R/readDTA.R
In jbrzusto/motus-R-package: Operate a server to process data for http://motus.org
#' read a lotek .DTA file
#'
#' .DTA Files are generated by Lotek receiver software, and contain interspersed
#' blocks of tag detections, antenna settings, and other metadata.
#'
#' @param filename if specified, gives the full path to the .DTA file
#'
#' @param lines if specified, this is a character vector of lines from the .DTA file
#' (helpful if it has already been read in for some reason). If NULL (the default),
#' this function reads the file specified by \code{filename}
#'
#' @param numLines the maximum number of lines to read from the file.
#' Useful if reading the file only to get a serial number, which
#' is within the first 20 lines. Default: -1, which reads all lines.
#'
#' @return A named list with some or all of these items:
#'
#' \itemize{
#' \item recv serial number; e.g. "Lotek-123"
#' \item siteCode; integer; code for site
#' \item tags a data.frame with these columns:
#' \itemize{
#'
#' \item ts numeric GMT timestamp (seconds since 1 Jan 1970)
#' \item id integer, no 999s
#' \item ant factor - Lotek antenna name
#' \item sig signal strength, in raw Lotek units (0..255)
#' \item lat if available, NA otherwise
#' \item lon if available, NA otherwise
#' \item dtaline line in the original .DTA file for this detection, beginning at 1
#' \item antfreq antenna listening frequency, in MHz
#' \item gain gain setting in place during this detection (0..99)
#' \item codeset factor - Lotek codeset name "Lotek3" or "Lotek4" so far
#'
#' }
#' \item pieces chunks of text of various types
#' \item piece.lines.before number of lines before pieces of various types
#' \item boottimes character of formatted boot timestamps
#' }
#'
#' @note The .DTA file is processed in lexical order, so that changes
#' to antenna frequency settings etc. are taken into account in
#' subsequent detection blocks.
#'
#' @export
#'
#' @author John Brzustowski \email{jbrzusto@@REMOVE_THIS_PART_fastmail.fm}
readDTA = function(filename="", lines=NULL, numLines=-1) {
if (is.null(lines))
## read the DTA file in; we don't sweat line endings this way
lines = readLines(filename, n = numLines)
## fix encoding: wherever there are non-ascii characters, assume 'Latin-1'
## see: https://github.com/jbrzusto/motusServer/issues/429
Encoding(lines) = "latin1"
date.format = "%m/%d/%y %H:%M:%OS"
## frequency and gain tables, needed for figuring out the antenna frequency and
## power for each detection
gain.tab = numeric()
freq.tab = numeric()
## paste text into one big string
lines = paste(lines, collapse="\n")
## start with a NULL tags dataframe
tags = NULL
## match against a regular expression to find tables - this splits the file
## up into recognizable blocks, in the order in which they appear there.
## We read and interpret those blocks later.
res = gregexpr(ltDTAregex, lines, perl=TRUE)[[1]]
clen = t(attr(res, "capture.length"))
cstart = t(attr(res, "capture.start"))
parts = clen != 0
pieces = stri_sub(lines, cstart[parts], length = clen[parts])
names(pieces) = rownames(clen)[1 + ((which(parts)-1) %% nrow(clen))]
newlines = gregexpr("\n", lines)[[1]]
piece.lines.before = sapply(cstart[parts], function(x) sum(newlines < x))
## each element of the character vector 'pieces' is the body of a
## table.
## Interpret these now.
codeset = as.character(NA)
boottimes = character(0)
site_code = NA
serno = NA
for (ip in seq(along=pieces)) {
if (nchar(pieces[ip]) == 0)
next
piece.name = names(pieces)[ip] ## can be repeated
## to keep line counts valid, retain blank lines within tables as rows of NA
con = textConnection(pieces[ip])
tab = read.table(con, as.is=TRUE, blank.lines.skip=FALSE)
close(con)
switch(piece.name,
model = {
model = tab[1, 1]
},
serial_no = {
serno = tab[1, 1]
},
boottime = {
boottimes = c(boottimes, paste(tab[1,1], tab[1, 2]))
},
site_code = {
site_code = tab[1, 1]
},
code_set = {
codeset = tab[1, 1]
},
active_scan = {
## make a lookup table for frequency by channel
freq.tab[as.character(tab[,1])] = tab[,2]
},
antenna_gain = {
## make a lookup table for gain by antenna
## We use this to adjust observed power i.e. we reduce
## power by a factor of gain. A brief lab trial
## showed an approximate increase of recorded signal
## strength of 40 units for each 10 unit increase in gain,
## so we reduce signal strength by 4 * gain before converting
## to dB way below.
gain.tab[as.character(tab[,1])] = tab[,2]
},
id_manual = {
## manually triggered readings are fully self-contained with these columns
## Date Time Freq [MHz] Gain Tag ID Antenna Power Data Latitude Longitude
## 1 2 3 4 5 6 7 8 9 10
## parse date / time from first two columns
tab = data.frame(
ts = as.numeric(as.POSIXct(strptime(paste(tab[[1]], tab[[2]]), date.format, tz="GMT"))),
id = tab[[5]],
ant = tab[[6]],
sig = tab[[7]],
lat = tab[[9]],
lon = tab[[10]],
dtaline = piece.lines.before[ip] + seq_len(nrow(tab)),
antfreq = tab[[3]],
gain = tab[[4]],
codeset = factor(1, labels=codeset),
stringsAsFactors = FALSE)
tags = rbind(tags, tab)
},
## default =
{
## this is a table of tag hits, either ID only or ID + GPS
tab[1] = as.numeric(as.POSIXct(strptime(paste(tab[[1]], tab[[2]]), date.format, tz="GMT")))
tab = tab[-2]
if (piece.name == "id_only")
tab = cbind(tab, NA, NA) ## lat and lon not available
names(tab) = c("ts", "chan", "id", "ant", "sig", "lat", "lon")
tab$dtaline = piece.lines.before[ip] + seq_len(nrow(tab))
tab$ant = as.character(tab$ant)
tab = subset(tab, id != 999)
## fill in the appropriate gain value, or a best guess
ants = unique(tab$ant)
bad.ants = is.na(gain.tab[ants])
if (any(bad.ants)) {
## the table refers to antenna for which we haven't seen a gain settings
## It appears that on the SRX-DL, if there are two antennas,
## and one of them is AH0, that antenna appears with a number in tag hit records
if (sum(bad.ants) == 1 && !is.na(gain.tab["AH0"]) && ! all(tab$ant == "AH0")) {
## use the gain for AH0, as this is presumably the same antenna
gain.tab[ants[bad.ants]] = gain.tab["AH0"]
} else {
## use the gain from the first antenna with known gain, otherwise, use
## 80 as this was common
if (all(is.na(gain.tab))) {
gain.to.use = 80
gain.source = " but NO GAIN VALUES WERE SPECIFIED FOR ANY ANTENNA!"
} else {
gain.to.use = gain.tab[which(!is.na(gain.tab))[1]]
gain.source = paste(" specified for antenna '", names(gain.tab)[which(!is.na(gain.tab))[1]], "'", sep="")
}
gain.tab[ants[bad.ants]] = gain.to.use
warning("Warning: No gain setting found for antenna number(s): ", paste(ants[bad.ants], collapse=", "),
" specified in ", piece.name, " table.\nUsing gain value of ", gain.to.use, gain.source, "\n")
}
}
## get frequency from latest frequency table
tab$antfreq = freq.tab[as.character(tab$chan)]
## report the gain setting in use
tab$gain = gain.tab[tab$ant]
## fill in the current codeset, if any rows were found
if(nrow(tab) > 0)
tab$codeset = factor(1, labels=codeset)
## remove the channel setting, which is redundant
tab$chan = NULL
tags = rbind(tags, tab)
}
)
}
## sort in order by time; record with and without GPS fixes are segregated
## in the DTA file, even though their timestamps might be interleaved.
## (why are GPS fixes intermittent? weird...)
if (! is.null(tags)) {
tags = subset(tags, ! is.na(tags$ts))
tags = tags[order(tags$ts),]
}
serno = paste0("Lotek-", serno)
if (! is.na(site_code)) {
## if a site_code was present, use it to possibly disambiguate duplicated
## receivers. Note that as soon as a rule matches, we use it and don't
## look at further rules.
rules = MetaDB("select * from serno_collision_rules where serno=%s order by id", serno, .QUOTE=TRUE)
for (i in seq_len(nrow(rules))) {
if (isTRUE(eval(parse(text = rules$cond[i])))) {
serno = paste0(serno, rules$suffix[i])
break
}
}
}
return (list(tags=tags, recv = serno, siteCode = site_code, pieces = pieces, piece.lines.before = piece.lines.before, boottimes = boottimes))
}
jbrzusto/motus-R-package documentation built on May 18, 2019, 7:03 p.m.
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#' read a lotek .DTA file
#'
#' .DTA Files are generated by Lotek receiver software, and contain interspersed
#' blocks of tag detections, antenna settings, and other metadata.
#'
#' @param filename if specified, gives the full path to the .DTA file
#'
#' @param lines if specified, this is a character vector of lines from the .DTA file
#' (helpful if it has already been read in for some reason). If NULL (the default),
#' this function reads the file specified by \code{filename}
#'
#' @param numLines the maximum number of lines to read from the file.
#' Useful if reading the file only to get a serial number, which
#' is within the first 20 lines. Default: -1, which reads all lines.
#'
#' @return A named list with some or all of these items:
#'
#' \itemize{
#' \item recv serial number; e.g. "Lotek-123"
#' \item siteCode; integer; code for site
#' \item tags a data.frame with these columns:
#' \itemize{
#'
#' \item ts numeric GMT timestamp (seconds since 1 Jan 1970)
#' \item id integer, no 999s
#' \item ant factor - Lotek antenna name
#' \item sig signal strength, in raw Lotek units (0..255)
#' \item lat if available, NA otherwise
#' \item lon if available, NA otherwise
#' \item dtaline line in the original .DTA file for this detection, beginning at 1
#' \item antfreq antenna listening frequency, in MHz
#' \item gain gain setting in place during this detection (0..99)
#' \item codeset factor - Lotek codeset name "Lotek3" or "Lotek4" so far
#'
#' }
#' \item pieces chunks of text of various types
#' \item piece.lines.before number of lines before pieces of various types
#' \item boottimes character of formatted boot timestamps
#' }
#'
#' @note The .DTA file is processed in lexical order, so that changes
#' to antenna frequency settings etc. are taken into account in
#' subsequent detection blocks.
#'
#' @export
#'
#' @author John Brzustowski \email{jbrzusto@@REMOVE_THIS_PART_fastmail.fm}
readDTA = function(filename="", lines=NULL, numLines=-1) {
if (is.null(lines))
## read the DTA file in; we don't sweat line endings this way
lines = readLines(filename, n = numLines)
## fix encoding: wherever there are non-ascii characters, assume 'Latin-1'
## see: https://github.com/jbrzusto/motusServer/issues/429
Encoding(lines) = "latin1"
date.format = "%m/%d/%y %H:%M:%OS"
## frequency and gain tables, needed for figuring out the antenna frequency and
## power for each detection
gain.tab = numeric()
freq.tab = numeric()
## paste text into one big string
lines = paste(lines, collapse="\n")
## start with a NULL tags dataframe
tags = NULL
## match against a regular expression to find tables - this splits the file
## up into recognizable blocks, in the order in which they appear there.
## We read and interpret those blocks later.
res = gregexpr(ltDTAregex, lines, perl=TRUE)[[1]]
clen = t(attr(res, "capture.length"))
cstart = t(attr(res, "capture.start"))
parts = clen != 0
pieces = stri_sub(lines, cstart[parts], length = clen[parts])
names(pieces) = rownames(clen)[1 + ((which(parts)-1) %% nrow(clen))]
newlines = gregexpr("\n", lines)[[1]]
piece.lines.before = sapply(cstart[parts], function(x) sum(newlines < x))
## each element of the character vector 'pieces' is the body of a
## table.
## Interpret these now.
codeset = as.character(NA)
boottimes = character(0)
site_code = NA
serno = NA
for (ip in seq(along=pieces)) {
if (nchar(pieces[ip]) == 0)
next
piece.name = names(pieces)[ip] ## can be repeated
## to keep line counts valid, retain blank lines within tables as rows of NA
con = textConnection(pieces[ip])
tab = read.table(con, as.is=TRUE, blank.lines.skip=FALSE)
close(con)
switch(piece.name,
model = {
model = tab[1, 1]
},
serial_no = {
serno = tab[1, 1]
},
boottime = {
boottimes = c(boottimes, paste(tab[1,1], tab[1, 2]))
},
site_code = {
site_code = tab[1, 1]
},
code_set = {
codeset = tab[1, 1]
},
active_scan = {
## make a lookup table for frequency by channel
freq.tab[as.character(tab[,1])] = tab[,2]
},
antenna_gain = {
## make a lookup table for gain by antenna
## We use this to adjust observed power i.e. we reduce
## power by a factor of gain. A brief lab trial
## showed an approximate increase of recorded signal
## strength of 40 units for each 10 unit increase in gain,
## so we reduce signal strength by 4 * gain before converting
## to dB way below.
gain.tab[as.character(tab[,1])] = tab[,2]
},
id_manual = {
## manually triggered readings are fully self-contained with these columns
## Date Time Freq [MHz] Gain Tag ID Antenna Power Data Latitude Longitude
## 1 2 3 4 5 6 7 8 9 10
## parse date / time from first two columns
tab = data.frame(
ts = as.numeric(as.POSIXct(strptime(paste(tab[[1]], tab[[2]]), date.format, tz="GMT"))),
id = tab[[5]],
ant = tab[[6]],
sig = tab[[7]],
lat = tab[[9]],
lon = tab[[10]],
dtaline = piece.lines.before[ip] + seq_len(nrow(tab)),
antfreq = tab[[3]],
gain = tab[[4]],
codeset = factor(1, labels=codeset),
stringsAsFactors = FALSE)
tags = rbind(tags, tab)
},
## default =
{
## this is a table of tag hits, either ID only or ID + GPS
tab[1] = as.numeric(as.POSIXct(strptime(paste(tab[[1]], tab[[2]]), date.format, tz="GMT")))
tab = tab[-2]
if (piece.name == "id_only")
tab = cbind(tab, NA, NA) ## lat and lon not available
names(tab) = c("ts", "chan", "id", "ant", "sig", "lat", "lon")
tab$dtaline = piece.lines.before[ip] + seq_len(nrow(tab))
tab$ant = as.character(tab$ant)
tab = subset(tab, id != 999)
## fill in the appropriate gain value, or a best guess
ants = unique(tab$ant)
bad.ants = is.na(gain.tab[ants])
if (any(bad.ants)) {
## the table refers to antenna for which we haven't seen a gain settings
## It appears that on the SRX-DL, if there are two antennas,
## and one of them is AH0, that antenna appears with a number in tag hit records
if (sum(bad.ants) == 1 && !is.na(gain.tab["AH0"]) && ! all(tab$ant == "AH0")) {
## use the gain for AH0, as this is presumably the same antenna
gain.tab[ants[bad.ants]] = gain.tab["AH0"]
} else {
## use the gain from the first antenna with known gain, otherwise, use
## 80 as this was common
if (all(is.na(gain.tab))) {
gain.to.use = 80
gain.source = " but NO GAIN VALUES WERE SPECIFIED FOR ANY ANTENNA!"
} else {
gain.to.use = gain.tab[which(!is.na(gain.tab))[1]]
gain.source = paste(" specified for antenna '", names(gain.tab)[which(!is.na(gain.tab))[1]], "'", sep="")
}
gain.tab[ants[bad.ants]] = gain.to.use
warning("Warning: No gain setting found for antenna number(s): ", paste(ants[bad.ants], collapse=", "),
" specified in ", piece.name, " table.\nUsing gain value of ", gain.to.use, gain.source, "\n")
}
}
## get frequency from latest frequency table
tab$antfreq = freq.tab[as.character(tab$chan)]
## report the gain setting in use
tab$gain = gain.tab[tab$ant]
## fill in the current codeset, if any rows were found
if(nrow(tab) > 0)
tab$codeset = factor(1, labels=codeset)
## remove the channel setting, which is redundant
tab$chan = NULL
tags = rbind(tags, tab)
}
)
}
## sort in order by time; record with and without GPS fixes are segregated
## in the DTA file, even though their timestamps might be interleaved.
## (why are GPS fixes intermittent? weird...)
if (! is.null(tags)) {
tags = subset(tags, ! is.na(tags$ts))
tags = tags[order(tags$ts),]
}
serno = paste0("Lotek-", serno)
if (! is.na(site_code)) {
## if a site_code was present, use it to possibly disambiguate duplicated
## receivers. Note that as soon as a rule matches, we use it and don't
## look at further rules.
rules = MetaDB("select * from serno_collision_rules where serno=%s order by id", serno, .QUOTE=TRUE)
for (i in seq_len(nrow(rules))) {
if (isTRUE(eval(parse(text = rules$cond[i])))) {
serno = paste0(serno, rules$suffix[i])
break
}
}
}
return (list(tags=tags, recv = serno, siteCode = site_code, pieces = pieces, piece.lines.before = piece.lines.before, boottimes = boottimes))
}
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