retistruct (version 0.6.3)

retistruct.batch: Batch operation using the parallel package

Description

This function reconstructs a number of datasets, using the R parallel package to distribute the reconstruction of multiple datasets across CPUs. If datasets is not specified the function recurses through a directory tree starting at tldir, determining whether the directory contains valid raw data and markup, and performing the reconstruction if it does.

Usage

retistruct.batch(
  tldir = ".",
  outputdir = tldir,
  datasets = NULL,
  device = "pdf",
  titrate = FALSE,
  cpu.time.limit = 3600,
  mc.cores = getOption("mc.cores", 2L)
)

Arguments

tldir

If datasets is not specified, the top level of the directory tree through which to recurse in order to find datasets.

outputdir

directory in which to dump a log file and images

datasets

Vector of dataset directories to reconstruct

device

string indicating what type of graphics output required. Options are "pdf" and "png".

titrate

Whether to "titrate" the reconstruction for different values of phi0. See titrate.reconstructedOutline.

cpu.time.limit

amount of CPU after which to terminate the process

mc.cores

The number of cores to use. Defaults to the value given by the option mc.cores