Collect all images of a species

This function will fetch all images of a particular species from all camera trap stations and copies these images to a new location. The images which are to be copied are found in one of 2 possible ways, 1) by providing an existing record table (created with recordTable) or 2) by reading species IDs from species directories or from metadata (calling ExifTool). Earlier in the workflow, i.e., before running this function, images should have been renamed (with imageRename) to give images unique file names based on station ID and date/time.

getSpeciesImages(
  species,
  recordTable,
  speciesCol = "Species",
  stationCol = "Station",
  inDir,
  outDir,
  createStationSubfolders = FALSE,
  IDfrom,
  metadataSpeciesTag,
  metadataHierarchyDelimitor = "|"
)

Arguments

species

character. Species whose images are to be fetched

recordTable

data frame. A data frame as returned by function recordTable. If you specify this argument, do not specify inDir

speciesCol

character. Name of the column specifying species ID in recordTable. Only required if recordTable is defined

stationCol

character. Name of the column specifying station ID in recordTable. Only required if recordTable is defined

inDir

character. Directory containing identified (species level) camera trap images sorted into station subdirectories (e.g. inDir/StationA/). If you specify this argument, do not specify recordTable.

outDir

character. Directory in which to save species images. A species subdirectory will be created in outDir automatically.

createStationSubfolders

logical. Save images in station directories within the newly created species directory in outDir?

IDfrom

character. Read species ID from image metadata ("metadata") of from species directory names ("directory")? Only required if inDir is defined.

metadataSpeciesTag

character. The species ID tag name in image metadata (if IDfrom = "metadata"). Only required if inDir is defined.

metadataHierarchyDelimitor

character. The character delimiting hierarchy levels in image metadata tags in field "HierarchicalSubject". Either "|" or ":" (if IDfrom = "metadata"). Only required if inDir is defined and IDfrom = "metadata".

Value

A data.frame with old and new directories and file names and the copy status (copy_ok; TRUE if copying was successful, FALSE if not).

Details

The function finds the images to be copied by either consulting a record table created with recordTable or by reading species IDs from images. The former is considerable faster because ExifTool is not called, but requires images to be in precisely the location given by the columns Directory and FileName in recordTable. To use this feature, provide the function with a record table in argument recordTable.

If you'd rather read species IDs from images within the function (to make sure all file paths are correct), images need to be in the directory structure required by the package, e.g.

> inDir/Station/Species

or

> inDir/Station/Camera/Species

if using species directories for species IDs, and

> inDir/Station

or

> inDir/Station/Camera

if reading IDs from species metadata tags. In the latter case, only station directories are needed. In any case, the argument species must match species IDs (either the speciesCol in recordTable, species directory names or species metadata tags).

Before running the function, first rename the images using function imageRename to provide unique file names and prevent several images from having the same name (if generic names like "IMGP0001.jpg" are used). The function will not copy images if there are duplicate filenames to prevent overwriting images unintentionally.

Author

Juergen Niedballa

Examples

if (FALSE) {
# define image directory
wd_images_ID <- system.file("pictures/sample_images_species_dir", package = "camtrapR")
wd_images_ID_copy <- file.path(tempdir(), "sample_images_species_dir")

species_to_copy <- "VTA"    # = Viverra tangalunga, Malay Civet

specImagecopy <- getSpeciesImages(species                 = species_to_copy,
                                  inDir                   = wd_images_ID,
                                  outDir                  = wd_images_ID_copy,
                                  createStationSubfolders = FALSE,
                                  IDfrom                  = "directory"
                                  )
}