complete pipeline

Complete Pupillometry Pipeline Walkthrough

📦 Introduction

This vignette will walk you through the basics of getting started with the eyeris package to preprocess your (eyelink) pupillometry data from start to finish. Here, we’ll walk through loading in the raw data, preprocessing, and quality control in a step-by-step manner.

We will specifically focus on demonstrating the eyeris::glassbox() function, which we built to streamline, in part, the process of collecting and preprocessing any freshly collected raw pupillometry dataset within minutes to assess the quality of those data while simultaneously running a full preprocessing pipeline in 1-to-2-ish lines of code.

🔎 The Glass Box Function

Our glassbox function – in contrast to a “black box” function where you run it and obtain a result with little-to-no idea as to how you got from raw input to cleaned output – provides a highly opinionated prescription of steps and starting parameters we (computational neuroscientists and signal processing experts at the Stanford Memory Lab) strongly believe any pupillometry researcher should use as their default starting point when preprocessing any set of pupillometry data.

We recommend starting out with the glassbox function to (ideally) reduce the probability of accidental mishaps when “reimplementing” the individual steps that make up the preprocessing pipeline both within and across projects.

Moreover, the glassbox function provides an “interactive” framework where you can evaluate the consequences of the parameters used within each step on your data in real time, therefore facilitating a fairly easy-to-use workflow for parameter optimization on your particular dataset.

In essence, this interactive process takes each opinionated step and allows you to see both pre and post timeseries plots so you can adjust parameters stepwise until you are satisfied with your choices (and their consequences on your pupil timeseries data).

Installing `eyeris`

If you haven’t already installed the eyeris package:

# Install latest stable release from CRAN
# install.packages("eyeris")

# pak
# install.packages("pak")
# pak::pak("shawntz/eyeris")

# Or install the development version from GitHub
# install.packages("devtools")
# devtools::install_github("shawntz/eyeris")

Loading `eyeris` Package

library(eyeris)
#> 
#> eyeris v3.2.0 - Lumpy Space Princess ꒰•ᴗ•｡꒱۶
#> Welcome! Type ?`eyeris` to get started.
#> ** DuckDB not found. Database features are disabled.
#> 
#> => To install DuckDB:
#>   - macOS: install.packages('duckdb', type = 'binary')
#>   - Linux: use system packages (e.g., `sudo apt-get install r-cran-duckdb`)
#>            or install.packages('duckdb') if binaries are available
#>   - Windows: install.packages('duckdb')
#> 
#> Once installed, restart R and reload eyeris to enable database storage
#> (bidsify(..., db_enabled = TRUE) and eyeris_db_* functions).
#> ** Arrow not found. Parquet operations will use DuckDB fallback (slower).
#> 
#> => To install Arrow:
#> 
#>   - macOS:
#>     1. First install system dependencies with Homebrew:
#>        brew update
#>        brew install pkg-config cmake apache-arrow
#>     2. Then install the R package:
#>        install.packages('arrow', type = 'binary')
#> 
#>   - Linux (Ubuntu/Debian):
#>     1. Install system dependencies:
#>        sudo apt-get update
#>        sudo apt-get install -y libcurl4-openssl-dev libssl-dev
#>     2. Then install the R package:
#>        install.packages('arrow')
#> 
#>   - Linux (Fedora/RHEL):
#>     1. Install system dependencies:
#>        sudo dnf install libcurl-devel openssl-devel
#>     2. Then install the R package:
#>        install.packages('arrow')
#> 
#>   - Windows:
#>     install.packages('arrow')
#> 
#> For more details, see: https://arrow.apache.org/docs/r/
#> 
#> Once installed, restart R and reload eyeris to enable faster parquet export/import
#> (eyeris_db_to_parquet(), read_eyeris_parquet(), and related functions).

Loading Your Raw Data

Using the Demo Dataset

For this demo, we’ll use our built in demo dataset, which contains a handful of trials from an associative memory task recorded in our lab.

demo_data <- eyelink_asc_demo_dataset()

Loading Your Own Custom Data

To load your own EyeLink pupillometry data, you need an .asc file converted from your original .edf file using the official EyeLink edf2asc command-line utility provided by SR Research.

Expected Data Format:

The .asc file should be a standard EyeLink ASCII output file containing:

Sample data with timestamps, gaze coordinates (x, y), and pupil size
Event messages (e.g., MSG lines with trial markers, stimulus onsets)
Recording metadata (sample rate, pupil measurement type, etc.)

Example Code for Loading Custom Data:

# Point to your own .asc file
my_data_path <- "/path/to/your/data/participant_01.asc"

# Load the data file
my_data <- eyeris::glassbox(my_data_path)

Important Notes:

File Path: Replace "/path/to/your/data/participant_01.asc" with the actual path to your .asc file.
Block Handling: Use block = "auto" (default) to automatically detect multiple recording segments within the same file. This is recommended for most use cases. See ?eyeris::load_asc for other options.

Binocular Data: If you have binocular recordings, you can specify how to handle them:

# Average both eyes (default)
my_data <- eyeris::glassbox(
  my_data_path,
  load_asc = list(binocular_mode = "average")
)

# Use only left eye
my_data <- eyeris::glassbox(
  my_data_path,
  load_asc = list(binocular_mode = "left")
)

# Use only right eye
my_data <- eyeris::glassbox(
  my_data_path,
  load_asc = list(binocular_mode = "right")
)

# Process both eyes independently
my_data <- eyeris::glassbox(
  my_data_path,
  load_asc = list(binocular_mode = "both")
)

Data Quality: Ensure your data was recorded without online filtering applied by the EyeLink Host PC. The eyeris pipeline expects raw, unfiltered data. See the Caveats section below for more details on this critical requirement.

Running the Fully-Automated Pipeline

Here, we use the example data along with the default prescribed parameters and pipeline recipe:

# Run an automated pipeline with no real-time inspection of parameters
output <- eyeris::glassbox(demo_data)
#> ✔ [2026-07-19 05:45:06] [OKAY] Running eyeris::load_asc()
#> ℹ [2026-07-19 05:45:06] [INFO] Processing block: block_1
#> ✔ [2026-07-19 05:45:06] [OKAY] Running eyeris::deblink() for block_1
#> ✔ [2026-07-19 05:45:06] [OKAY] Running eyeris::detransient() for block_1
#> ✔ [2026-07-19 05:45:06] [OKAY] Running eyeris::interpolate() for block_1
#> ✔ [2026-07-19 05:45:06] [OKAY] Running eyeris::lpfilt() for block_1

#> ! [2026-07-19 05:45:06] [WARN] Skipping eyeris::downsample() for block_1
#> ! [2026-07-19 05:45:06] [WARN] Skipping eyeris::bin() for block_1
#> ! [2026-07-19 05:45:06] [WARN] Skipping eyeris::detrend() for block_1
#> ✔ [2026-07-19 05:45:06] [OKAY] Running eyeris::zscore() for block_1
#> ℹ [2026-07-19 05:45:06] [INFO] Block processing summary:
#> ℹ [2026-07-19 05:45:06] [INFO] block_1: OK (steps: 6, latest:
#> pupil_raw_deblink_detransient_interpolate_lpfilt_z)
#> ✔ [2026-07-19 05:45:06] [OKAY] Running eyeris::summarize_confounds()

# Preview first and second steps of the pipeline
plot(
  output,
  steps = c(1, 2),
  preview_window = c(0, max(output$timeseries$block_1$time_secs)),
  seed = 0
)
#> ℹ [2026-07-19 05:45:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
#> possible blocks: 1

Automatic Sampling-Grid Repair

Before any rate-dependent step runs, glassbox() places each recording block onto the expected uniform sampling grid via eyeris::resample(). Most trackers (e.g., EyeLink) zero-fill missing pupil samples, so their time vector is already evenly spaced and this step is a guaranteed no-op. Some hardware instead drops samples when pupil data is missing, leaving holes that would silently distort filtering, downsampling, and any other step that assumes a fixed sampling rate.

When irregular sampling is detected, resample() repairs the time axis in two stages: it anchors a uniform grid on the first reliable regular interval (so early timing jitter doesn’t offset the whole grid), interpolates local sub-period jitter onto that grid, and inserts NA rows at any longer-than-expected gaps (the dropped samples). Those NA gaps are then filled by the interpolate() step later in the pipeline, and the inserted rows are flagged in an is_resampled column (also surfaced by summarize_confounds() as n_resampled / prop_resampled).

This step runs automatically by default. To disable it, pass resample = FALSE to glassbox().

Running the Pipeline Interactively

output <- eyeris::glassbox(demo_data, interactive_preview = TRUE, seed = 0)

Overriding the Default Parameters

To override the default glassbox parameters directly within the glassbox() function call, you need to pass in the appropriate parameter(s) for each pipeline step to glassbox().

Example

output <- eyeris::glassbox(
  demo_data,
  interactive_preview = FALSE, # TRUE to visualize each step in real-time
  deblink = list(extend = 40),
  lpfilt = list(plot_freqz = FALSE)
)
#> ✔ [2026-07-19 05:45:08] [OKAY] Running eyeris::load_asc()
#> ℹ [2026-07-19 05:45:08] [INFO] Processing block: block_1
#> ✔ [2026-07-19 05:45:08] [OKAY] Running eyeris::deblink() for block_1
#> ✔ [2026-07-19 05:45:08] [OKAY] Running eyeris::detransient() for block_1
#> ✔ [2026-07-19 05:45:08] [OKAY] Running eyeris::interpolate() for block_1
#> ✔ [2026-07-19 05:45:08] [OKAY] Running eyeris::lpfilt() for block_1
#> ! [2026-07-19 05:45:08] [WARN] Skipping eyeris::downsample() for block_1
#> ! [2026-07-19 05:45:08] [WARN] Skipping eyeris::bin() for block_1
#> ! [2026-07-19 05:45:08] [WARN] Skipping eyeris::detrend() for block_1
#> ✔ [2026-07-19 05:45:08] [OKAY] Running eyeris::zscore() for block_1
#> ℹ [2026-07-19 05:45:08] [INFO] Block processing summary:
#> ℹ [2026-07-19 05:45:08] [INFO] block_1: OK (steps: 6, latest:
#> pupil_raw_deblink_detransient_interpolate_lpfilt_z)
#> ✔ [2026-07-19 05:45:08] [OKAY] Running eyeris::summarize_confounds()

Pipeline Steps with Overridable Parameters

eyeris::load_asc(): > block
eyeris::deblink(): > extend
eyeris::detransient(): > n, mad_thresh
eyeris::lpfilt(): > wp, ws, rp, rs, plot_freqz

Advanced: Building the Pipeline Manually

glassbox() is the recommended entry point, but every preprocessing function it wraps is also exported and can be chained together directly as a “building block.” For a complete, deconstructed reference pipeline — each eyeris preprocessing function called in sequence, mapped one-to-one to the default glassbox() recipe — see the Building Blocks Under the Hood section of the Anatomy of an eyeris Object vignette.

💬 Caveats

`Detrend` Step

Detrending is turned off by default.

To enable detrending in the pipeline, pass detrend = TRUE to glassbox(). This removes a straight-line (linear) trend by default. To instead remove a smooth, potentially nonlinear trend with a natural cubic spline of time, pass detrend = list(method = "spline") (optionally tuning the spline degrees of freedom with spline_df, e.g. detrend = list(method = "spline", spline_df = 5)).

**Note: Detrending your pupil timeseries can have unintended consequences; ** **we thus recommend that users understand the implications of detrending – in ** **addition to whether detrending is appropriate for the research design and ** question(s) – before using this function.

I received this message… what does it mean and what should I do?

You (hopefully) shouldn’t encounter this, but if you do, let us explain:

***WARNING: SOMETHING OUTRAGEOUS IS HAPPENING WITH YOUR PUPIL DATA!*** 

The median absolute deviation (MAD) of your pupil speed is 0.
 This indicates a potential setup / hardware issue which has likely propogated 
 into your pupil recording. Most often, this is due to online filtering being 
 applied directly to your pupil data via the EyeLink Host PC.

 WE DO NOT RECOMMEND USING ANY ONLINE AUTO FILTERING DURING YOUR DATA RECORDING.

 ***ADDITIONAL INFO***
The default setting for communicating with the EyeLink
 machine is to have filtering enabled on either live-streamed data or saved data 
 in EDF files.

We do not want these filters because:
 (1) it is unclear how the EyeLink machine is specifying their low-pass filter,
 and (2) it conflicts with an assumption here in `eyeris::detransient()` to use 
 one-step difference to compute a threshold for detecting large jumps in pupil 
 data (suggesting blinking or other artifacts).

 ***GENERAL TIP***
 You should aim to have your data as raw as possible so you can 'cook' it fresh!

 ***WHAT TO DO NEXT***
 If you would like to continue preprocessing your current pupil data file,
 you should consider skipping the `eyeris::detransient()` step of the pipeline 
 altogether. Advanced users might consider additional testing by manually 
 passing in different `mad_thresh` override values into `eyeris::detransient()` 
 and then carefully assessing the consequences of any given override value on 
 the pupil data; however, this step is not recommended for most users.

 PLEASE CONTINUE AT YOUR OWN RISK.

Basically the default setting for communicating with an EyeLink machine is to have filtering enabled on either live-streamed data or saved data in EDF files. You do not want these filters because

it’s unclear what are their low-pass filter specifications, and
it conflicts with an assumption in eyeris::detransient() to use one-step difference to compute a threshold for detecting large jumps in pupil data (suggesting blinking or other artifacts).

In general, you’d like to have your data as raw as possible so you can “cook” it fresh.

So, if your data aren’t as raw as possible, you will need to run eyeris without the detransient step.

To skip the detransient step, pass detransient = FALSE into your glassbox() call.

To skip the detransient step within the glassbox pipeline, pass detrend = TRUE to glassbox().

Some additional notes about preventing live filtering in future recordings…

Unfortunately the Live Sample Filter and Saved Sample Filter are two common settings when experiment software communicates with EyeLink. For example, PsychoPy incorporates them in the eyetracking setting panel, and if you use pylink directly, these two settings are also included in their example script / function used to connect to EyeLink. The same goes for Eprime and NBS Presentation, where these two filter settings are users’ responsibilities to set.

Adjusting the config.ini file on your EyeLink host PC to set the defaults to be OFF is not sufficient as they will get overwritten when experiment software (PsychoPy, Eprime, NBS Presentation, etc.) make the initial connect request.

Therefore, unfortunately all users for all future experiments need to be cognizant of this setting. This is why eyeris::detransient() will yell the long warning message at you (as a reminder to turn off hardware filters).

So moving forward, please consider taking the following recommendations into consideration:

Use pylink directly, add additional optional settings beyond what the SR Research example scripts set so you ping down all the optional settings. In terms of the filter settings, it boils down to calling pylink.EyeLink.setHeuristicLinkAndFileFilter(), but there are other settings that you likely want to hard-code into your experiments.
Use pylink directly, but don’t code additional optional settings into you scripts. Instead, you must manually inspect the settings on the console screen of host PC at the start of each experiment to make sure they are set correctly. Specifically, in terms of the filter settings, you just need to make sure both Online and Saved Sample Filtering are set to OFF on the EyeLink setup screen. It’s on the left column along with the button to auto-threshold and toggle which eye to track. This applies to all the other optional settings too.
Use the builder and ioHub directly, and set these settings in the eyetracking setting panel, which saves to each experiment, so you don’t need to worry about it. Specifically, in terms of the filter settings, you should set FILTER_LEVEL_OFF for both live and saved sample filtering. You can see all the different optional settings here: https://github.com/mh105/psychopy-eyetracker-sr-research/blob/main/psychopy_eyetracker_sr_research/sr_research/eyelink/eyetracker.py.
For most users, we simply recommend using the PsychoPy builder for PsychoPy experiments and use the psychopy-eyetracker-sr-research plug-in maintained by the PsychoPy development team + Alex He, Ph.D., Stanford Postdoctoral Scholar in the Purdon lab under the Department of Anesthesiology and in the Wagner lab under the Department of Psychology, and co-author of eyeris.

📚 Citing `eyeris`

If you use the eyeris package in your research, please cite it!

Run the following in R to get the citation:

citation("eyeris")
#> To cite package 'eyeris' in publications use:
#> 
#>   Schwartz ST, Yang H, Xue AM, He M (2025). "eyeris: A flexible,
#>   extensible, and reproducible pupillometry preprocessing framework in
#>   R." _bioRxiv_, 1-37. doi:10.1101/2025.06.01.657312
#>   <https://doi.org/10.1101/2025.06.01.657312>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {eyeris: A flexible, extensible, and reproducible pupillometry preprocessing framework in R},
#>     author = {Shawn T Schwartz and Haopei Yang and Alice M Xue and Mingjian He},
#>     journal = {bioRxiv},
#>     year = {2025},
#>     pages = {1--37},
#>     doi = {10.1101/2025.06.01.657312},
#>   }

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complete pipeline

Complete Pupillometry Pipeline Walkthrough

📦 Introduction

🔎 The Glass Box Function

Installing `eyeris`

Loading `eyeris` Package

Loading Your Raw Data

Using the Demo Dataset

Loading Your Own Custom Data

Running the Fully-Automated Pipeline

Automatic Sampling-Grid Repair

Running the Pipeline Interactively

Overriding the Default Parameters

Example

Pipeline Steps with Overridable Parameters

Advanced: Building the Pipeline Manually

💬 Caveats

`Detrend` Step

I received this message… what does it mean and what should I do?

Some additional notes about preventing live filtering in future recordings…

📚 Citing `eyeris`

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complete pipeline

Complete Pupillometry Pipeline Walkthrough

📦 Introduction

🔎 The Glass Box Function

Installing eyeris

Loading eyeris Package

Loading Your Raw Data

Using the Demo Dataset

Loading Your Own Custom Data

Running the Fully-Automated Pipeline

Automatic Sampling-Grid Repair

Running the Pipeline Interactively

Overriding the Default Parameters

Example

Pipeline Steps with Overridable Parameters

Advanced: Building the Pipeline Manually

💬 Caveats

Detrend Step

I received this message… what does it mean and what should I do?

Some additional notes about preventing live filtering in future recordings…

📚 Citing eyeris

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Clone this wiki locally

Installing `eyeris`

Loading `eyeris` Package

`Detrend` Step

📚 Citing `eyeris`