#!/usr/bin/perl
# 2008-07-08 Bryan Bishop kanzure@gmail.com
# Extract information from the humancortex XML files for specimen ID numbers.

open(DOOR, ">>specimen_list.txt") or die $!;
for ($i = 1; $i <= 190; $i++) {
	print "Iterating to file $i.xml.\n";
	open(FILE, "<imageseries/$i.xml") or die $!;
	while(my $line = <FILE>) {
		if($line =~ /\<specimenid type\=\"integer\"\>(\d+)/) {
			print DOOR "$1\n"; print "XML fetch. Initializing wget fetch sequence on specimen with ID number $1\n";
			`wget -nc http://humancortex.alleninstitute.org/has/human/specimen/summary/$1.xml `;
			print "\nJPEG  fetch on human cortex specimen $1.\n";
			`wget -nc http://humancortex.alleninstitute.org/ImageWeb/GetImage?imageId=$1&zoom=3&size=max`;
			print "Successfully fetched human cortex specimen (from $i) $1.\n";
		}
	}
	print "Closing file $i.\n";
	close(FILE);
	#print "\n\nDone.\n\n";
}
close(DOOR);