#! /bin/sh
# get_apdet Joe Mietus Dec 19 2001
#
#-------------------------------------------------------------------------------
# get_apdet: Hilbert transform based apnea detector
# Copyright (C) 2000 Joe Mietus
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
# Place - Suite 330, Boston, MA 02111-1307, USA.
#
# You may contact the author by e-mail (joe at physionet dot org) or postal mail
# (MIT Room E25-505A, Cambridge, MA 02139 USA). For updates to this software,
# please visit PhysioNet (http://www.physionet.org/).
#_______________________________________________________________________________
USAGE="$0 record annotator
This program takes a record name and the name of an annotation file
and produces an output listing the times of sleep apnea detections
and the total fraction of time with such detections.
"
BINDIR=/usr/local/bin
PATH=$BINDIR/apdet:$PATH
NFLAG='-a N'
FILT="0.2 20 -x 0.4 2.0"
RESAMP=1.0
DETREND=40
SMOOTH=5
MEDFILT=60 # length of filter (in units of 1/RESAMP seconds)
NORM=1
AVSDOUT="1:00 5:00"
MINLEN=15:00
AMPTHRES="-0.555 1.3"
# thresholds
AVAMP0=0.65
AVAMP1=2.5
SDAMP0=0
SDAMP1=0.6
AMPTIME0=0.006
AMPTIME1=1
AVFREQ0=0.01
AVFREQ1=0.055
SDFREQ0=0
SDFREQ1=0.01
FREQTIME0=0.7
FREQTIME1=1
if test $# -lt 2
then
echo "$USAGE"
exit 1
fi
REC=$1
ANN=$2
INCR=`echo $AVSDOUT | awk '{print $1}'`
set $AVSDOUT
if test $# -eq 2
then WIN=`echo $AVSDOUT | awk '{print $2}'`
else WIN=$INCR
fi
AVSDARGS="$INCR $WIN"
# get hilbert transform
rrlist $ANN $REC $NFLAG -s |
awk "{printf \"%.3f %g\n\", \$1, \$2}" >foo.rr
cat foo.rr |
filt $FILT |
linsamp $RESAMP |
ldetrend $DETREND |
smooth $SMOOTH >foo.filt
# MEDFILT=`echo "$MEDFILT / $RESAMP" | bc`
cat foo.filt |
ht |
awk "{\$3 /= $RESAMP; print}" |
htmedfilt $MEDFILT >foo.ht
AVAMP=`awk '{print $2}' <foo.ht | av | awk '{print $2}'`
awk "{\$2 /= $AVAMP; print}" <foo.ht >foo.ht.norm
mv foo.ht.norm foo.ht
# get ht avs and sds
AMPLIMS=`awk '{print $2}' <foo.ht | mm`
MID=`echo "$AMPLIMS" | awk '{printf "%g\n", ($1+$2)/2}'`
THRES=`echo "$AMPTHRES $MID" | awk '{print $1 + $2*($3+1)/2}'`
cat foo.ht |
htavsd $AVSDARGS $THRES >foo.avsd
# get ht detections
awk "\$2>=$AVAMP0 && \$2<=$AVAMP1 && \
\$3>=$SDAMP0 && \$3<=$SDAMP1 && \
\$4>=$AMPTIME0 && \$4<=$AMPTIME1 && \
\$5>=$AVFREQ0 && \$5<=$AVFREQ1 && \
\$6>=$SDFREQ0 && \$6<=$SDFREQ1 && \
\$7>=$FREQTIME0 && \$7<=$FREQTIME1 \
{print \$1}" foo.avsd >foo.avsd.det
if test -s foo.avsd.det
then
cat foo.avsd.det |
detruns $INCR $WIN $MINLEN >foo.det
DETLEN=`tail -1 foo.det`
else
DETLEN=00:00:00
fi
DETLENSEC=`echo $DETLEN | awk -F: '{print $1*3600+$2*60+$3}'`
RRSTART=`head -1 foo.rr | awk '{print $1}'`
RREND=`tail -1 foo.rr | awk '{print $1}'`
TOTLEN=`echo $RRSTART $RREND |
awk '{T=$2-$1; printf "%02d:%02d:%02d\n", \
T/3600, (T%3600)/60, int(T%60)}'`
TOTLENSEC=`echo $TOTLEN | awk -F: '{print $1*3600+$2*60+$3}'`
cat foo.det 2>/dev/null |
awk "NF==2 {printf \"%s - %s\n\", \$1, \$2}
END {printf \"\ntot = $DETLEN / $TOTLEN = %.3f\n\", \
$DETLENSEC / $TOTLENSEC}"
rm -f foo.rr foo.filt foo.ht foo.avsd foo.avsd.det foo.det