Cfrtjryk

I need to process files in couples.
So if I have:

00000.nii.gz   

00001.nii.gz

00002.nii.gz

00003.nii.gz 

and so on... (nii.gz is an extension used during imaging resonance processing) I need to process the file 00000.nii.gz and 00001.nii.gz together, then 0002.nii.gz and 00003.nii.gz and so on. For each output, I need to rename it.

I'm assuming that the number in the file names are five-digit zero-filled numbers and that the occasional four-digit string in the question and in the comments are typos.

#!/bin/bash



for (( i = 0; i <= 99999; i += 2 )); do

    name1=$( printf '%05d.nii.gz' "$i" )

    name2=$( printf '%05d.nii.gz' "$(( i + 1 ))" )



    if [ -f "$name1" ] && [ -f "$name2" ]; then

        printf 'Processing "%s" and "%s" together...n' "$name1" "$name2" >&2

        # use the two files here

    else

        printf '"%s" or "%s" not found, exiting.n' "$name1" "$name2" >&2

        break

    fi

done

The loop goes from zero to a large number in increments of two. For each iteration, it constructs the two filenames using the variable i in two calls to printf (once for i and once for i+1). The format specifier %05d formats an integer to a zero-filled five-digit string.

As soon as the constructed filenames no longer corresponds to any existing files (in the current directory), the loop exits.

If the files are located in another directory than in the current, change the printf format string from '%05d.nii.gz' to '/path/to/dir/%05d.nii.gz'.

To keep with the DRY principle ("Don't Repeat Yourself"):

#!/bin/bash



dir='/path/to/dir'

name_fmt="$dir/%05d.nii.gz"



for (( i = 0; i <= 99999; i += 2 )); do

    name1=$( printf "$name_fmt" "$i" )

    name2=$( printf "$name_fmt" "$(( i + 1 ))" )



    if [ -f "$name1" ] && [ -f "$name2" ]; then

        printf 'Processing "%s" and "%s" together...n' "$name1" "$name2" >&2

        # use the two files here

    else

        printf '"%s" or "%s" not found, exiting.n' "$name1" "$name2" >&2

        break

    fi

done

Suppose you had a number of files like this:

echo z?

z1 z2 z3 z4 z5 z6 z7 z8 z9

Then to get couples, you could use:

echo z? | xargs -n2

z1 z2

z3 z4

z5 z6

z7 z8

z9

To get triples:

echo z? | xargs -n3

z1 z2 z3

z4 z5 z6

z7 z8 z9

The default command for xargs is echo, but you can supply your own command. The man page for xargs, while long, includes a few examples at the end.

Best wishes ... cheers, drl