Scientific Toolkit for Java'

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Scientific Toolkit for Java.

• Mark Pollack
• (formerly BNL-PHENIX now
• TIBCO Software)

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Goals for Toolkit (I)

• Develop scientific specific interfaces.
• Data Points with error bars, Histograms, Fitting,
  Functions, Plotting.
• Take advantage of inherit multithreaded nature of
  Java (Online monitoring)
• Stick to Model-View-Controller design.
• Avoid package dependencies.
• Note Not a attack on Java Analysis Studio my
  side project to learn more about JDK1.2

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Goals for Toolkit (II)

• Bundle together useful components for building a
  real world application.
• Advanced GUI components, icons.
• Editor.
• Interpreters.
• Regular Expressions.
• Source code management. (cvs)
• Code scrapbook. (tricks of the trade)

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State of Java

• Plethora of new extensions
• JavaHelp
• New features in JDK 1.2
• Collection classes.
• Java 2D.
• Growing collection of open-source components.
• Reuse and integration.

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Java2D Overview

• Graphics2D class
• Acquire g2d object for an output device
• Screen, Printer, Offscreen buffer.
• Set rendering context
• Font, Transform, Stroke, Paint, Clip, Hints
• g2d.setPaint(Color.blue)
• Draw shapes, text, images
• g2d.draw(aShape), g2d.drawText(hi)
• g2d.draw(new Rectangle(0,0,100,100)

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STJ Drawing Framework

• Based on HotDraw framework.
• Simplify Java2D API
• ltltGShapegtgt
• Appearance.
• Delegates drawing to a ltltRenderergtgt.
• isFixedSize, isMoveable, isVisible.
• ltltShapeChangeListnergtgt
• draw(Graphics2D)

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STJ Drawing Framework Interfaces
GDrawingView
GDrawingEditor
Implementation inherits from JComponent
Current tool
GDrawing
Implementation inherits from JFrame
GTool
GLayer
GShape
Text
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GShapes
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Transformations

• Easy to transform a Shape
• Non-linear transformations.
• Can use PathIterator to walk shape and convert
  points as necessary.

Fish-eye
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Graphs

• Interfaces
• ltltDataPoint2Dgtgt, ltltGraphModelgtgt
• Models
• AbstractGraphModel (Listener management)
• DefaultGraphModel
• GraphModelEvent events fired when model changes.
• View Graph. (GAxis, ltltTickMakergtgt)

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Simple Graph
Axis scale with data changes
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Histograms

• Interfaces
• ltltHistoModelgtgt, ltltHistoModel1Dgtgt, ltltPartitiongtgt
• Models
• AbstractHistoModel, FixedPartition,
  FixedHistoModel1D
• HistoModelEvent events fired. (manage up to 3D)
• Abstract Histogram Factory
• STJHistoFactory implementation.

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Simple Histogram
Random Number Generation via CERN Colt package.
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Functions

• Interfaces
• ltltFunctiongtgt,ltltFunction1Dgtgt
• Models
• AbstractFunction, AbstractFunction1D
• 1D Gaussian, Exponential, Polynomial
• ParsedFunction1D (use interpreter)
• View Graph, GFunction1D

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Functions
Math.abs(x) is a parsed function.
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Interactive use

• Many interpreted languages available in Java.
• Allow access to Java objects.
• Managed like JDBC drivers
• ltltInterpreterDrivergtgt InterpreterDriverManager
• BshInterpreterDriver (Java) etc
• Generic Swing console.

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Interactive use
It actually works!
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Generic Console

• For packages that do not provide a swing based
  console.

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Persistence

• Use Bridge pattern for locating and archiving
  objects.
• ltltObjectFindergtgt,ltltObjectStorergtgt
• Responsible for finding object and how to
  decompose object for storage on physical media.
• RawSerializationStorer, ReflectionStorer
• Physical storage ltltObjectStoragegtgt
• JDBCStorage, RawSerializationFileStorage
• Objects can be located from Serialized file DB
  and saved to JDBC Database.

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Persistance

• Java Reflection picks apart objects
• Class, Name, Value put in StorageFields.
• Basic types, arrays to come, (SQL3 Data Types)
• Bean Reflection, persistence based on public API.
  (more stable?) New RFC from Sun.

(SQL generated on the fly)
TMessage
(TFile to come)
File DB
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Code snip for JDBC Storage
ObjectStorage storage new JDBCStorage()
ObjectManager.setObjectStorer(new
ReflectionStorer(storage)) ObjectManager om
new ObjectManager() Person p new
Person("mark",30,6.0f) om.storeObject(p)
ObjectFinderImpl of new JDBCObjectFinder(storage
) om.setObjectFinder(of) //work with object
Iterator it om.selectAll() //Iterator itt
om.select(QueryString)
Specific Implementations
Similar to ODMG DCollection
OQL grammar now available in Java.
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Code snip for Serialization Storage
RawObjectStorage storage new
RawSerializationFileStorage("D\\mark\\java\\dataf
iles\\myfile.ser", "RECREATE")
ObjectManager om new ObjectManager()
ObjectManager.setObjectStorer(new
RawSerializationStorer(storage)) //Work with
objects. GraphModel gmodel new
DefaultGraph2DModel() om.storeObject(gmodel
) ObjectFinderImpl of new
SERObjectFinder(storage) om.setObjectFinder(of)
Iterator it om.selectAll() //work with
objects.
Specific Implementations
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GUI Components/Icons

• Nice components from Claude Duguay.
• JBorder, JCalendar, JConfigure, JExplore,
  JGradient, JGraph, JIconEditor, JMaskField,
  JOutlookBar, JPalette, JReportForm, JScrollView,
  JSpinner.
• JavaLobby, 200 20x20 icons.
• Converted to 16x16.

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Component Snapshots
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Other Components

• JavaHelp
• Integration with application context.
• jEdit
• Extensible via plug-ins
• jCVS
• JUnit, framework for Unit testing.
• Colt

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Status

• Proof of principle
• Early stages, feedback needed.
• Drawing metaphor too clumsy?
• To do Fitting Implementation, TFile support, TeX
  Labels.
• Need to make API more concise, scripting
  friendly.
• Performance, Interpreters General

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Contact

• markp_at_bnl.gov
• More information _at_
• www.phenix.bnl.gov/markp