Building DataViewer Compatible Interest Area Files

Eye movement data can be analyzed by using interest area definitions to pick out specific screen areas for summarizing local gaze behavior. For reading experiments, interest areas may focus on a single word or a multi-word unit depending on needs of the analysis. Given an interest area specification, SRR DataViewer can generate an interest area report to provide information on various gaze measures for each area: fixation count, summed fixation duration, regressions into an interest area, etc.

Using R Package FDBeye to Create SRR Interest Area Files

At this point we assume that the user has created paired bitmap (used as experimental stimuli in, e.g., SRR Experiment Builder) and comma separated region files. File names for the latter will typically end with "region.csv". R and the package FDBeye can be used to create Interest Area Templates compatible with SRR DataViewer.

The following R packages are required:

Steps to get from a *.region.csv file to an SRR *.ias file.

  1. Read the *.region.csv file into a data.frame.
  2. Use its content to generate a region definition character vector.
  3. Write the region definition vector to a region.def file.
  4. Hand edit the region.def file to specify the desired regions.
  5. Use the region.def file to generate an *.ias file suitable for use in DataViewer.

Here are the first three steps in R code:

reg <- read_csv("trial1.region.csv", trim_ws=FALSE)
tmp <- reg2regdef(reg, mrgn.left=86, rgn.maxH=60, rgn.minH=43, rgn.padL=18, rgn.padR=18)
outf <- "trial1.region.def"
writeLines(tmp, con=outf)

The region definition file will typically end with *.region.def. Once the file is saved to the working directory it can be hand edited in any text editor. The text document will include a block of information text layout on the screen as seen by the study participants. This appears in a 'yaml' block at the beginning of the file. Some of this information is read directly from the region.csv file, and some is specified in the function call reg2regdef(). It is easiest to specify this information when the region definition file is created, rather than hand editing it in the region.def file.

The text you want to edit to specify interest area locations will be at the bottom of the *.region.def file and will look something like this:

The quick brown fox jumps over the lazy dog.
...|.....|.....|...|.....|....|...|....|....

Each line of a text stimulus is paired with a 'regioning string'. Within a regioning string, each letter and punctuation mark in the stimulus sentence is marked with a dot, ".", and regions are separated with pipe character, "|". The pipe character marks the first character of a new region. In this example, all regions in the stimulus sentence but the first will begin with a "space". (The first region of a line always begins with the first character.) To edit locations of the interest areas, add or remove "|" characters from the regioning string. Note that the regioning string must be the same length as its paired text line. To maintain the same length between text line and regioning string, any removed "|" must be replaced with a ".".

An edited regioning string in the text document will look like this:

The quick brown fox jumps over the lazy dog.
...................|.....|........|.........

Once you have hand edited the text document to reflect the interest area locations you want save the file.

Preview the new interest areas:

  1. Use the *.region.def file to build a set of regions.
  2. Load the bitmap corresponding to the regions.
  3. Plot the new interest areas over the bitmap.

Here are the steps in R code:

ias2 <- regdef2ias("trial1.region2.def")
write_delim(ias2, "trial1.region2.ias", "\t", col_names=FALSE)
fp2 <- fixPlot(data = data.frame(x=-1, y=-1),
              bgImage = "trial1.png", bgAlpha=1,
              xyMap = ggplot2::aes_string(x='x', y='y'),
              pointMap=ggplot2::aes_string(alpha=0)
              )
fp2 + geom_rect(data=ias2, inherit.aes=FALSE,
               aes(xmin=x1+1, xmax=x2, ymin=y1, ymax=y2,
                   fill=NULL, color=as.factor(regnum%%2)), alpha=0) +
     guides(color=FALSE)

Note that for our purposes, we renamed the *region.def file to reflect the changes made (*region.def > *region2.def). We chose to save and document the process and all the steps included in generating the new interest areas. Unless specified in your own code to be saved with a new name, the original *region.def and *.ias files will be overwritten.

Once the bitmaps and interest area regions have been displayed in R Plots you can visualize the regions as they will appear in DataViewer. If the text regions are not what you want/expect, then you can re-edit your *region.def file, and re-run regdef2ias(), and reload the plot. If the top and bottom boundaries of the regions are not placed appropriately, they can be adjusted by changing argument values rgn.maxH, and rgn.minH to reg2regdef(). See help page for that function.

reg2regdef(reg, mrgn.left=86, rgn.maxH=60, rgn.minH=43, rgn.padL=18, rgn.padR=18)

It is recommended that one *region.def file be hand edited and one *.ias file be generated and checked for accuracy before creating multiple files. Then when you are sure the interest areas locations are appearing as you would like you can generate a full set of region definition files to edit.

Create all the *region.def and *.ias files you need:

  1. Set your working directory to the folder containing all of the *region.csv.
  2. Make a vector of all the files located in your working directory and remove all files that are not *region.csv.
  3. Using a loop function, create one *region.def for each *region.csv.
  4. Hand edit the regioning string in each *region.def.
  5. Then return to R and make a vector of all the files located in your working directory and remove all files that are not *region.def.
  6. Using a loop function, create one *.ias for each *region.def.

Here are steps 2-3 in R code:

flist <- dir()
flist <- flist[str_detect(flist, "region[.]csv")] ## change the regexp as needed to pick out your files
for (ff in flist) {
    reg <- read_csv(ff, trim_ws=FALSE)
    rdef <- reg2regdef(reg, mrgn.left=86, rgn.maxH=60, rgn.minH=43, rgn.padL=18, rgn.padR=18)
    outf <- str_replace(ff, "region.csv$", "region2.def")
    writeLines(rdef, con=outf)
}

Here are steps 5-6 in R code:

flist <- dir()
flist <- flist[str_detect(flist, "region2[.]def")]
for (ff in flist) {
    ias <- regdef2ias(ff)
    outf <- str_replace(ff, "def$", "ias")
    write_delim(ias, outf, delim="\t", col_names=FALSE)
}

Now that your interest area files have been created for each trial you will need to load them into DataViewer. For these steps refer to Interest Areas for Data Analysis.



davebraze/FDBeye documentation built on Nov. 21, 2017, 11:23 a.m.