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test_read.myacc.csv.R
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test_read.myacc.csv.R
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library(GGIR)
context("read.myacc.csv")
test_that("read.myacc.csv can handle files without header, no decimal places in timestamps, temperature", {
skip_on_cran()
old_options = options()
# create test files
N = 30
sf = 30
options(digits.secs = 4)
# NOTE THIS UNIT TEST STILL USES POSIXlt A LOT
# BECAUSE OLDER R RELEASE CANNOT HANDLE POSIXct for this purpose
t0 = as.POSIXlt(x = "2022-11-02 14:01:16.00", tz = "Europe/Amsterdam")
timeseq = t0 + ((0:(N - 1))/sf)
time = as.POSIXlt(timeseq, origin = "1970-1-1", tz = "Europe/London")
testfile = matrix("", 4, 1)
set.seed(100)
accx = rnorm(N)
set.seed(200)
accy = rnorm(N)
set.seed(300)
accz = rnorm(N)
set.seed(400)
temp = rnorm(N)
wear = c(rep(TRUE,N/3),rep(FALSE,N/6),rep(TRUE,N/3),rep(TRUE,N/6))
# No header, but otherwise normal
S1 = data.frame(x = accx, time = time,
y = accy, z = accz, temp = temp + 20,
stringsAsFactors = TRUE)
testfile[1] = "testcsv1.csv"
write.csv(S1, file = testfile[1], row.names = FALSE)
# With decimal places in seconds removed
testfile[2] = "testcsv2.csv"
S1$time = round(S1$time)
write.csv(S1, file = testfile[2], row.names = FALSE)
# Without temperature
S2 = data.frame(x = accx, time = time, y = accy, z = accz, stringsAsFactors = TRUE)
testfile[3] = "testcsv3.csv"
write.csv(S2, file = testfile[3], row.names = FALSE)
# Without temperature, without time, with a wear channel
S3 = data.frame(x = accx, y = accy, z = accz, wear = wear, stringsAsFactors = TRUE)
testfile[4] = "testcsv4.csv"
write.csv(S3, file = testfile[4], row.names = FALSE)
# attempt to load
D1 = read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS", rmc.origin = "1970-01-01",
desiredtz = "Europe/London", rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID")
expect_equal(mean(D1$data$x), 0.1078671, tol = 0.0001)
expect_equal(mean(D1$data$y), -0.06675716, tol = 0.0001)
# attempt to load as if values are in mg and scale by 100
D1B = read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "mg", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS", rmc.origin = "1970-01-01",
rmc.scalefactor.acc = 100,
desiredtz = "Europe/London", rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID")
expect_equal(mean(D1B$data$x), 0.01078671, tol = 0.0001)
expect_equal(mean(D1B$data$y), -0.006675716, tol = 0.0001)
#------------------------
# Warnings and errors related to desiredtz and configtz
# warning if desiredtz not provided but rmc.desiredtz provided:
expect_warning(read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
rmc.desiredtz = "Europe/London", rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID"))
# now also with configtz
expect_warning(read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London",
rmc.configtz = "Europe/Madrid",
rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID"))
# error if none of rmc.desiredtz and desiredtz are provided:
expect_error(read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID"))
# error if both rmc.desiredtz and desiredtz are provided:
expect_error(read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London", rmc.desiredtz = "Europe/Madrid",
rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID"))
# Evaluate with decimal places in seconds
expect_equal(nrow(D1$data), 20)
expect_equal(ncol(D1$data), 5)
expect_equal(strftime(as.POSIXct(D1$data$time[1:5], tz = "Europe/London", origin = "1970-01-01"),
format = '%Y-%m-%d %H:%M:%OS2', tz = "Europe/London"),
c("2022-11-02 13:01:16.00",
"2022-11-02 13:01:16.03",
"2022-11-02 13:01:16.06",
"2022-11-02 13:01:16.09",
"2022-11-02 13:01:16.13"))
expect_that(D1$header,equals("no header"))
# Evaluate without decimal places decimal places in seconds and
# different config timezone
D2 = read.myacc.csv(rmc.file = testfile[2], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C", rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London", rmc.sf = sf,
configtz = "America/Chicago",
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID")
expect_equal(nrow(D2$data), 20)
expect_equal(ncol(D2$data), 5)
expect_equal(strftime(as.POSIXct(D2$data$time[1:5], tz = "Europe/London", origin = "1970-01-01"),
format = '%Y-%m-%d %H:%M:%OS2', tz = "Europe/London"),
c("2022-11-02 18:01:16.50", "2022-11-02 18:01:16.53",
"2022-11-02 18:01:16.56", "2022-11-02 18:01:16.59",
"2022-11-02 18:01:16.63"))
expect_that(D2$header,equals("no header"))
D3 = read.myacc.csv(rmc.file = testfile[3], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = c(1,3,4), rmc.col.temp = c(),
rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London",
rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID")
expect_that(nrow(D3$data),equals(20))
expect_that(ncol(D3$data),equals(4))
expect_that(D3$header,equals("no header"))
D4 = read.myacc.csv(rmc.file = testfile[4], rmc.nrow = 20,
rmc.dec = ".",
rmc.firstrow.acc = 1, rmc.firstrow.header = c(),
rmc.col.acc = 1:3, rmc.col.temp = c(), rmc.col.time = c(),
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London", rmc.sf = sf,
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID",
rmc.col.wear = 4)
expect_that(nrow(D4$data), equals(20))
expect_true(D4$data[1, 4])
expect_that(ncol(D4$data), equals(4))
expect_that(D4$header, equals("no header"))
for (i in 1:length(testfile)) {
expect_true(file.exists(testfile[i]))
if (file.exists(testfile[i])) file.remove(testfile[i])
}
options(old_options)
})
test_that("read.myacc.csv can handle header and bit-value acceleration", {
skip_on_cran()
old_options = options()
# create test files
N = 30
sf = 30
options(digits.secs = 4)
t0 = as.POSIXlt(x = "2022-11-02 14:01:16.00", tz = "Europe/Amsterdam")
timeseq = t0 + ((0:(N - 1))/sf)
time = as.POSIXlt(timeseq, origin = "1970-1-1", tz = "Europe/London")
testfile = matrix("", 3, 1)
set.seed(100)
accx = rnorm(N)
set.seed(200)
accy = rnorm(N)
set.seed(300)
accz = rnorm(N)
set.seed(400)
temp = rnorm(N)
wear = c(rep(TRUE, N / 3), rep(FALSE, N / 6),
rep(TRUE, N / 3), rep(TRUE, N / 6))
# 1: With 2-column header, with temperature, with time
S1 = as.matrix(data.frame(x = accx, time = time, y = accy,
z = accz, temp = temp + 20, stringsAsFactors = TRUE))
hd_NR = 10
hd = matrix("", hd_NR + 1, ncol(S1))
hd[1, 1:2] = c("ID","12345")
hd[2, 1:2] = c("sample_rate","30")
hd[3, 1:2] = c("serial_number","30")
hd[4, 1:2] = c("bit","8")
hd[5, 1:2] = c("dynamic_range","6")
S1 = rbind(hd, S1)
S1[hd_NR + 1,] = colnames(S1)
colnames(S1) = NULL
testfile[1] = "testcsv1.csv"
write.table(S1, file = testfile[1], col.names = FALSE, row.names = FALSE)
# 2: With 2-column header, with temperature, with time, bit-value acceleration unit
bits = 8
set.seed(100)
xb = sample(x = 1:(2^bits),size = N,replace = TRUE)
set.seed(200)
yb = sample(x = 1:(2^bits),size = N,replace = TRUE)
set.seed(300)
zb = sample(x = 1:(2^bits),size = N,replace = TRUE)
set.seed(400)
temp3 = rnorm(N)
S3 = S2 = as.matrix(data.frame(x = xb, time = time, y = yb,
z = zb, temp = temp3 + 20, stringsAsFactors = TRUE))
S2 = rbind(hd, S2)
S2[hd_NR + 1, ] = colnames(S2)
colnames(S2) = NULL
testfile[2] = "testcsv2.csv"
write.table(S2, file = testfile[2], col.names = FALSE, row.names = FALSE)
# 2. A header in 1 column:
hd2 = matrix("", hd_NR + 1, ncol(S3))
hd2[1, 1:2] = c("ID: 12345", "")
hd2[2, 1:2] = c("sample_rate: 30", "")
hd2[3, 1:2] = c("serial_number: 30", "")
hd2[4, 1:2] = c("bit: 8", "")
hd2[5, 1:2] = c("dynamic_range: 6", "")
S3 = rbind(hd2, S3)
S3[hd_NR + 1,] = colnames(S3)
colnames(S3) = NULL
testfile[3] = "testcsv3.csv"
write.table(S3, file = testfile[3], col.names = FALSE, row.names = FALSE)
#------------------------
# Test 1 - 2 column header
D1 = read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 11, rmc.firstrow.header = 1,
rmc.col.acc = c(1, 3, 4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London",
rmc.headername.sf = "sample_frequency",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID")
expect_that(nrow(D1$data), equals(20))
expect_that(ncol(D1$data), equals(5))
expect_that(nrow(D1$header), equals(5))
expect_that(ncol(D1$header), equals(1))
expect_equal(as.numeric(D1$header["sample_rate",1]), 30)
# Test 2 - 2 column header, bit-valued acceleration
D2 = read.myacc.csv(rmc.file = testfile[2], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 11, rmc.firstrow.header = 1,
rmc.col.acc = c(1,3,4), rmc.col.temp = 5,
rmc.col.time = 2,
rmc.unit.acc = "bit", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London", rmc.sf = sf,
rmc.headername.sf = "sample_rate",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID", rmc.bitrate = "bit",
rmc.dynamic_range = "dynamic_range",
rmc.header.structure = c())
expect_that(nrow(D2$data),equals(20))
expect_that(ncol(D2$data),equals(5))
expect_that(nrow(D2$header),equals(5))
expect_that(ncol(D2$header),equals(1))
# Test 3 - 1 column header, bit-valued acceleration
D3 = read.myacc.csv(rmc.file = testfile[3], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 11, rmc.firstrow.header = 1,
rmc.header.length = 5,
rmc.col.acc = c(1,3,4), rmc.col.temp = 5,
rmc.col.time = 2,
rmc.unit.acc = "bit", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London", rmc.sf = sf,
rmc.headername.sf = "sample_rate",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID",
rmc.bitrate = "bit", rmc.dynamic_range = "dynamic_range",
rmc.header.structure = ": ", rmc.check4timegaps = TRUE)
#
expect_equal(mean(D3$data[,2]), 0.761, tolerance = 3)
expect_equal(mean(D3$data[,3]), -0.62, tolerance = 2)
expect_equal(mean(D3$data[,4]), -0.36, tolerance = 1)
expect_equal(mean(D3$data[,5]), 20.1, tolerance = 1)
expect_equal(D3$data[2,2], 0.9768219, tolerance = 3)
expect_equal(ncol(D3$data), 5)
expect_equal(nrow(D3$header),5)
expect_equal(ncol(D3$header), 1)
expect_equal(as.numeric(D3$header[1,]), 12345)
expect_equal(as.numeric(D3$header[2,]), 30)
for (i in 1:length(testfile)) {
expect_true(file.exists(testfile[i]))
if (file.exists(testfile[i])) file.remove(testfile[i])
}
options(old_options)
})
test_that("read.myacc.csv can handle gaps in time and irregular sample rate", {
skip_on_cran()
old_options = options()
# create test files
N = 30
sf = 30
options(digits.secs = 4)
t0 = as.POSIXlt(x = "2022-11-02 14:01:16.00", tz = "Europe/Amsterdam")
timeseq = t0 + ((0:(N - 1))/sf)
time = as.POSIXlt(timeseq, origin = "1970-1-1", tz = "Europe/London")
testfile = matrix("", 1, 1)
set.seed(100)
accx = rnorm(N)
set.seed(200)
accy = rnorm(N)
set.seed(300)
accz = rnorm(N)
set.seed(400)
temp = rnorm(N)
wear = c(rep(TRUE, N / 3), rep(FALSE, N / 6),
rep(TRUE, N / 3), rep(TRUE, N / 6))
# 1: With 2-column header, with temperature, with gap in time, variation in sample rate
time_gap = time
time_gap[10:length(time_gap)] = time_gap[10:length(time_gap)] + 5 # add gap of 5 seconds
time_gap = time_gap + rnorm(n = length(time_gap), mean = 0, sd = 0.0001)
S1 = as.matrix(data.frame(x = accx, time = time_gap, y = accy,
z = accz, temp = temp + 20, stringsAsFactors = TRUE))
hd_NR = 10
hd = matrix("", hd_NR + 1, ncol(S1))
hd[1, 1:2] = c("ID","12345")
hd[2, 1:2] = c("sample_rate","30")
hd[3, 1:2] = c("serial_number","30")
S1 = rbind(hd, S1)
S1[hd_NR + 1,] = colnames(S1)
colnames(S1) = NULL
testfile[1] = "testcsv1.csv"
write.table(S1, file = testfile[1], col.names = FALSE, row.names = FALSE)
#------------------------
# Test 1 - time gaps but otherwise regular sample rate
D1 = read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 11, rmc.firstrow.header = 1,
rmc.col.acc = c(1, 3, 4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London",
rmc.sf = sf,
rmc.headername.sf = "sample_rate",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID",
rmc.check4timegaps = TRUE, rmc.doresample = FALSE)
expect_that(nrow(D1$data), equals(170)) # because data expands with 5 seconds that are now imputed
expect_that(ncol(D1$data), equals(5))
#------------------------
# Test 2 - time gaps and irregular sample rate
D2 = read.myacc.csv(rmc.file = testfile[1], rmc.nrow = 20, rmc.dec = ".",
rmc.firstrow.acc = 11, rmc.firstrow.header = 1,
rmc.col.acc = c(1, 3, 4), rmc.col.temp = 5, rmc.col.time = 2,
rmc.unit.acc = "g", rmc.unit.temp = "C",
rmc.format.time = "%Y-%m-%d %H:%M:%OS",
rmc.origin = "1970-01-01",
desiredtz = "Europe/London",
rmc.sf = sf,
rmc.headername.sf = "sample_rate",
rmc.headername.sn = "serial_number",
rmc.headername.recordingid = "ID",
rmc.check4timegaps = TRUE, rmc.doresample = TRUE)
expect_that(nrow(D2$data), equals(170)) # because data expands with 5 seconds that are now imputed
expect_that(ncol(D2$data), equals(5))
for (i in 1:length(testfile)) {
expect_true(file.exists(testfile[i]))
if (file.exists(testfile[i])) file.remove(testfile[i])
}
options(old_options)
})