Modules

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QIT includes a module framework for making making it easy to analyze data. This page describes how modules are used, outlines the basic components of the module framework, and provides an example of a module . If you're not interested in the software development aspects, you can probably just read the first section.

Why use a Module?

The QIT module system is meant to make it easier to use the many useful data processing algorithms that are out there. Many researchers develop sophisticated new methods, but unfortunately, they often end up as prototypes that aren't more widely used. The module framework is an attempt to bridge the gap between these methods and people who can use them in their research. The basic idea is to provide a simple interface for implementing an algorithm that doesn't require the developer to worry about file formats, user interfaces, etc.

Module.diagram.png

All of these things are automatically handled by QIT once a Module has been implemented, making it easy to share a new tool with a wider audience. Any QIT Module can be run on the command line, applied to data interactively in qitview, or run on the LONI Pipeline. In addition, documentation can be made from a Module and a preferred set of parameter settings can be saved for later use or archival purposes.

What is a Module?

A Module is an object that processes data in some way. That may sound too general to be useful, but there are a number of elements common to each Module that make life easier for both software developers and users. From the perspective of a developer, a Module makes life easier by providing a framework for implementing both simple and complex algorithms that use any of the available Datatypes. This framework isn't specific to any file format, so any new Module automatically supports the file formats listed in for each of the Datatypes. It also provides automatically generated command line and graphical user interfaces for using the Module. For command line applications, each Module will have an automatically generated usage page and option parsing available. For graphical applications, each Module will be listed in 3d data viewer qitview, along with a dialog for controlling how the it operates on data loaded in the viewer. For the user, this framework also simplifies the analysis of data by providing a consistent interface across algorithms, reducing the need to learn how to use each tool as it comes along. It also means that an algorithm is more widely available than if it was developed as an independent program or as a MATLAB script, which are not typically integrated into data viewers or support many file formats. Finally, each Module also supports meta-data that includes the author, associated publications, and plain english descriptions.

What makes up a Module?

Each Module has some number of fields with annotations to indicate how they should be treated. There are three main types:

  • @ModuleInput: a Datatypes object that will be processed, which is provided by the user
  • @ModuleParameter: a numerical, string, or boolean parameter, which is provided by the user
  • @ModuleOutput: a Datatypes object that will be the result, which will be received by the user

There can be multiple @ModuleInput and @ModuleOutput fields, each of which belongs to one of the types listed in Datatypes. There can be any number of @ModuleParameter components, but they must also be primitive types, such Integer, Double, String, or Boolean. @ModuleParameter field can also have default values. There are also modifiers on fields, including:

  • @ModuleOptional: a component is not required for the Module to run
  • @ModuleAdvanced: a component is not typically modified (only used when making documentation)

There can also be annotations for provenance, for example:

  • @ModuleDescription: a plain english description of a module or field
  • @ModuleAuthor: the person implementing the Module (not necessarily the author of the underlying algorithm or paper)
  • @ModuleCitation: a reference that should be cited when using this module in analysis for academic publication

Beyond this, each Module also contains the procedures for data processing, which is why you would use the Module in the first place!

What is an example of a Module?

Below, we provide an example Module named VolumeThreshold that thresholds a Volume to produce a binary Mask. While there are many more complex examples, this demonstrates the basic features of a Module.

The code for the module looks like this:

@ModuleDescription("Threshold a volume to make a mask")
@ModuleAuthor("Ryan Cabeen")
public class VolumeThreshold implements Module
{
    @ModuleInput
    @ModuleDescription("input volume")
    public Volume input;
    
    @ModuleInput
    @ModuleDescription("a mask restricting which voxels are processed")
    public Mask mask;
    
    @ModuleParameter
    @ModuleDescription("threshold value")
    public double threshold = 0.5;
    
    @ModuleOutput
    @ModuleDescription("output mask")
    public Mask output;

    public VolumeThreshold run()
    {
        Mask out = new Mask(this.input.getSampling());

        for (Sample sample : this.input.getSampling())
        {
            if (this.input.valid(sample, this.mask))
            {
                double value = this.input.get(sample, 0);
                if (value >= this.threshold)
                {
                    out.set(sample, 1);
                }
            }
        }
        
        this.output = out;

        return this;
    }
}

The command line interface for this module looks like this:

$ qit VolumeThreshold --help

Name:

  VolumeThreshold

Description:

  threshold a volume to make a mask

Required Arguments:

  --input <Volume>

    input volume

  --output <Mask>

    output mask

Optional Arguments:

  --mask <Mask>

    a mask restricting which voxels are processed

  --threshold <double>

    threshold value (Default: 0.5)

Author:

  Ryan Cabeen

The graphical user interface looks like this:

Module.threshold.png

Note: the module dialog supports tooltips, which means if you hover the mouse over a @Parameter it will pop up a box showing more information.