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add functionality for Actical csv format #68
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| readActicalCount = function(filename = file, desiredEpochSize = NULL, | ||
| timeformat = "%m/%d/%Y %H:%M:%S", tz = "", timeformatName = "timeformat") { | ||
| # In GGIR set timeformatName to extEpochData_timeformat | ||
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| # ! Assumptions that timeseries start before line 1000 | ||
| index = 300 | ||
| while (index > 0) { | ||
| quote = detectQuote(fn = filename, index = index) | ||
| testraw = data.table::fread(input = filename, | ||
| header = FALSE, sep = ",", skip = index, | ||
| nrows = 2, data.table = FALSE, quote = quote) | ||
| if (length(testraw) > 0) { | ||
| if (nrow(testraw) == 2) { | ||
| if (testraw$V1[2] == testraw$V1[1] + 1) { | ||
| break | ||
| } | ||
| } | ||
| } | ||
| index = index - 100 | ||
| } | ||
| # ! Assumption that first column are the epoch numbers | ||
| delta = 1 - testraw$V1[1] | ||
| index = index + delta | ||
| startFound = FALSE | ||
| while (startFound == FALSE) { | ||
| Dtest = data.table::fread(input = filename, sep = ",", skip = index, quote = quote, nrows = 1) | ||
| if (Dtest$V1[1] == 1) { | ||
| startFound = TRUE | ||
| } else { | ||
| # This happens when file is has an empty row between each measurement point is stored | ||
| index = index - 1 | ||
| if (index < 1) stop("Could not find start of recording", call. = FALSE) | ||
| } | ||
| } | ||
| D = data.table::fread(input = filename, sep = ",", skip = index, quote = quote, data.table = FALSE) | ||
| # ! Assumption that column names are present 2 lines prior to timeseries | ||
| dashedlineFound = FALSE | ||
| dashedLineIndex = index | ||
| while (dashedlineFound == FALSE) { | ||
| linedata = data.table::fread(input = filename, data.table = FALSE, | ||
| header = FALSE, sep = ",", | ||
| skip = dashedLineIndex, nrows = 1, quote = quote) | ||
| if (length(grep(pattern = "------", x = linedata[1])) == 1) { | ||
| dashedlineFound = TRUE | ||
| } else { | ||
| dashedLineIndex = dashedLineIndex - 1 | ||
| } | ||
| } | ||
| colnames = data.table::fread(input = filename, data.table = FALSE, | ||
| header = FALSE, sep = ",", | ||
| skip = dashedLineIndex + 1, nrows = (index - dashedLineIndex) - 2, quote = quote) | ||
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| collapse = function(x) { | ||
| return(paste0(x, collapse = "_")) | ||
| } | ||
| colnames = tolower(as.character(apply(colnames, MARGIN = 2, FUN = collapse))) | ||
| colnames(D) = colnames | ||
| # ! Assumptions about columns names | ||
| colnames(D)[grep(pattern = "time", x = colnames(D))] = "time" | ||
| colnames(D)[grep(pattern = "date", x = colnames(D))] = "date" | ||
| colnames(D)[grep(pattern = "activity_counts", x = colnames(D))] = "counts" | ||
| colnames(D)[grep(pattern = "steps", x = colnames(D))] = "steps" | ||
| D = D[, grep(pattern = "time|date|counts|steps", x = colnames(D))] | ||
| timestamp_POSIX = as.POSIXct(x = paste(D$date[1:4], D$time[1:4], sep = " "), | ||
| format = timeformat, | ||
| tz = tz) | ||
| checkTimeFormat(timestamp_POSIX[1], | ||
| rawValue = paste(D$date[1], D$time[1], sep = " "), | ||
| timeformat = timeformat, | ||
| timeformatName = timeformatName) | ||
| epSizeShort = mean(diff(as.numeric(timestamp_POSIX))) | ||
| timestamp_POSIX = timestamp_POSIX[1] | ||
| D = D[, -which(colnames(D) %in% c("date", "time"))] | ||
| D = as.matrix(D, drop = FALSE) | ||
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| # If requested, aggregate data to lower resolution to match desired | ||
| # epoch size in argument windowsizes | ||
| if (!is.null(desiredEpochSize)) { | ||
| if (desiredEpochSize > epSizeShort) { | ||
| step = desiredEpochSize %/% epSizeShort | ||
| D = sumAggregate(D, step) | ||
| epSizeShort = epSizeShort * step | ||
| } | ||
| checkEpochMatch(desiredEpochSize, epSizeShort) | ||
| } | ||
| if (quote == "") D = apply(D, 2, as.numeric) | ||
| invisible(list(data = D, epochSize = epSizeShort, | ||
| startTime = timestamp_POSIX)) | ||
| } |
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