National Alliance for Medical Image Computing http://na-mic.org

Anatomy of a plugin

Common architecture for interactive and batch processing

National Alliance for Medical Image Computing http://na-mic.org

Objectives

• Provide a simple mechanism for integrating user code with the rich user experience of Slicer3

• Support GUI application processing• Support batch processing

National Alliance for Medical Image Computing http://na-mic.org

Grand vision

UserDesktopAlgorithms ITK VTK Slicer

Modules

VTK AppsUsing ITK

Scripts ofSlicer Mods

BatchPrograms

Non-NAMICCmd tools BatchMake

BIRN GridWizard

Slicer 3.0

National Alliance for Medical Image Computing http://na-mic.org

Design

• Specification of parameters to control a plugin– Command line style parameter specification

– XML description

• Automatic discovery process for plugins– Searchpath for plugins

– Queries for XML description of parameters

• Automatic construction of GUI for plugins– Each parameter/attribute type maps to a specific style of GUI

element

Plugin writer focuses on algorithm, not GUI nor integration

National Alliance for Medical Image Computing http://na-mic.org

Each module has …

… an entry in the module menu

… a panel of user interface controls

National Alliance for Medical Image Computing http://na-mic.org

Plugin overview

National Alliance for Medical Image Computing http://na-mic.org

Parameters

<integer> | <float> | <double> | <boolean> | <string> | <integer-vector> | <float-vector> | <double-vector> | <string-vector> | <integer-enumeration> | <float-enumeration> | <double-enumeration> | <string-enumeration> | <file> | <directory> | <image>[type="scalar|label|tensor|diffusion-weighted|vector|model"] | <geometry> [type="fiberbundle|model"] | <point>[multiple="true|false"] [coordinateSystem="lps|ras|ijk"] | <region>[multiple="true|false"] [coordinateSystem="lps|ras|ijk"]

National Alliance for Medical Image Computing http://na-mic.org

Parameter description

<name> * C++ variable name of the parameter

<description> * Help message for parameter

<label> * GUI label for the parameter

<default> Default value

<flag> * Single character flag, e.g. –f

<longflag> * Single word flag, e.g. --outputImage

<constraints> Block around minimum/maximum/step. Trigger a slider to be used.

<minimum> Minimum parameter value

<maximum> Maximum parameter value

<step> Step size

<channel> * Input or output parameter (image, geometry, file, directory)

<index> * Position of a parameter without a flag. Starts at 0

<enumeration> * Block around element

<element> * Choice value for an enumeration

* Required tags

* Required under certain conditions

National Alliance for Medical Image Computing http://na-mic.org

Behind the scenes

• Tasks queued for processing thread• Three types of modules:

– executable,

– shared object, and

– Python modules

• Scalar images sent via files for executables and memory* for shared objects and python

• Vector images, tensor images, geometry, tables, transforms sent via files

• Scalars, file names, directories, fiducials, regions sent via command line

* VTK-based modules using scalar images are only supported as executable (command line) modules.

National Alliance for Medical Image Computing http://na-mic.org

(Current) Limitations

• Limited/restricted access to Slicer3 internals• Supported parameter types are prescribed by Slicer3

– Request new parameter types

• Some parameter types can only (currently) be sent to plugins, not returned from plugins

• Some parameters types are (currently) sent via files not mapped through memory

• Conditional parameter specification tricky• Non-interactive• Intermediate results not (currently) supported

National Alliance for Medical Image Computing http://na-mic.org

The next level

Full Slicer3 modules are also supported as plugins• Model-view-controller design: Node, GUI, Logic• Access to all Slicer3 services

o Exposed to Slicer3 architectureo Batch processing requires running all of Slicer3

National Alliance for Medical Image Computing http://na-mic.org

Slicer3 Plugins

Common architecture for interactive and batch processing