dptools / dpsleep-freq

DPSleep Frequency Analysis

DPSleep Pipeline Step #2 (frequency analysis)

Table of contents

1. Requirements
2. Installation
3. Usage examples

Requirements

• To run the freq pipeline, make sure that you have time files saved in mtl1. To do so, you need to run the dpsleep-extract pipeline first.

• The output is saved as mtl2_YYYY_MM_DD.mat per day.

• After running this pipeline you should run dpsleep-act.

Installation

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

git clone [e-mail]:harvard-nrg/dpsleep-freq.git 
cd freq
pip install -r requirements.txt

Usage examples

# The default is that the pipeline runs for the "new" files. The --ext_mode can be [new, all, specific]. If "all" it runs for all the files in the subject folder. If "specific" the files after --ext_date argument is analyzed.

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

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

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

# To generate reports for subject A and subject C in STUDY_PILOT under their processed folders
geneactiv_freq.py --study STUDY_PILOT --subject A C --data-type actigraphy --pipeline geneactiv_freq --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_freq.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_freq --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 
# Define extract mode and date
geneactiv_freq.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_freq --data-dir GENERAL --ext-mode specific --ext-date YYYY-MM-DD

For more information, please run:

geneactiv_freq.py -h