#!/usr/bin/perl -w

#work on current dir unless otherwise noted
@ARGV = qw(.) unless @ARGV;

use File::Find;
use File::Copy;
use Cwd;

sub process_file {

	#only want files
	return unless -f ;

#	$fname = $_;

	open (DICOM, "/usr/local/AFNI/src/linux_mdk72/dicom_hdr $_ |") or die "Couldn't run the DICOM header program";
	#pull out revelant DICOM fields
	while (<DICOM>) {
		if (/PAT Patient Name/) {
			($a,$b,$patname) = split('/+');
			chomp $patname;
		}
		if (/PAT Patient ID/) {
			($a,$b,$patID) = split('/+');
			chomp $patID;
		}

		if (/REL Study ID/) {
			($a,$b,$studyID) = split('/+');
			chomp $studyID;
		}
		if (/ID Study Date/) {
			($a,$b,$studydate) = split('/+');
			chomp $studydate;
		}
		if (/ID Study Description/) {
			($a,$b,$studydesc) = split('/+');
			chomp $studydesc;
		}


		if (/ID Series Description/) {
			($a,$b,$serdesc) = split('/+');
			chomp $serdesc;
		}
		if (/REL Series Number/) {
			($a,$b,$sernum) = split('/+');
			chomp $sernum;
		}


		if (/REL Acquisition Number/) {
			($a,$b,$acq) = split('/+');
			chomp $acq;
		}
		if (/REL Image Number/) {
			($a,$b,$image) = split('/+');
			chomp $image;
		}

	}
	close (DICOM);

	#create subject, study, series, image - strip out any spaces and change carets to underscores
	$pat = $patID . "-" . $patname;
	$pat =~ s/\s//g;
	$pat =~ s/\^/_/g;
	$study = $studydate . "-" . $studyID . "-" . $studydesc;
	$study =~ s/\s//g;
	$study =~ s/\^/_/g;
	$series = $sernum . "-" . $serdesc;
	$series =~ s/\s//g;
	$series =~ s/\^/_/g; 

	#zeropad acq and image by reversing, adding zeros, re-reversing and taking the last chars
	$acq =~ s/\s//g;
	$acq =~ s/\^/_/g;
	$acq = reverse($acq)."0000000000";
	$acq = substr(reverse($acq), -5);
	$image =~ s/\s//g;
	$image =~ s/\^/_/g;
	$image = reverse($image)."0000000000";
	$image = substr(reverse($image), -6);
	$im = $acq . "-" . $image;
	
	if (! -e $parentdir."/".$pat) {
		mkdir($parentdir."/".$pat, 0777) || die "couldn't create a directory for $pat  :$!\n";
	}
	if (! -e $parentdir."/".$pat."/".$study) {
		mkdir($parentdir."/".$pat."/".$study, 0777) || die "couldn't create a directory for $study  :$!\n";
	}
	if (! -e $parentdir."/".$pat."/".$study."/".$series) {
		mkdir($parentdir."/".$pat."/".$study."/".$series, 0777) || die "couldn't create a directory for $series  :$!\n";
	}

	copy($parentdir."/".$File::Find::name, $parentdir."/".$pat."/".$study."/".$series."/image-".$im.".IMA") || die "couldn't copy files $!\n";
#	print $fname, "  ", $pat, "  ", $study, "  ", $series,"  ", $im,"\n";
}

$parentdir = cwd();
find(\&process_file, @ARGV);