Skip to contents

Import a PNG class folder and backfill the rest as "unclassified"

Source: R/database.R
import_png_folder_with_unclassified.Rd

Convenience wrapper that runs import_png_folder_to_db followed by fill_unclassified_db in a single call. After importing the selected-taxa PNGs, it backfills the remaining ROIs of only the samples that were just imported as "unclassified", so each imported sample is fully represented in the database without touching samples from earlier import sessions.

Usage

import_png_folder_with_unclassified(
  png_folder,
  db_path,
  class2use,
  roi_folder,
  class_mapping = NULL,
  annotator = "imported",
  fill = TRUE
)

Arguments

png_folder

Path to the top-level folder containing class subfolders

db_path

Path to the SQLite database file

class2use

Character vector of class names (preserves index order for .mat export)

roi_folder

Base ROI folder path, following the standard IFCB folder structure (roi_folder/YYYY/DYYYYMMDD/sample_name.adc). Used by the backfill step to read each sample's complete ROI list.

class_mapping

Optional named character vector mapping scanned class names to target class names. Passed to import_png_folder_to_db.

annotator

Annotator name (defaults to "imported"). Applied to both the import and the backfill.

fill

Logical. When TRUE (the default), backfill the imported samples with "unclassified" ROIs. Set to FALSE to import only.

Value

Named list with two elements: import (the result of import_png_folder_to_db) and filled (the result of fill_unclassified_db, or zero counts when fill is FALSE or no samples were imported).

See also

import_png_folder_to_db, fill_unclassified_db

Examples

if (FALSE) { # \dontrun{
db_path <- get_db_path("/data/manual")
class2use <- c("Diatom", "Dinoflagellate", "Ciliate")
result <- import_png_folder_with_unclassified(
  "/data/png_export", db_path, class2use,
  roi_folder = "/data/ifcb/raw"
)
cat(result$import$success, "imported,",
    result$filled$added, "backfilled\n")
} # }