Run the gray leaf spot pipeline — simplified entry point — grayleafspot

A streamlined wrapper around the SmallUNet pipeline. Python dependencies are resolved automatically via basilisk — no manual environment setup is required.

Usage

grayleafspot_run(
  input_dir,
  output_dir,
  run_name = "run",
  engine_model = "localunet",
  plate_diameter_mm = 90
)

Arguments

input_dir: Character. Path to the folder containing plate images.
output_dir: Character. Directory to write outputs into (created if absent).
run_name: Character. Human-readable label for the run (default "run").
engine_model: Character. Must be "localunet".
plate_diameter_mm: Numeric. Known petri dish diameter in mm (default 90).

Value

A named list parsed from the pipeline JSON output, containing $results (per-image feature records) and $run (manifest metadata).

Details

Workflow

library(grayleafspotr)

res <- grayleafspot_run(
  input_dir  = "path/to/images",
  output_dir = "outputs",
  run_name   = "trial_01"
)
res$results   # per-image feature table

Advanced: developer Python override

Set GRAYLEAFSPOTR_PYTHON in ~/.Rprofile to use a specific interpreter (e.g. a local rvenv_arm_311). This is not needed for normal use.

# ~/.Rprofile — developer only
Sys.setenv(GRAYLEAFSPOTR_PYTHON = "/path/to/rvenv_arm_311/bin/python")

Examples

# \donttest{
  img_dir <- system.file("extdata", "testdata", "06FEB", package = "grayleafspotr")
  result <- grayleafspot_run(img_dir, tempdir())
# }

Run the gray leaf spot pipeline — simplified entry point