add script to restructure directory to future BEP020 conformity #13
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182
code/restructure.sh
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182
code/restructure.sh
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#!/bin/bash
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# This script is intended to restructure and/or rename contents of the
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# studyforrest-phase2 dataset into future BIDS compatibility with BIDS Extension
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# Proposal 20 (BEP020
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# https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw/edit#).
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# To execute run the following datalad run command:
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# datalad run --input 'sub*/*/*/sub*_task-movie_run*_events*' --input
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# 'sub*/*/*/sub*_task-movie_run*eyelink*' --input
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# 'sub*/*/*/sub*_task-movie_run*eyegaze*' 'code/restructure.sh'
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set -e
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set -u
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##create eyetrack dir if it doesn't exist
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#initial_dir=/home/adina/Repos/studyforrest-data-phase2
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initial_dir='../studyforrest-data-phase2'
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subs=$(find -type d -name "sub-*" -printf "%f\n" | sort)
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for sub in $subs; do
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root_dir=${initial_dir}/${sub}/ses-movie/
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eyetrack_dir=${root_dir}/eyetrack/
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[ ! -d "$eyetrack_dir" ] && mkdir -p "$eyetrack_dir";
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[ ! -d "$eyetrack_dir/sourcedataa" ] && mkdir -p "$eyetrack_dir/sourcedata";
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[ ! -d "$eyetrack_dir/derivatives" ] && mkdir -p "$eyetrack_dir/derivatives";
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done
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#move raw and derived eyetracking data into respective sub/eyetrack/ directories
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for sub in $subs; do
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if [ ! -d ${initial_dir}/${sub}/beh ]; then
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mv ${initial_dir}/${sub}/ses-movie/func/${sub}_ses-movie_task-movie_run-*_eyelinkraw.asc.gz ${initial_dir}/${sub}/ses-movie/eyetrack/sourcedata/
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mv ${initial_dir}/${sub}/ses-movie/func/${sub}_ses-movie_task-movie_run-*recording-eyegaze_physio* ${initial_dir}/${sub}/ses-movie/eyetrack/derivatives/
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mv ${initial_dir}/${sub}/ses-movie/func/${sub}_ses-movie_task-movie_run-*events* ${initial_dir}/${sub}/ses-movie/eyetrack/sourcedata ;
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fi
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if [ -d ${initial_dir}/${sub}/beh ]; then
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mv ${initial_dir}/${sub}/beh/${sub}_task-movie_run-*event* ${initial_dir}/${sub}/ses-movie/eyetrack/sourcedata
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mv ${initial_dir}/${sub}/beh/${sub}_task-movie_run-*eyelink* ${initial_dir}/${sub}/ses-movie/eyetrack/sourcedata
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mv ${initial_dir}/${sub}/beh/*physio* ${initial_dir}/${sub}/ses-movie/eyetrack/derivatives;
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mv ${initial_dir}/${sub}/*beh.json ${initial_dir}/${sub}/ses-movie/eyetrack;
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rm -r -f ${initial_dir}/${sub}/beh
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fi
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done
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#rename raw data
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for sub in $subs; do
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for i in $(find $sub/ses-movie/eyetrack/sourcedata -name '*eyelinkraw*'); do
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mv $i $(echo $i | sed -e 's/eyelinkraw/eyetrack/')
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done
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for i in $(find $sub/ses-movie/eyetrack/sourcedata -name '*task-movie*'); do
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mv $i $(echo $i | sed -r 's/task-movie_/task-avmovie_/');
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done
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done
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#rename the deriv data
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for sub in $subs; do
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for i in $(find $sub/ses-movie/eyetrack/derivatives -name '*recording-eyegaze_physio*'); do
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mv $i $(echo $i | sed -e 's/task-movie_/task-avmovie_/');
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done
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done
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#unify naming of lab subj data
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for sub in sub-22 sub-23 sub-24 sub-25 sub-26 sub-27 sub-28 sub-29 sub-30 sub-31 sub-32 sub-33 sub-34 sub-35 sub-36; do
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for i in $(find ${sub}/ses-movie/eyetrack/derivatives -name '*recording-eyegaze_physio*'); do
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mv $i $(echo $i | sed -e 's/task-avmovie_/ses-movie_task-avmovie_/');
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done
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for i in $(find ${sub}/ses-movie/eyetrack/sourcedata -name '*run*'); do
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mv $i $(echo $i | sed -e 's/task/ses-movie_task/');
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done
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for i in $(find ${sub}/ses-movie/eyetrack -name '*beh.json'); do
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mv $i $(echo $i | sed -e 's/task-movie_beh/ses-movie_task-avmovie_eyetrack/');
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done
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done
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list_include_item() {
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local list="$1"
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local item="$2"
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if [[ $list =~ (^|[[:space:]])"$item"($|[[:space:]]) ]] ; then
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# yes, list include item
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result=0
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else
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result=1
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fi
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return $result
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}
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#generate _eyetrack.json file based on whether subject has lab or scanner data
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mri="sub-01 sub-02 sub-03 sub-04 sub-05 sub-06 sub-09 sub-10 sub-14 sub-15 sub-16 sub-17 sub-18 sub-19 sub-20"
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for sub in $subs; do
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if `list_include_item "sub-01 sub-02 sub-03 sub-04 sub-05 sub-06 sub-09 sub-10 sub-14 sub-15 sub-16 sub-17 sub-18 sub-19 sub-20" "${sub}"`; then
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cat <<EOT > ${initial_dir}/${sub}/ses-movie/eyetrack/sourcedata/${sub}_ses-movie_task-avmovie_eyetrack.json
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{
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"SamplingFrequency": 1000,
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"FileFormat": "*.asc.gz",
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"StartMessage": "<TODO>",
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"EndMessage": "<TODO>",
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"EventIdentifier": "custom log message at onset of every movie frame",
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"InstitutionName": "Psychoinformatics Lab",
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"InstitutionAddress": "Otto-von-Guericke-Universitaet, Universitaetsplatz 2, Building 23, Magdeburg, D-39106",
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"Manufacturer": "SR-Research",
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"ManufacturersModelName": "Eye-link 1000",
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"SoftwareVersions": 4.594,
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"TaskDescription": "Participants watch the movie 'Forrest Gump' in eight segments",
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"Instructions": "Enjoy the movie",
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"CalibrationTyoe": "13-point sequence",
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"RecordedEye": "Left",
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"AverageCalibrationError": 0.5753018209378478
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}
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EOT
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else
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cat <<EOT >${initial_dir}/${sub}/ses-movie/eyetrack/sourcedata/${sub}_ses-movie_task-avmovie_eyetrack.json
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{
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"SamplingFrequency": 1000,
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"FileFormat": "*.asc.gz",
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"StartMessage": ,
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"EndMessage": ,
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"EventIdentifier": ,
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"InstitutionName": "Psychoinformatics Lab",
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"InstitutionAddress": "Otto-von-Guericke-Univer,
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"Manufacturer": "SR-Research",
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"ManufacturersModelName": "Eye-link 1000",
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"SoftwareVersions": 4.594,
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"TaskDescription": "Participants watch the movie 'Forrest Gump' in eight segments",
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"Instructions": "Enjoy the movie",
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"CalibrationTyoe": "13-point sequence",
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"RecordedEye": "Left",
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"AverageCalibrationError": 0.4534103524447244
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}
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EOT
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fi
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done
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#create .bidsignore file for all files not yet supported in BIDS
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cat <<EOT >${initial_dir}/.bidsignore
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ISSUES
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LICENSE
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Makefile
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README.rst
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README
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tests/
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EOT
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#create data dictionary for participants.tsv file
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cat <<EOT >${initial_dir}/participants.json
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{
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"gender": "Gender (m = male, f = female)",
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"age": "Age, specified in age groups of 5 years",
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"handedness": "r = right, l = left",
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"hearing_problems_current": "n = no, y = yes",
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"hearing_problems_past": "n = no, y = yes",
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"vision_problems_current": "n = no, y = yes",
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"vision_problems_past": "n = no, y = yes",
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"forrest_seen": "n = no, y = yes",
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"forrest_seen_dist": "time since the last time the movie was watched",
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"forrest_seen_count": "number of previous viewing of the movie",
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"forrest_seen_languages": "language(s) the movie was previously seen in",
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"forrest_ad_known": "audio-version known? n = no, y = yes",
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"forrest_av_rating": "average rating",
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"forrest_av_storydepth": "subjective rating of story depth",
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"forrest_av_fatigue": "subjective rating of fatique",
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"forrest_av_feeling": "average subjective feeling",
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"forrest_av_artist_count": "average artist count"
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}
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EOT
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#generate README in derivatives directory
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for sub in $subs; do
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cat << EOT >${initial_dir}/${sub}/ses-movie/eyetrack/derivatives/README
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studyforrest-phase2/sub*/ses-movie/eyetrack/derivatives/
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This directory contains the following files:
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- sub-{subid}_ses-movie_task-avmovie_run-{runid}_recording-eyegaze_physio.tsv.gz:
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A .tsv file with columns "x", "y", "pupil_dil", "movieframe:idx" (no
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header)
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EOT
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done
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