Merge branch 'master' into issue991_v2_tempcolumn_adhoccsv_calibration

wadpac · Dec 13, 2023 · 83fe8dd · 83fe8dd
2 parents 574131c + 4a1ee62
commit 83fe8dd
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Showing 4 changed files with 24 additions and 10 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -16,6 +16,8 @@
 
 - Part 1: Fix bug in adhoc-csv format calibration process as it could not extract temperature column #991
 
+- Part 1: Fix bug that caused a mismatch between IDs and filenames in part 1 when movisens participant folders did not contain the acc.bin file #994.
+
 # CHANGES IN GGIR VERSION 3.0-1
 
 - Part 2: Added option to provide a csv file with start and end dates when accelerometer is expected to be worn #943

diff --git a/R/datadir2fnames.R b/R/datadir2fnames.R
@@ -12,8 +12,24 @@ datadir2fnames = function(datadir,filelist) {
       fnamesfull = fnamesRD
     }
   } else {
-    fnamesfull = datadir
-    fnames = basename(fnamesfull)
+    if (ismovisens(datadir)) {
+      fnamesfull = dir(datadir, recursive = TRUE, pattern = "acc.bin", full.names = TRUE)
+      fnames = basename(dirname(fnamesfull))
+      nfolders = length(dir(datadir))
+      if (nfolders > length(fnamesfull)) { # meaning there are movisens data folder without acc.bin
+        # folders without acc.bin
+        allfolders = dir(datadir, full.names = TRUE)
+        foldersWithAccBin = dirname(fnamesfull)
+        noAccBin = allfolders[which(!allfolders %in% foldersWithAccBin)]
+        warning(paste0("The following movisens data folders do not contain the ",
+                       "acc.bin file with the accelerometer recording, and ",
+                       "therefore cannot be processed in GGIR: ",
+                       paste(noAccBin, collapse = ", ")), call. = FALSE)
+      }
+    } else {
+      fnamesfull = datadir
+      fnames = basename(fnamesfull)
+    }
   }
   invisible(list(fnames = fnames, fnamesfull = fnamesfull))
 }
diff --git a/R/g.part1.R b/R/g.part1.R
@@ -18,17 +18,12 @@ g.part1 = function(datadir = c(), metadatadir = c(), f0 = 1, f1 = c(), myfun = c
 
   if (f1 == 0) warning("\nWarning: f1 = 0 is not a meaningful value")
   filelist = isfilelist(datadir)
+  if (ismovisens(datadir)) filelist = TRUE
 
   # list all accelerometer files
   dir2fn = datadir2fnames(datadir, filelist)
   fnames = dir2fn$fnames
   fnamesfull = dir2fn$fnamesfull
-
-  # check whether these are movisens files
-  if (filelist == FALSE & ismovisens(datadir) == TRUE) {
-    fnamesfull = dir(datadir, recursive = TRUE, pattern = "acc.bin", full.names = TRUE)
-    fnames = dir(datadir, recursive = FALSE)
-  }
   filesizes = file.size(fnamesfull) # in bytes
   bigEnough = which(filesizes/1e6 > params_rawdata[["minimumFileSizeMB"]])
   fnamesfull = fnamesfull[bigEnough]

diff --git a/vignettes/GGIR.Rmd b/vignettes/GGIR.Rmd
@@ -159,8 +159,9 @@ additional packages:
         the absence of timestamps GGIR will calculate timestamps from
         the sample frequency, the start time and start date as presented
         in the file header.
-    -   [Movisens](https://www.movisens.com/en/) with data stored in
-        folders.
+    -   [Movisens](https://www.movisens.com/en/) .bin files with data 
+        stored in folders. GGIR expects that each participant's folder 
+        contains at least a file named acc.bin.
     -   Any other accelerometer brand that generates csv output, see
         documentation for functions `read.myacc.csv` and argument
         `rmc.noise` in the [GGIR function documentation