R/readBinTemplates.R

In jonkatz2/monitoR: Acoustic Template Detection in R

# For reading in one or more binary template files and creating a template list
# Modified: 2015 APR 2

readBinTemplates <-
function(
   files = NULL,                # Named vector of files to read in
   dir = '.',                   # Or a directory to look in for files with a specified ext
   ext = 'bt',                  # Extension for binary template files
   parallel = FALSE
) {

   # Select lapplyfun
   if(parallel) {
      lapplyfun <- function(X, FUN) parallel::mclapply(X, FUN, mc.cores = parallel::detectCores())
   } else lapplyfun <- lapply

   # If needed, determine files
   if(is.null(files)) {
      filesfull <- list.files(path = dir, full.names = TRUE, pattern = paste('\\.', ext, '$', sep = ''))
      files <- list.files(path = dir, pattern = paste('\\.', ext, '$', sep = ''))
      names(filesfull) <- gsub("\\.[^.]*$", "", files)
      #names(filesfull) <- sapply(files, function(x) strsplit(x, '\\.')[[1]][1])
   } else {
      filesfull <- paste(dir, '/', files, sep = '')
      names(filesfull) <- if(is.null(names(files))) gsub("\\.[^.]*$", "", files) else names(files)
   }

   # Read in templaes
   template.L <- lapplyfun(filesfull, function(x) readOneBinTemplate(file = x))

   # Return template list
   templates <- new('binTemplateList', templates = template.L)
   return(templates)
}