procPhotos2 — procPhotos2 • easyfulcrum

procPhotos2 copies raw sample photos, renames them with the C-label and strain name if CeNDR is set to TRUE, and pastes them in data/processed/fulcrum/photos folder. The function also makes thumbnails for use with interactive maps and calculates md5 checksums for images.

procPhotos2(
  dir,
  data,
  max_dim = 500,
  overwrite = FALSE,
  CeaNDR = FALSE,
 
    pub_url = "https://storage.googleapis.com/elegansvariation.org/photos/isolation/fulcrum/"
)

Arguments

dir: The path to the base fulcrum directory, raw/fulcrum/photos. This directory must contain the raw sample photos exported from Fulcrum.
data: a data frame output from the joinGenoFulc function.
max_dim: This value sets the maximum dimension of the resized images in pixels. The default value is 500.
overwrite: Logical, passed to fs::file_copy. If TRUE then existing files with similar names will be written over. Default is FALSE.
CeaNDR: Logical, determines whether to also rename photos to strain names for Caenorhabditis briggsae, Caenorhabditis elegans, Caenorhabditis tropicalis positive collections and add those images to the data/processed/fulcrum/photos/CeaNDR/ directory.
pub_url: A public url that holds sample images organized by <your project>/sampling_thumbs/<C-label>.jpg. For example, if the full url for C-5133 is https://storage.googleapis.com/elegansvariation.org/photos/isolation/fulcrum/2020JanuaryHawaii/sampling_thumbs/C-5133.jpg, the pub_url should be set to https://storage.googleapis.com/elegansvariation.org/photos/isolation/fulcrum/. The project name, "sampling_thumbs", C-label, and file extension will be filled by the function.

Value

A folder named photos in the data/processed/fulcrum directory. The folder contains sample photos renamed with C-labels. If CeNDR is set to TRUE sample photos will be renamed with strain names as well organized by species. A dataframe identical to input data with old and new image file names, md5 photo hash values, and a public url to find images. The function also saves a .rds file to the data/processed/fulcrum directory.