Skip to content

IntrospectingOps.md

Latest commit

 

History

History
126 lines (86 loc) · 6.57 KB

IntrospectingOps.md

File metadata and controls

126 lines (86 loc) · 6.57 KB

Reasoning about Ops

The declarative nature of Ops is convenient for matching and execution, but sometimes it is necessary to know where an Op comes from. This page describes the tools provided by SciJava Ops to understand the code underneath.

Naturally, to understand where an Op came from, you first need an Op:

var img = ...;
var out = ...;
var sigma = 5.0;

// This Op call finds a "filter.gauss Op" that blurs an image using a provided
// sigma, placing the result in the output container "out".
//
// NB the Op is saved within the variable "op"
var op = ops.op("filter.gauss").input(img, sigma).output(out).computer();

Introduction

Each Op is generated from an OpInfo object, describing an Op's source code, version, and other associated metadata. If you've matched an Op op, you can obtain its OpInfo using the method Ops.info(op):

import org.scijava.ops.api.Ops;

var info = Ops.info(op);

The OpInfo often provides all needed information, but if op utilizes dependencies or other framework features, you may wish to introspect the "rich" Op instead, using the method Ops.rich(op). This method returns a RichOp object which wraps the Op up with its OpInfo and the OpInfos of its dependencies, along with other metadata.

var richOp = Ops.rich(op);

These two methods provide gateways into learning more about where your Op came from!

Implementations and Versions

For reproducibility, it is important to know not only the underlying implementations, or discrete lines of code, backing each executed Op, but additionally the version of that implementation if it changes over time. Fortunately, SciJava Ops provides mechanisms to determine both!

A unique identifier to an Op's implementation can be obtained from its OpInfo using the method OpInfo.implementationName(). For example, the following

System.out.println(Ops.info(op).implementationName());

might print out (if you're using scijava-ops-image version 1.0.0):

:class: no-copybutton
org.scijava.ops.image.filter.gauss.Gaussians.gaussRAISingleSigma(net.imglib2.RandomAccessibleInterval<I>,double,net.imglib2.outofbounds.OutOfBoundsFactory<I, net.imglib2.RandomAccessibleInterval<I>>,net.imglib2.RandomAccessibleInterval<O>)Reduction1

Note that in many cases, including the case above, the implementation name may not itself be an explicit piece of code, however it must always explain how an explicit piece of code became the Op you've matched.

Similarly, the method OpInfo.version() describes the version of the Op, which is set by whichever component declares the Op. This version might change due to:

  • An update in the version of the underlying implementation (such as a bump in the version of scijava-ops-image)
  • An update to the Op itself (such as the inclusion of an additional alias, or a change in the Op priority)

SciJava Ops guarantees identical outputs from an Op execution given identical inputs and an identical OpEnvironment. Your results may differ if you:

  • Add new Ops into your OpEnvironment, if a new Op takes precedence over an existing Op
  • Change the version of an Op within the OpEnvironment by updating a component
  • Pass different inputs to the Op

Op Signatures

While SciJava Ops requires the aforementioned constraints to ensure reproducible Op matches, the concept of Op Signatures enables SciJava Ops to reproducibly reconstruct prior matches in new environments (assuming all required Ops are still available).

Given a matched Op op, its signature can be obtained using the static method Ops.signature(op), which distills all Op implementation names and versions into a single string. For example, the following

System.out.println(Ops.signature(op));

might print out (again using scijava-ops-image version 1.0.0):

:class: no-copybutton
|Reduction:|ParamsReduced:1|OriginalInfo:|Info:org.scijava.ops.image.filter.gauss.Gaussians.gaussRAISingleSigma(net.imglib2.RandomAccessibleInterval<I>,double,net.imglib2.outofbounds.OutOfBoundsFactory<I, net.imglib2.RandomAccessibleInterval<I>>,net.imglib2.RandomAccessibleInterval<O>)@1.0.0{}

Assuming all utilized Ops and Op features are still available, the Op can then be reconstructed using the method OpEnvironment.opFromSignature(signature, opType):

// The value of signature could be saved within a script for future reconstruction
String signature = Ops.signature(op);

...

// NB: This generic type construct is needed for the OpEnvironment to provide a Computer Op.
var opType = new Nil<Computers.Arity2<Img<DoubleType>, Double, Img<DoubleType>>>() {};
// Reconstruct the Op
var sameOp = ops.opFromSignature(signature, opType);
// We could then call this Op with our input image, real-valued sigma, and output image container
sameOp.compute(img, sigma, out);

There still exist limitations with reconstructive features, including:

Info Trees

Ops often utilize Op dependencies, which may have dependencies themselves. As such, the Ops returned by SciJava Ops are best thought of as a tree. While an Op's signature, described above, represents the entire Tree, it is often more convenient to interrogate dependencies using the InfoTree data structure, obtained using the method Ops.infoTree(op):

var tree = Ops.infoTree(op);

The InfoTree API allows users to interrogate:

  • The root OpInfo, accessible using InfoTree.info()
  • All dependencies, which are each themselves an InfoTree, using InfoTree.dependencies().

Op History

It is often useful to determine the list of Ops responsible for the current state of a given Object. To aid in this task, each OpEnvironment records Op executions within an OpHistory object, accessible using the method OpEnvironment.history().

// OpEnvironment.history() provides access to a OpHistory object
var history = ops.history();

// Since an Op was responsible for the results written into the "out" object, it is listed in OpHistory.executionsUpon()
var usedOps = history.executionsUpon(out);

Using the OpHistory object, we can see that our gaussian blur Op op is at the end of the list, since it wrote to out last. If out was additionally created using SciJava Ops, the Op(s) responsible for creating the image would also be included.