From e6a302ba97e1572cc496d18514b2b8dd8e4682ee Mon Sep 17 00:00:00 2001 From: Vincent van Hees Date: Thu, 26 Sep 2024 10:48:00 +0200 Subject: [PATCH] migrate function for reading ActiGraph csv from GGIR to GGIRread #68 --- DESCRIPTION | 2 +- NAMESPACE | 8 +- NEWS.md | 1 + R/readActiGraphCount.R | 176 +++ inst/testfiles/ActiGraph13.csv | 1000 ++++++++++++++++ .../ActiGraph13_timestamps_headers.csv | 1011 +++++++++++++++++ inst/testfiles/ActiGraph61.csv | 1000 ++++++++++++++++ man/readActiGraphCount.Rd | 37 + tests/testthat/test_readActiGraphCount.R | 66 ++ 9 files changed, 3298 insertions(+), 3 deletions(-) create mode 100644 R/readActiGraphCount.R create mode 100644 inst/testfiles/ActiGraph13.csv create mode 100644 inst/testfiles/ActiGraph13_timestamps_headers.csv create mode 100644 inst/testfiles/ActiGraph61.csv create mode 100644 man/readActiGraphCount.Rd create mode 100644 tests/testthat/test_readActiGraphCount.R diff --git a/DESCRIPTION b/DESCRIPTION index 5044519..0536150 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,7 +22,7 @@ URL: https://github.com/wadpac/GGIRread/ BugReports: https://github.com/wadpac/GGIRread/issues License: Apache License (== 2.0) Suggests: testthat -Imports: matlab, bitops, Rcpp (>= 0.12.10) +Imports: matlab, bitops, Rcpp (>= 0.12.10), data.table Depends: stats, utils, R (>= 3.5.0) NeedsCompilation: yes LinkingTo: Rcpp diff --git a/NAMESPACE b/NAMESPACE index b1cd31b..f5834ae 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,5 +1,9 @@ -export(readGenea, readAxivity, readGENEActiv, GENEActivReader, resample, readWav) +export(readGenea, readAxivity, readGENEActiv, + GENEActivReader, resample, readWav, + readActiGraphCount) useDynLib(GGIRread, .registration = TRUE) importFrom(Rcpp, sourceCpp) +importFrom(data.table, fread) importFrom("utils", "setTxtProgressBar", "txtProgressBar") -importFrom("utils", "read.csv") \ No newline at end of file +importFrom("utils", "read.csv") +importFrom("utils", "available.packages") \ No newline at end of file diff --git a/NEWS.md b/NEWS.md index acb326b..0f48dfd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ - Added a `NEWS.md` file to track changes to the package. - Stops interactive calling of `chooseCRANmirror` on `.onAttach` if interactive and CRAN mirror not set GGIR #1141. +- Migrate read function for ActiGraph count data (csv) to GGIRread #68. # Changes in version 1.0.1 (release date:03-06-2024) diff --git a/R/readActiGraphCount.R b/R/readActiGraphCount.R new file mode 100644 index 0000000..4f3c3d7 --- /dev/null +++ b/R/readActiGraphCount.R @@ -0,0 +1,176 @@ +readActiGraphCount = function(filename = file, desiredEpochSize = NULL, + timeformat = "%m/%d/%Y %H:%M:%S", tz = "") { + deviceSerialNumber = NULL + # Test if file has header by reading first ten rows + # and checking whether it contains the word + # serial number. + headerAvailable = FALSE + header = data.table::fread( + input = filename, + header = FALSE, + nrows = 10, + data.table = FALSE, + sep = "," + ) + if (nrow(header) < 10) { + stop(paste0("File ", filename, " cannot be processed because it has less than ten rows")) + } + splitHeader = function(x) { + tmp = unlist(strsplit(x, " ")) + item = gsub( + pattern = ":| ", + replacement = "", + x = paste0(tmp[1:(length(tmp) - 1)], collapse = "") + ) + df = data.frame(item = tolower(item), value = tmp[length(tmp)]) + return(df) + } + fileHeader = NULL + for (hh in header[2:9,1]) { + fileHeader = rbind(fileHeader, splitHeader(hh)) + } + if (any(grepl("serialnumber", fileHeader$item))) headerAvailable = TRUE + + # Depending on whether header is present assign number of rows to skip: + if (headerAvailable == TRUE) { + skip = 10 + } else { + tmp = data.table::fread(input = filename, + header = FALSE, + data.table = FALSE, + skip = 0, + nrows = 1) + if (any(grepl("data|scoring", tmp[1,]))) { + skip = 1 + } else { + skip = 0 + } + } + + # Check if file was exported with column names: + colnames = FALSE + colnames_test = data.table::fread(input = filename, + header = FALSE, + data.table = FALSE, + skip = skip, + nrows = 1) + if (any(grepl("Axis|vector magnitude|vm", colnames_test[1,], ignore.case = TRUE))) { + colnames = TRUE + } + # Increment skip if column names are present + Dtest = data.table::fread(input = filename, + header = colnames, + data.table = FALSE, + skip = skip, nrows = 1) + if (length(grep(pattern = "time|date", x = Dtest[1, 1], ignore.case = TRUE)) > 0) { + skip = skip + 1 + } + # Read all data from file + D = data.table::fread(input = filename, + header = colnames, + data.table = FALSE, + skip = skip) + + # Ignore time and date column if present + D = D[, grep(pattern = "time|date", x = Dtest[1, ], ignore.case = TRUE, invert = TRUE), drop = FALSE] + D = D[, grep(pattern = "time|date", x = colnames(Dtest), ignore.case = TRUE, invert = TRUE), drop = FALSE] + if (inherits(x = D[1,1], what = "POSIXt")) { + D = D[, -1, drop = FALSE] + } + # Identify columns with count data + acccol = vmcol = NA + if (colnames == TRUE) { + acccol = grep("axis|activity", colnames(D), ignore.case = TRUE) + vmcol = grep("vector magnitude|vm", colnames(D), ignore.case = TRUE) + } else { + # Then assume first 3 columns are axis1, axis2, axis3 if ncol(D) >= 3 + # First column is VM if ncol(D) < 3 + # Note that in ActiLife software the user can select + # the columns to export (e.g, it could be "Axis1", "Vector Magnitude", "Steps") + # which may mean that our assumptions here are not necessarily true. + if (ncol(D) >= 3) { + acccol = 1:3 + } else { + vmcol = 1 + } + } + # Assign colnames and formatting + if (is.na(acccol[1]) == FALSE) { + colnames(D)[acccol] = c("y", "x", "z") # ActiGraph always stores y axis first + } + if (is.na(vmcol[1]) == FALSE) { + D = as.matrix(D, drop = FALSE) # Convert to matrix as data.frame will auto-collapse to vector + colnames(D)[vmcol] = c("vm") + } + keep = c(acccol, vmcol)[!is.na(c(acccol, vmcol))] + D = D[, keep, drop = FALSE] + if (ncol(D) == 3 & is.na(vmcol)) { + D$vm = sqrt(D[,1]^2 + D[,2]^2 + D[,3]^2) + } + # Extract information from header, if present + if (headerAvailable == TRUE) { + deviceSerialNumber = fileHeader$value[grep(pattern = "serialnumber", x = fileHeader$item)] + epochSize = fileHeader$value[grep(pattern = "epochperiod|cycleperiod", x = fileHeader$item)] + epSizeShort = sum(as.numeric(unlist(strsplit(epochSize, ":"))) * c(3600, 60, 1)) + starttime = fileHeader$value[grep(pattern = "starttime", x = fileHeader$item)] + startdate = fileHeader$value[grep(pattern = "startdate", x = fileHeader$item)] + timestamp = paste0(startdate, " ", starttime) + timestamp_POSIX = as.POSIXlt(timestamp, tz = tz, + format = timeformat) + } else if (headerAvailable == FALSE) { + # Extract date/timestamp from first values of column + tmp = data.table::fread(input = filename, + header = colnames, + data.table = FALSE, + skip = skip, + nrows = 2) + if (colnames == TRUE) { + datecol = grep("date", colnames(tmp), ignore.case = TRUE) + timecol = grep("time|epoch", colnames(tmp), ignore.case = TRUE) + time = tmp[, timecol] + date = tmp[, datecol] + + starttime = time[1] + starttime = date[1] + timestamp = paste0(date, " ", time) + format = timeformat + timestamp_POSIX = as.POSIXlt(timestamp, tz = tz, format = format) + if (all(is.na(timestamp_POSIX))) { + stop(paste0("\nTimestamps are not available in the file, neither has", + " it a header to extract the timestamps from. Therefore, the file", + " cannot be processed.\n")) + } + epochSize = difftime(timestamp_POSIX[2], timestamp_POSIX[1], + units = "secs") + epSizeShort = as.numeric(epochSize) + timestamp_POSIX = timestamp_POSIX[1] # startTime + } + } + # Check timestamp is meaningful + if (all(is.na(timestamp_POSIX))) { + stop(paste0("\nTime format in data ", timestamp, " does not match with time format ", + timeformat, + " as specified by argument extEpochData_timeformat, please correct.\n")) + } + # 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) + D = apply(D, 2, cumsum) + D = D[seq(1, nrow(D), by = step), , drop = FALSE] + D = apply(D, 2, diff) + epSizeShort = epSizeShort * step + } + if (epSizeShort != desiredEpochSize) { + stop(paste0("\nThe short epoch size as specified by the user as the first value of argument windowsizes (", + desiredEpochSize, + " seconds) does NOT match the short epoch size we see in the data (", epSizeShort), + " seconds). Please correct.", call. = FALSE) + } + } + invisible(list(data = D, epochSize = epSizeShort, + startTime = timestamp_POSIX, + deviceSerialNumber = deviceSerialNumber)) +} \ No newline at end of file diff --git a/inst/testfiles/ActiGraph13.csv b/inst/testfiles/ActiGraph13.csv new file mode 100644 index 0000000..3b1d0ab --- /dev/null +++ b/inst/testfiles/ActiGraph13.csv @@ -0,0 +1,1000 @@ +------------ Data File Created By ActiGraph wGT3XPlus ActiLife v6.10.2 Firmware v2.2.1 date format M/d/yyyy Filter Normal -----------,,, +Serial Number: CLE2A2123456,,, +Start Time 09:00:00,,, +Start Date 8/26/2013,,, +Epoch Period (hh:mm:ss) 00:00:15,,, +Download Time 12:54:04,,, +Download Date 9/3/2013,,, +Current Memory Address: 0,,, +Current Battery Voltage: 4.03 Mode = 13,,, +--------------------------------------------------,,, +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 +0,0,0,0 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b/man/readActiGraphCount.Rd @@ -0,0 +1,37 @@ +\name{readActiGraphCount} +\alias{readActiGraphCount} +\title{ + Read ActiGraph Count data files (csv) +} +\description{ + Reads ActiGraph Count data file. Currently a variety of csv format are facilitated. +} +\usage{ + readActiGraphCount(filename = file, desiredEpochSize = NULL, + timeformat = "\%m/\%d/\%Y \%H:\%M:\%S", tz = "") +} +\arguments{ + \item{filename}{ + filename (required) + } + \item{desiredEpochSize}{ + Numeric, desired epoch size in seconds. If set aggregate data by summation to + this epochsize. + } + \item{timeformat}{ + Character, timestemp format. + } + \item{tz}{ + Character, timezone name from the timezone database names. + } +} +\value{ + \item{data}{Matrix with one or multiple columns} + \item{epochSize}{epoch size in seconds of data} + \item{startTime}{POSIXlt format timestamp on which recording starts } + \item{deviceSerialNumber}{Device serial number if it could be extracted + from the file header} +} +\author{ + Vincent T van Hees +} \ No newline at end of file diff --git a/tests/testthat/test_readActiGraphCount.R b/tests/testthat/test_readActiGraphCount.R new file mode 100644 index 0000000..22ae117 --- /dev/null +++ b/tests/testthat/test_readActiGraphCount.R @@ -0,0 +1,66 @@ +library(GGIRread) +context("read ActiGraph csv files") +test_that("ActiGraph61 is correctly read", { + file = system.file("testfiles/ActiGraph61.csv", package = "GGIRread") + D = readActiGraphCount(filename = file, desiredEpochSize = 10, timeformat = "%m/%d/%Y %H:%M:%S", tz = "") + expect_equal(D$deviceSerialNumber, "MOS2D16160581") + expect_equal(D$epochSize, 10) + expect_equal(format(D$startTime), "2016-08-15 21:35:00") + expect_equal(nrow(D$data), 495) + expect_equal(ncol(D$data), 4) + expect_equal(sum(D$data), 63952.33) + + D = readActiGraphCount(filename = file, desiredEpochSize = 5, timeformat = "%m/%d/%Y %H:%M:%S", tz = "") + expect_equal(D$deviceSerialNumber, "MOS2D16160581") + expect_equal(D$epochSize, 5) + expect_equal(format(D$startTime), "2016-08-15 21:35:00") + expect_equal(nrow(D$data), 990) + expect_equal(ncol(D$data), 4) + expect_equal(sum(D$data), 63952.33) +}) + +test_that("ActiGraph31 is correctly read", { + file = system.file("testfiles/ActiGraph13.csv", package = "GGIRread") + D = readActiGraphCount(filename = file, desiredEpochSize = 15, timeformat = "%m/%d/%Y %H:%M:%S", tz = "") + expect_equal(D$deviceSerialNumber, "CLE2A2123456") + expect_equal(D$epochSize, 15) + expect_equal(format(D$startTime), "2013-08-26 09:00:00") + expect_equal(nrow(D$data), 990) + expect_equal(ncol(D$data), 4) + expect_equal(sum(D$data), 272870.6, tol = 0.1) + + D = readActiGraphCount(filename = file, desiredEpochSize = 30, timeformat = "%m/%d/%Y %H:%M:%S", tz = "") + expect_equal(D$deviceSerialNumber, "CLE2A2123456") + expect_equal(D$epochSize, 30) + expect_equal(format(D$startTime), "2013-08-26 09:00:00") + expect_equal(nrow(D$data), 495) + expect_equal(ncol(D$data), 4) + expect_equal(sum(D$data), 272870.6, tol = 0.1) +}) + +test_that("ActiGraph13_timestamps_headers.csv is correctly read", { + file = system.file("testfiles/ActiGraph13_timestamps_headers.csv", package = "GGIRread") + D = readActiGraphCount(filename = file, desiredEpochSize = 1, timeformat = "%d-%m-%Y %H:%M:%S", tz = "") + expect_equal(D$deviceSerialNumber, "TAS1D48140206") + expect_equal(D$epochSize, 1) + expect_equal(format(D$startTime), "2017-12-09 15:00:00") + expect_equal(nrow(D$data), 1000) + expect_equal(ncol(D$data), 4) + expect_equal(sum(D$data), 256047) + + + D = readActiGraphCount(filename = file, desiredEpochSize = 5, timeformat = "%d-%m-%Y %H:%M:%S", tz = "") + expect_equal(D$deviceSerialNumber, "TAS1D48140206") + expect_equal(D$epochSize, 5) + expect_equal(format(D$startTime), "2017-12-09 15:00:00") + expect_equal(nrow(D$data), 200) + expect_equal(ncol(D$data), 4) + expect_equal(sum(D$data), 256047) + + expect_error(readActiGraphCount(filename = file, + desiredEpochSize = 5, + timeformat = "%m/%d/%Y %H:%M:%S")) + expect_error(readActiGraphCount(filename = file, + desiredEpochSize = 0.5, + timeformat = "%d-%m-%Y %H:%M:%S")) +}) \ No newline at end of file