Skip to content

Commit

Permalink
Merge pull request #28 from wadpac/issue14_speedAx_attemp2023
Browse files Browse the repository at this point in the history 
Speeding up readAxivity
  • Loading branch information
@vincentvanhees
vincentvanhees authored May 17, 2023
2 parents fa62993 + 4b8f084 commit 7e566ab
Show file tree
Hide file tree
Showing 3 changed files with 39 additions and 27 deletions.
4 changes: 2 additions & 2 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Package: GGIRread
Type: Package
Title: Wearable Accelerometer Data File Readers
Version: 0.2.6
Date: 2022-12-05
Version: 0.2.7
Date: 2022-05-12
Authors@R: c(person("Vincent T","van Hees",role=c("aut","cre"),
email="[email protected]"),
person(given = "Patrick",family = "Bos",
Expand Down
57 changes: 32 additions & 25 deletions R/readAxivity.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
#############################################################################

# Internal functions
timestampDecoder = function(coded, fraction, shift, struc) {
timestampDecoder = function(coded, fraction, shift, struc, configtz) {
year = struc[[1]]
if (year == 0) {
# Extract parts of date
Expand All @@ -70,7 +70,6 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
struc <- list(year,secs)
# Add fractional part and shift
start = year + fraction / 65536 + shift

invisible(list(start = start, struc = struc))
}

Expand Down Expand Up @@ -102,7 +101,6 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# data is matrix with three columns "x", "y", and "z"
# matrix data is presented if complete == TRUE only.
#

if (!is.null(parameters)) {
accelScaleCode = parameters$accelScaleCode
accelScale = parameters$accelScale
Expand All @@ -114,7 +112,6 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
# Check the block header
# idstr = readChar(fid,2,useBytes = TRUE)
# seek(fid, 2, origin = 'current') # idstr and assume it is AX

# Read the data block. Extract several data fields
# offset 4 contains u16 with timestamp offset
seek(fid, 4, origin = 'current') # skip packetlength
Expand All @@ -124,8 +121,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
timeStamp = readBin(fid, integer(), size = 4)
# Get light u16 in offset 18
offset18 = unsigned16(readBin(fid, integer(), size = 2))
# light = 2 ^ (3.0 * (offset18 / 512.0 + 1.0)) # used for AX3, but this seems to have been incorrect
light = bitwAnd(offset18, 0x03ffL) # this seems to match better what is shown in OMGUI
light = bitwAnd(offset18, 0x03ffL)
# Read and recalculate temperature u16 in offset 20
temperature = (150.0 * readBin(fid, integer(), size = 2) - 20500.0) / 1000.0;
if (loadbattery == TRUE) {
Expand Down Expand Up @@ -167,13 +163,14 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
if (is.null(parameters)) {
if (bitwAnd(tsOffset, 0x8000L) != 0) {
format = 1
} else if (bitwAnd(tsOffset, 0x8000L) == 0) { # & class(frequency_data) == "function") {
frequency_data = round( 3200 / bitwShiftL(1, 15 - bitwAnd(samplerate_dynrange, 15)))
accrange = bitwShiftR(16,(bitwShiftR(abs(samplerate_dynrange),6)))
} else { # & class(frequency_data) == "function") {
format = 2
frequency_data = round( 3200 / bitwShiftL(1, 15 - bitwAnd(samplerate_dynrange, 15)))
}
}
if (format == 1) {
frequency_data = round( 3200 / bitwShiftL(1, 15 - bitwAnd(samplerate_dynrange, 15)))
accrange = bitwShiftR(16,(bitwShiftR(abs(samplerate_dynrange),6)))
# Need to undo backwards-compatible shim:
# Take into account how many whole samples the fractional part
# of timestamp accounts for:
Expand All @@ -185,19 +182,17 @@ 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);
} else if (format == 2) { # & class(frequency_data) == "function") {
if (is.null(parameters)) {
frequency_data = round( 3200 / bitwShiftL(1, 15 - bitwAnd(samplerate_dynrange, 15)))
}
}
} else {
#Very old format, where offset 26 contains frequency
frequency_data = temp
}
# Read data if necessary
if (complete) {

if (packed) { #32 bit
# Read 4 byte for three measurements
packedData = readBin(fid, integer(), size = 4, n = blockLength)
Expand All @@ -208,8 +203,8 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
temp = 482 - 4 * (Naxes/3) * blockLength
} else {
# Read unpacked data
xyz = readBin(fid, integer(), size = 2, n = blockLength * Naxes) #*3
data = matrix(xyz, ncol = Naxes,byrow = T) #3
xyz = readBin(fid, integer(), size = 2, n = blockLength * Naxes)
data = matrix(xyz, ncol = Naxes, byrow = T)
# Calculate number of bytes to skip
temp = 482 - (2 * Naxes * blockLength)
}
Expand Down Expand Up @@ -241,8 +236,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
frequency_data = frequency_data,
format = format)
}

tsDeco = timestampDecoder(timeStamp, fractional, -shift / frequency_data, struc)
tsDeco = timestampDecoder(timeStamp, fractional, -shift / frequency_data, struc, configtz)
start = tsDeco$start
struc = tsDeco$struc
rawdata_list = list(
Expand All @@ -258,6 +252,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
if (complete) {
rawdata_list$data = data
}

return(invisible(rawdata_list))
}
readHeader = function(fid, numDBlocks) {
Expand Down Expand Up @@ -371,7 +366,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
return(invisible(list(header = header, data = NULL)))
}
#############################################################################
# reinitiate file and start reading of data and sesrch the beginning of required
# reinitiate file and start reading of data and search the beginning of required
seek(fid,0)
# skip header
seek(fid, 1024, origin = 'current')
Expand Down Expand Up @@ -408,21 +403,34 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
rawAccel = matrix(0, nrow = 300 * Npages, ncol = 6)
}
rawPos = 1
for (i in 2:numDBlocks) {
raw = readDataBlock(fid, header_accrange = header$accrange, struc = struc,
parameters = prevRaw$parameters)
i = 2
while (i <= numDBlocks) {
time2Skip = start - prevRaw$start
blockDur = prevRaw$length / prevRaw$frequency
Nblocks2Skip = floor(time2Skip/blockDur) - 1

if (i >= Nblocks2Skip) { # start of recording
raw = readDataBlock(fid, header_accrange = header$accrange, struc = struc,
parameters = prevRaw$parameters)
} else {
# skip blocks
seek(fid, 512 * Nblocks2Skip, origin = 'current')
i = i + Nblocks2Skip
next
}
if (is.null(raw)) {
break
}
# Save start and length of the previous block
prevStart = prevRaw$start
prevLength = prevRaw$length
struc = raw$struc
# Check are previous data block necessary
if (raw$start < start) {
prevRaw = raw
i = i + 1
next
}
struc = raw$struc
# Create array of times
time = seq(prevStart, raw$start, length.out = prevLength + 1)

Expand Down Expand Up @@ -470,12 +478,11 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
if (pos > nr) {
break
}
i = i + 1
}

#############################################################################
# Process the last block of data if necessary
if (pos <= nr) { # & ignorelastblock == FALSE) {
# print("last block of data")
if (pos <= nr & exists("prevStart") & exists("prevLength")) {
# Calculate pseudo time for the "next" block
newTimes = (prevRaw$start - prevStart) / prevLength * prevRaw$length + prevRaw$start
prevLength = prevRaw$length
Expand Down
5 changes: 5 additions & 0 deletions inst/NEWS.Rd
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
\name{NEWS}
\title{News for Package \pkg{GGIRread}}
\newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
\section{Changes in version 0.2.7 (release date:12-05-2022)}{
\itemize{
\item Speeding up readAxivity function by approximately 75 percent.
}
}
\section{Changes in version 0.2.6 (release date:05-12-2022)}{
\itemize{
\item New CRAN release, only minor improvements to syntax
Expand Down

0 comments on commit 7e566ab

Please sign in to comment.