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##
## Metric to determine times of DC offsets
##
## Copyright (C) 2013 Mazama Science, Inc.
## by Jonathan Callahan, jonathan@mazamascience.com
##
## 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
################################################################################
#
DCOffsetTimesMetric <- function(st, windowSecs=1800, incrementSecs=windowSecs/2, threshold=0.9) {
# Merge traces
tr <- mergeTraces(st,"fillNA")@traces[[1]]
# Get information from the trace
snclq <- tr@id
starttime <- tr@stats@starttime
endtime <- tr@stats@endtime
# Bail out if we have a DC signal
if (isDC(tr)) {
stop(paste("DCOffsetTimesMetric: Trace data is a DC signal."))
}
# Calculate chunk information
windowSamples <- windowSecs * tr@stats@sampling_rate
incrementSamples <- incrementSecs * tr@stats@sampling_rate
outLength <- length(tr) / (incrementSamples)
# Initialize vectors
means <- vector("numeric",outLength) * NA
sds <- vector("numeric",outLength) * NA
indices <- vector("integer",outLength) * NA
# Loop through all chunks
for (i in seq(outLength)) {
lo <- (i-1) * incrementSamples + 1
hi <- lo + windowSamples
means[i] <- mean(tr@data[lo:hi],na.rm=TRUE)
sds[i] <- sd(tr@data[lo:hi],na.rm=TRUE)
indices[i] <- as.integer(lo)
}
# NOTE: diff() returns a vector that is one less than the incoming vector.
# NOTE: Thus, diff(mean)[1] = mean[2]-mean[1].
# NOTE: indices[N] referes to the location at the beginning of mean[N] so we
# NOTE: really want to associate indices[N] with diff(mean[N+1])
metric <- abs(diff(means)) / max(mean(sds,na.rm=TRUE),1)
jumps <- which(metric > threshold) + 1 # because metric is one shorter than indices
dcOffsetTimes <- starttime + indices[jumps]/tr@stats@sampling_rate
# Create and return a MultipleTimeValue metric
m1 <- new("MultipleTimeValueMetric", snclq=snclq, starttime=starttime, endtime=endtime, metricName="dc_offset_times", values=dcOffsetTimes)
return(c(m1))
}
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