standardise filename and calendar date in reports from parts 2, 4, 5,…

… and 6
wadpac · Sep 13, 2024 · e349942 · e349942
1 parent a70a430
commit e349942
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Showing 4 changed files with 28 additions and 5 deletions.
diff --git a/R/g.part6.R b/R/g.part6.R
@@ -29,6 +29,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
   # Identify correct subfolder
   expected_ts_path = paste0(metadatadir, "/meta/ms5.outraw/", params_phyact[["part6_threshold_combi"]])
   expected_ms5raw_path = paste0(metadatadir, "/meta/ms5.outraw")
+  expected_ms5_path = paste0(metadatadir, "/meta/ms5.out")
   if (!dir.exists(expected_ts_path)) {
     if (!dir.exists(expected_ms5raw_path)) {
       stop("\nPath ", expected_ms5raw_path, " does not exist", call. = FALSE)
@@ -44,6 +45,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
     }
   }
   fnames.ms5raw = dir(expected_ts_path)
+  fnames.ms5 = dir(expected_ms5_path)
   # It can be that the use stored rdata and csv files
   # only use rdata in that case
   getExt = function(x) {
@@ -95,7 +97,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
   # Declare recording level functionality, which at the end of this g.part6 is either
   # applied to the file in parallel with foreach or serially with a loop
   main_part6_recordlevel = function(i, metadatadir = c(), f0 = c(), f1 = c(),
-                                    fnames.ms5raw, ffdone, EXT, verbose) {
+                                    fnames.ms5raw, ffdone, EXT, verbose, fnames.ms5) {
     if (length(ffdone) > 0) {
       if (length(which(ffdone == fnames.ms5raw[i])) > 0) {
         skip = 1 #skip this file because it was analysed before")
@@ -109,6 +111,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
 
     if (skip == 0) {
       # Load time series:
+      lookfor = unlist(strsplit(fnames.ms5raw[i], "_"))[1] # filename without extension and without sib detection indicator (e.g., _T5A5.csv)
       if (EXT == "RData") {
         load(file = paste0(metadatadir, "/meta/ms5.outraw/",
                            params_phyact[["part6_threshold_combi"]], "/", fnames.ms5raw[i]))
@@ -117,6 +120,17 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
         mdat = data.table::fread(file = paste0(metadatadir, "/meta/ms5.outraw/", 
                                                params_phyact[["part6_threshold_combi"]],  "/", fnames.ms5raw[i]), data.table = FALSE)
       }
+      # also load corresponding ms5 file to extract filename
+      ms5toload = grep(pattern = lookfor, fnames.ms5, fixed = T, value = T)
+      if (length(ms5toload) == 1) {
+        output = c()
+        load(file.path(metadatadir, "meta/ms5.out", ms5toload))
+        filename = gsub(".RData$", "", unique(output$filename))
+        rm(output)
+      } else {
+        # if couldn't match the ms5 data, then use the ms5raw as filename as it was done before
+        filename = gsub(pattern = "[.]RData|[.]csv", replacement = "", x = fnames.ms5raw[i])
+      }
       nfeatures = 50
       summary = matrix(NA, nfeatures, 1)
       s_names = rep("", nfeatures)
@@ -188,7 +202,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
       summary[fi] = format(starttime)
       s_names[fi] = "starttime"
       fi = fi + 1
-      summary[fi] = gsub(pattern = "[.]RData|[.]csv", replacement = "", x = fnames.ms5raw[i])
+      summary[fi] = filename
       s_names[fi] = "filename"
       fi = fi + 1
       summary[fi] = ifelse(test = nrow(ts) == 1,
@@ -333,7 +347,8 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
                                      .export = functions2passon, .errorhandling = errhand) %myinfix% {
                                        tryCatchResult = tryCatch({
                                          main_part6_recordlevel(i, metadatadir, f0, f1,
-                                                                fnames.ms5raw, ffdone, EXT, verbose)
+                                                                fnames.ms5raw, ffdone, EXT, verbose,
+                                                                fnames.ms5)
                                        })
                                        return(tryCatchResult)
                                      }
@@ -348,7 +363,8 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
       for (i in f0:f1) {
         if (verbose == TRUE) cat(paste0(i, " "))
         main_part6_recordlevel(i, metadatadir, f0, f1,
-                               fnames.ms5raw, ffdone, EXT, verbose)
+                               fnames.ms5raw, ffdone, EXT, verbose,
+                               fnames.ms5)
       }
     }
   }

diff --git a/R/g.report.part2.R b/R/g.report.part2.R
@@ -239,7 +239,8 @@ g.report.part2 = function(metadatadir = c(), f0 = c(), f1 = c(), maxdur = 0,
       # tidy up data.frames
       SUMMARY_clean = tidyup_df(SUMMARY)
       daySUMMARY_clean = tidyup_df(daySUMMARY)
-
+      # format calendar dates (dates are stored as iso8601, so date is in the first 10 characters )
+      daySUMMARY_clean$calendar_date = substr(daySUMMARY_clean$calendar_date, 1, 10)
       #===============================================================================
       # store final matrices again
       data.table::fwrite(x = SUMMARY_clean, file = paste0(metadatadir, "/results/part2_summary.csv"),

diff --git a/R/g.report.part4.R b/R/g.report.part4.R
@@ -76,6 +76,9 @@ g.report.part4 = function(datadir = c(), metadatadir = c(), loglocation = c(),
     }
     nightsummary2 = as.data.frame(do.call(rbind, lapply(fnames.ms4, myfun)), stringsAsFactors = FALSE)
     nightsummary2$night = as.numeric(gsub(" ", "", nightsummary2$night))
+    nightsummary2$calendar_date = as.Date(nightsummary2$calendar_date, format = "%d/%m/%Y")
+    nightsummary2$calendar_date = as.character(nightsummary2$calendar_date)
+    nightsummary2$filename = gsub(".RData$", "", nightsummary2$filename)
     # ====================================== Add non-wearing during SPT from part 5, if it is availabe:
     ms5.out = "/meta/ms5.out"
     if (file.exists(paste(metadatadir, ms5.out, sep = ""))) {

diff --git a/R/g.report.part5.R b/R/g.report.part5.R
@@ -184,6 +184,9 @@ g.report.part5 = function(metadatadir = c(), f0 = c(), f1 = c(), loglocation = c
       outputfinal = outputfinal[,-cut]
     }
 
+    # revise filename
+    outputfinal$filename = gsub(".RData$", "", outputfinal$filename)
+
     # order data.frame
     outputfinal$window_number = as.numeric(gsub(" ", "", outputfinal$window_number))
     outputfinal = outputfinal[order(outputfinal$filename, outputfinal$window_number, outputfinal$window), ]