# Building Your Own Custom Pipeline Extensions

One key strength of the preprocessing framework within `eyeris` is its modularity.

While we encourage most users to use the `glassbox()` function for simplicity and reproducibility, advanced users can create custom preprocessing steps that seamlessly integrate into the pipeline.

This vignette walks you through the structure required to write your own `eyeris`-compatible preprocessing functions.

## 🧩 How the Pipeline Works

Under the hood, each preprocessing function in `eyeris` is a wrapper around a core operation that gets tracked, versioned, and stored using the `pipeline_handler()`.

Custom pipeline steps must conform to the `eyeris` protocol for maximum compatibility with the downstream functions we provide.

Following the `eyeris` protocol also ensures: - all operations follow a predictable structure, and - that new pupil data columns based on previous operations in the chain are able to be dynamically constructed within the core `timeseries` data frame.

For instance: `pupil_raw -> pupil_raw_deblink -> pupil_raw_deblink_detransient -> ...`

If you’re unfamiliar with how these columns are structured and tracked, first check out the companion vignette: 📦 Anatomy of an `eyeris` Object.

## 🛠️Creating a Custom Extension for `eyeris`

Let’s say you want to write a new `eyeris` extension function called `winsorize()` to apply winsorization to extreme pupil values.

### 1) Write the core operation function

This function should accept a data frame `x`, a string `prev_op` (i.e., the name of the previous pupil column), and any custom parameters.

#### To illustrate:

    winsorize_pupil <- function(x, prev_op, lower = 0.01, upper = 0.99) {
      vec <- x[[prev_op]]
      q <- quantile(vec, probs = c(lower, upper), na.rm = TRUE)
      vec[vec < q[1]] <- q[1]
      vec[vec > q[2]] <- q[2]
      vec
    }

### 2) Create the wrapper using the `eyeris::pipeline_handler()`

The `pipeline_handler()` enables your function to automatically:

- track your function within the `eyeris` list object’s `params` field,
- append a new column to each block within the `timeseries` list of data frames, and
- update the object’s `latest` pointer.

#### To illustrate:

    #' Winsorize pupil values
    #'
    #' Applies winsorization to extreme pupil values within each block.
    #'
    #' @param eyeris An `eyeris` object created by [load_asc()].
    #' @param lower Lower quantile threshold. Default is 0.01.
    #' @param upper Upper quantile threshold. Default is 0.99.
    #' @param call_info A list of call information and parameters. If not provided,
    #'   it will be generated from the function call.
    #'
    #' @return Updated `eyeris` object with new winsorized pupil column.
    winsorize <- function(eyeris, lower = 0.01, upper = 0.99, call_info = NULL) {
      # create call_info if not provided
      call_info <- if (is.null(call_info)) {
        list(
          call_stack = match.call(),
          parameters = list(lower = lower, upper = upper)
        )
      } else {
        call_info
      }

      # handle binocular objects
      if (is_binocular_object(eyeris)) {
        # process left and right eyes independently
        left_result <- eyeris$left |>
          pipeline_handler(
            winsorize_pupil,
            "winsorize",
            lower = lower,
            upper = upper,
            call_info = call_info
          )

        right_result <- eyeris$right |>
          pipeline_handler(
            winsorize_pupil,
            "winsorize",
            lower = lower,
            upper = upper,
            call_info = call_info
          )

        # return combined structure
        list_out <- list(
          left = left_result,
          right = right_result,
          original_file = eyeris$original_file,
          raw_binocular_object = eyeris$raw_binocular_object
        )

        class(list_out) <- "eyeris"

        return(list_out)
      } else {
        # regular eyeris object, process normally
        eyeris |>
          pipeline_handler(
            winsorize_pupil,
            "winsorize",
            lower = lower,
            upper = upper,
            call_info = call_info
          )
      }
    }

### 3) Understanding Call Stack Tracking

The `call_info` parameter is crucial for maintaining reproducibility and debugging in `eyeris`. It captures:

- `call_stack`: The exact function call that was made (using `match.call()`)
- `parameters`: A list of all parameters passed to your function

This information is automatically stored in `eyeris$params[[new_suffix]]` and can be used for: - Generating reproducible reports - Debugging pipeline issues - Tracking parameter changes across different runs

Important Notes: - Always include `call_info = NULL` as the last parameter in your function signature - Use `match.call()` to capture the function call - Pass all your function parameters in the `parameters` list - Always pass `call_info = call_info` as the last argument to `pipeline_handler()`

### 4) Function Structure Breakdown

1. Function signature: Always include `call_info = NULL` as the last parameter
2. Call info creation: Create the call_info list if not provided
3. Pipeline handler call: Pass all parameters including call_info
4. Parameter order:
   - First: `eyeris` object
   - Second: your core operation function name
   - Third: the suffix for column naming
   - Fourth+: your function parameters
   - Last: `call_info = call_info`

## 🎉 And that’s it!

You should now be able to use your new function extension as a component within a new custom `eyeris` pipeline declaration. To illustrate:

    system.file("extdata", "memory.asc", package = "eyeris") |>
      eyeris::load_asc(block = "auto") |>
      eyeris::deblink(extend = 50) |>
      winsorize()

## 💪 Best Practices

- Use consistent naming: i.e., match your suffix (e.g. `"winsorize"`) to the column and log structure:
  - If you call `pipeline_handler(..., "winsorize")`
  - Then, your function names should reflect that:
    - the public facing `winsorize()` wrapper function, and
    - the private `winsorize_pupil()` logic implementation function.
  - You will then see `pupil_raw_*_winsorize` as the new output column!
- Respect previous steps: Your custom function should rely only on `prev_op`, not on any hardcoded column names!
- Return the expected data type: Be sure that you private function always returns a modified vector type, as the underlying `pipeline_handler()` is looking out for a vector it can transpose into the new column that will be added to the `timeseries` data frame within the resulting `eyeris` object.
- Test on individual blocks: Always try your private function logic on a single data block (e.g., `eyeris$timeseries[[1]]`) to debug before integrating it with the `eyeris` pipeline protocol.
- Include call stack tracking: Always implement proper `call_info` handling for reproducibility and debugging capabilities.

## 🔍 Advanced: Custom Call Info Handling

For more complex functions, you might want to customize the `call_info` structure:

    custom_function <- function(eyeris, param1, param2, call_info = NULL) {
      # custom call_info with additional metadata
      call_info <- if (is.null(call_info)) {
        list(
          call_stack = match.call(),
          parameters = list(param1 = param1, param2 = param2),
          metadata = list(
            timestamp = Sys.time(),
            version = "1.0.0",
            description = "Custom processing step"
          )
        )
      } else {
        call_info
      }

      pipeline_handler(
        eyeris,
        custom_pupil_function,
        "custom",
        param1 = param1,
        param2 = param2,
        call_info = call_info
      )
    }

## ✨ Summary

We hope you are now convinced at the power and extensibility the `eyeris` protocol enables! As we demonstrated here, with just a little bit of structure, you can create custom extension steps tailored to your specific analysis needs – all while preserving the reproducibility and organizational core principles `eyeris` was designed and built around.

If you’d like to contribute new steps to `eyeris`, feel free to open a pull request or discussion on GitHub!

## 📚 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},
    #>   }