README.md

If you have any questions regarding this repository, please contact Ruida Zeng at ruida dot zeng at vanderbilt dot edu

Cluster Analysis on Subject Data in Immersive Virtual Environments

This repository contains my work from the 2019 VUSE undergraduate summer research program, at the Learning in Virtual Environments (LIVE) research lab at Vanderbilt University's School of Engineering. The graduate research assistant for this project is Richard Paris, who is responsible for the creation of the immersive virtual environments using Unity, and promptly conducted the experiments on around 200 subjects. The primary investigator for the project is Dr. Bobby Bodenheimer, associate professor at the Department of Electrical Engineering and Computer Science.

It mainly consists of 143 parsed .csv files in the "Parsed Data" sub-folder and several machine learning source codes with a detailed explanation on the methodology attempted. I also included an appendix, which contains useful information regarding the raw data and the parsed data.

Note: Future research, either through a variety machine learning algorithms or otherwise, is encouraged on the 143, nicely parsed, .csv files containing information of the maze.

Python modules required to be installed: numpy, pandas, sklearn, matplotlib and their dependencies.

Parsed Data

The attributes of the parsed .csv files are date/time, seconds since started, posX, posY, posZ, rotX, rotY, rotZ, respectively. The raw tab-separated .txt files before parsing contained more unimportant attributes but was sliced.

1color.py

Visual representation of one singular .csv file using matplotlib module based on the temporal attributes, with red indicates early and blue indicates late.

This script will not compile in its current form, due to it being legacy code.

2color.py

Visual representation of two .csv files using matplotlib module based on the temporal attributes, with red indicates early and blue indicates late.

This script will not compile in its current form, due to it being legacy code.

failed_km.py

Failed attempt at k-means clustering all (posX, posZ) in tuple forms in a numpy array, from 5 distinct pandas dataframes which were imported from the first 5 parsed data alphabetically. Returned ValueError: Found array with dim 3. Estimator expected <= 2.

km_3d.py

Temporal attribute (time) is added as the Z-axis for 3D visual representation of the clusters.

km_avg.py

A 3D representation, with time as the Z-axis, of the average (mean) position of the clusters. Returned IndexError: list index out of range for certain clusters (yet to be debugged).

km_linear.py

Successful k-means clustering on (posX, posZ) tuples on a subject dataframe, imported from a singular parsed data file. In this example, I set the number of clusters to 8 for AAAA.csv, but they can be easily modified.

km_quadruple.py

Traverse through all .csv files in the Parsed Data folder. Successful k-means clustering on (posX, posZ) tuples on each subject dataframe from all parsed data file. The quadruples are calculated from time spent around the vicinity of 4 decision points (intersections) in the maze.

km_vector.py

Successful k-means clustering on decimated posY stacked on top of posX, forming a vector for each of the subject dataframe from all parsed data files. Since the codes require uniformity of vector size, we had to slice out 2 data files because of the particular decimation.

km_vector_more.py

Successful k-means clustering on "less" decimated posY stacked on top of posX, forming a vector for each of the subject dataframe from all parsed data files. Since the codes require uniformity of vector size, we had to slice out 39 data files because of the particular decimation.

km_color.py

Successful k-means clustering on decimated posY stacked on top of posX, forming a vector for each of the subject dataframe from all parsed data files. Since the codes require uniformity of vector size, we had to slice out 2 data files because of the particular decimation. The graphs are coded with the temporal attributes, with red indicates early and blue indicates late.

km_color_more.py

Successful k-means clustering on "less" decimated posY stacked on top of posX, forming a vector for each of the subject dataframe from all parsed data files. Since the codes require uniformity of vector size, we had to slice out 39 data files because of the particular decimation. The graphs are coded with the temporal attributes, with red indicates early and blue indicates late.

makecsv.py

This source code generates a .csv file from the original, tab-separated, .txt file by applying my "find 10 min" slicing algorithm.

matplotlibfullalgo.py

Returns a visual representation using matplotlib module of a 10 minutes slot found by my "find 10 min" slicing algorithm. This visual is used to determine whether or not my algorithm has found the correct 10 minutes.

This script will not compile in its current form, due to it being legacy code.

subdir.py

This is the code I applied on the original, raw, data in order to find the 10 minutes of useful data. However, since this piece of "find 10 min" algorithm his code does not work on all, I wrote this script to iterate through every original raw data file to determine the efficiency of my algorithms.

This script will not compile in its current form, due to it being legacy code.

subdir_multiple.py

This is a modification on the subdir.py, such that it will tell me which are the files that my "find 10 min" slicing algorithm found two or more candidates.

This script will not compile in its current form, due to it being legacy code.

subdir_unique.py

This is a modification on the subdir.py, such that it will tell me which are the files that my "find 10 min" slicing algorithm found only one candidate.

This script will not compile in its current form, due to it being legacy code.

visual.py

Visual representation using matplotlib module.

turtle.py

Visual representation using turtle module (live animation).

Appendix

I prepared a poster presentation for 2019 Vanderbilt School of Engineering Summer Undergraduate Research Experience Program as 2019 Summer Research Fellow.

The following tables contain the manuever I had to apply based on the graphic representation given by applying matplotlibfullalgo.py to each individual raw data, which is significantly larger, containing more unuseful data.

Y indicates that the data was parsed out perfectly, N indicates that I hardcoded a shift of 10 minutes because the visual gave us a visual representation of the training maze which procedes the learning maze, and X indicates throwing out the data completely because the visual made no sense even after hardcoded tinkering.

Subject ID	Status	Additional Notes
LABELED DATA
IZZO	X
SVBB	X
RCEH	N
VUUK	X
IXRA	N
FMVE Bad	X
CXIJ	N
DKAF	X
RTUG	V
CPSL	V
JHMW	X
NWTC	X
YBRX	X
MLOS	X
KMRY	X
CDYY	X
LQKJ	V
AOXY	N
WGNY	V
UVRZ	N
OGTB	N
BPPX	N
GJJJ	N
YFDE	N
RIKR	N
YJKM	N
XLLZ	X
UNWN	X
VPQA	N
MPOB	N
UPCV	X
OUWM	N
JBXP	N
VZYX	N
RSXQ	X
YPQL	N
WMKQ	N
HASK	N
UFNF	N
IHGX	N
TMPJ	N
ZTAL	N
VNWM	N
ODJH	N
SIUT	N
XLZQ	X
DRDQ	N
FXXV	N
EGRU	N
ZDGH	N
TEYQ	N
VKPD	N
TYJR	N
YNRZ	N
RGYJ	N
ANAV	N
URXR	N
NGVO	N
QQTV	N
RTBV	N
OWHE	N
QVFJ	N
CGWN	N
LAWW	N
BVEH	N
DXJP	N
PGBB	N
MRPD	N
JVRV	N
MTXB	N
KSQU	N	2 candidates
NUAO	N
FWPA	V	2 candidates
CXQX	N
EOPT	N
OGBK	N
WTIY	N
GZTO	N
EUDK	N
GQYU	X	2 candidates
UPGW	N
SSNK	N	2 candidates
IQMQ	N
GGWU	N
DBQH	N
ZDNA	X
YYTZ	N	2 candidates
XQJO	N
UICN	N
HRGF	N
ONVA	N
TWJS	X	2 candidates
WONG	N
MCCO	N
UNLABELED DATA
AAAA	N
ACGN	N
AELV	N
BBBB	X
BBHD	V
BFFT	V
BFJK	N
BPUF	V
BQHT	N
BWNF	V
BYOU	N
CBDG	N
CFLN	X
CXYL	V
DIJR	V
EMBJ	N
FAFH	V
FGTV	N	2 candidates
FIVC	N
FJAJ	X
FJEB	V
FMKJ	N
FMRE	N
FPIT	N
FQGS	N
FQMM	V
FVZI	V
FWVY	V
GCIV	V
GGMO	N
HCWV	V
HDNQ	V
HIXM	V
HTLW	N
IAHA	X
IIMV	V
ITCT	V
JKOY	V
JYVB	V
KRKM	N
KXKS	N
LCPU	V
LFWZ	N
LMUU	V
LVEY	V
MEPW	X
MHGM	V
NEQV	X
OVOW	N
PGJC	N
QHTL	N
QKVF	X
QMGI	N
QMUX	V
QZPJ	V
RRSK	V
RVQO	N
SFUG	N
SGLD	N
SSXP	V
test	ROFL
TRTT	V
TRUK	V
TWBG	V
UING	N
UREH	N
UZMT	N
VAGY	V
VCVG	V
VJGB	V
WFKT	V
WJJU	N
WOKD	N
WRED	V
WTYX	X
XBCP	V
XKAL	N
XPRU	N
YDJH	X
YLTR	V
YPGZ	N