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readGENEActiv = function(filename, start = 0, end = 0, progress_bar = FALSE,
desiredtz = "", configtz = NULL) {
# Extract information from the fileheader
suppressWarnings({fh = readLines(filename, 69)})
SN = gsub(pattern = "Device Unique Serial Code:", replacement = "",
x = fh[grep(pattern = "Device Unique Serial Code", x = fh)[1]])
firmware = gsub(pattern = "Device Firmware Version:", replacement = "",
x = fh[grep(pattern = "Device Firmware Version", x = fh)[1]])
Lux = as.numeric(gsub(pattern = "Lux:", replacement = "",
x = fh[grep(pattern = "Lux", x = fh)[1]]))
Volts = as.numeric(gsub(pattern = "Volts:", replacement = "",
x = fh[grep(pattern = "Volts", x = fh)[1]]))
# We use first Page Time and not Start time from the file header
# because start time from the file header is known to be incorrect
# when battery runs out prior to end of recording
starttime = gsub(pattern = "Page Time:", replacement = "",
x = fh[grep(pattern = "Page Time", x = fh)[1]])
tzone = gsub(pattern = "Time Zone:", replacement = "",
x = fh[grep(pattern = "Time Zone", x = fh)[1]])
tzone = as.numeric(unlist(strsplit(tzone, "[:]| "))[2]) * 3600
Handedness = gsub(pattern = "Handedness Code:", replacement = "",
x = fh[grep(pattern = "Handedness Code", x = fh)[1]])
ID = gsub(pattern = "Subject Code:", replacement = "",
x = fh[grep(pattern = "Subject Code", x = fh)[1]])
DeviceLocation = gsub(pattern = "Device Location Code:", replacement = "",
x = fh[grep(pattern = "Device Location Code", x = fh)[1]])
DeviceModel = gsub(pattern = " ", replacement = "",
x = gsub(pattern = "Device Model:", replacement = "",
x = fh[grep(pattern = "Device Model", x = fh)[1]]))
# Read acceleration, lux and temperature data
rawdata = GENEActivReader(filename = filename,
start = start, end = end,
progress_bar = progress_bar)
rawdata$time = rawdata$time / 1000
# Construct header object
header = list(serial_number = SN,
firmware = firmware,
tzone = tzone,
ReadOK = rawdata$info$ReadOK,
SampleRate = rawdata$info$SampleRate,
ReadErrors = rawdata$info$ReadErrors,
numBlocksTotal = rawdata$info$numBlocksTotal,
StarTime = starttime,
Handedness = Handedness,
RecordingID = ID,
DeviceLocation = DeviceLocation,
DeviceModel = DeviceModel)
s0 = unlist(strsplit(starttime, ":"))
if (length(s0) == 4) {
starttime = paste0(s0[1], ":", s0[2], ":", s0[3], ".", s0[4])
}
# Establish starttime in the correct timezone
if (is.null(configtz)) {
starttime_posix = as.POSIXlt(x = starttime, tz = desiredtz,
format = "%Y-%m-%d %H:%M:%OS", origin = "1970-01-01")
} else {
starttime_posix = as.POSIXlt(starttime, tz = configtz,
format = "%Y-%m-%d %H:%M:%OS", origin = "1970-01-01")
}
# Correct timestamps
if (start > 1) {
page_offset = (((start - 1) * 300) / rawdata$info$SampleRate)
} else {
page_offset = 0
}
starttime_num = as.numeric(starttime_posix) + page_offset
rawdata$time = rawdata$time + abs(rawdata$time[1]) + starttime_num
return(invisible(list(
header = header,
data.out = data.frame(time = rawdata$time,
x = rawdata$x, y = rawdata$y, z = rawdata$z,
light = rawdata$lux * (Lux/Volts),
temperature = rawdata$temperature,
stringsAsFactors = TRUE)
)))
}
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