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#' ---
#' title: Wrapper for changepoint.np package in TCPDBench
#' author: G.J.J. van den Burg
#' date: 2019-09-30
#' license: See LICENSE file.
#' copyright: 2019, The Alan Turing Institute
#' ---
library(argparse)
library(changepoint.np)
load.utils <- function() {
# get the name of the current script so we can load utils.R (yay, R!)
cmd.args <- commandArgs(trailingOnly=F)
file.arg <- "--file="
this.script <- sub(file.arg, "", cmd.args[grep(file.arg, cmd.args)])
this.dir <- dirname(this.script)
utils.script <- file.path(this.dir, 'utils.R')
source(utils.script)
}
parse.args <- function() {
parser <- ArgumentParser(description='Wrapper for changepoint.np package')
parser$add_argument('-i',
'--input',
help='path to the input data file',
required=TRUE
)
parser$add_argument('-o',
'--output',
help='path to the output file')
parser$add_argument('-p',
'--penalty',
choices=c(
'None',
'SIC',
'BIC',
'MBIC',
'AIC',
'Hannan-Quinn',
'Asymptotic'
),
help='Choice of penalty in the cpt function',
default='MBIC'
)
parser$add_argument('-q',
'--nquantiles',
type='integer',
help='Number of quantiles to use',
default=10
)
return(parser$parse_args())
}
main <- function() {
args <- parse.args()
# load the data
data <- load.dataset(args$input)
# get the parameter list
defaults <- list(method='PELT',
test.stat='empirical_distribution',
minseglen=1)
params <- make.param.list(args, defaults)
if (data$origina$n_dim > 1) {
# changepoint.np package can't handle multidimensional data
exit.error.multidim(data$original, args, params)
}
vec <- as.vector(data$mat)
start.time <- Sys.time()
result <- tryCatch({
locs <- cpt.np(vec,
penalty=params$penalty,
method=params$method,
test.stat=params$test.stat,
minseglen=params$minseglen,
nquantiles=params$nquantiles,
class=FALSE
)
list(locations=locs, error=NULL)
}, error=function(e) {
return(list(locations=NULL, error=e$message))
})
stop.time <- Sys.time()
runtime <- difftime(stop.time, start.time, units="secs")
if (!is.null(result$error)) {
exit.with.error(data$original, args, params, result$error)
}
# convert indices to 0-based indices
locations <- as.list(result$locations - 1)
exit.success(data$original, args, params, locations, runtime)
}
load.utils()
main()
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