. Likely the Xpert Epitaxy software also does this when it reports contour lines at various levels.

There is more work to be done with my code, however. In particular, I’m stepping the meshgrid by “1″ degree, which may not be an appropriate data-density depending on the full scale of your scan. [i.e., it might be too much, or too little.] So, I need to run a simple set of code to run a fixed number of data points per scan-range, allowing the data-density to stay the same irregardless of the data-range. I also need to improve the 3D image plotting, as MATLAB does some strange z-axis scaling while plotting in 3D. I suspect the aspect command will solve the problem for me and allow camera moves without re-scaling the axes. Worst case scenario, I’ll take the data into OpenDX (DXHDF5) and use rubber-sheet and camera commands to get a better three-dimensional image than MATLAB can provide.

So, for now, because of the data-density problem, and not having the code in a form to release (properly commented and code-snippets referenced), I’m going to ask that you contact me via the contact page for a copy of the current set of m-files for the RLM scans if you need them. I’ll happily send them off with some caveats about their short-comings.

Here are some example plots capable with the simple m-files. Note that the data below is plotted with Log(Intensity) scale to show low-intensity nuances in the data.

I guess I should explain the above a little bit. If you need more info on how x-ray diffraction works, check here: [Xray Diffraction (XRD)] In my present work, I work with bicrystalline GaAs and epitaxially grown copper indium diselenide. In the xrd micrographs above, there are two primary diffraction spots. The first, which is fairly sharp and localized (high intensity) is the GaAs substrate peak. The second, the more diffuse, is my thin-film CIGS peak. The distance between them, as well as the projections of the distance in both Qx and Qy give us information regarding d-spacing difference and in-plane and out-of-plane strains. The spreads of peaks give us information regarding crystal quality, or rather, local crystal variations (which may be due to numerous reasons including stoichiometric changes). For those of you a bit familiar with XRD, for some of the pictures above, a rocking curve would give you the side-to-side breadth of the peak and the omega-2theta scans would give you your standard broad film peak along with the sharp lorentzian like reflection of the substrate peak. However, doing simple 2d line scans, you miss a lot of information regarding the peak shape in reciprocal space, which may be important to how your film is grown and what residual stresses or variations of crystal structure exist in your film.

As a kid I always hated the horrible yellow number 2. It was hard to carry in my back-pack without the point breaking, couldn’t be carried in any pockets without fear of lack of future off-spring, and sharp for only a small instance of time (delta-t before writing). So, I was the insane geek with numerous mechanical pencils to my name. The mechanical pencil mostly solved the carry problem (point didn’t break- or rather was always breaking to the same size) as well as the sharpness issue (always was a 0.5mm man myself). And only in the last few instances of the Staedler I had did I have a truly retractable point mechanical pencil worthy of safe-pocket use.

Enter the brilliant mind of the Faber-Castell engineers. They realized all three of these problems and solved them (and then some) with their Perfect Pencil line. I don’t know the history of the perfect pencil, but I know when I saw the nice shiney one I was enthralled (until I saw the price-tag, and about had a heart-attack). Someone pointed me towards the cheaper plastic FC 9000 perfect pencil. Thank goodness they did! I need to buy a handful so I’m never without, because I’m now hooked.

The perfect pencil consists of a slightly shorter FC-9000 B hardness pencil with a plastic add-on piece. The plastic piece acts as all the following: 1) pencil extender (for when the pencil gets dinky- I’ve gone almost all the way to the eraser end), 2) Shirt-pocket clip, 3) point protector, 4) Sharpener (inside!!)

So, not only did they solve the point breaking, point jabbing sensitive man-parts, and lack of pencil clip, they added to that the ability to have a sharp tip anytime you want, as well as using more of the pencil itself.

I’ll have to post some pictures of how mine’s held up over this year’s use! It’s looking great still with almost every-day carry (and knocking around in the bag). Best yet, it’s light, good looking, and cheap! (For the Ramen and peanut-butter eating grad-students!) Big cheers, Faber-Castell! Please don’t stop producing this one anytime soon!

Here’s a link to Faber-Castell’s webstore where you can buy your own. (They’re somewhat hard to find online, and even insanely harder to find locally.) – Buy from Faber-Castell [Price is $10 at time of writing, and $6 for 3 more 9000 pencils with erasers (shorter for less awkward initial use with the perfect-pencil cap.]

There are two other products likely also excellent. One is a perfect pencil that was Porsche Designed (approximately $45 at time of writing) and the other is the absolutely gorgeous Graf von Faber-Castell Perfect Pencil which will set you back $250 for the platinum coated and $395 for the solid-silver (and no, I didn’t confuse a decimal place). [Let's hope those links worked as it's very difficult to find some of those on the FC website- especially the FC 9000 Perfect Pencil.]

One of the first research programs I worked on as an undergraduate was taking large amounts of data from an HPGC running a fixed-bed reactor. There were many problems with the work: (1) since our filter materials were very good at filtering the chemicals used, the run-times to breakthrough were very long (which meant that I had to come into the lab every 4 hours and restart the machine), (2) even with the lowest data setting, we had gobs and gobs of data (gigabytes in a day we were used to kilobytes of data), and (3) the data was saved in the form of: A 1 B 2 C3 (return) D4 E5 F6 (return). To the rescue was a friend of mine, Nicolas, who was an excellent coder. He turned me onto AWK and it worked beautifully. The code he came up with is more complex than the following, and I’ve misplaced the old code, so for now, let’s deal with a simple case…

Let’s say you have too much data (you set the machine wrong, or you can’t set the machine properly), and you don’t care about throwing away the data, as the trends you want to see aren’t on the order of the data you wish to pitch. If you have thousands of data-points and you only need say every 5th line, or every other line- do you really put it in Excel and edit it manually? If so, you shouldn’t get a pay-raise next quarter- you can save crap tons of time by using the right tools.

Enter Awk – a great command-line program available on almost every linux/unix computer (maybe yours is called Gawk). [A huge book on how to use all the aspects of awk is available here: The Gnu Awk User's Guide.]

With a single one-liner of code in the terminal, you can accomplish your goal of reducing your data. My pal Brandon wanted to keep only every 5th line from his data:

cat "$@" | awk -F, '{if (count++%5==0) print $0;}' >~/Desktop/AwkOutput5thLines.txt

This is the code I used within Automator to accomplish his data-throw-away needs. (there was an error with line-endings I fix later on down in this post…) cat “$@” uses the output of the choose-file automator task (as argument) to feed the file to the awk command (in -F mode for piping). The count++ command is doing the dirty work. Hat-tip to Duane’s Brain blog for the awk portion of the code which does the dirty work here! Details of how to pass strings as arguments came from this great post on MacOsXHints.com.

Another frequent problem is throwing away every other line. Here’s the code to pitch every 2nd line:
cat "$@" | awk -F, 'NR % 2 == 1' > ~/Desktop/AwkOutput.txt

One of the errors my pal had with his data was the line-endings. So, note that awk requires linefeeds (unix format text) in order to accomplish it’s goals. A simple way to translate is to use tr (translate text) the line-endings into things unix understands.

So, I solved the text line-ending problems by adding the following code:
tr '\r' '\n'
making the final code appear like this (within automator) (all in one line):
cat "$@" | tr '\r' '\n' | awk -F, '{if (count++%5==0) print $0;}' >~/Desktop/AwkOutput5thLines.txt

Some more great awk links you may find useful:

• Awk Examples
• Famous Awk One Liners Explained

Finally, to give you a few presents for dropping in to read this meager blog, here’s a finished Automator script as well as an application form of the script in case you need exactly every 5th line like my pal, Brandon.

• Keep Every 5th Line Of My Data (ZIP file)
• Keep Every 5th Line Of My Data With Encoding (ZIP file)
• Throw Away Every Other Line (ZIP file)

Working a bit with my old q-space map code, I’m able to accomplish the following:

Note the strange love-handles the data gains. I suspect this might be due to the Gridfit function (see MATLAB files repository) I used for regridding the data. Gridfit.m uses an extrapolant method. My suspicion is it is trying to fill out the square of the data matrix and is accomplishing relatively correct values for near-by-data that is outside the scanned range. I’ll try it again with regrid or something similar in the future when I have time.

If anyone knows where the current site for XRDMLread.m is, I’d love to link to it. It appears the site may be down (graduated student I suspect). You can obtain the wonderful XRDMLread.m function and examples on the XRDMLread.m website. For now, I have to wait until I hear from the authors before I can share the file. I also don’t yet trust my icky 3D code, so I prefer not to release that until I have things hashed out. Sorry!

I’m extremely happy that Panalytical has published their XRDML file format and that the makers of XRDML.m have released their .m files for MATLAB. In the past, when Philips had the Xpert systems, the data was stuck for the most part in proprietary data formats. [You could slice the data and output in ascii- but making that work was a pain- which is why I never released that previous code.] I’m much closer to the 3d plotting now, and hope to finish it up before the thesis (my primary work which is not this plotting) is published.

Wishing you luck in you research!

I have to admit as a scientist I love to see graceful solutions to any problem. Prof. Josh Silver at the University of Oxford has come up with just such a brilliant simple solution that any scientist who understands index of refraction will say: “Ahhh… yes!” about. Prof. Silver has made plastic glasses with adaptive lenses for third world countries. In third world countries to get glasses right now you have to either already know (by magic) your prescription, or try and somehow happen across an optometrist (and you thought it was just about affording a roof over your head!). Unfortunately, optometrists don’t grow on trees in third world countries, and so you’re pretty much out of luck.

Enter the “dial a prescription” solution of Prof. Josh Silver’s. With his glasses you simply turn a few dials which push plungers in or out of a syringe attached to each lens. These syringes hold a fluid which has the same index of refraction as a polymer film which flexes under pressure (positive and negative pressure). This pressure of course will bow out or bow in the surface of the “lens” (which is fixed on the edges to a certain thickness). How to know your prescription? Simple- is it clearer or not? [Much like the old A or B, A or B, A or B, 1 or 2, 1 or 2 hassle we all go through at the optometrist's office- but cut out all that binary testing... just dial it in or out- bam, there's your prescription- in fact, it's fractions of diopters even- so it's much more analog than the current system.] Pure brilliance. Such a simple problem to a complex issue.

The impact to those who can’t see? Huge! I suggest it’s almost as huge as teaching someone how to farm. People are illiterate because they can’t see things clearly enough to learn how to read or write. Prof. Silver’s solution has the possibility of changing all of that.

So, my hat is off to him as a scientist- excellent work, and much needed work!!

Here are some links to the adaptive lenses:

• Guardian: Inventor’s 2020 vision: to help 1bn of the world’s poorest see better
• Prof. Josh Silver’s Organization: Center For Vision In The Developing World

And here are some talks that highlight these new adjustable lens glasses:

If you’ve been moved by this simple idea, consider sending a donation to them to help support vision for those around the developing world: Donate.

Well, here’s the fix… it turns out that Leopard uses launchd to set the display. So, the old method of launching MATLAB was to set the display to 0.0, but this will fail after the first instance, hence the bug. What you can do is simply remove this line from the startup script in matlab (located within the startup application contents).

The line that was:

$SHELL -c 'bin/'$ARCH'/setsid bin/matlab -desktop -display :0.0 &'

should now be:
$SHELL -c 'bin/'$ARCH'/setsid bin/matlab -desktop &'

Once I changed that, everything started up fine!

ps- you will know you have this problem if you look at your console log immediately after launching MATLAB and it says something like:
6/29/10 9:03:34 AM [0x0-0x78078].StartMATLAB[23469] Warning: Unable to open display :0.0, MATLAB is starting without a display.

Speaking of our own struggles, what most of the public often does not get a feel for is the absolute devotion, almost to insanity, towards finding the solutions we are looking for. Many of the comments by the graduate’s spouses touched home for me. In each of the graduates followed in this film I saw bits of myself. One thing however, that is different, is the struggle for the specific protein structure. Often that struggle is a lot less well-defined. In this situation, you either get the structure of AMPK or you don’t. I guess it’s a lot like their attempts at creating crystals. Sure, you get crystals, but if they don’t have a periodic structure, you’ll never get diffraction. In my situation, the variables in our studies are very difficult to control, and so often one doubts one’s work solely on the question of reproducibility. Many scientists struggle with this same situation. People think that doing things like “measuring temperature” is a very easy thing. In reality, it is a very very difficult thing. Especially in a vacuum. That question just arose the other day in discussing our science with a new undergraduate assistant. As we talked more and more on the difficulties of measuring temperature we all saw his eyes grow larger in wonder. The simplest of problems can often be the most difficult. How accurate do you need to measure it? What standard will you use? Do you believe your thermocouple, your thermometer, or your pyrometer? What if the emissivity of the surface changes?

This is the life of a scientist. And the film below attempts to capture the lives and struggles of a few graduate students who are hoping for a career in science. It’s a struggle. But, you have heard me say that enough. To learn more about it I strongly suggest you watch this film. For the graduate student, I warn you: you’ll see yourself in this. For those who aren’t scientists: this may end up being a comedy, and I kindly refer you to Marg Simpson’s commentary on graduate students posted earlier in this blog.

My congratulations to Thirteen for doing such an excellent job on this one hour film. They didn’t have a lot of time to share with you everything regarding our struggles and achievements, but they distilled it quite well in the time available.