Spirals
by mikez0r on Mar.01, 2010, under Uncategorized
Some interesting maths from working on the dissertation. Yes, maths. I have to get used to the Queen’s proper manner of speech.
I study a material that is readily exfoliated into sheets. The sides of each sheet are not the same. This dissimilarity causes the sheet to roll up. You might be wanting a figure right about now. Me too. The sheet structure is easy – that’s just a matter of getting the crystal structure from some published source (e.g. ICSD). But how to turn this into a scroll? I tried Illustrator’s spiral tool to create a path, but got lazy trying to re-create the brush that would represent the structure. Plus, a friend noticed that when the diamond patterns get too close to one another, illustrator puts white space between them (makes one or both of them thinner). That won’t do for representations of reality!
So, I turned to the dark, non-artistic side: maths. You can draw a spiral pretty easily using polar coordinates. Check it out: if you have a line of length X, you can make a spiral by setting 2 things:
radius = x+inner radius of spiral
theta(angle) = some range of angles – how many times you want the spiral to make a complete circle.
In python with numpy and matplotlib:
import numpy as np
import matplotlib.pyplot as plt
r=numpy.arange(0,10,0.001)
theta=numpy.arange(0,4*numpy.pi,4*numpy.pi/len(r)
plt.polar(theta,r)
and you get
2 circles, no offset from 0.
Well, cool, but I need the spacing between layers to be some well-defined value. You can play with starting radii and/or number of times around the circle (and I did, before I got tired of it). Mathematically, you can set the either of these, and determine the other based on the spacing you want.
Spacing = length of line / number of times around.
So, when I want a spiral with 5 unit spacing, and I start with an initial radius of 100, I get 20 spins around the circle:
And you want Cartesian coordinates, because what good molecular modeling software recognizes polar coordinates? The nearest plot already shows this, but here’s how I got them. See how bumpy my lines are? Those are atoms! OOOO!
x=r*cos(theta)
y=r*sin(theta)
Basic geometry, I know, but I was proud of myself. Especially since I’ve been intending to figure this out for nearly a year and finally did it. And it only took me a day.
Dissertation writing tips: Latex and Mendeley
by mikez0r on Jan.18, 2010, under Nerd, Uncategorized
Some odd notes of potential usefulness as I stumble through dissertation writing:
- Proper figure numbering is accomplished by including the \label{} command inside the \caption{caption} command. Otherwise, it catches the section number…
- Mendeley is great for managing references. Set the web importer up as a bookmark in the bookmark toolbar. It can grab references from Google Scholar, Google books, and many others. I find that the direct grabs from a Google Scholar search are incomplete – where possible click the link through to the page with the abstract, and import the article from there.
- Store your articles with Mendeley’s web storage to keep them in sync across multiple computers. To start storing them, right click your “All Documents” collection, then “Edit settings” (Why isn’t there any reference to this in Mendeley’s program settings? I had a hell of a time finding this.)
- \ref and \cite are very different Latex commands. If a bibtex reference refuses to show up, you probably tried to cite it using \ref, rather than \cite. \ref is for references defined by \label.
And… my theme here apparently has a problem showing bulleted and numbered lists…
Get motivated!
by mikez0r on Dec.28, 2009, under Uncategorized
Sarah Palin is coming to Houston! Yippeee!
“Sarah Palin made history as the first woman ever to be elected Governor of Alaska, and the youngest person to ever hold that office.Her straightforward, no-nonsense approach to politics and life captivated the nation and jettisoned her new book to an instant mega-bestseller. ”
I think jettisoning her book is the only appropriate action for it, though I worry about overflowing landfills.
Courtesy of Answer.com, the definition of jettison:
verb
To let go or get rid of as being useless or defective, for example: discard, dispose of, dump, junk, scrap, throw away, throw out. Informal chuck, shuck (off). Slang ditch.
noun
The act of getting rid of something useless or used up: disposal, dumping, elimination, riddance.
jettison indeed.
Bomb Threats in Britain
by mikez0r on Dec.16, 2009, under Travels
Just in case you ever need to politely respond to one of these…
1. On receipt of a telephoned bomb threat:
(a) Try to be calm and courteous.
(b) If at all possible keep the caller talking, for example, by pretending difficulty in hearing, and repeat all the information you receive alound
2. Try to find out:
(a) Exactly where is the bomb?
(b) When will it go off?
(c) What does it look like?
(d) What organization do they represent or why are they making the threat?
(e) How does the bomb work?
(f) Where is the caller phoning from?
OS X 10.6 problems & fix
by mikez0r on Dec.16, 2009, under Uncategorized
Oh boy, was I seething at Apple after upgrading to 10.6. It seemed like just about everything broke. All of my Python development stuff went to hell in a handbasket (a stylish, well-designed handbasket). My 600$ (educational) copy of the Adobe CS3 Design pack would not even install. To boot, X11 did not work, so I couldn’t even use trusty old NXclient to remote desktop on my linux box.
I’m not sure why, but I didn’t bother searching for anyone with similar problems at the time. After going through the trouble to revert to 10.5, I did that search, and found all kinds of exactly similar problems, mostly caused by cruft from the old system. After a fresh OS X 10.6 install, things are in much better shape. Yes, there are other ways to clean up the cruft, but fresh installs feel so nice. CS3 still won’t install, but I can live with Inkscape and the GIMP.
Long story short: OS X is not the bulletproof OS that it is often advertised as, but it’s also not as bad as I thought.
Oh, one quirk:
Everyone mentions how much space 10.6 frees up on their hard drive. That’s nonsense. It may use a tiny bit less space, but the real “increase” in hard disk space comes because they switched to calling kilobytes 1000 bytes, rather than 1024 bytes (and MB are 1000 KB, and so forth). Because it divides the total number of bytes by an accordingly smaller number, you end up with a “bigger” hard drive. This has long been what the hard drive manufacturers do, but it’s awfully shady and very arbitrary for Apple to make that switch now.
OpenCV image registration
by mikez0r on Oct.13, 2009, under Uncategorized
This is more a note to self than anything else, but if you find it useful, hooray!
I’m trying to register images for school. There’s a neat trick to get rotation & scale roughly aligned, without doing any kind of brute forcing (which is really important, because my images can be any angle offset from one another). You take the log-polar transform of each image, and then cross-correlate the two transformed images. The distance from the center to the cross correlation maximum along the Y axis tells you the rotation, and the same on the X axis tells you the scale (on a logarithmic scale). The end result is that you can avoid the local alignment maxima associated with brute forcing, and save a whole lot of time in the process.
However, it doesn’t work perfectly for me yet. Here’s a few steps I’ve taken to improve it:
1. Pad the image that you’re going to match the template on.
Python with ctypes_opencv:
pad_img=ocv.cvCreateImage(ocv.cvSize(cropWidth*3,cropHeight*3),
expIPLimg.depth,expIPLimg.nChannels)
offset=ocv.cvPoint(cropWidth,cropHeight)
ocv.cvCopyMakeBorder(expLP, pad_img, offset,
ocv.IPL_BORDER_CONSTANT, ocv.cvAvg(expLP))
2. Do not cross-correlate the entire template to match. Instead, match only the central strip. There’s plenty of good stuff to match there, and you avoid the correlation penalties of having your template overlap with the padding. If you don’t do this, then the scale correction possible will be limited.
resultWidth = pad_img.width – refLP.width/2 + 1
resultHeight = pad_img.height – refLP.height + 1
result = ocv.cvCreateMat(resultHeight,resultWidth,ocv.CV_32F)
ocv.cvSetImageROI(refLP,ocv.cvRect(refLP.width/4,
0, refLP.width/2, refLP.height))
ocv.cvMatchTemplate(pad_img,refLP,result,ocv.CV_TM_CCOEFF_NORMED)
You smell like beer.
by mikez0r on Aug.24, 2009, under Uncategorized
Funny encounter today with some jailbait at the Woodstocks bar. Here’s how it went:
(2 young girls walk up next to me at the bar, and are wondering what the trinkets in the glass at the bar are)
Me: “those are bottle openers.”
Them: “you smell like beer.”
Me: “that’s because I’m drinking it.”
The real question, though, is how they know what beer smells like, but don’t know what a bottle opener looks like. Hmmmm….
How to annoy your TA/group elder
by mikez0r on Apr.21, 2009, under Uncategorized
1. Copy and paste answers from Wikipedia. Don’t bother paraphrasing them – leave them in their (somewhat) good English, so that they’re easy to pick up as plagiarized. Better yet, leave the blue text and active hyperlinks. Then justify it by saying the information was hard to find.
2. Treat your elder as the group secretary. He doesn’t get enough of this shit from the boss, and he looked lonely. Ask him to find you a desk, or better yet, make space for you.
3. Declare that it’s the TA’s fault that you don’t have a good sample to work with for lab. Demand that he provide a better one for next time. Ignore that other classmates got good results from the same sample, just a different region.
4. Do all of the above with charming enthusiasm and smiley faces.
Garlic
by mikez0r on Mar.19, 2009, under Uncategorized
On the suggestion of one of my new co-op friends, I tried eating a raw garlic clove to try to nip my cold in the bud. My body was unhappy with me the first time, and downright refused the second. I think I’ll stick to vitamins and horrible-tasting cough syrup.
In other news, I passed my qualifying exam. I’m now a dissertation away from being a mad doctor. Excitement abounds.
Fixed width string formatting in python
by mikez0r on Feb.25, 2009, under Nerd, Uncategorized
I wanted to make a nice, pretty text file from some log info, but python didn’t want to cooperate with string formatting.
I was trying something like this:
f=open(‘file’,'w’)
f.write(‘%-10s’ %string)
At the interactive prompt, the equivalent print command would give the desired result.
I got it to work by replacing f.write() with
print >> f, mystring.ljust(10)
This code has the same net result of printing to the file, but it actually does the spacing properly.
This thread gave me the hint I needed, though it looks like the poor guy never resolved his issue – he should have tried the print suggestion.
http://bytes.com/groups/python/25205-using-string-ljust-try-hold-fixed-width#links