#! /bin/sh
# file: genresults.sh G. Moody 22 March 2012
# Shell script for processing a Challenge 2012 data set with a Challenge entry
# Version 1.0 (22 March 2012)
# A script similar to this one will be used as part of the evaluation of
# Challenge entries written in C. A companion script will be used to perform
# the same function for Challenge entries written in MATLAB m-code. We have
# provided these scripts so that Challenge participants can test their entries
# to verify that they run properly in the environment that will be used to test
# them.
# Each Challenge .txt file (record) contains data for one patient, in 3 columns
# (timestamp, parameter, and value). The three Challenge data sets contain
# 4000 records each.
# This script supplies a complete set of 4000 records, one at a time, to an
# entry, and collects its output for each record (a binary prediction of
# survival, for event 1, and an estimate of mortality risk, for event 2)
# in a summary output file.
# The summary output file is then scored by comparing its contents with the
# patients' known outcomes. This script invokes a small C program ('score')
# that can calculate unofficial scores for the training data (set A), for which
# the known outcomes are provided to participants. Entries will be ranked using
# official scores obtained using the same methods, but based on testing with
# sets B and C, for which the outcomes are not provided to participants.
# If your entry is written in C, it must be compilable into an executable
# program named physionet2012, which reads the contents of a Challenge record
# from its standard input and writes the results of its analysis to its
# standard output, as a single line containing the RecordID (read from the
# input), a binary prediction (0: survival, 1: death), and a risk estimate
# (0: certain survival, 1: certain death). Example:
# 123456,0,0.16
# See the sample entry at http://physionet.org/challenge/2012/physionet2012.c
# for details.
# To use this script to obtain an unofficial score for your entry on set A:
# 1. Download these files from http://physionet.org/challenge/2012/ and save
# them in your working directory:
# genresults.sh (this file)
# score.c (program needed to calculate scores)
# set-a.zip or set-a.tar.gz (zip archive or tarball of set A files)
# Outcomes-a.txt (known outcomes for set A)
# 2. Compile score.c . Using gcc, this can be done by:
# gcc -o score score.c
# 3. Unzip set-a.zip (or unpack set-a.tar.gz), creating a subdirectory within
# your working directory called 'set-a'. When you have completed this
# step, the set-a directory should contain 4000 individual .txt files.
# 4. Save an executable version of your entry (physionet2012) in your working
# directory.
# 5. Run this script by:
# ./genresults set-a
# You can also use this script to run your entry on test set B, but it will
# not be able to calculate scores in this case, since the outcomes are provided
# for set A only. To do this, download and unzip/unpack set B into a 'set-b'
# subdirectory as you did for set A, and run:
# ./genresults set-b
if [ $# != 1 ]
then
echo Supply the name of the directory containing the data set. Type either
echo " $0 set-a"
echo or
echo " $0 set-b"
exit
fi
case $1 in
set-a) S=a; OUT=Outputs-a.txt ;;
set-b) S=b; OUT=Outputs-b.txt ;;
*) echo Choose either set-a or set-b.
exit ;;
esac
for R in $1/*.txt
do
./physionet2012 <$R >>$OUT
echo $R
done
if [ -s Outcomes-$S.txt ]
then
./score $OUT Outcomes-$S.txt >Score-$S.txt 2>Plot-$S.txt
echo
cat Score-$S.txt
fi