Simplify and parallel bash if statement script

Question

I have written a script that finds files in directories, and brings through if statement, here is a code:

for dirname in /input/*; do

    id=${dirname#/input/}    # remove "/input/sub-"
    id=${id%/}             # remove trailing "/"

    printf 'Adding ID to recon-all processing list: %s\n' "${id}" >&2

    T11=`find /input/${id}/unprocessed/3T -name "*T1*MPR1*" -type f`
    T12=`find /input/${id}/unprocessed/3T -name "*T1*MPR2*" -type f`

    T21=`find /input/${id}/unprocessed/3T -name "*T2*SPC1*" -type f`
    T22=`find /input/${id}/unprocessed/3T -name "*T2*SPC2*" -type f`

    if [ -z "$T11" ] || [ -z "$T12" ] || [ -z "$T21" ] || [ -z "$T22" ]; then
        recon-all -s "${id}" -i "${T11}" -i "${T12}" -i "${T21}" -i "${T22}"
    elif [ -z "$T11" ] || [ -z "$T12" ] || [ -z "$T21" ]; then
        recon-all -s "${id}" -i "${T11}" -i "${T12}" -i "${T21}"
    elif [ -z "$T11" ] || [ -z "$T12" ] || [ -z "$T22" ]; then
        recon-all -s "${id}" -i "${T11}" -i "${T12}" -i "${T22}"
    elif [ -z "$T11" ] || [ -z "$T21" ]; then
        recon-all -s "${id}" -i "${T11}" -i "${T21}"
    elif [ -z "$T11" ] || [ -z "$T22" ]; then
        recon-all -s "${id}" -i "${T11}" -i "${T22}"
    else 
        recon-all -s "${id}" -i "${T11}" -i "${T21}" 
    fi

    if [ -e "/output/$subj_id" ]; then
        # no output file corresponding to this ID found,
        # add it to he list
        all_ids+=( "$subj_id" )
    fi
done

The problem is that there could be different combination inside directories, and T12 and T22 could sometimes be missed, that's why I made a recon-all for every statement. How could I simplify if statements and parallel this script?

Your logic is suspect: If any of the variables is empty, then you "recon-all" with all the variables. All the "elif" conditions are redundant. If the vars are all non-empty then you fall into the "else" block. I think you need to reconsider the logic. — glenn jackman
– glenn jackman, Commented Jun 28, 2019 at 18:12

glenn jackman · Accepted Answer · 2019-06-28 18:18:51Z

2

I wonder if you want to call recon-all with all of the non-empty variables. If that's the case, you might want this:

opts=( -s "$id" )
for val in "$T11" "$T12" "$T21" "$T22"; do
    [[ -n "$val" ]] && opts+=( -i "$val" )
done
recon-all "${opts[@]}"

answered Jun 28, 2019 at 18:18

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glenn jackman

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