niiMover

#/bin/bash

# modify this as needed to arrange .nii files into subfolders for preprocessing
# 
# input: a directory of .nii files named nnAAA.nii
# where n are numberical digits and AAA is any other non digit characters
#
# .nii files will be moved into sub-directories named sub0000nn
#
# James Valenti, October 2015

if [[ $# -lt 1 ]]
then
    echo "take a path to a directory of files and move them into subfolders"
    echo "Where subfolders are based upon the file name (look at code for regex)"
    echo "Usage: $0 PATH"
    echo "or to test what would be done: $0 -t PATH" 
    echo " ie ./ret -t /data2/archived/CMU_60"
    exit 1
fi

test=0

if [[ "$1" == '-t' ]]
then
	test=1
	# remove -t, the next paramater should be a directory
	shift
fi

##########################################
# Edit this regular expression as needed #
##########################################

# select the leading numbers from the file name
regex='(^[0-9]+)*'

if [ -d "$1" ]
then

    # for all files in the path passed into the script
    for file_name in $(ls $1)
    do
        # if there is a match
        if [[ $file_name =~ $regex ]]
        then
	    # directory name to create and file to move into it
	    newDir=$(printf "$1/sub%06d/\n" ${BASH_REMATCH[1]})
	    fq_fn="$1/$file_name"
	
	    if [[ $test -eq 1 ]]
	    then
	       # test: jsut show what would be done
                echo "$fq_fn --> $newDir"
	    else
	        # create directory and move file
	        mkdir $newDir
                mv $fq_fn $newDir
	    fi
        else
	    # warn that there is something in the directory that doesnt match
            echo "** $1 does not match regular expression, skipping"
        fi
    done
else
    echo "ERROR: $1 is not a directory or does not exist"
fi