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miloswrathmiloswrath
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Merge pull request #1 from HBClab/dev
Dev
2 parents 348ea4a + dab14b5 commit f8e4714

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‎.github/workflows/main.yml‎

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

‎README.md‎

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

‎app/.gitkeeper‎

Whitespace-only changes.

‎code/core/acc.R‎

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#!/usr/bin/env Rscript
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library(tidyr)
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library(plyr)
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library(optparse)
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library(GGIR)
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main <- function() {
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# Define the option list
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option_list <- list(
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make_option(c("-p", "--project_dir"), type="character",
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default="/mnt/nfs/lss/vosslabhpc/Projects/BOOST/InterventionStudy/3-Experiment/data/act-int-test/",
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help="Path to the project directory", metavar="character"),
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make_option(c("-d", "--deriv_dir"), type="character",
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default="/derivatives/GGIR-2.8.2-test2/",
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help="Path to the derivatives directory", metavar="character")
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)
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# Parse the options
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opt_parser <- OptionParser(option_list=option_list)
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opt <- parse_args(opt_parser)
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# Assign variables
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ProjectDir <- opt$project_dir
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ProjectDerivDir <- opt$deriv_dir
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# Print values to verify
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print(paste("Project Directory:", ProjectDir))
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print(paste("Derivatives Directory:", ProjectDerivDir))
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# Helper functions
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SubjectGGIRDeriv <- function(x) {
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a <- dirname(x)
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paste0(ProjectDir, ProjectDerivDir, a)
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}
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datadirname <- function(x) {
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b <- dirname(x)
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paste0(ProjectDir, b)
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}
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# Gather subject directories
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directories <- list.dirs(ProjectDir, recursive = FALSE)
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subdirs <- directories[grepl("sub-*", directories)]
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print(paste("subdirs: ", subdirs))
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# Create project-specific derivatives GGIR folder if it doesn't already exist
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if (!dir.exists(paste0(ProjectDir, ProjectDerivDir))) {
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dir.create(paste0(ProjectDir, ProjectDerivDir))
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}
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# List accel.csv files within subject-specific folders
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filepattern <- "*accel.csv"
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GGIRfiles <- list.files(subdirs, pattern = filepattern, recursive = TRUE,
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include.dirs = TRUE, full.names = TRUE, no.. = TRUE)
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print(paste("GGIR Files before splitting: ", GGIRfiles))
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# Split files at the "//" so we only have paths from sub-XXX/ses-.....
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GGIRfiles <- sapply(strsplit(GGIRfiles, "//", fixed = TRUE), function(x) paste(x[2]))
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print(paste("GGIR Files after splitting: ", GGIRfiles))
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# Ensure directory structure exists for GGIR processing
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for (i in GGIRfiles) {
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if (!dir.exists(SubjectGGIRDeriv(i))) {
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dir.create(SubjectGGIRDeriv(i), recursive = TRUE)
68+
}
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}
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# Run GGIR loop
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for (r in GGIRfiles) {
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if (dir.exists(paste0(SubjectGGIRDeriv(r), "/output_beh"))) {
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next
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} else {
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datadir <- paste0(normalize(path(datadirname(r)))
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outputdir <- paste0(SubjectGGIRDeriv(r))
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print(paste("datadir: ", datadir))
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print(paste("outputdir: ", outputdir))
81+
if (!dir.exists(datadir)) {
82+
stop(paste("Error: datadir does not exist ->", datadir))
83+
}
84+
# Force evaluation before calling GGIR
85+
assign("datadir", datadir, envir = .GlobalEnv)
86+
assign("outputdir", outputdir, envir = .GlobalEnv)
87+
88+
try(g.shell.GGIR(
89+
mode = 1:5,
90+
datadir = get("datadir", envir = .GlobalEnv),
91+
outputdir = get("outputdir", envir = .GlobalEnv),
92+
overwrite = FALSE,
93+
print.filename = TRUE,
94+
storefolderstructure = FALSE,
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windowsizes = c(5, 900, 3600),
96+
desiredtz = "America/Chicago",
97+
do.enmo = TRUE, do.anglez = TRUE,
98+
dayborder = 0,
99+
strategy = 1, hrs.del.start = 0, hrs.del.end = 0,
100+
maxdur = 0, includedaycrit = 0,
101+
idloc = 1,
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dynrange = 8,
103+
chunksize = 1,
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do.cal = TRUE,
105+
use.temp = FALSE,
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spherecrit = 0.3,
107+
minloadcrit = 72,
108+
printsummary = TRUE,
109+
do.imp = TRUE,
110+
epochvalues2csv = TRUE,
111+
L5M5window = c(0,24),
112+
M5L5res = 10,
113+
winhr = c(5,10),
114+
qlevels = c(960/1440, 1320/1440, 1380/1440, 1410/1440, 1430/1440, 1435/1440, 1438/1440),
115+
ilevels = seq(0,600, by = 25),
116+
iglevels = c(seq(0,4000, by = 25), 8000),
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bout.metric = 4,
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do.visual = TRUE,
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excludefirstlast = FALSE,
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includenightcrit = 0,
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anglethreshold = 5,
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timethreshold = 5,
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ignorenonwear = TRUE,
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acc.metric = "ENMO",
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do.part3.pdf = TRUE,
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outliers.only = FALSE,
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def.noc.sleep = 1,
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excludefirstlast.part5 = FALSE,
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maxdur = 0,
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threshold.lig = c(45),
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threshold.mod = c(100),
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threshold.vig = c(430),
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boutdur.mvpa = c(1,5,10),
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boutdur.in = c(10,20,30),
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boutdur.lig = c(1,5,10),
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boutcriter.mvpa = 0.8,
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boutcriter.in = 0.9,
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boutcriter.lig = 0.8,
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timewindow = c("MM", "WW"),
140+
acc.metric = "ENMO",
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do.report = c(2,4,5),
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visualreport = TRUE,
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do.parallel = TRUE
144+
))
145+
}
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}
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}
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# Run main if executed as a script
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if (!interactive()) {
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main()
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}

‎code/core/acc_new.R‎

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#!/usr/bin/env Rscript
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# 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/"
5+
library(tidyr)
6+
library(plyr)
7+
library(optparse)
8+
if (!requireNamespace("remotes", quietly = TRUE)) {
9+
install.packages("remotes")
10+
}
11+
if (!requireNamespace("GGIR", quietly = TRUE) || packageVersion("GGIR") != "3.2.6") {
12+
remotes::install_version("GGIR", version = "3.2.6", repos = "https://cloud.r-project.org")
13+
}
14+
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library(GGIR)
16+
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main <- function() {
18+
# Define the option list
19+
option_list <- list(
20+
make_option(c("-p", "--project_dir"), type = "character",
21+
default = "/mnt/nfs/lss/vosslabhpc/Projects/BOOST/InterventionStudy/3-Experiment/data/act-int-test/",
22+
help = "Path to the project directory", metavar = "character"),
23+
make_option(c("-d", "--deriv_dir"), type = "character",
24+
default = "/derivatives/GGIR-3.2.6-test/",
25+
help = "Path to the derivatives directory", metavar = "character")
26+
)
27+
28+
# Parse the options
29+
opt_parser <- OptionParser(option_list = option_list)
30+
opt <- parse_args(opt_parser)
31+
32+
# Assign variables
33+
ProjectDir <- opt$project_dir
34+
ProjectDerivDir <- opt$deriv_dir
35+
36+
# Print values to verify
37+
print(paste("Project Directory:", ProjectDir))
38+
print(paste("Derivatives Directory:", ProjectDerivDir))
39+
40+
# Helper functions
41+
SubjectGGIRDeriv <- function(x) {
42+
a <- dirname(x)
43+
paste0(ProjectDir, ProjectDerivDir, a)
44+
}
45+
46+
datadirname <- function(x) {
47+
b <- dirname(x)
48+
paste0(ProjectDir, b)
49+
}
50+
51+
# Gather subject directories
52+
directories <- list.dirs(ProjectDir, recursive = FALSE)
53+
subdirs <- directories[grepl("sub-*", directories)]
54+
print(paste("subdirs: ", subdirs))
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56+
# Create project-specific derivatives GGIR folder if it doesn't exist
57+
if (!dir.exists(paste0(ProjectDir, ProjectDerivDir))) {
58+
dir.create(paste0(ProjectDir, ProjectDerivDir))
59+
}
60+
61+
# List accel.csv files
62+
filepattern <- "*accel.csv"
63+
GGIRfiles <- list.files(subdirs, pattern = filepattern, recursive = TRUE,
64+
include.dirs = TRUE, full.names = TRUE, no.. = TRUE)
65+
print(paste("GGIR Files before splitting: ", GGIRfiles))
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# Adjust path formatting
68+
GGIRfiles <- sapply(strsplit(GGIRfiles, "//", fixed = TRUE), function(x) paste(x[2]))
69+
print(paste("GGIR Files after splitting: ", GGIRfiles))
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# Ensure directory structure exists
72+
for (i in GGIRfiles) {
73+
if (!dir.exists(SubjectGGIRDeriv(i))) {
74+
dir.create(SubjectGGIRDeriv(i), recursive = TRUE)
75+
}
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}
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# Run GGIR loop
79+
for (r in GGIRfiles) {
80+
if (dir.exists(paste0(SubjectGGIRDeriv(r), "/output_beh"))) {
81+
next
82+
} else {
83+
datadir <- normalizePath(datadirname(r), mustWork = FALSE)
84+
outputdir <- SubjectGGIRDeriv(r)
85+
print(paste("datadir: ", datadir))
86+
print(paste("outputdir: ", outputdir))
87+
if (!dir.exists(datadir)) {
88+
stop(paste("Error: datadir does not exist ->", datadir))
89+
}
90+
91+
assign("datadir", datadir, envir = .GlobalEnv)
92+
assign("outputdir", outputdir, envir = .GlobalEnv)
93+
94+
try({
95+
GGIR(
96+
mode = 1:6,
97+
datadir = datadir,
98+
outputdir = outputdir,
99+
studyname = "boost",
100+
overwrite = FALSE,
101+
do.report = c(2, 4, 5, 6),
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visualreport = TRUE,
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old_visualreport = FALSE,
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windowsizes = c(5, 900, 3600),
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desiredtz = "America/Chicago",
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print.filename = TRUE,
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dayborder = 0,
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idloc = 2,
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epochvalues2csv = TRUE,
110+
ignorenonwear = TRUE,
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do.ENMO = TRUE,
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acc.metric = "ENMO",
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hrs.del.start = 4,
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hrs.del.end = 3,
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maxdur = 9,
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loglocation = "/Shared/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test/sleep.csv",
117+
colid = 1,
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coln1 = 2,
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sleepwindowType = "SPT",
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timewindow = c("WW", "MM", "OO"),
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part6CR = TRUE
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)
123+
})
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}
125+
}
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}
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# Run main if executed as script
129+
if (!interactive()) {
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main()
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}

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