running the qc on newest verion

Author: miloswrath

code/core/acc_new.R

@@ -0,0 +1,124 @@
+
+#!/usr/bin/env Rscript
+
+# Usage: Rscript new_gg.R --project_dir "/Shared/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test/" --deriv_dir "derivatives/GGIR-3.2.6-test/"
+library(tidyr)
+library(plyr)
+library(optparse)
+library(GGIR)
+
+main <- function() {
+  # Define the option list
+  option_list <- list(
+    make_option(c("-p", "--project_dir"), type = "character",
+                default = "/mnt/nfs/lss/vosslabhpc/Projects/BOOST/InterventionStudy/3-Experiment/data/act-int-test/",
+                help = "Path to the project directory", metavar = "character"),
+    make_option(c("-d", "--deriv_dir"), type = "character",
+                default = "/derivatives/GGIR-3.2.6-test/",
+                help = "Path to the derivatives directory", metavar = "character")
+  )
+
+  # Parse the options
+  opt_parser <- OptionParser(option_list = option_list)
+  opt <- parse_args(opt_parser)
+
+  # Assign variables
+  ProjectDir <- opt$project_dir
+  ProjectDerivDir <- opt$deriv_dir
+
+  # Print values to verify
+  print(paste("Project Directory:", ProjectDir))
+  print(paste("Derivatives Directory:", ProjectDerivDir))
+
+  # Helper functions
+  SubjectGGIRDeriv <- function(x) {
+    a <- dirname(x)
+    paste0(ProjectDir, ProjectDerivDir, a)
+  }
+
+  datadirname <- function(x) {
+    b <- dirname(x)
+    paste0(ProjectDir, b)
+  }
+
+  # Gather subject directories
+  directories <- list.dirs(ProjectDir, recursive = FALSE)
+  subdirs <- directories[grepl("sub-*", directories)]
+  print(paste("subdirs: ", subdirs))
+
+  # Create project-specific derivatives GGIR folder if it doesn't exist
+  if (!dir.exists(paste0(ProjectDir, ProjectDerivDir))) {
+    dir.create(paste0(ProjectDir, ProjectDerivDir))
+  }
+
+  # List accel.csv files
+  filepattern <- "*accel.csv"
+  GGIRfiles <- list.files(subdirs, pattern = filepattern, recursive = TRUE,
+                          include.dirs = TRUE, full.names = TRUE, no.. = TRUE)
+  print(paste("GGIR Files before splitting: ", GGIRfiles))
+
+  # Adjust path formatting
+  GGIRfiles <- sapply(strsplit(GGIRfiles, "//", fixed = TRUE), function(x) paste(x[2]))
+  print(paste("GGIR Files after splitting: ", GGIRfiles))
+
+  # Ensure directory structure exists
+  for (i in GGIRfiles) {
+    if (!dir.exists(SubjectGGIRDeriv(i))) {
+      dir.create(SubjectGGIRDeriv(i), recursive = TRUE)
+    }
+  }
+
+  # Run GGIR loop
+  for (r in GGIRfiles) {
+    if (dir.exists(paste0(SubjectGGIRDeriv(r), "/output_beh"))) {
+      next
+    } else {
+      datadir <- normalizePath(datadirname(r), mustWork = FALSE)
+      outputdir <- SubjectGGIRDeriv(r)
+      print(paste("datadir: ", datadir))
+      print(paste("outputdir: ", outputdir))
+      if (!dir.exists(datadir)) {
+        stop(paste("Error: datadir does not exist ->", datadir))
+      }
+
+      assign("datadir", datadir, envir = .GlobalEnv)
+      assign("outputdir", outputdir, envir = .GlobalEnv)
+
+      try({
+        GGIR(
+          mode = 1:6,
+          datadir = datadir,
+          outputdir = outputdir,
+          studyname = "boost",
+          overwrite = FALSE,
+          do.report = c(2, 4, 5, 6),
+          visualreport = TRUE,
+          old_visualreport = FALSE,
+          windowsizes = c(5, 900, 3600),
+          desiredtz = "America/Chicago",
+          print.filename = TRUE,
+          dayborder = 0,
+          idloc = 2,
+          epochvalues2csv = TRUE,
+          ignorenonwear = TRUE,
+          do.ENMO = TRUE,
+          acc.metric = "ENMO",
+          hrs.del.start = 4,
+          hrs.del.end = 3,
+          maxdur = 9,
+          loglocation = "/Shared/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test/sleep.csv",
+          colid = 1,
+          coln1 = 2,
+          sleepwindowType = "SPT",
+          timewindow = c("WW", "MM", "OO"),
+          part6CR = TRUE
+        )
+      })
+    }
+  }
+}
+
+# Run main if executed as script
+if (!interactive()) {
+  main()
+}

code/core/gg.py

@@ -17,7 +17,7 @@ def __init__(self, matched, intdir, obsdir):
         self.matched = matched
         self.INTDIR = intdir.rstrip('/') + '/'
         self.OBSDIR = obsdir.rstrip('/') + '/'
-        self.DERIVATIVES = "/derivatives/GGIR-3.1.4"  # Defined within the class
+        self.DERIVATIVES = "/derivatives/GGIR-3.2.6-test"  # Defined within the class
 
     def run_gg(self):
         """
@@ -28,7 +28,7 @@ def run_gg(self):
         from utils.qc import QC 
 
         for project_dir in [self.INTDIR, self.OBSDIR]:
-            command = f"Rscript core/acc.R --project_dir {project_dir} --deriv_dir {self.DERIVATIVES}"
+            command = f"Rscript core/acc_new.R --project_dir {project_dir} --deriv_dir {self.DERIVATIVES}"
 
             try:
                 # Execute the command in a new subprocess