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Run the gray leaf spot pipeline — simplified entry point

Source: R/python_engine.R
grayleafspot_run.Rd

A streamlined wrapper around the SmallUNet pipeline designed for everyday use. Unlike grayleafspot_analyze(), this function:

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 appended to the timestamped run folder name (default "run").

engine_model

Character. Must be "localunet" (the only supported pipeline).

plate_diameter_mm

Numeric. Known petri dish diameter in mm (default 90).

Value

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

Details

  • reads the Python interpreter from GRAYLEAFSPOTR_PYTHON (fail-fast with a clear message if it is not set),

  • creates output_dir automatically if it does not exist,

  • returns the raw parsed JSON payload so you can work with results directly.

One-time Python setup

Set the environment variable once per session, or add it to ~/.Rprofile so it is loaded automatically every time R starts:

# In ~/.Rprofile  (open with file.edit("~/.Rprofile"))
Sys.setenv(GRAYLEAFSPOTR_PYTHON = "/path/to/rvenv_arm_311/bin/python")

See also

grayleafspot_analyze() for the full-featured interface that returns a grayleafspot_run S3 object with tidy plotting helpers.