- Day 1: Data files
- Experiment Builder Script Setup
- EDF files
- Other EB files
- Day 2: Data viewer
- Visualizing data; QC
- Interest areas
- Creating reports
- Day 3: ET data in R
- Reading EDF ASCII files
- Creating Reports
- Interest areas
- Visualizing data (ggplot)
June 23, 2017
Outline for the Week
Outline for Today
- Reading EDF ASCII files
- Creating Reports
- Interest areas
- Visualizing data (ggplot)
Reading EDF ASCII files
EDF2ASC
Command line utility for converting EDF files to ASC files.
- There is a GUI version of the tool.
- There is a Mac OS version called EDFconverter.
Eyelink Data files
- Gaze Data
- Samples
- Fixations
- Saccades
- other Data
- Trial Variables
- Visual displays
EDF2ASC
EDF2ASC
FDBeye package
https://github.com/davebraze/FDBeye
install.packages("devtools") ## if you don't already have it
library(devtools)
install_github("davebraze/FDBeye", build_vignettes=TRUE)
edf2asc()
library(FDBeye)
Need to Tell FDBeye where to find the edf2asc utility.
edf2asc()
options(FDBeye_edf2asc_exec = "C:/Program Files (x86)/SR Research/EyeLink/EDF_Access_API/Example/edf2asc64.exe")
getOption("FDBeye_edf2asc_exec")
## [1] "C:/Program Files (x86)/SR Research/EyeLink/EDF_Access_API/Example/edf2asc64.exe"
## Set some options. Here '-y' forces overwrite of existing ## ASC files. options(FDBeye_edf2asc_opts = "-y")
edf2asc()
Get a list of EDF files and process them with edf2asc.
edffiles <- list.files(".", pattern = "edf$", recursive = TRUE)
edffiles
## [1] "data/RAN/1950180/1950180.edf"
ascfiles <- edf2asc(edffiles) ascfiles
## [1] "data/RAN/1950180/1950180.asc"
Returns a list of the ASC files that are created.
readELascii()
eldat <- readELascii(ascfiles[1])
## X1 X2 X3 X4 X5 X6 X7 X8 ## 1 4318226 613.4 493.9 803.0 640.1 493.4 656.0 ..... ## [1] "Sbinoc && !(Svel||Sres)" ## X1 X2 X3 X4 X5 X6 X7 X8 ## 1 4341642 -63.3 720.5 276.0 . . 0.0 ...C. ## [1] "Sbinoc && !(Svel||Sres)" ## X1 X2 X3 X4 X5 X6 X7 X8 ## 1 4364730 626.6 527.3 789.0 658.2 525.4 613.0 ..... ## [1] "Sbinoc && !(Svel||Sres)" ## X1 X2 X3 X4 X5 X6 X7 X8 ## 1 4382990 616.1 536.3 892.0 641.8 528.6 683.0 ..... ## [1] "Sbinoc && !(Svel||Sres)" ## X1 X2 X3 X4 X5 X6 X7 X8 ## 1 4402394 612.1 520.8 861.0 649.3 502.7 664.0 ..... ## [1] "Sbinoc && !(Svel||Sres)" ## X1 X2 X3 X4 X5 X6 X7 X8 ## 1 4427690 557.0 445.8 864.0 587.1 433.5 703.0 ..... ## [1] "Sbinoc && !(Svel||Sres)"
readELascii()
names(eldat)
## [1] "session" "trials"
names(eldat$session)
## [1] "subj" "script" "sessdate" "srcfile"
names(eldat$trials)
## [1] "0" "1" "2" "3" "4" "5"
names(eldat$trials$"0")
## [1] "fix" "sacc" "blink" "trialvar" "samp" "msg"
Fixation Report
fixdat <- fixReport(eldat) names(fixdat)
## [1] "subject" "trialn" ## [3] "time0" "event" ## [5] "eye" "stime" ## [7] "etime" "dur" ## [9] "xpos" "ypos" ## [11] "pupil" "currentEyeTrackerTime" ## [13] "currentDisplayPCTime" "AudioRecordingStartTime" ## [15] "AlignVoiceTriggerTime" "trial" ## [17] "p1" "p2" ## [19] "p3" "p4" ## [21] "p5" "p6" ## [23] "p7" "p8" ## [25] "p9" "p10" ## [27] "p11" "p12" ## [29] "p13" "p14" ## [31] "p15" "p16" ## [33] "p17" "p18" ## [35] "p19" "p20" ## [37] "p21" "p22" ## [39] "p23" "p24" ## [41] "p25" "p26" ## [43] "p27" "p28" ## [45] "p29" "p30" ## [47] "p31" "p32" ## [49] "p33" "p34" ## [51] "p35" "p36" ## [53] "cell_width" "cell_height"
Fixation Report: Clean It Up
fixdat <- fixdat %>% select(c(subject, trialn, time0, event,
eye, stime, etime, dur, xpos, ypos, pupil, trial))
str(fixdat)
## 'data.frame': 679 obs. of 12 variables: ## $ subject: chr "1950180" "1950180" "1950180" "1950180" ... ## $ trialn : Factor w/ 6 levels "0","1","2","3",..: 1 1 1 1 1 1 1 1 1 1 ... ## $ time0 : int 4318226 4318226 4318226 4318226 4318226 4318226 4318226 4318226 4318226 4318226 ... ## $ event : chr "FIX" "FIX" "FIX" "FIX" ... ## $ eye : Factor w/ 2 levels "L","R": 1 2 1 2 1 1 2 1 2 1 ... ## $ stime : num 4318242 4318242 4318510 4318470 4318642 ... ## $ etime : num 4318414 4318414 4318614 4318802 4318806 ... ## $ dur : num 176 176 108 336 168 192 188 124 112 264 ... ## $ xpos : num 613 638 131 229 185 ... ## $ ypos : num 521 515 418 300 307 ... ## $ pupil : num 824 669 937 727 901 904 717 862 674 923 ... ## $ trial : chr "letters1" "letters1" "letters1" "letters1" ...
Look at your Data
Individual Trial: FDBeye::fixPlot()
Under Repair.
Now for some generic ggplot.
Individual Trial
letters2 <- filter(fixdat, trial == "letters2")
p1 <- ggplot(aes(x = xpos, y = ypos, size = dur, color = eye),
data = letters2) + geom_point()
Individual Trial
p2 <- p1 + geom_point(alpha = 1/2) + scale_x_continuous(limits = c(0,
1279)) + scale_y_reverse(limits = c(1023, 0)) + coord_fixed() +
guides(size = FALSE, color = FALSE)
Individual Trial: read region file
regions <- read_tsv("data/RAN/Interest Area and Canvas Overlay Setup in DV/letters1-big.ias",
col_names = c("type", "regnum", "left", "top", "right", "bottom",
"reglabel"))
Region files, in the form of Data Viewer ias files, are just tab-separated variable files, without headers.
Individual Trial: add regions to plot
p3 <- p2 + geom_rect(aes(xmin = left, ymin = top, xmax = right,
ymax = bottom), fill = NA, color = "blue", data = regions,
inherit.aes = FALSE)
Individual Trial: zoom in
p4 <- p3 + ylim(875, 200) + xlim(175, 1100)
Individual Trial: closest line
regions <- regions %>% mutate(vcenter = (top+bottom)/2,
hcenter = (left+right)/2)
lines <- unique(regions$vcenter)
p5 <- p2 + ylim(875, 200) +
xlim(175, 1100) +
geom_hline(yintercept=lines, color="orange")Individual Trial: closest line
Individual Trial: closest line
getNearestLine <- function(y, lines) {
which.min(abs(y-lines))
}
line <- apply(matrix(letters2$ypos), 1, getNearestLine, lines)
line
## [1] 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 ## [36] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ## [71] 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 2 2 ## [106] 1 1 3 3
letters2 <- data.frame(letters2, line)
Color fixations according to nearest line (vcenter, line).
Individual Trial: closest line
p6 <- p5 + geom_point(aes(color=as.factor(line)))
Individual Trial: closest line
letters2r <- filter(letters2, eye=="R")
p10 <- ggplot(aes(x=xpos, y=ypos, size=dur), data=letters2r) +
geom_point(aes(color=as.factor(line)), alpha=1/2) +
scale_y_reverse(limits=c(875,200)) +
scale_x_continuous(limits=c(175,1100)) +
coord_fixed() +
guides(size=FALSE, color=FALSE) +
geom_hline(yintercept=lines, color="orange")
Putting everything together.
Individual Trial: closest line
Individual Trial: fix out of sequence
letters2r$line
## [1] 2 2 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 ## [36] 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 2 1 3
tmp <- FDButils::series(letters2r$line, step = 0, minseries = 3) ffix <- tmp[1, 2] lfix <- sum(tmp[4, 2:3]) - 1 letters2r$line[ffix:lfix]
## [1] 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 ## [36] 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4
letters2r.trim <- letters2r[ffix:lfix, ]
Individual Trial: trimmed
Multiple Trials/Conditions
s180 <- filter(fixdat, eye=="R")
p11 <- ggplot(aes(x=xpos, y=ypos, size=dur), data=s180) +
geom_point(aes(color=(stime-time0)), alpha=1/2) +
scale_color_gradientn(colors=rainbow(4)) +
scale_y_reverse(limits=c(875,200)) +
scale_x_continuous(limits=c(175,1100)) +
coord_fixed() +
guides(size=FALSE) +
geom_hline(yintercept=lines, color="orange") +
facet_wrap(~trial, nrow=2, dir="v")
Also color fixations according to onset time (stime).
Multiple Trials
Color highlights relative durations of trials and helps show fixations out sequence.
Recap of Today
- Reading EDF ASCII files
- Creating Reports
- Interest areas
- Visualizing data (ggplot)
Outline for the Week
- Day 1: Data files
- Experiment Builder Script Setup
- EDF files
- Other EB files
- Day 2: Data viewer
- Visualizing data; QC
- Interest areas
- Creating reports
- Day 3: ET data in R
- Reading EDF ASCII files
- Creating Reports
- Interest areas
- Visualizing data (ggplot)