Merge pull request #62 from wadpac/issue61_increamenting_time_GENEActiv

Increment time correctly between pages GENEActiv

Author: vincentvanhees

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: GGIRread
 Type: Package
 Title: Wearable Accelerometer Data File Readers
-Version: 0.3.3
-Date: 2024-01-24
+Version: 1.0.0
+Date: 2024-03-27
 Authors@R: c(person("Vincent T","van Hees",role=c("aut","cre"),
                   email="v.vanhees@accelting.com"),
              person(given = "Patrick",family = "Bos",

R/readGENEActiv.R

@@ -70,7 +70,11 @@ readGENEActiv = function(filename, start = 0, end = 0, progress_bar = FALSE,
   }
 
   # Correct timestamps
-  page_offset = (((start - 1) * 300) / rawdata$info$SampleRate)
+  if (start > 1) {
+    page_offset = (((start - 1) * 300) / rawdata$info$SampleRate)
+  } else {
+    page_offset = 0
+  }
   starttime_num = as.numeric(starttime_posix) + page_offset
   rawdata$time = rawdata$time + abs(rawdata$time[1]) + starttime_num
   return(invisible(list(

inst/NEWS.Rd

@@ -2,9 +2,10 @@
 \title{News for Package \pkg{GGIRread}}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
-\section{Changes in version 0.3.4 (release date:??-??-2024)}{
+\section{Changes in version 1.0.0 (release date:27-03-2024)}{
     \itemize{
-      \item GENEActiv no longer prints error to console when more data is requested than is in the file because this is not an error, issue #58
+      \item GENEActiv no longer prints error to console when more data is requested 
+      than is in the file because this is not an error, issue #58
     }
 }
 

man/GGIRread-package.Rd

@@ -14,8 +14,8 @@
   \tabular{ll}{
   Package: \tab GGIRread\cr
   Type: \tab Package\cr
-  Version: \tab 0.3.3\cr
-  Date: \tab 2024-01-24\cr
+  Version: \tab 1.0.0\cr
+  Date: \tab 2024-03-27\cr
   License: \tab LGPL (>= 2.0, < 3)\cr
   }
 }

src/GENEActivReader.cpp

@@ -127,18 +127,14 @@ Rcpp::List GENEActivReader(std::string filename, std::size_t start = 0, std::siz
         while (std::getline(input_file, line)) {
             ++blockCount;
             if (blockCount >= start && blockCount <= end) {
+                blockTime = lastvalue;
                 // header: "Recorded Data" (0), serialCode (1), seq num (2),
                 // blockTime (3), unassigned (4), temp (5), batteryVolt (6),
                 // deviceStatus (7), freq (8), data (9)
                 for (int i = 1; i < blockHeaderSize; i++) {
                     try {
                         std::getline(input_file, header);
-                        if (i == 3) {
-                            std::stringstream ss(header);
-                            int milliseconds;
-                            ss >> milliseconds;
-                            blockTime = lastvalue + milliseconds;
-                        } else if (i == 5) {
+                        if (i == 5) {
                             std::stringstream ss(header);
                             ss.ignore(max_streamsize, ':');
                             ss >> temperature;
@@ -168,7 +164,6 @@ Rcpp::List GENEActivReader(std::string filename, std::size_t start = 0, std::siz
                 double y = 0.0;
                 double z = 0.0;
                 double t = 0.0;
-
                 int i = 0;
                 while (hexPosition < data.size() - 1) {
                     try {
@@ -182,9 +177,8 @@ Rcpp::List GENEActivReader(std::string filename, std::size_t start = 0, std::siz
                         x = (xRaw * 100. - mfrOffset[0]) / mfrGain[0];
                         y = (yRaw * 100. - mfrOffset[1]) / mfrGain[1];
                         z = (zRaw * 100. - mfrOffset[2]) / mfrGain[2];
-
                         t = (double)blockTime + (double)i * (1.0 / freq) * 1000;  // Unix millis
-                        lastvalue = t;
+                        lastvalue = t + (1.0 / freq) * 1000;
                         time_array.push_back(t);
                         x_array.push_back(x);
                         y_array.push_back(y);

tests/testthat/test_readGENEActiv.R

@@ -9,6 +9,7 @@ test_that("GENEActivReader reads data from file correctly", {
   expect_equal(cppdata$info$SampleRate, 85.7)
   expect_equal(cppdata$info$numBlocksTotal, 222048)
   expect_equal(length(cppdata$time), 300)
+  expect_equal(cppdata$time[300], 3488)
   expect_equal(length(cppdata$x), 300)
   expect_equal(length(cppdata$y), 300)
   expect_equal(length(cppdata$z), 300)
@@ -21,7 +22,7 @@ test_that("GENEActivReader reads data from file correctly", {
 test_that("readGENEActiv reads data from file correctly", {
   old <- options(digits.secs = 3)
   binfile  = system.file("testfiles/GENEActiv_testfile.bin", package = "GGIRread")[1]
-  rdata = readGENEActiv(filename = binfile, start = 1, end = 1, desiredtz = "Europe/London")
+  rdata = readGENEActiv(filename = binfile, start = 1, end = 2, desiredtz = "Europe/London")
 
   expect_equal(rdata$header$ReadOK, 1)
   expect_equal(rdata$header$ReadErrors, 0)
@@ -31,12 +32,13 @@ test_that("readGENEActiv reads data from file correctly", {
   expect_equal(rdata$header$RecordingID, "")
   expect_equal(rdata$header$DeviceLocation, "")
   expect_equal(rdata$header$DeviceModel, "1.1")
-  expect_equal(length(rdata$data$time), 300)
-  expect_equal(length(rdata$data$x), 300)
-  expect_equal(length(rdata$data$y), 300)
-  expect_equal(length(rdata$data$z), 300)
-  expect_equal(length(rdata$data$temperature), 300)
-  expect_equal(length(rdata$data$light), 300)
+  expect_equal(length(rdata$data$time), 600)
+  expect_equal(rdata$data$time[600], 1369905181)
+  expect_equal(length(rdata$data$x), 600)
+  expect_equal(length(rdata$data$y), 600)
+  expect_equal(length(rdata$data$z), 600)
+  expect_equal(length(rdata$data$temperature), 600)
+  expect_equal(length(rdata$data$light), 600)
   expect_equal(rdata$data$temperature[1], 21.5)
   expect_equal(rdata$data$light[2], 2.666667, tolerance = 4)
   expect_equal(rdata$data$z[300], -0.80836403369903564453, tolerance = 15)