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Analyze plate images with the SmallUNet pipeline

Source: R/python_engine.R
grayleafspot_analyze.Rd

Calls the bundled Python pipeline (inst/python/pipeline/analysislocal.py) via rvenv_arm_311, performs dish detection and SmallUNet segmentation on each image, and returns a grayleafspot_run object with tidy results.

Usage

grayleafspot_analyze(
  input_dir,
  output_dir = "outputs",
  filenames = NULL,
  plate_diameter_mm = 90,
  run_name = NULL,
  save_outputs = TRUE,
  verbose = TRUE,
  python = NULL,
  engine_model = "localunet"
)

Arguments

input_dir

Character. Path to the folder containing plate images.

output_dir

Character. Base output directory. A timestamped sub-folder is created for each run.

filenames

Optional character vector. Names of specific image files inside input_dir to analyze. If NULL, all images in input_dir are processed.

plate_diameter_mm

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

run_name

Optional character. Human-readable suffix appended to the timestamped run folder name.

save_outputs

Logical. If FALSE, outputs are written to a temporary directory and deleted after the results are returned.

verbose

Logical. Print the saved run path to the console.

python

Optional character. Override the Python executable (see grayleafspot_python_executable()).

engine_model

Character. Must be "localunet".

Value

A grayleafspot_run object with elements $run, $results, and $raw_results.