R/appendRecords.R

In wadpac/GGIR: Raw Accelerometer Data Analysis

appendRecords = function(metadatadir, desiredtz = "", idloc = 1, maxRecordingInterval = NULL) {
  
  # Declare local functions:
  getInfo = function(fn, idloc, tz) {
    load(fn)
    if (is.null(M$metashort)) return()
    hvars = g.extractheadervars(I)
    if (exists("Clist")) {
      ID = NA # If Clist exists then ignore this file as it was previously appended
    } else {
      ID = extractID(hvars, idloc, fname = I$filename)
    }
    start = as.POSIXct(x = M$metashort$timestamp[1], format = "%Y-%m-%dT%H:%M:%S%z", tz = tz)
    end = as.POSIXct(x = M$metashort$timestamp[nrow(M$metashort)], format = "%Y-%m-%dT%H:%M:%S%z", tz = tz)
    info = data.frame(ID = ID, start = start, end = end, filename = fn, brand = I$monn)
    return(info)
  }
  mergePair = function(M1, M2, overlap, tz) {
    # overlap in epochs
    if (overlap < 0) { 
      # there is a gap
      fillgaps = function(df, overlap, epochSize, pattern) {
        if (overlap < 0) {
          N = abs(overlap) - ifelse(pattern == "long", yes = 0, no = 1)
        } else {
          N = overlap - 1
        }
        if (N > 0) {
          NEWSHORT = df[nrow(df), ]
          NEWSHORT[1:N, ] = NEWSHORT
          T0 = as.POSIXct(x = NEWSHORT$timestamp[1], format = "%Y-%m-%dT%H:%M:%S%z", tz = tz) + epochSize
          NEWSHORT$timestamp = POSIXtime2iso8601(seq(T0, T0 + (N * epochSize) - 1, by =  epochSize), tz)
          if (pattern != "long") {
            NEWSHORT[, grep(pattern = pattern, x = colnames(NEWSHORT), invert = TRUE, ignore.case = TRUE)] = 0
          } else {
            enCol = grep("en", colnames(NEWSHORT), ignore.case = TRUE)
            NEWSHORT[, enCol] = 1
            NEWSHORT$clippingscore = 0
            NEWSHORT$nonwearscore = 3
            if (any(colnames(NEWSHORT) %in% c("lightmean", "lightpeak"))) {
              NEWSHORT$lightmean = 0
              NEWSHORT$lightpeak = 0
            }
            if ("temperaturemean" %in% colnames(NEWSHORT)) {
              NEWSHORT$temperaturemean = 0
            }
          }
          df = rbind(df, NEWSHORT)
        }
        return(df)
      }
      # insert missing values in metashort
      M1$metashort = fillgaps(df = M1$metashort, overlap = round(overlap / M1$windows[1]),
                              epochSize = M1$windows[1], pattern = "time|angle")
      # insert missing values in metalong
      M1$metalong = fillgaps(df = M1$metalong,
                             overlap = round(overlap / M1$windows[2]),
                             epochSize = M1$windows[2], pattern = "long")
      if (length(which(duplicated(M1$metashort$timestamp) == TRUE) > 0) |
          length(which(duplicated(M1$metalong$timestamp) == TRUE) > 0)) {
        stop("\nDuplicated timestamps found, something may have gone wrong with appending the timeseries")
      }
      
    }
    
    # Append data.frames (yes, we may expect duplicates here, which are going to be dealt with)
    M1$metashort = rbind(M1$metashort, M2$metashort)
    M1$metalong = rbind(M1$metalong, M2$metalong)
    # Omit oldest duplicated timestamps
    M1$metashort = M1$metashort[rev(!duplicated(rev(M1$metashort$timestamp))),]
    M1$metalong = M1$metalong[rev(!duplicated(rev(M1$metalong$timestamp))),]
    return(M1)
  }
  #==================================================
  # Main code:
  filefoldername = filename_dir = tail_expansion_log = NULL
  # Create overview of all recordings ID, start time, end time, and filename
  fns = dir(paste0(metadatadir, "/meta/basic"), full.names = TRUE)
  
  S = do.call("rbind", lapply(X = fns, FUN = getInfo, idloc = idloc, tz = desiredtz)) 
  if (length(S) > 0 & !is.null(maxRecordingInterval)) {
    S = S[!is.na(S$ID),]
    S = S[order(S$ID, S$start), ]
    S$overlap = NA
    # Identify recordings that can be appended (ID and brand need to match)
    doubleID = unique(S$ID[duplicated(S[, c("ID", "brand")])])
    if (length(doubleID) > 0) {
      for (j in 1:length(doubleID)) {
        Mlist = Ilist = Clist = list()
        # Does time interval overlap?
        # Label the recordings that are groups, this can be more than 2 recordings
        rowsOfInterest = which(S$ID == doubleID[j])
        Nrec = length(which(S$ID == doubleID[j]))
        for (k in Nrec:2) {
          overlap = as.numeric(difftime(S$end[rowsOfInterest[k - 1]], S$start[rowsOfInterest[k]], units = "secs"))
          # positive overlap is true overlap, negative overlap is a gap
          # Add load number
          S$overlap[rowsOfInterest[k]] = overlap 
          load(S$filename[rowsOfInterest[k]])
          Mlist[[k]] = M
          Ilist[[k]] = I
          Clist[[k]] = C
        }
        # First recording
        load(S$filename[rowsOfInterest[1]])
        Mlist[[1]] = M
        Ilist[[1]] = I
        Clist[[1]] = C
        
        # Append all recordings if they are a sequence of nearby recordings
        cnt = 0
        for (k in (Nrec:1)) {
          if (!is.na(S$overlap[rowsOfInterest[k]])) {
            interval = S$overlap[rowsOfInterest[k]]
          } else {
            interval = -2e10
          }
          if (interval > -abs(maxRecordingInterval) * 3600 & k > 1) {
            # Merge this pair
            Mlist[[k - 1]] = mergePair(M1 = Mlist[[k - 1]],
                                       M2 =  Mlist[[k]],
                                       overlap = S$overlap[rowsOfInterest[k]],
                                       tz = desiredtz)
            interval = round(interval / 3600, digits = 3)
            if ("interval" %in% names(Ilist[[k]])) {
              Ilist[[k - 1]]$interval = c(Ilist[[k]]$interval, interval)
            } else {
              Ilist[[k - 1]]$interval = interval
            }
            # Remove duplicate files
            unlink(S$filename[rowsOfInterest[k]], recursive = TRUE)
            cnt = cnt + 1 # keep track of how many files were appended
          } else {
            if (cnt > 0) {
              # we need to have at least two recording appended to make it worth saving the data
              M = Mlist[[k]]
              C = Clist[[k]]
              I = Ilist[[k]]
              # save as new milestone data for part 1
              # Note that we also keep copy of I and C for each of the original recordings
              # this to retain this information for reporting in part 2
              Nappended = cnt
              C_list = Clist[c(k:(cnt + 1))]
              I_list = Ilist[c(k:(cnt + 1))]
              save(M, C, I, C_list, I_list,
                   filefoldername, filename_dir, tail_expansion_log, Nappended,
                   file = S$filename[rowsOfInterest[k]])
            }
            cnt = 0 # start again
          }
        }
      }
    }
  }
  # THIS FUNCTION DOES NOT PRODUCE OUTPUT IT ONLY APPENDS FILES
  return(NULL)
}