Dev

.github/workflows/main.yml

@@ -2,44 +2,48 @@ name: run act workflow
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "main", "dev" ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: '4.2.0' # Specify the R version
 
       - name: Install R packages
         run: |
-          Rscript -e 'install.packages(c("ggplot2", "plyr", "optparse", "tidyr", "GGIR"), repos="https://cloud.r-project.org")'
-
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.10"
-    - name: Install python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        if [ -f code/requirements.txt ]; then pip install -r code/requirements.txt; fi
-    - name: Run Python script
-      run: |
-        python code/main.py
-    - name: Commit and push changes to main
-      run: |
-        git config --global user.name "GitHub Actions Bot"
-        git config --global user.email "github-actions[bot]@users.noreply.github.com"
-        git checkout main
-        git add .
-        git commit -m "Automated changes from GitHub Actions"
-        git push origin main
+          Rscript -e 'install.packages(c("ggplot2","plyr","optparse","tidyr","remotes"), repos="https://cloud.r-project.org", dependencies=TRUE)'
+          Rscript -e 'remotes::install_version("GGIR", version = "3.2.6", repos = "https://cloud.r-project.org")'
 
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
 
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8 pytest
+          if [ -f code/requirements.txt ]; then pip install -r code/requirements.txt; fi
 
+      - name: Run Python script
+        env:
+          RC_TOKEN: ${{ secrets.RC_TOKEN }}
+        run: |
+          python code/main.py 1 "$RC_TOKEN"
 
+      - name: Commit and push changes to main
+        run: |
+          git config --global user.name "GitHub Actions Bot"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git checkout main
+          git add .
+          git commit -m "Automated changes from GitHub Actions"
+          git push origin main

README.md

@@ -20,3 +20,12 @@
 - [ ] add study rule ->
     - if sub already in obs -> move to int 
     - all need to be after start date 
+
+### adding sleep logs
+- [x] need to return the sleep files from `/sleep` inside the accel folder in RDSS
+- [x] modify `code/utils/comparison_utils` to also add the sleep logs to the linkage, storing the correct study inside
+    - [ ] need to split running by session and split sleep logs by session
+
+
+
+- [ ] create a new util that transforms the current logs into the GGIR available one

code/core/acc.R

@@ -0,0 +1,152 @@
+#!/usr/bin/env Rscript
+
+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-2.8.2-test2/",
+                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 already exist
+  if (!dir.exists(paste0(ProjectDir, ProjectDerivDir))) {
+    dir.create(paste0(ProjectDir, ProjectDerivDir))
+  }
+
+  # List accel.csv files within subject-specific folders
+  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))
+
+  # Split files at the "//" so we only have paths from sub-XXX/ses-.....
+  GGIRfiles <- sapply(strsplit(GGIRfiles, "//", fixed = TRUE), function(x) paste(x[2]))
+
+  print(paste("GGIR Files after splitting: ", GGIRfiles))
+
+
+  # Ensure directory structure exists for GGIR processing
+  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 <- paste0(normalize(path(datadirname(r)))
+      outputdir <- paste0(SubjectGGIRDeriv(r))
+      print(paste("datadir: ", datadir))
+      print(paste("outputdir: ", outputdir))
+      if (!dir.exists(datadir)) {
+        stop(paste("Error: datadir does not exist ->", datadir))
+      }
+    # Force evaluation before calling GGIR
+    assign("datadir", datadir, envir = .GlobalEnv)
+    assign("outputdir", outputdir, envir = .GlobalEnv)
+
+      try(g.shell.GGIR(
+        mode = 1:5,
+        datadir = get("datadir", envir = .GlobalEnv),
+        outputdir = get("outputdir", envir = .GlobalEnv),
+        overwrite = FALSE,
+        print.filename = TRUE,
+        storefolderstructure = FALSE,
+        windowsizes = c(5, 900, 3600),
+        desiredtz = "America/Chicago",
+        do.enmo = TRUE, do.anglez = TRUE,
+        dayborder = 0,
+        strategy = 1, hrs.del.start = 0, hrs.del.end = 0,
+        maxdur = 0, includedaycrit = 0,
+        idloc = 1,
+        dynrange = 8,
+        chunksize = 1,
+        do.cal = TRUE,
+        use.temp = FALSE,
+        spherecrit = 0.3,
+        minloadcrit = 72,
+        printsummary = TRUE,
+        do.imp = TRUE,
+        epochvalues2csv = TRUE,
+        L5M5window = c(0,24),
+        M5L5res = 10,
+        winhr = c(5,10),
+        qlevels = c(960/1440, 1320/1440, 1380/1440, 1410/1440, 1430/1440, 1435/1440, 1438/1440),
+        ilevels = seq(0,600, by = 25),
+        iglevels = c(seq(0,4000, by = 25), 8000),
+        bout.metric = 4,
+        do.visual = TRUE,
+        excludefirstlast = FALSE,
+        includenightcrit = 0,
+        anglethreshold = 5,
+        timethreshold = 5,
+        ignorenonwear = TRUE,
+        acc.metric = "ENMO",
+        do.part3.pdf = TRUE,
+        outliers.only = FALSE,
+        def.noc.sleep = 1,
+        excludefirstlast.part5 = FALSE,
+        maxdur = 0,
+        threshold.lig = c(45),
+        threshold.mod = c(100),
+        threshold.vig = c(430),
+        boutdur.mvpa = c(1,5,10),
+        boutdur.in = c(10,20,30),
+        boutdur.lig = c(1,5,10),
+        boutcriter.mvpa = 0.8,
+        boutcriter.in = 0.9,
+        boutcriter.lig = 0.8,
+        timewindow = c("MM", "WW"),
+        acc.metric = "ENMO",
+        do.report = c(2,4,5),
+        visualreport = TRUE,
+        do.parallel = TRUE
+      ))
+    }
+  }
+}
+
+# Run main if executed as a script
+if (!interactive()) {
+  main()
+}

code/core/acc_new.R

@@ -0,0 +1,131 @@
+
+#!/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)
+if (!requireNamespace("remotes", quietly = TRUE)) {
+  install.packages("remotes")
+}
+if (!requireNamespace("GGIR", quietly = TRUE) || packageVersion("GGIR") != "3.2.6") {
+  remotes::install_version("GGIR", version = "3.2.6", repos = "https://cloud.r-project.org")
+}
+
+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()
+}