#!/usr/bin/env Rscript
# Parallelization based on:
# http://gforge.se/2015/02/how-to-go-parallel-in-r-basics-tips/
# library(parallel)
library(heyexr)
library(argparser)
library(dplyr)
p <- arg_parser("Render OCT summaries in parallel")
p <- add_argument(p, "--vol",
help = "Heidelberg VOL file to parse")
p <- add_argument(p, "--xml",
help = "XML segmentation from OCT Explorer",
default = NULL)
p <- add_argument(p, "--center",
help="XML file specifying the grid center",
default = NULL)
p <- add_argument(p, "--np",
help="Number of cores to use",
default = 1)
# p <- add_argument(p, "--indir",
# help="Directory containing VOL files",
# default = ".")
p <- add_argument(p, "--outdir",
help="Directory to write results",
default = ".")
argv <- parse_args(p)
# Echo the arguments
cat("Parameters:\n")
argv %>% (function(x) data.frame(argument = names(argv), value = unlist(argv)))
# For all the VOL files within a directory, generate SLO images.
# (Capture the nulls from parLapply into a list to prevent them from echoing at the end.)
# temp_list <- parLapply(cl,
# list.files(argv$indir, full.names = TRUE, pattern="VOL"),
# temp_list <- parLapply(cl,
# list.files("~/Desktop/oct_controls", full.names = TRUE, pattern="VOL"),
# render_slo, out_dir = "~/Desktop/oct_controls_slo", draw_margins = FALSE)
render_oct_summary(vol_file = argv$vol,
xml_file = argv$xml,
center_file = argv$center,
out_dir = argv$outdir,
n_cores = as.numeric(argv$np))
cat("Done\n")
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