main

#!/bin/bash
#PBS -l nodes=1:ppn=6
#PBS -l vmem=16gb
#PBS -l walltime=10:00:00

set -e
set -x

cmd=`jq -r .command config.json`
case "$cmd" in

    dipy_fit_mapmri)
        cat > script.sh <<EOF
#!/bin/bash
LAPLACIAN_OPT=`jq -r '.laplacian' config.json`
POSITIVITY_OPT=`jq -r '.positivity' config.json`
if [ "$LAPLACIAN_OPT" = true ]; then
    LAPLACIAN_OPT="--laplacian"
else
    LAPLACIAN_OPT=" "
fi
if [ "$POSITIVITY_OPT" = true ]; then
    POSITIVITY_OPT="--positivity"
else
    POSITIVITY_OPT=" "
fi
$cmd --force \
    --out_dir $(pwd) \
    --b0_threshold $(jq -r .b0_threshold config.json) \
    $LAPLACIAN_OPT  $POSITIVITY_OPT   \
    --bval_threshold $(jq -r .bval_threshold config.json) \
    --laplacian_weighting $(jq -r .laplacian_weighting config.json) \
    --radial_order $(jq -r .radial_order config.json) \
    --out_strat what \
    $(jq -r .dwi config.json) $(jq -r .bvals config.json) $(jq -r .bvecs config.json) $(jq -r .small_delta config.json) $(jq -r .big_delta config.json)
EOF
        ;;
    *)
        echo "invalid command: $cmd"
        exit 1
esac

chmod +x script.sh
SINGULARITYENV_PYTHONNOUSERSITE=true singularity exec -e docker://brainlife/dipy:1.1.1 ./script.sh

echo "done"