Contributing to GumTree (Version 1.1)

Contributing to GumTree(Version 1.1)

Presenter:

Tony Lam (Gumnix Lab)

Tutorial Prerequisite

• GumTree Development Environment should be correctly setup on your machine Check out the latest “GumTree Platform” and “GumTree

Common Library” from Sourceforge Run Gumzilla demo instrument to check your GumTree

installation Have the tutorial note & source ready in your Eclipse workspace

• Basic J2SE 5.0 Programming Skill

• Some ideas on using Java Development Tool (JDT) and under Eclipse

Tutorial Outcomes

• What can you expect:1. Be able to write simple plug-in for GumTree and

Eclipse

2. Understand the design philosophy of GumTree

3. Contribute to GumTree by using the GumTree Platform API

• An instrument plug-in (Gumnut) for you to take home

Tutorial Outline

Basic GumTree Concept

• Say “Hello World” to GumTree

• Data Handling

• Experiment Modelling

• Data Acquisition

• Instrument Adaptation

What is GumTree?

• Official GUI for NBIP instruments

• A highly Integrated Scientific Experiment Environment ISEE!!

• An Eclipse based Rich Client Platform (RCP) application

• An open source GUI framework for collaboration

• ANSTO’s secret software weapon for total world domination (just kidding)

• http://gumtree.sourceforge.net

http://gumtree.sourceforge.net/

http://gumtree.sourceforge.net/

GumTree Architecture

core

cs

device

experiment

Java 5 VM

Instrument Control System Bridge

Instrument Specific Component

Data Acquisition

(DAQ)

Data Reduction and Analysis

(DRA)

Workbench Modelling

Instrument Specific

Leveraged Technology

GumTree Platform

Instrument Plugin

ui vis data

RCPEclipse

EcosystemOpen Source Technology

PlatformInfrastructure

common

Contributing to GumTree• What can be extended in

GumTree? Control System adaptation Visualisation Rendering Engine Data Format Support… and more

• When? Integrating new features to existing

instrument Writing new instrument front end

• Where? In a new GumTree plug-in

• How? Using Eclipse IDE and GumTree

Framework API

Eclipse RCP Runtime

Data

CS

DeviceACC

DRAVIS

UI

GumTree Platform

GumTree Project

Core

Your Plug-ins

Games

Clock

Other Eclipse Plug-ins

Their Plug-ins

HIPD

HRPD

TAS

SANS

REFL

REST

MRPD

GumNIX

Multimedia

Accessaries

Simulation Device

Environment Control Device

(Ancillary)

SDK Testing Framework

Data Analysis Algorithm

Instrument Operation Procedure

Contribution Rules

• Everything is a contributionAdd, do not modify

• Contribution code is only loaded when it is needed.Lazy loading mechanism

• Separate core functionality from UI functionality.

• Keep non-API codes to internal packagesDo not risk your plug-in

Eclipse Plugin Architecture• Plug-in – set of contributions

Example: Instrument specific data reduction & analysis (DRA) module

• Extension point - named entity for collecting contributions Example: Data format support

• Extension - a contribution Example: customised data format reader

Eclipse Plugin Architecture

• Plug-in details spelled out in the plug-in manifest Manifest declares

contributions Code implements

contributions and provides API

plugin.xml file in root of plug-in subdirectory

Tutorial Outline

Basic GumTree ConceptSay “Hello World” to GumTree

• Data Handling

• Experiment Modelling



Tutorial 1.1

• Learning ObjectivesWriting plug-in and simple Eclipse UI extension for

GumTreeFirst touch with the GumTree Visualisation API

• Performance IndicatorsA new plug-in with view to be displayed in the

GumTree WorkbenchGroup view into a view categoryDisplay “Hello World” in 1D GraphTwo buttons to control display on/off

Tutorial 1.2

• Learning ObjectivesGrouping UI contribution to a single screenUsing existing GumTree UI component

• Performance IndicatorsA perspective with Hello World view and

GumTree device navigator

Tutorial Outline

Basic GumTree ConceptSay “Hello World” to GumTreeExperiment Modelling


• Data Handling


Experiment Framework

• Experiments are modelled as objects users can operate GumTree in their familiar

scientific domainEssential elements are modelled as

experiment components eg, user metadata, instrument operations

• GumTree manages experiment lifecycleOnly one experiment to be activated at a time

Experiment LifecycleLogin

Hardware Setup (Expert Only)

Experiment Setup

Scan(Single Run)

Batch Run(Automated Data Collection /

Scheduled Scan)

Visualise / Process / Analyse Result

Export Data

Typical lifecycle

Modelling Gumnut Experiment

• For this tutorial, we will create a simple experiment which is capable of:Storing user metadata (name, address and email)

Performing a simple scan without driving any device

Collecting 2 monitor counts for each scan point

Importing and exporting experiment data with customised HDF5 reader and writer

Tutorial 2.1

• Learning ObjectivesUsing experiment extension pointUsing dummy SICS extension point

• Performance IndicatorsCreate a new experiment objectCreate dummy SICS objects

Four different SICS variables Two dummy SICS monitors A dummy SICS scan object

New contributions

Experiment Component Library

• Each experiment object has a group of experiment components Components are grouped in an experiment component library Components are stored in a tree structure Each component has an unique path, eg, /user/name,

/sample/sampleInfo/NaCl, /acquisition/scan/centerScan

• Experiment should provide the structure of the component library via a component library advisor Advisor provides basic tree structure and hooks for further

expansion

Gumnut Library Advisor

Root/

User/user

Instrument/instrument

Scan/scan

Name (user metadata)/user/name

Address (user metadata)/user/address

Email (user metadata)/user/email

(hook)/instrument/additions

(hook)/scan/additions

(hook)/user/additions

Tutorial 2.2

• Learning Objectives Experiment component and component library Tasting the adaptor design pattern Using experiment component extension point Basic device proxy concept (more on Data Acquisition section)

• Performance Indicators Setup a new component library Create user metadata objects (experiment components) Create a experiment browser UI adaptor for user metadata

objects Customise the appearance of component group Create an instrument info object and hook to the component

library

AdaptorFactory(IAdapterFactory)

Client:Experiment Browser

Adaptor Pattern

UserMetadata(IUserMetadata)

UserMetadataBrowserPart(IBrowserUIPart)

1. Experiment Browser wants User Metadata class to provide the functionalities which are specified in IBrowserUIPart

2. If User Metadata object cannot provide this, the Experiment Browser will use the adaptor factory to resolve this

3. Adaptor Factory returns an object that implements IBrowserUIPart. This object knows how to communicate with User Metadata

Advantages:

• Customisable and reusable

• All User Metadata share only a single instance of IBrowserUIPart

Tutorial Outline

Basic GumTree ConceptSay “Hello World” to GumTreeExperiment ModellingData Acquisition

• Data Handling


Data Acquisition• Data acquisition (DAQ) in GumTree is a set of sequential

(and possibly combinational) logic for controlling and sampling data from hardware.

• DAQ module in GumTree stores data in the experiment data object for data export and further data analysis

• DAQ module can be a scan, batch or any other possible method

• GumTree controls hardware via device proxy

• Control system adaptor in GumTree is responsible to provide the handle of device proxy

Working with Device Proxy• Device Proxy is a thin wrapper for objects in control system

SICS object: sics variable, monitor, virtual motor, etc TANGO object: device proxy EPICS object: process variable or artificial device object Device proxy interface is consist regardless which control system

GumTree connects to

• Device Proxy supports Execute commands synchronously / asynchronously Read attributes synchronously / asynchronously Write attributes synchronously / asynchronously Generate events and deliver them to event listeners

• Writing device proxy for GumTree will NOT be covered in this tutorial

Device Proxy API

DeviceData data = monitor1.syncReadAttribute(

ISicsGenericMonitor.Attribute.COUNT, DeviceSource.EXTERNAL);

int value = ((Integer)data.getData()).intValue();

Scan Template

• GumTree support generic scan routine via the scan template pattern

• Scan template is an object forControlling control system to perform scanVisualising live data during the scan processStoring data to centralised data object during an

experiment lifecycle

• Current GumTree scan framework requires scan template to supply UI for scan control and visualisation

Scan Template in Gumnut

SimpleExperimentGumnutScanTemplate

(IScanTemplate)

GumnutScanController

(IScanControlUIPart)

GumnutScanVisualiser(IScanVisUIPart)

CountCollector

Data(GTD)

SICSmonitor1

SICSScan object

SICSmonitor2

= SICS object

= Java class

= GumTree Data Object

1D Plot

Data Visualisation

• GumTree is capable of displaying 1D, 2D and 3D data with various rendering engine

1D

Tutorial 3.1

• Learning ObjectivesUnderstanding scan template design pattern

• Performance IndicatorsCreate a scan template for collecting 2

monitor counts at each scan pointDisplay live scan data

Tutorial Outline

Basic GumTree ConceptSay “Hello World” to GumTreeExperiment ModellingData AcquisitionData Handling


GumTree Data Object• GumTree Data (GTD) Object is a data container for internal

application data• GTD has hierarchy data structure

GTDItem (data set container) GTDGroup (GTDItem container) GTDAttribute (attrbitute for GTDItem and GTDGroup)

root(GTDGroup)

Node 1(GTDGroup)

Node 2(GTDGroup)

Data(GTDItem)

Attribute 1(GTDAttribute)

Data 1(GTDItem)

Node 2.1(GTDGroup)

Data 2(GTDItem)

Attribute 2(GTDAttribute)

Data Exchange

• GTD can be used forChanging data format

Storing experiment data

XML GTD NeXus

HistogramDevice

Device Data GTD NeXus

GumTree

GumTree

Tutorial 4.1

• Learning ObjectivesUsing GTD ObjectWrite data to experiment data object

• Performance IndicatorsMake experiment object to handle data from

scan

Data Format

• A GTD object can be import from and export to different data format if adaptors exist. GumTree supports:HDF, NeXus, CSV, XML, etc.

• Data reader (importing) and data writer (exporting) can be customised to preserve the structure of GTD

Tutorial 4.2

• Learning ObjectivesUsing file formatCustomise file format reader and writer

• Performance IndicatorsA new HDF5 reader and writer for the Gumnut

experimentBe able to export data from experiment

Tutorial Outline

Basic GumTree ConceptSay “Hello World” to GumTreeExperiment ModellingData AcquisitionData HandlingInstrument Adaptation

Instrument Support

• GumTree supports one (or zero) instrument at runtime

• Each instrument in GumTree needs to map to a control system adaptor

• Instrument feature plug-in defines plug-in set for an instrument

Product, Feature and Plug-in

• Product Basic unit of an application Eclipse (RCP) support 0 or 1 product definition

• Feature Defining a group of plug-ins Disabling a feature will disable all its declared plug-ins

• Plug-in Set of contributions wrapped in a single unit

• Instrument Plug-in A plug-in with a single instrument extension declared

• Instrument Feature Feature which contains an instrument plug-in Feature should have id identical to its instrument id

Final Goal

• Toward the end of this tutorial:Create a GUI for out imaginary instrument,

GumnutPass all our contributions to GumnutRun GumTree with Gumnut, not Gumzilla

We do not want any contribution from Gumzilla!


FeatureGumzilla

FeatureGumTreePlatform

ProductISEE

Plug-inSycamore

InstrumentPlug-inGumzilla

Plug-inGumnut

Plug-in…

Plug-in…

Plug-in…

#Instrument Plug-in: 1


FeatureGumnut

FeatureGumzilla


ProductISEE

Plug-inSycamore


InstrumentPlug-inGumnut

Plug-in…

Plug-in…

Plug-in…

#Instrument Plug-in: 2 -> Bad


FeatureGumnut

FeatureGumzilla


ProductISEE

Plug-inSycamore


InstrumentPlug-inGumnut

Plug-in…

Plug-in…

Plug-in…

#Instrument Plug-in: 1

Tutorial 5.1

• Learning ObjectivesUnderstanding instrument plug-in activation

with GumTree

• Performance IndicatorsWrapping contributions to a new instrument

plug-inLaunch GumTree with Gumnut

Reference

• Contributing to Eclipse: Understanding and Writing Plug-ins http://eclipsecon.org/2005/presentations/EclipseCon2005_Tutorial1.pdf

• GumTree Wiki

http://gumtree.sourceforge.net/wiki

http://eclipsecon.org/2005/presentations/EclipseCon2005_Tutorial1.pdf





Contributing to GumTree (Version 1.1)

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