DPSleep Pipeline Step #7 (upact - Update Sleep Parameters after QC)

Table of contents

1. Requirements
2. Installation
3. Usage examples

Requirements

• Make sure to run the "dpsleep-qcact" pipeline before this step
• Run this step after doing Quality Control on "dpsleep-qcact" results and saving the .csv file with adding "_qcd" to the name
• The output is saved as a .csv file in mtl7 with all sleep parameters

Installation

To install dpsleep-upact on your system, run the following commands:

git clone [email protected]:harvard-nrg/dpsleep-upact.git 
cd upact
pip install -r requirements.txt

Usage examples

# To generate reports under every subject's processed directory in PHOENIX
geneactiv_upact.py --data-type actigraphy --pipeline geneactiv_upact --data-dir GENERAL

# To generate reports for every subject and save them in ~/dp_test1 directory
geneactiv_upact.py --output-dir ~/dp_test1 --data-type actigraphy --pipeline geneactiv_upact --data-dir GENERAL
# or
geneactiv_upact.py --output-dir ~/dp_test1/ --data-type actigraphy --pipeline geneactiv_upact --data-dir GENERAL

# To generate reports for STUDY_A's subject B under ~/dp_test1 directory
geneactiv_upact.py --output-dir ~/dp_test1/ --study STUDY_A --subject B --data-type actigraphy --pipeline geneactiv_upact --data-dir GENERAL

# To generate reports for subject A and subject C in STUDY_PILOT under their processed folders
geneactiv_upact.py --study STUDY_PILOT --subject A C --data-type actigraphy --pipeline geneactiv_upact --data-dir GENERAL

# To generate reports for subject A and subject C in STUDY_PILOT under their processed folders
# Define the PHOENIX, consent and MATLAB directories 
geneactiv_upact.py --study STUDY_PILOT --phoenix-dir /data/PHOENIX --consent-dir /data/PHOENIX/GENERAL --mtl-dir MATLAB_DIRECTORY --subject A C --data-type actigraphy --pipeline geneactiv_upact --data-dir GENERAL

For more information, please run:

geneactiv_upact.py -h