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migrate function for reading Actiwatch to GGIRread and revise impleme…
…ntation for ActiGraph #68
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,129 @@ | ||
| readActiwatchCount = function(filename = file, desiredEpochSize = NULL, | ||
| timeformat = "%m/%d/%Y %H:%M:%S", tz = "", timeformatName = "timeformat") { | ||
| # In GGIR set timeformatName to extEpochData_timeformat | ||
|
|
||
| fileExtension = tolower(getExtension(filename)) | ||
|
|
||
| if (fileExtension == "csv") { | ||
| #========================================================= | ||
| # CSV | ||
| #========================================================= | ||
| # ! Assumptions that timeseries start before line 1000 | ||
| index = 1000 | ||
| 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) | ||
| # ! Assumption that column names are present 2 lines prior to timeseries | ||
| colnames = data.table::fread(input = filename, | ||
| header = FALSE, sep = ",", | ||
| skip = index - 2, nrows = 1, quote = quote) | ||
| if (all(is.na(colnames))) { | ||
| colnames = data.table::fread(input = filename, | ||
| header = FALSE, sep = ",", | ||
| skip = index - 4, nrows = 1, quote = quote) | ||
| } | ||
| colnames(D) = as.character(colnames)[1:ncol(D)] | ||
| # ! Assumptions about columns names | ||
| colnames(D) = gsub(pattern = "datum|date", replacement = "date", x = colnames(D), ignore.case = TRUE) | ||
| colnames(D) = gsub(pattern = "tijd|time", replacement = "time", x = colnames(D), ignore.case = TRUE) | ||
| colnames(D) = gsub(pattern = "activiteit|activity", replacement = "ZCY", x = colnames(D), ignore.case = TRUE) | ||
| 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[, "ZCY"] | ||
| } else if (fileExtension == "awd") { | ||
| #========================================================= | ||
| # AWD | ||
| #========================================================= | ||
| # ! Assumption that first data row equals the first row with 3 columns | ||
| index = 0 | ||
|
|
||
| quote = detectQuote(fn = filename, index = 50) | ||
| NC = 1 | ||
| while (NC >= 3) { | ||
| testraw = data.table::fread(input = filename, | ||
| header = FALSE, sep = ",", skip = index, | ||
| nrows = 1, data.table = TRUE, quote = quote) | ||
| NC = ncol(testraw) | ||
| if (NC >= 3) { | ||
| break() | ||
| } else { | ||
| index = index + 1 | ||
| } | ||
| } | ||
| D = data.table::fread(input = filename, header = FALSE, sep = ",", | ||
| skip = index, quote = quote) | ||
| D = D[,1] | ||
| colnames(D)[1] = "ZCY" | ||
| header = data.table::fread(input = filename, header = FALSE, sep = ",", | ||
| nrows = 7, quote = quote) | ||
| # Get epoch size | ||
| optionalEpochs = data.frame(code = c("1", "2", "4", "8", "20", "81", "C1", "C2"), | ||
| size = c(15, 30, 60, 120, 300, 2, 5, 10)) | ||
| epSizeShort = optionalEpochs$size[which(optionalEpochs$code == as.character(header[4]))] | ||
| # Get starttime | ||
| timestampFormat = paste0(unlist(strsplit(timeformat, " "))[1], " %H:%M") | ||
| timestamp_POSIX = as.POSIXct(x = paste(header[2], header[3], sep = " "), | ||
| format = timestampFormat, tz = tz) | ||
| checkTimeFormat(timestamp_POSIX, | ||
| rawValue = header[2], | ||
| timeformat = timeformat, | ||
| timeformatName = timeformatName) | ||
|
|
||
| } | ||
| D = as.matrix(D, drop = FALSE) | ||
|
|
||
| # 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 = rbind(rep(0, ncol(D)), D) | ||
| cumsum2 = function(x) { | ||
| x = cumsum(ifelse(is.na(x), 0, x)) + x*0 | ||
| return(x) | ||
| } | ||
| D = apply(D, 2, cumsum2) | ||
| D = D[seq(1, nrow(D), by = step), , drop = FALSE] | ||
| D = apply(D, 2, diff) | ||
| epSizeShort = epSizeShort * step | ||
| } | ||
| checkEpochMatch(desiredEpochSize, epSizeShort) | ||
| } | ||
| if (quote == "") D$ZCY = as.numeric(D$ZCY) | ||
| invisible(list(data = D, epochSize = epSizeShort, | ||
| startTime = timestamp_POSIX)) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| # Collection of short function used in functions readActigraphCount, readActiwatchCount | ||
| checkTimeFormat = function(timestamp_POSIX, rawValue = " ?? ", timeformat = " ?? ", | ||
| timeformatName = NULL) { | ||
| if (is.na(timestamp_POSIX)) { | ||
| stop(paste0("\nTime format in data ", rawValue, | ||
| " does not match with time format ", timeformat, | ||
| " as specified by argument ", timeformatName, | ||
| ", please correct.\n"), call. = FALSE) | ||
| } | ||
| } | ||
|
|
||
| checkEpochMatch = function(desiredEpochSize, epSizeShort) { | ||
| if (!is.null(desiredEpochSize) && epSizeShort != desiredEpochSize) { | ||
| stop(paste0("\nThe short epoch size as specified by the user (", | ||
| desiredEpochSize, " seconds) does NOT match the short", | ||
| " epoch size we see in the data (", epSizeShort, | ||
| " seconds). Please correct."), call. = FALSE) | ||
| } | ||
| return() | ||
| } | ||
|
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||
| detectQuote = function(fn, index) { | ||
| # data.table::fread has argument quote. | ||
| # On some computers the quotes in the files are | ||
| # not recognised, to catch this first try to check whether this is the case: | ||
| quote = "\"" | ||
| Dtest = NULL | ||
| try(expr = {Dtest = data.table::fread(input = fn, | ||
| header = FALSE, sep = ",", skip = index, | ||
| nrows = 20, quote = quote)}, silent = TRUE) | ||
| if (length(Dtest) == 0) { | ||
| quote = "" | ||
| } else { | ||
| if (nrow(Dtest) <= 1) { | ||
| quote = "" | ||
| } | ||
| } | ||
| return(quote) | ||
| } | ||
|
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||
| getExtension <- function(filename){ | ||
| ex <- unlist(strsplit(basename(filename), split = "[.]")) | ||
| if (length(ex) < 2) stop(paste0("Cannot recognise extension from '", filename, "' as filename, please check"), call. = FALSE) | ||
| return(ex[-1]) | ||
| } |
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