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Latest revision as of 06:25, 12 June 2015

Personal Information

My name is Amanda Wert and I am a double major in Math and Computer Science at Benedictine College in Kansas. I am planning on graduating in December of 2012 and hopefully move back to Appleton, Wisconsin and be a software developer.

Time Log

Week 1

Tuesday, May 31

  • Was orientated
  • Learned expectations
  • Toured campus
  • Filed paperwork

Time: 6 1/2 hrs

Wednesday, June 1

  • Worked with the Wiki
    • Created user page and updated recent activities
  • Met with Dr. Spiller and Dr. Scott and received readings
  • Read the first chapter of a textbook on Chaotic Dynamics
  • Read Driscoll, Tobin A. Learning MATLAB. 2009 Chapters 1-4 and 6
  • Played around with MATLAB
  • Reread Learning MATLAB chapter 2
  • Read Chapter 6 (Diff Eq) section 1 (IVP and Euler's Method) of a textbook on Numerical Analysis

Time: 8 hrs

Thursday, June 2

  • Reread Learning MATLAB chapters 3 and 4
    • Feel very comfortable with MATLAB and prepared to examine the code I'll be working with
  • Researched Linear Shallow Water Equations online
    • Found general background information but did not find an understandable technical description of the equations or how to use them
  • Met with Dr. Scott and discussed:
    • The code for the program that measures how a fluid particle's path covers the sample space among other things
    • Goals for the summer
    • Pere the super computer
  • Logged onto Pere
  • Went to the talk by Dr. Factor on good research practices and learned:
    • To be careful because internet sources can lie
    • To be both thorough and reasonable
    • The goal of the summer is to gather information to make a conjecture and then support it
  • Listened to a presentation on how to use the library online resources
  • Familiarized myself with the Ergodic Defect script
    • I am comfortable with what the program is doing though not with all the technical math behind it
  • Read about how to submit jobs to Pere and looked up words/concepts I didn't know
  • Began skimming Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.

Time: 8 hrs

Friday, June 3

  • Reviewed the Ergodic Defect script
    • I am now very comfortable with everything the program does though still not with all of the technical math behind it
  • Reviewed the Runge Kutta 4 script
  • Reread the first chapter of a textbook on Chaotic Dynamics
  • Played with the Ergodic Defect script
  • Researched Condor
    • Unsure how to submit MATLAB jobs but does not matter as I will be now using PBS/Torque
  • Met with Dr. Scott
    • Discussed goals
    • Emailed Feng for help with Condor
    • Answered my questions on the scripts
  • Worked with Feng
    • He showed my how to submit jobs using PBS :)
  • Worked with PBS on my own
    • I now know how to submit jobs and edit things on ssh
  • Added goals and project page to wiki

Time: 6 hrs

Saturday, June 4

  • Read Chapter 6 (Diff Eq) sections 1-4 of a textbook on Numerical Analysis
  • Skimmed Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.

Time: 4 hrs

Week 2

Sunday, June 5

  • Read Chapter 6 (Diff Eq) sections 5-7 of a textbook on Numerical Analysis
  • Read Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.
    • Sections 1 and 2
  • Looked at running Ergodic Defect script in Pere
    • How to put changing inputs in and get intelligible outputs out

Time: 3 hrs

Monday, June 6

  • Reread the first chapter of a textbook on Chaotic Dynamics
  • Worked with MATLAB and Pere
    • Ran MATLAB functions that took input and output files on both
    • Made an edited version of the Ergodic Defect script that takes an input file and writes to an output file
    • Ran the edited version on Pere
    • Ran an array of jobs using different inputs of the edited version on Pere
  • Reviewed the two uses of Runge Kutta 4 Methods for Ergodic Defect Script
  • Became more familiar with LSW equations
  • Made a generic Runge Kutta 4 method for a system of up to 4 equations
    • Put as a sub-function into a modified Erg Def script and used for flow field RK
      • Same speed (maybe a bit slower)
    • Should be useful when the third dimension will be added
  • Wrote a program that will generate input files for the parameter sweep
    • Still needs to be tested
  • Reexamined Ergodic Defect code to prepare for adding a third dimension
    • Marked places where dimension matters
    • Re-went through variables to better understand calculations
      • Need to finish this tomorrow morning

Time: 9 hrs

Tuesday, June 7

  • Tested the input writing program
  • Got everything ready in Pere to run a parameter sweep
  • Finished going over variables to better understand calculations
  • Edited Ergodic Defect code to easily take a third dimension
  • Met with Dr. Spiller, Regis, and Paul to discuss Numerical Analysis theory
  • Looked at previous posters and made a rough outline for presentation
  • Read for background information

Time: 9 hrs

Wednesday, June 8

  • Read Learning MATLAB chapter 5 for knowledge of graphics
  • Researched MATLAB graphics functions
  • Sketched out what would needed for a grayscale picture of the ergodic defects of individual trajectories
  • Met with Dr. Scott to discuss making the ergodic defect picture
  • Implemented the code and got a picture
  • Tried to run on Pere
    • Had problems with writing/displaying the picture as output
    • Found out I was using functions from the Image Procession Toolkit which the version of MATLAB on Pere does not have
    • Feng Xizhou fixed that for me :)
    • Now it works perfectly and is the version I am using
  • Worked on a method of drawing the picture that does not use those functions
    • Continued working after the problem was fixed because this way may be better overall
    • Ended up failing
  • Changed the script to calculate the average of individual ergodic defects at 5 scales

Time: 9 hrs

Thursday, June 9

  • Added additional outputs to average picture script
  • Got Pere ready
  • Skimmed Rypina, I.I., et al. "Investigating the connection between complexity of isolated trajectories and Lagrangian coherent structures." 2011
  • Met with Dr. Scott
  • Submited the base case
  • Went to the working lunch
  • Worked on adding a title to the picture--didn't work
  • Worked on creating a scale diagram to go with the pictures
  • Tried to remote log onto Pere from home but it didn't work

Time: 7 hrs

Friday, June 10

  • Tried to log onto Pere
    • Had to go through Pascal and then Pere shut down
  • Tried to download Octave
    • Didn't work
  • Handwrote plan for some cases Dr. Scott requested because text editor on Pascal wasn't working
  • Typed up and ran the cases until Pere shut down again
    • Pretty sure they are bug free and will quickly run in the morning

Time: 4 hrs

Saturday, June 11

  • Ran the cases Dr. Scott had asked for
    • The base case with the same gray scale
    • The trajectories of the two particles
  • Started the parameter sweep
    • Ran the first 500
    • Found out Monday I had made a mistake and would have to rerun

Time: 3 hrs

Week 3

Monday, June 13

  • Discovered I had a problem with the inputs for my parameter sweep
    • Fixed it and restarted the sweep
  • Made a gray scale diagram for the LSW pictures
  • Met with Dr. Scott and discussed:
    • Parameter sweep
    • MMW flows
    • Future applications
  • Reread Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.
  • Read the beginning of Malhotra, Mezic, Wiggins. Patchiness: A New Diagnostic for Lagrangian Trajectory Analysis in Time-Dependent Fluid Flows. 1998.
    • Compared the equations for the two
  • Adjusted the Ergodic Defect code to use the MMW equations
  • Edited/cleaned up my project page on the wiki
  • Found out I was doing the parameter sweep inefficiently

Time: 8 hrs

Tuesday, June 14

  • Printed off pictures of MMW in preparation for meeting with Dr. Scott
  • Added titles to the pictures
  • Troubleshooted with Pere
    • No jobs I submit will run
  • Met with Dr. Scott and discussed:
    • MMW flows
    • Trajectories
    • She gave me code that another student had made that made a movie of the flow
  • Went to a talk on Good Research Presentations and Good Research Papers by Dr. Brylow
  • Worked with the MMW trajectories
    • Realized my problem--I had forgotten to modify the mod function when I modified the rest of the code
    • Fixed that
  • Made the ergodic defect picture drawing scripts more efficient
    • Combined loops and used a build in function in find(...) instead of max(find(...))
  • Thought about where I wanted to go with my research
  • Tried different things on Pere to get it to work
  • Worked with trajectories to make sure I had the correct code

Time: 9 3/4 hrs

Wednesday, June 15

  • My birthday! whoot!
  • Worked with the trajectories to try to make Fig. 2 from the MMW paper
  • Went to the conference on cloud computing in Appleton

Time: Conference + 3/4 hrs

Thursday, June 16

  • Used Gabe's code to make a movie of the MMW trajectories
  • Tried to run the parameter sweep
    • Pere was working but then it stopped...:/
  • Working lunch
  • Went to a required NSF talk on Research Ethics
  • Met with Dr. Scott
  • Made small edits to MMW script
    • Started the 10 T's but again, Pere won't run any jobs
  • Started reading Bullitt, Elizabeth, et al. "Measuring Tortuosity of the Intracerebral Vasculature from MRA Images." 2003.

Time: 8 1/2 hrs

Friday, June 17

  • Read Bullitt paper
  • Thought about how to measure ergodic defect of sine graphs
  • Edited code to measure the ergodic defect of sine graphs
    • Varying frequency and amplitude
  • Tried to submit jobs in Condor because Pere still wasn't running the jobs
    • Didn't work
  • Ran sine graph code to see if there is a correspondence with tortuosity
    • I couldn't find one
  • Made a code that drew the trajectories for the sine graphs
  • Learned how to use Condor from Adam
  • Met with Dr. Scott

Time: 7 hrs

Week 4

Monday, June 20

  • Organized and prioritized tasks to be completed
  • Run MMW sweep for the various T's
  • Skimmed Rom-Kedar, V., and Poje, A. C. "Universal Properties of Chaotic Transport in teh Presence of Diffusion." 1999.
  • Set up the Rom-Kedar flow script
    • Did not find explicit u and v so used my calculator to solve for the complicated partial derivatives
  • Fixed the dxdy problem for MMW, tortuosity, and Rom-Kedar
    • Hadn't been using the correct area
  • Skimmed Scott, Sherry E., et al. “Capturing deviation from ergodicity at different scales.” Physica D, 2009.
    • Researched various terms on google to try to understand the underlying math and notation
  • Adjusted domain of tortuosity d value calculations
  • Made code for the coil tortuosity

Time: 9 1/2 hrs

Tuesday, June 21

  • Collected output from LSW parameter sweep
  • Tried to print the toruosity trajectories for the new domain
    • There was some problem either with the mod-ing or the plot function, the trajectories were unintelligible
  • Looked at the problems in the script with calculating the defect
    • The normalization factor and maybe another constant had gotten lost from the code
  • Fixed Rom-Kedar code for ln instead of log10
  • Skimmed Capturing deviation from ergodicity at different scales some more
  • Fixed the sine trajectory picture
  • Cleaned up various scripts
  • Added normalization factors to various scripts
    • May not be needed...
  • Skimmed some papers on chaotic advectation
  • Went through the LSW parameter sweep data to look for patterns

Time: 9 hrs

Wednesday, June 22

  • Looked at the temperature data
  • Consolidated the LSW parameter sweep data into a single matrix
    • Made graphs using data
  • Skyped/talked with Dr. Scott
  • Found a way to save the trajectories of the particles in the flow
  • Started jobs to get more detail on h1=+-.5
  • Thought about how to make the code faster

Time: 8 hrs

Thursday, June 23

  • Made trajectory movies
  • Examined data
    • Grayscale pictures
    • Individual trajectory
  • Made combined graphs for Avg d vs u1 and Avg d vs h1 with the varying other parameter (u1 or h1)
  • Working lunch
  • Made the script much faster
  • Wrote outline for presentation
  • Worked more with the movies
  • Skyped with Dr. Scott

Time: 9 hrs

Friday, June 24

  • Made more combined graphs
  • Adjusted code for mapping
  • Made tortuosity pictures
  • Worked with the LSW movie
  • Obtained tortuosity sine data
  • Worked with coil toruosity
  • Varies u0 to see if the step size needs to be increased

Time: 8 1/2 hrs

Week 5

Monday, June 27

  • Finished varying u0
    • Do not need to change step size
  • Made pictures of the coil trajectories
  • Wrote setup sheets for tortuosity and MMW
  • Obtained tortuosity coil data
    • d values, xyindcounts, and pictures
  • Tested for number of uncounted boundary cases
    • Very few compared to the number of counts so its ok
  • Skimmed the chapter on LSW to review for presentation
  • Ensured synthetic tortuosity matched the Bullitt et al 2003 paper
    • Had trouble with corresponding same start/end voxel
  • Reread the tortuosity paper
  • Worked on my presentation
  • Met with Dr. Scott
  • Worked u0

Time: 9 hrs

Tuesday, June 28

  • Worked on presentation
  • Made the start/end voxels the same for tort
  • Ready Rypina paper on Largrangian structures and Scott paper on ergodic defect
  • Met with Dr. Scott
  • Set up u0 varying parameter sweep

Time: 8 hrs

Wednesday, June 29

  • Worked on presentation
  • Made the coil 3d
  • Worked with u0 data
    • Finished collecting and consolidated data
  • Reread Scott, et. al on the Ergodic Defect

Time: 7 hrs

Thursday, June 30

  • Worked on presentation
  • Thought about how to use ergodic defect to measure tortuosity effectively
  • Listened to other present and gave my presentation
  • Worked with u0 data
    • Tried to figure out an informative way to graph

Time: 8 hrs

Friday, July 1

  • Read various papers for background info
    • Looking for inspiration on how to process LSW data and how to measure tortuosity
  • Worked with u0 data
  • Researched vessel segmentation
  • Read on chaotic advection

Time: 7 hrs

Week 6

Tuesday, July 5

  • Worked on making tortuosity sampling evenly spaced
  • Read on chaotic advection
  • Went to a talk on making a good poster
  • Started 3 small parameter sweeps exploring
    • LSW for h1=0:0.01:0.1 and u1=-0.5:0.1:0.5
    • LSW for h1=0.3:0.1:0.5 and u1=-5:0.1:-1.9
    • MMW for Epsilon 0:.05:0.5 and T=0.5:0.5:3
      • Found out I made a mistake and so restarted the run on Thursday

Time: 9 hrs

Wednesday, July 6

  • Worked with the temperature data
    • Consolidated and calculated ergodic defects
    • Made grayscale pictures
    • Dealt with the NaN values
    • Broke the data into 4 sets for more detailed graphing
  • Worked with tortuosity

Time: 8 hrs

Thursday, July 7

  • Consolidated data from the small parameter sweeps from Tuesday
  • Fixed MMW and restarted small sweep
  • Worked with the tortuosity data
  • Cleaned up folders
  • Working lunch
  • Listened to a talk by Dr. Struble

Time: 7 hrs

Week 7

Monday, July 11

  • Worked with the tortuosity data
  • Wrote a program to automatically write the excel file for me
  • Consolidated the MMW data
  • Edited the sine and coil scripts so that the number of scales can be varied

Time: 8 hrs

Tuesday, July 12

  • Worked with the tortuosity averaging scales 3 to 5
  • Put comments in code describing purpose and reasoning
    • Tortuosity
    • LSW

Time: 8 hrs

Wednesday, July 13

  • Fixed the Arclength program
    • Used it to calculate the ergodic defect of the sine waves
  • Made the tortuosity set up sheet more detailed
  • Worked with the Rom Kedar flows
    • Fixed the equations
    • Attempted ways to make it faster

Time: 7 1/2 hrs

Thursday, July 14

  • Made sure everything in the tortuosity and Rom Kedar sections were good to go
  • Made the LSW set up and observations sheet more detailed
  • Added observations to the detailed tortuosity set up sheet
  • Went to the working lunch
  • Further commented the code
    • MMW
    • Rome Kedar
    • Temperature
  • Started editing code to calculate the ergodicity defect of the temperature of the floats

Time: 8 1/2 hrs

Friday, July 15

  • Finished editing the code to calculate the ergodicity defect of the temperature of the floats
    • Made grayscale pictures
    • Made a comparison graph between the two types of defects--position and temperature
  • Proofed comments of various codes and made more detailed
  • Went over comments from the presentation to improve for next time
  • Read the paper on the Loop Current in the Gulf of Mexico
  • Calculated the defect for more detailed synthetic sine wave data
  • Met with Dr. Scott and went over:
    • MMW-how to get fig 2.
    • Rom Kedar - how to get fig 3 and 4

Time: 7 1/2 hrs

Week 8

Monday, July 18

  • Tried various ways to make fig 2 pic 1 for MMW
  • Tried to make fig 3 for Rom Kedar
    • Didn't succeed at all
  • Met with Dr. Scott and discussed:
    • Other ways to get MMW and Rom Kedar right

Time: 7 1/2 hrs

Tuesday, July 19

  • Set up more detailed u0 sweep
  • Made movies of various trajectories
  • Tried to make fig 2 pic 1 for MMW
    • Somewhat succeeded but mine is more continuous
  • Tried to make fig 3 for Rom Kedar
    • Didn't succeed at first
    • Ran for a much longer time interval and it worked
  • Met with Dr. Scott to discuss achievements so far
  • Played around with LSW trajectory movies

Time: 8 1/2 hrs

Wednesday, July 20

  • Examined relationship and effects of parameters
    • Why white line is where it is when u0=0
    • What happens as you vary u1 and h1 for u0=0
  • Examined change as u0 approaches 0
    • Made trajectory movies
  • Documented observations so far
  • Consolidated u0 data and graphed
  • Tried to get fig 3 from Rom Kedar
    • Succeeded in fig 3c
  • Met with Dr. Scott to discuss current progress
  • Tried to obtain fig 2 from MMW

Time: 8 hrs

Thursday, July 21

  • Ran some trials with u1=u0=0 for a larger endt
  • Tried to obtain fig 2 from MMW
    • Was able to get a discrete grayscale like theirs
  • Worked on my final presentation
    • Made some movies of LSW gray scale pictures
  • Went to the working lunch
  • Met with Dr. Scott and discussed
    • Tortuosity data to come tomorrow! :D
    • Crazy LSW behavior
  • Thought about why certain LSW behavior occurs
  • Got a script ready to process the real tortuosity data for tomorrow

Time: 9 1/2 hours

Friday, July 22

  • Explored why the the white line appears where it does
  • Reread MMW and tortuosity
  • Looked at LSW with different endt
  • Tried to reproduce fig 2 of MMW

Time: 6 hrs

Week 9

Monday, July 25

  • Found the mean Temperature values
  • Worked on my poster
  • Tried to get the tortuosity software to work
  • Met with Dr. Scott
  • Extracted vessel XYZ data and tested with script

Time: 9 hrs

Tuesday, July 26

  • Played around with Paraview
  • Worked on my poster
  • Met with Dr. Scott
  • Made graphs for the tortuosity

Time: 7 1/2 hrs

Wednesday, July 27

  • Worked on my poster
  • Fixed the problem with LSW quiver plots
  • Played around with tortuosity data

Time: 7 1/2 hrs

Thursday, July 28

  • Worked with tortuosity data
  • Documented my work with LSW
  • Went to the working lunch
  • Met with Dr. Scott

Time: 8 hours

Friday, July 29

  • Worked on my abstract for my final talk
  • Worked with tortuosity data
  • Met with Dr. Scott

Time: 10 1/2 hrs

Week 10

Monday, August 1

  • Worked with tortuosity data
  • Met with Dr. Scott
  • Submitted our abstract for the SPIE conference
  • Worked on presentation

Time: 7 hrs

Tuesday, August 2

  • Presented posters
  • Worked on presentation

Time: 5 hrs

Wednesday, August 3

  • Worked on presentation
  • Gave and listened to presentations
  • Worked on final paper

Time: hrs