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_median_otsu)
        #bypass bvals / bvecs for masked output
        cp $(jq -r .bvals config.json) dwi.bvals
        cp $(jq -r .bvecs config.json) dwi.bvecs

        # Todo: Add these options after dipy release 0.14.0
        ext_arg=""
        autocrop=$(jq -r .autocrop config.json)
        if [ $autocrop == "true" ]; then
            ext_arg="--autocrop"
        fi

        cat > script.sh <<EOF
#!/bin/bash
$cmd $ext_arg --force  \
    --out_dir $(pwd) \
    --save_masked \
    --numpass $(jq -r .numpass config.json) \
    --median_radius $(jq -r .median_radius config.json) \
    --out_mask mask.nii.gz \
    --out_masked dwi.nii.gz \
    $(jq -r .dwi config.json)
EOF
        ;;

    dipy_fit_dti)
        cat > script.sh <<EOF
#!/bin/bash
$cmd --force \
    --out_dir $(pwd) \
    --b0_threshold $(jq -r .b0_threshold config.json) \
    --bvecs_tol $(jq -r .bvecs_tol config.json) \
    --out_strat what \
    $(jq -r .dwi config.json) $(jq -r .bvals config.json) $(jq -r .bvecs config.json) $(jq -r .mask config.json)
EOF
        ;;
    
    dipy_fit_dki)
        cat > script.sh <<EOF
$cmd --force \
    --out_dir $(pwd) \
    --b0_threshold $(jq -r .b0_threshold config.json) \
    --out_strat what \
    $(jq -r .dwi config.json) $(jq -r .bvals config.json) $(jq -r .bvecs config.json) $(jq -r .mask config.json)
EOF
        ;;
    
    dipy_fit_csa)
        cat > script.sh <<EOF
#!/bin/bash
$cmd --force \
    --out_dir $(pwd) \
    --b0_threshold $(jq -r .b0_threshold config.json) \
    --out_strat what \
    $(jq -r .dwi config.json) $(jq -r .bvals config.json) $(jq -r .bvecs config.json) $(jq -r .mask config.json)
        ;;
    
    dipy_fit_csd)
        cat > script.sh <<EOF
#!/bin/bash
$cmd --force \
    --out_dir $(pwd) \
    --b0_threshold $(jq -r .b0_threshold config.json) \
    --out_strat what \
    $(jq -r .dwi config.json) $(jq -r .bvals config.json) $(jq -r .bvecs config.json) $(jq -r .mask config.json)
        ;;
    
    dipy_fit_mapmri)
        cat > script.sh <<EOF
#!/bin/bash
$cmd --force \
    --out_dir $(pwd) \
    --b0_threshold $(jq -r .b0_threshold 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)
        ;;

    dipy_nlmeans)
        cat > script.sh <<EOF
#!/bin/bash
$cmd --force \
    --out_dir $PWD \
    --sigma $(jq -r .sigma config.json) \
    --out_denoised dwi.nii.gz \
    $(jq -r .dwi config.json)
        ;;
        
    dipy_mask:dwi)
        cat > script.sh <<EOF
#!/bin/bash
dipy_mask --force \
    --out_dir $PWD \
    --out_mask mask.nii.gz \
    $(jq -r .dwi config.json) $(jq -r .lb config.json)
      ;;

    dipy_mask:tensor)
        cat > script.sh <<EOF
#!/bin/bash
dipy_mask --force \
    --out_dir $PWD \
    --out_mask mask.nii.gz \
    $(jq -r .fa config.json) $(jq -r .lb config.json)
        ;;
    
    dipy_reslice)
        # pass through bvecs/bvals
        cp $(jq -r .bvecs config.json) dwi.bvecs
        cp $(jq -r .bvals config.json) dwi.bvals

        cat > script.sh <<EOF
#!/bin/bash
$cmd --force \
    --out_dir $PWD \
    --out_resliced dwi.nii.gz \
    $(jq -r .dwi config.json) $(jq -r .new_vox_size config.json)
EOF
        ;;

    dipy_recobundles)
        #TODO - maybe we could do this in the Dockerfile? Ping Josh as he is doing something similar I believe
        mkdir -p "atlas"
        if [ ! -f "atlas/Atlas_in_MNI_Space_16_bundles.zip" ]; then
            wget -O "atlas/Atlas_in_MNI_Space_16_bundles.zip" https://ndownloader.figshare.com/files/11921522
            unzip -d "atlas" "atlas/Atlas_in_MNI_Space_16_bundles.zip"
        fi

        cat > script.sh <<EOF
#!/bin/bash
set -e
set -x

#no ~/.dipy inside dipy container.. 
#dipy_slr ~/.dipy/bundle_atlas_hcp842/Atlas_in_MNI_Space_16_bundles/whole_brain/whole_brain_MNI.trk csa_track.trk --mix_names
#dipy_recobundles --force --out_dir $PWD --mix_names --refine $(jq -r .tracks_target config.json) \
#    "\$(python -c "from dipy.data import get_bundle_atlas_hcp842; print(get_bundle_atlas_hcp842()[1])")" #double-double quotes ok?

#dipy_labelsbundles $(jq -r .tracks_target config.json) *.npy --mix_names --out_dir original_space
dipy_recobundles --force --out_dir $PWD --mix_names --refine $(jq -r .tracks_target config.json) "atlas/Atlas_in_MNI_Space_16_bundles/bundles/*.trk"
EOF

        ;;
    dipy_info)
        cat > script.sh << EOF
#!/bin/bash
$cmd --force $(jq -r .dwi config.json) $(jq -r .bvals config.json) $(jq -r .bvecs config.json)
EOF
        ;;
    
    dipy_track_det)
        cat > script.sh << EOF
#!/bin/bash
$cmd --force --out_dir $PWD $(jq -r .peaks config.json) $(jq -r .stop config.json) $(jq -r .seed config.json)
EOF
        ;;
    *)
        echo "invalid command: $cmd"
        exit 1
esac

chmod +x script.sh
SINGULARITYENV_PYTHONNOUSERSITE=true singularity exec -e docker://brainlife/dipy:0.16.0 ./script.sh

echo "done"