IJ2 Plugin Proposal

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Nov 24, 2010, 4:26:09 PM11/24/10
to ImageJX
I'm proposing a more dynamic way of running plugins and sending images
from one plugin to another that would lend itself to workflows and
pipelines. This could also be used within plugins and within IJ2 as
an architectural building block to chain chunks of image processing
code together.

Basically I propose that a plugin can have multiple named input and
output images and that whenever an output image is ready it is passed
on to become the input image to the next plugin in the chain.


I feel the need for this from a couple of plugins I have worked on
(actually my only plugins!).

I worked on a Deep Zoom plugin. This takes a huge image, tiles it,
then the tiles are written out in a particular directory/file name
structure. Next we halve the original image and repeat, until the
image gets halved to a miniscule size.

While working on this plugin I thought about writing the code to halve
the image and to tile it in the most general-purpose, reusable way.
Also I wanted to be memory-efficient: I didn't want to just make all
the halves, then go through them and make all the tiles, then go
throughout those and write out all the files.

What I came up with at that time was a chainable plugin. In pseudo-

interface IChainablePlugin {

// chains one plugin to next; called from outside the plugin
public chain(IChainablePlugin plugin);

// gets the input image; called from within plugin
Image get();

// puts the output image; called from within plugin
put(Image image);

An abstract base class kept track of the next, chained plugin instance
and handed off the output image to that next plugin, using the same

I wrote a chainable plugin class to halve the image, one to tile it,
and had a third one that was just an inner class to my Deep Zoom
plugin that handled the specifics of writing out the tiled image
files. Presumably the first two classes would be reusable code and
the third was just specific to Deep Zoom.

Obviously as-is this is limited to one input and one output. I
started thinking about having an image dispatcher class that would
keep track of which images a plugin required and hand them off from
one plugin to another.

I'll just briefly mention the SLIM plugin I am working on. Since the
SLIM fitting process is time consuming I display a very coarse
colorized version of the fitted results that is refined as the fit
progresses. So there I want to pass on my output image before the
plugin finishes and I want to put out successive versions of this
image. This is similar to my wanting to process the individual tiles
before the whole image is tiled.


We could label the input and output images using Java annotations.
(Note that the current Declarative Plugin annotations allow one to
label input and output image member variables but the outputs are
harvested only once the plugin is finished. There is no way to put out
an output image within the plugin code.)

Here is some sample code for what I'm proposing:

@Output({ @Img(Plugin1.BLUE), @Img(Plugin1.GREEN) })
public class Plugin1 extends AbstractPlugin {
public static final String BLUE = "Blue";
public static final String GREEN = "Green";

void process() {
Image image = get();
put(BLUE, image);
put(GREEN, image);

Here the annotations result in an input name set of ["Default"] and an
output set of ["Blue","Green"]. (If there are no parameters the
default name is used.) Of course, there could also be named input
images (i.e. "get(ORANGE)") or default output images (i.e. "put()").

Instances of plugins such as these could be chained together:
plugin1.chain(Plugin1.BLUE, plugin2); // named output goes to
default input
plugin1.chain(Plugin1.GREEN, plugin2, Plugin2.ORANGE); // named
output goes to named input
plugin2.chain(plugin3); // default output goes to default input
plugin2.chain(plugin4, Plugin4.PURPLE); // default output goes to
named input

Using strings as identifiers might seem less than ideal. However, the
strings are unique to the plugin they belong to. If they are
specified as static constants, as above, that would prevent spelling
mismatches. Once a chain of plugins is established and before we run
it we could make sure that all of the inputs have been chained to. We
can detect if a plugin asks for an input or output that has not been
annotated and warn the plugin programmer.

Of course, once we have named input and output images we could build
on that and give the IJ end-user ways to link up plugins in workflows
or pipelines, a la CellProfiler.

I have a prototype implementation of this, so the sample code above
works, details upon request.


(P.S. It's the Thanksgiving holiday in the U.S. so you might not hear
from us until Monday. Happy Thanksgiving!)
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