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added progress bar fix for axivity #64

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merged 2 commits into from
Apr 9, 2024
Merged

added progress bar fix for axivity #64

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04da6e6
added progress bar fix for axivity
muschellij2 Apr 8, 2024
52a8fc2
added a test
muschellij2 Apr 8, 2024
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62 changes: 31 additions & 31 deletions R/readAxivity.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
blockBytes = 512
headerBytes = 1024

# Credits: The original version of this code developed outside GitHub was
# Credits: The original version of this code developed outside GitHub was
# contributed by Dr. Evgeny Mirkes (Leicester University, UK)
#========================================================================
# Documentation moved to standard place for documentation which is readAxivity.Rd
Expand Down Expand Up @@ -108,13 +108,13 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
if (packetLength != 508) {
stop("Packet length is incorrect, should always be 508.")
}

# offset 4: if the top bit set, this contains a 15-bit fraction of a second for the timestamp
tsOffset = readBin(block[5:6], integer(), size = 2, signed = FALSE, endian = "little")

# offset 10: sequence ID
blockID = readBin(block[11:14], integer(), size = 4, endian = "little")

# read data for timestamp u32 at offset 14
timeStamp = readBin(block[15:18], integer(), size = 4, endian = "little") # the "signed" flag of readBin only works when reading 1 or 2 bytes

Expand All @@ -123,7 +123,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
light = bitwAnd(offset18, 0x03ffL)

# Read and recalculate temperature, lower 10 bits of u16 at offset 20.
# Formula for the temperature is specified at
# Formula for the temperature is specified at
# https://github.com/digitalinteraction/openmovement/blob/545564d3bf45fc19914de1ad1523ed86538cfe5e/Docs/ax3/cwa.h#L102
# Also see the following discussion:
# https://github.com/digitalinteraction/openmovement/issues/11#issuecomment-1622278513
Expand All @@ -133,34 +133,34 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# https://github.com/digitalinteraction/openmovement/blob/master/Docs/ax3/ax3-auxiliary.md#battery-voltage
# Battery is sampled as a 10-bit ADC value, but only the middle 8 bits are stored (the lowest bit is lost, and the highest bit is always 1).
# So to restore the ADC value, double the packed value and add 512.
# Then voltage = ADC_value * 6 / 1024
# Then voltage = ADC_value * 6 / 1024
battery = 3.0 * (readBin(block[24], integer(), size = 1, signed = FALSE) / 256.0 + 1.0);
} else {
battery = 0
}

# offset 25, per documentation:
# "top nibble: number of axes, 3=Axyz, 6=Gxyz/Axyz, 9=Gxyz/Axyz/Mxyz;
# offset 25, per documentation:
# "top nibble: number of axes, 3=Axyz, 6=Gxyz/Axyz, 9=Gxyz/Axyz/Mxyz;
# bottom nibble: packing format" (2 means unpacked, 0 packed).
offset25 = readBin(block[26], integer(), size = 1, signed = FALSE)
packed = (bitwAnd(offset25,15) == 0)

# offset 26 has a int16 (not uint16) value.
# offset 26 has a int16 (not uint16) value.
# It's the "relative sample index from the start of the buffer where the whole-second timestamp is valid"
offset26 = readBin(block[27:28], integer(), size = 2, endian = "little")

# number of observations in block U16 at offset 28
# blockLength is expected to be 40 for AX6, 80 or 120 for AX3.
# Note that if AX6 is configured to only collect accelerometer data
# this will look as if it is a AX3
blockLength = readBin(block[29:30], integer(), size = 2, signed = FALSE, endian = "little")
blockLength = readBin(block[29:30], integer(), size = 2, signed = FALSE, endian = "little")

if (is.null(parameters)) {
accelScaleCode = bitwShiftR(offset18, 13)
accelScale = 1 / (2^(8 + accelScaleCode))
# top nibble of offset25 is the number of axes
Naxes = bitwShiftR(offset25, 4)
}
}

# auxiliary variables
shift = 0
Expand Down Expand Up @@ -194,15 +194,15 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# [0][1][2][3][4][5][6][7][8][9]
# use 15-bits as 16-bit fractional time
fractional = bitwShiftL(bitwAnd(tsOffset, 0x7fffL), 1);

# frequency is truncated to int in firmware
shift = shift + bitwShiftR((fractional * frequency_data), 16);
}
}

# Read data if necessary
if (complete) {

if (packed) {
# Read 4 bytes for three measurements
packedData = readBin(block[31:510], integer(), size = 4, n = blockLength, endian = "little")
Expand Down Expand Up @@ -233,12 +233,12 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
frequency_data = frequency_data,
format = format)
}

if (blockID == 0) {
# force timestampDecoder to extract full timestamp
# this could for example happen when curious participant plugs
# AX device into computer
struc[[1]] = 0
struc[[1]] = 0
}
tsDeco = timestampDecoder(timeStamp, fractional, -shift / frequency_data, struc, configtz)
start = tsDeco$start
Expand All @@ -258,7 +258,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
if (complete) {
rawdata_list$data = data
}

return(invisible(rawdata_list))
}

Expand All @@ -278,7 +278,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# blocks is number of datablocks with 80 or 120 observations in each
# Unfortunately frequency of measurement is varied in this device.
#

# Start from the file origin
seek(fid,0)
block = readBin(fid, raw(), n=headerBytes)
Expand Down Expand Up @@ -333,14 +333,14 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
}
stop("Error reading file. The first ", maxAllowedCorruptBlocks+1, " blocks are corrupt.")
}

if (frequency_header != datas$frequency) {
warning("Inconsistent value of measurement frequency: there is ",
frequency_header, " in header and ", datas$frequency, " in the first data block. ")
}

blockLength = datas$length # number of samples in a block

start = as.POSIXct(datas$start, origin = "1970-01-01", tz = desiredtz)

return(invisible(list(
Expand All @@ -354,7 +354,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire

################################################################################################
# Main function

# Parse input arguments
nargin = nargs()
if (nargin < 1) {
Expand Down Expand Up @@ -389,11 +389,6 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
return(invisible(list(header = header, data = NULL)))
}

# Create progress bar if it is necessary
if (progressBar) {
pb = txtProgressBar(1, nr, style = 3)
}

# Read the end block, to determine the end timestamp.
struc = list(0,0L,0)
if (end < numDBlocks) { # the end block isn't part of the data we'll read, but its start will be our ending timestamp
Expand All @@ -408,7 +403,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# and between the two requests, all 20 blocks will be accounted for.
is_corrupt = TRUE
for (ii in end : min(numDBlocks-1, end+maxAllowedCorruptBlocks)) {
endBlock = readDataBlock(fid, struc = struc)
endBlock = readDataBlock(fid, struc = struc)

if (endBlock$checksum_pass) {
is_corrupt = FALSE
Expand Down Expand Up @@ -465,7 +460,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# Skip any corrupt blocks, up to maxAllowedCorruptBlocks in number.
is_corrupt = TRUE
for (ii in 1 : min((end-start), maxAllowedCorruptBlocks+1)) {
prevRaw = readDataBlock(fid, struc = struc)
prevRaw = readDataBlock(fid, struc = struc)

if (prevRaw$checksum_pass) {
is_corrupt = FALSE
Expand Down Expand Up @@ -505,6 +500,11 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
battery = vector(mode = "double", nr)
light = vector(mode = "double", nr)

# Create progress bar if it is necessary
if (progressBar) {
pb = txtProgressBar(1, nr, style = 3)
}

# Allocate enough space for the expected number of samples in a block, plus an extra ones needed for resampling.
# Don't rely on the type of device to determine the dimensionality of the data
# because AX6 can be configured to only collect accelerometer data.
Expand Down Expand Up @@ -588,13 +588,13 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# The following code checks whether any of the following conditions are met:
# - blockID is not zero and not consecutive from previous blockID
# - checksum_pass is FALSE
# - observed and expected sampling frequency differ by a fraction larger
# - observed and expected sampling frequency differ by a fraction larger
# than frequency_tol
# If yes, then we consider the block faulty
# and impute the acceleration and if applicable gyroscope values
# We log this event in output object QClog, which will allow the user to
# decide on alternative imputation strategies.

impute = FALSE
doQClog = FALSE
frequency_bias = abs(frequency_observed - prevRaw$frequency) / prevRaw$frequency
Expand All @@ -605,7 +605,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# Log and impute this event
doQClog = TRUE
impute = TRUE

# Prepare imputation with last recorded value, from the last non-faulty block,
# normalized to vector 1 g
imputedValues = rawAccel[1, 1:3]
Expand Down Expand Up @@ -650,7 +650,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
last = last + positions2add
if (last > nr) last = nr
}

if (impute == FALSE) {
tmp = resample(rawAccel, rawTime, timeRes[pos:last], rawLast, type = interpolationType)
} else {
Expand All @@ -667,7 +667,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
tmp = matrix(0, numImp, prevRaw$parameters$Naxes)
for (axi in 1:3) tmp[, axi] = imputedValues[axi]
}

# put result into specified position
last = nrow(tmp) + pos - 1

Expand Down
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