Progress Report - 15 Jun 2007

1. What were my goals for this week?

• Literature search for motion segmentation and clustering
• Get comfortable with PyMol
• Go through a Python tutorial
• Start playing around with some two-dimensional analogues from Gleicher, generate some images
• Speak to Aaron re: 3ANK with motion

2. What did I accomplish this week?

• Did a quick run-through of PyMol with Aaron
• Got open/closed AKE states and ran the open state through elNemo, did some visualization in PyMol
• Ran through Dive into Python
• Wrote three affine transform calculating programs in Matlab:
  - CalculateAffine.m: calculates exact affine transform given start and end positions of three non-colinear points
  - newAffine.m: calculates least-squares fit affine transform of an arbitrary (>3) number of points
  - Affine.m: calculates least-squares fit affine transform of points from data in an external text file

3. Why are numbers 1 and 2 different?

Spoke with Mike on Monday regarding aims for the week, and instead of continuing the literature search, decided to change course toward implementation. As I hadn't done this sort of affine transform calculation (all prior math experience was with ideal situations using basis vectors), I needed to do a fairly extensive search through textbooks and internet resources regarding methods and tricks in Matlab and in general, which took longer than expected, and resulted in me being unable to design or implement even a simple clustering algorithm. It's on the to-do list for next week.

Also ended up getting very little done Friday afternoon as the Registrar and the math department apparently weren't in very good communication, and I had to spend a good hour sorting out whether I actually got to graduate or not, which was a bit on the emotionally taxing side and kind of sapped the rest of my motivation for the afternoon.

4. What are my goals for next week?

• Literature search for clustering
• Speak to Aaron about implementing a clustering algorithm in the Matlab program
• Interface program with Mike's motion program
• Generate some IMAGES!!

5. How does this fit in my bigger picture?

Get some basis images in two dimensions to build on later with a more general model in three dimensions (the proteins). Also develop a base program from which to develop the next stage of the calculations and images.

6. What did I read this week?

• Huitema, Henk and Robert van Liere, Interactive visualization of protein dynamics.
• Horn, Berthold K. P. and John G. Harris, Rigid body motion from range image sequences.
• Unser, Michael, Matthew A. Neimark, and Chulhee Lee, Affine transformations of images: a least squares formulation.
• Lecture 4: Affine transformations (lecture notes from intro graphics class at Rice)