my $referencepixels=countpixels($referencefile);
@data=ls($datadir)
foreach my $file (@data){
  my $cover=countpixels($file)/$referencepixels;
  $datahash{$file}=$cover;
}
output_to_datafile(%datahash);
[download]

This is untested; just going from memory and a quick look at the Image::Magick API Reference. Basically it should read in the image, figure out which colour is transparent, then loop through every pixel and increment a counter when the pixel isn’t transparent. Again, it’s untested. I’m unsure if the pixel index starts at 1 (as I used) or 0. I’m also not totally sure on the $image->Get('transparent') call -- read the API for the exact method -- it’s been a while since I've used it. This should give you a good jumping off point though.

use Image::Magick;

my $image = new Image::Magick;

$image->Read('foo.png');

my $count;                                     # The number of non-tra
+nsparent pixels.
my $transparent = $image->Get('transparent');  # Index of the transpar
+ent colour.
my $height      = $image->Get('height');       # Image height.
my $width       = $image->Get('width');        # Image width.

for my $x ( 1 .. $height ) {
    for my $y ( 1 .. $width ) {
        $count++ if $image->Get("pixel[$x,$y]") != $transparent;
    }
}
[download]

If I get what you're trying to do, it might be beneficial to store each species as a mask. If you save it as a black and white bitmap counting becomes really fast, since you can read the file as one long binary string and just count the 1’s.

Another possibility (again I’m assuming you're generating these masks by hand) is to use a format that allows multiple layers. Storing the image as a photoshop PSD or something similar would allow you to keep all the masks as named channels or layers. The Gimp might be a great tool here as it allows Perl extensions and has said layers. This way the masks stay embedded right in the original image for easy archiving, and you could even store the result of those counts in the image comments. With a little Perl magic, Gimp could become a biology workdesk :).

Fantastic - thanks! Unfortunately, I can follow neither of your two above suggestions, although don't think I haven't contemplated it. Unfortunately a variety of the species involved have multiple color morphs, or are exactly the same color as another species (I mean you have to zoom in on individual zooids in a colony to tell the difference- hence we're using a high-res digital underwater camera).

Saving different layers in a PSD would be nice, but the problem there is that often we have species overgrowing each other in a non-lethal way (e.g. a colonial sea squirt overgrows a mussel. Both live, and both need to be counted). The current scheme I'm going with is copying the area of each species, putting it into its own .gif, and using some filename information for the final data file.

Although if you know a way to do all of that in GIMP, I'd love to hear it!

That's what I figured. Have you decided yet how (ie. what tools. I can see the process will probably need to be manual) you are to use to create the cut-outs?

---

Examine what is said, not who speaks.
"Efficiency is intelligent laziness." -David Dunham
"When I'm working on a problem, I never think about beauty. I think only how to solve the problem. But when I have finished, if the solution is not beautiful, I know it is wrong." -Richard Buckminster Fuller

Oh, it's a manual process given the complexity of species identification, etc.