This tutorial is designed to guide developers through the options, processes and motivations for adding Ops outside the core imagej-ops project. Because this tutorial caters to external developers, in this tutorial we show how a BAR function could be converted to an Op.
Make your first Op
At the most fundamental level, an Op is a SciJava Plugin encapsulating a piece of functionality, which can be discovered and used by a central OpService.
At a minimum, creating an Op requires two pieces - an interface, and an implementation
Create your Interface
package bar;
import net.imagej.ops.Op;
/**
* Op interface for calculating the greatest common divisor (GCD)
*/
public interface GCD extends Op {
// Ops can be called by name, defined as properties of the Op interface
String NAME = "gcd";
// An alias is OPTIONAL but gives users additional ways to call your Op.
// For example - the GCD is also called greatest common factor (GCF).
String ALIASES = "gcf";
}
Implement your Op
package bar;
import net.imagej.ops.AbstractOp;
import org.scijava.ItemIO;
import org.scijava.plugin.Attr;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
// The Plugin annotation allows this Op to be discovered by the OpService.
// We declare the type of op; the name and any aliases will be auto-detected.
@Plugin(type = GCD.class)
public class DefaultGCD implements GCD extends AbstractOp {
// -- Inputs --
// We want our GCD function to have two inputs. These are declared using @Parameter notation
@Parameter
private double a;
@Parameter
private double b;
// -- Outputs --
// This op will return a single value (the computed GCD) so we declare an output parameter
@Parameter(type = ItemIO.OUTPUT)
private double result;
@Override
public void run() {
// The job of the run method is to populate any outputs using the inputs
result = computeGCD(a, b);
}
private double computeGCD(final double p1, final double p2) {
return p2 == 0 ? p1 : computeGCD(p2, p1%p2);
}
}
Use your Op
With these two components, you can start using your Op - for example, in the script editor:
# @OpService ops
from bar import GCD
# We look up our Op by asking the framework to find an implementation of the
# GCD interface that could handle these inputs
gcd = ops.op(GCD, 7, 10);
# Print the Op instance, to verify our Op is picked up
print(gcd)
# The OpService can print useful information about any Op..
print(ops.info(gcd))
# .. including its usage
print(ops.help("gcd"))
# We can also run an Op by passing the name or alias we defined
# Print the result of running our Op
print(ops.run("gcf", 20, 7))
Group your Ops in a Namespace
Calling our Ops by name is not type-safe, and importing each interface is tedious. If you are going to provide a collection of Ops, a useful way to package them is within a custom Namespace.
Create your Interface(s)
package bar;
import org.scijava.plugin.Plugin;
import net.imagej.ops.AbstractNamespace;
import net.imagej.ops.Namespace;
import net.imagej.ops.Op;
import net.imagej.ops.OpMethod;
@Plugin(type = Namespace.class)
public class BAR extends AbstractNamespace {
@Override
public String getName() {
return "name";
}
// -- BAR Namespace Op interfaces --
// We can make all of our interfaces nested classes.
// This allows references to take the form of "Namespace.Op" which
// can make things easier to understand.
public interface GCD extends Op {
// Note that the name and aliases are prepended with Namespace.getName
String NAME = "bar.gcd";
String ALIASES = "bar.gcf";
}
// -- BAR Namespace built-in methods --
// Built-in methods provide type-safe methods for accessing Ops
// in a namespace.
// We always provide an Object... constructor that can be passed directly to the
// OpService.run method
@OpMethod(op = bar.BAR.GCD.class)
public Object gcd(final Object... args) {
return ops().run(bar.BAR.GCD.class, args);
}
// But we can also type-narrow our inputs and returns with our knowledge of the Op
// implementations
@OpMethod(op = bar.BAR.GCD.class)
public double gcd(final double a, final double b) {
return (Double) ops().run(bar.BAR.GCD.class, a, b);
}
}
Implement your Op(s)
The implementation is essentially the same as with single Ops, although we do have to update our class references.
Since the implementations are not accessed directly typically, whether they are grouped as nested classes or provided individually is less important than for the interfaces.
package bar;
import net.imagej.ops.AbstractOp;
import org.scijava.ItemIO;
import org.scijava.plugin.Attr;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
@Plugin(type = BAR.GCD.class, name = BAR.GCD.NAME, attrs = { @Attr(name = "aliases", value = BAR.GCD.ALIASES) })
public class DefaultGCD extends AbstractOp implements BAR.GCD {
// -- Inputs --
@Parameter
private double a;
@Parameter
private double b;
// -- Outputs --
@Parameter(type = ItemIO.OUTPUT)
private double result;
@Override
public void run() {
result = computeGCD(a, b);
}
private double computeGCD(final double p1, final double p2) {
return p2 == 0 ? p1 : computeGCD(p2, p1%p2);
}
}
Use your Op(s)
We can still use our Op through the OpService:
# @OpService ops
print(ops.run("bar.gcd", 20, 15))
But we can also use our built-in methods:
# @bar.BAR bar
print(bar.gcd(20, 15))
This is especially useful in environments with code completion.
Namespaces also present an easy way for users to find information about available functionality using the base Help ops:
# @OpService ops
# @bar.BAR bar
# Print usage for all ops in the BAR namespace
print(ops.help(bar))
Potential next steps
Create a helper service for your Namespace
SciJava Services are a general workhorse in a given SciJava context. There is a single instance of each Service created per context, so they are a common container for static utility style methods.
When developing an external Namespace, an immediate benefit to creating a corresponding Service is that it provides an initialization hook for registering your new Namespace outside the Ops framework - in particular, with the SCriptService:
package bar;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.script.ScriptService;
import org.scijava.service.AbstractService;
import org.scijava.service.Service;
import net.imagej.ImageJService;
@Plugin(type = Service.class)
public class BARService extends AbstractService implements ImageJService {
@Parameter
private ScriptService scriptService;
@Override
public void initialize() {
// Register this namespace with the ScriptService so we can drop package prefixes
// in script parameters, allowing:
// @BAR
// instead of
// @bar.BAR
scriptService.addAlias(bar.BAR.class);
}
}
Now we can drop package prefixes when using our Namespace in scripts:
# @OpService ops
# @BAR bar
# Print usage for all ops in the BAR namespace
print(ops.help(bar))
Distribute scripts demonstrating how your Ops should be used
The ImageJ script editor automatically collects scripts located in src/main/resources/script_templates. For example, if we create a file:
src/main/resources/script_templates/BAR/GCD.py
with contents:
# @BAR bar
# @float a
# @float b
print("Greatest common divisor of " + str(a) + " and " + str(b) + " is: " + str(bar.gcd(a, b)))
[On GitHub](https://github.com/tferr/Scripts/blob/-/BAR/src/main/resources/script_templates/BAR/GCD.py)
Then users will be able to select Templates > BAR > GCD from the script editor window, to automatically load the script and select the correct script language (python in this case).
This is an easy way to provide a starting point for development using your Ops.
Advanced Topics
There are many conveniences in Op development that have not been covered in this tutorial, including:
- Create additional implementations for a given Ops interfaces
- Specializing Ops for a variety of input types
- Auto-generate your Op implementations using templates
- Write unit-tests to ensure coverage of built-in methods for your Ops
However, all of this is done in the core imagej-ops project and could be deduced by careful study. If you do take the time to independently attempt any of these topics, consider documenting your experience and sharing it as a tutorial on this wiki.
