#! /usr/bin/perl
{
 use Shell;
 use Cwd; # module for finding the current working directory
$|=1;    # turn off I/O buffering

print "\n";

if ($#ARGV == -1) { # if no arguments are entered
	instructions(); 
print "\n";
}
else { # read in the arguments
	for ($j=0; $j<$#ARGV+1; $j++) {
		$tempdir = $ARGV[$j];
		chomp($tempdir);
		if ($tempdir eq "."){
			$tempdir = &cwd
		}
		opendir(DIR,$tempdir) or die "$tempdir does not exist or I can't open it\n"; # check the directories inputted
		closedir(DIR);
		@dirlist = $tempdir;
		foreach my $name (@dirlist) {
			&ScanDirectory($name);
			print "\n";
		} 
	}
}

sub ScanDirectory {
    my ($p) = 0;
	my ($workdir) = shift; 
    my($startdir) = &cwd; # keep track of where we began
	print "Processing Directory $workdir \n";
    chdir($workdir) or die "\nUnable to enter dir $workdir:$!\n";
    opendir(DIR, ".") or die "\nUnable to open $workdir:$!\n";
    my @names = readdir(DIR);
    closedir(DIR);
	$command = "mkdir backupimg";
	system ($command); 
    foreach my $name (@names){
        next if ($name eq "."); 
        next if ($name eq "..");
		next if ($name eq "backupimg");
        if (-d $name){                     # is this a directory?
            &ScanDirectory($name);
            next;
        }
		#do something with file
		if (grep(/\.MRDC\./, $name)){
			$p = $p + 1;
			$command = "cp $name backupimg/";
			system ($command); 
			$old_name = $name;
			$name =~ s/i(.*)\.MRDC\.(.*)/i\.CFMRI\.$2/;
			$num = "";
			$num = sprintf("%5d", $2);
			$num=~ tr/ /0/;
			$name = "i$num\.CFMRI\.$2";
			rename("$old_name", "$name") || die "Cannot rename $old_name: $!";
		}
		#done
    }
	print "     Directory $workdir has $p files processed \n"; # print size
	$command = "rm -rf backupimg";
	system ($command); 
    chdir($startdir) or die "Unable to change to dir $startdir:$!\n";
}

sub instructions {
print "This program renames and reorders the dicom files acquired on the GE scanners at UCSD - CFMRI.\n";
  print "Usage: imseq [directories to convert] \n";
  print "Example:  imseq directory1 directory2 directory3 \n\n";

  }

}