# User:Awert

## Contents

## 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
- Need to find out how to run the job in Octave
- Skimmed Condor manual: http://www.cs.wisc.edu/condor/manual

- 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

- Put as a sub-function into a modified Erg Def script and used for flow field RK
- 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
- Shalizi, Cosma
*Ergodic Theory* - Scott, Sherry E., et al. “Capturing deviation from ergodicity at different scales.” Physica D, 2009.
- Vreugdenhil C.B. "Numerical Methods for Shallow-Water Flow" Kluwer Academic Publishers. Dordrecht, The Netherlands. 1994.
- Acheson D.J. "Elementary Fluid Dynamics" Oxford University Press, Oxford. 1990.

- Shalizi, Cosma

Time: 9 hrs

**Wednesday, June 8**

- Read
*Learning MATLAB*chapter 5 for knowledge of graphics - Researched MATLAB graphics functions
- Found | MathwWorks' MATLAB Help Section very useful

- 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