Merge pull request #86 from wadpac/issue85_actical_csv_start

improve detection of Actical start

Author: vincentvanhees

NEWS.md

@@ -1,3 +1,7 @@
+# Changes in version 1.0.6 (release date:??-??-2025)
+
+- Actical: Improve detection of recording start #85
+
 # Changes in version 1.0.5 (release date:09-05-2025)
 
 - Fitbit: Now also loads heart rate data #78

R/findStartData.R

@@ -1,6 +1,26 @@
-findStartData = function(filename, quote, startindex) {
+findStartData = function(filename, quote, startindex, blockname = NULL) {
   # Function used to find start of time series in Actiwatch and Actical data
-  # ! Assumptions that timeseries start before line 1000
+  if (!is.null(blockname)) {
+    # Default approach when blockname is specified (used for Actical)
+    # ! Assumption that time series start in first 3000 lines
+    # ! Assumption count data are preceded by a block header with name blockname
+    data_head = data.table::fread(input = filename,
+                                header = FALSE, sep = ",",
+                                nrows = 3000, data.table = FALSE, 
+                                quote = quote, fill = TRUE)
+    block_start = grep(pattern = blockname, x = data_head[, 1], ignore.case = TRUE)
+    if (length(block_start) != 0) {
+      block_head = data_head[(block_start + 1):(block_start + 20), 1]
+      block_head = unlist(lapply(block_head, FUN = function(x) unlist(strsplit(x, ","))[1]))
+      epochnumbers = suppressWarnings(as.numeric(block_head))
+      block_start = block_start + which(!is.na(epochnumbers))[1]
+    }
+    if (length(block_start) != 0) return(block_start)
+    startindex = block_start
+  }
+  # Original approach:
+  # ! Assumption that timeseries start before line 1000
+  # ! Assumption that epoch column start with 1
   while (startindex > 0) {
     testraw = data.table::fread(input = filename,
                                 header = FALSE, sep = ",", skip = startindex,

R/readActicalCount.R

@@ -8,7 +8,7 @@ readActicalCount = function(filename = NULL,
   # ! Assumptions that timeseries start before line 1000
   startindex = 300
   quote = detectQuote(filename = filename, skip = startindex)
-  startindex = findStartData(filename, quote, startindex)
+  startindex = findStartData(filename, quote, startindex, blockname = "epoch-by-epoch")
   # -1 because Actical starts at epoch 0 while function looks for epoch 1
   startindex = startindex - 1 
   D = data.table::fread(input = filename, sep = ",", skip = startindex,
@@ -29,7 +29,7 @@ readActicalCount = function(filename = NULL,
   colnames = data.table::fread(input = filename, data.table = FALSE,
                                header = FALSE, sep = ",",
                                skip = dashedLineIndex + 1,
-                               nrows = (startindex - dashedLineIndex) - 2, quote = quote)
+                               nrows = (startindex - dashedLineIndex) - 2, quote = quote, fill = TRUE)
   collapse = function(x) {
     return(paste0(x, collapse = "_"))
   }

R/readAxivity.R

@@ -361,7 +361,7 @@ readAxivity = function(filename, start = 0, end = 0, progressBar = FALSE, desire
     stop("At least file must be specified")
   }
   # Get file size in data blocks
-  numDBlocks = round(file.info(filename)$size / blockBytes) - 2
+  numDBlocks = round(file.size(filename) / blockBytes) - 2
   # Open file
   fid = file(filename,"rb")
   on.exit({

man/findStartData.Rd

@@ -8,7 +8,7 @@
   Actiwatch and Actical data.
 }
 \usage{
-  findStartData(filename, quote, startindex)
+  findStartData(filename, quote, startindex, blockname = NULL)
 }
 \arguments{
   \item{filename}{
@@ -21,6 +21,10 @@
     Start index where to start searching. For Actical we start at 300 while
     for Actiwatch we start at 1000.
   }
+  \item{blockname}{
+    Character with name of data block to search for.
+    For Actical we use "epoch-by-epoch".
+  }
 }
 \value{
   Start index