scientific visualization in scirun

Scientific Computing and Imaging InstituteScientific Computing and Imaging InstituteSchool of ComputingSchool of Computing

University of UtahUniversity of Utah

Scientific Computing and Imaging InstituteScientific Computing and Imaging InstituteSchool of ComputingSchool of Computing

University of UtahUniversity of Utah

David Weinstein

SIAM CSE

02.09.2003

David Weinstein

SIAM CSE

02.09.2003

Scientific Visualization inSCIRun

Scientific Visualization inSCIRun

SCIRun

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OverviewOverview

Examples

Tour of SCIRun

- How To Get / Install It

- Dataflow

- Building A Module

Live Demos

SCIRun

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Natalie: Surgical PlanningNatalie: Surgical Planning

SCIRun

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Aneurysm: Volume RenderingAneurysm: Volume Rendering

SCIRun

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Forward and Inverse EEGForward and Inverse EEG

SCIRun

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ElectrocardiographyElectrocardiography

SCIRun

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ElectroencephalographyElectroencephalography

SCIRun

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MEG / Diffusion TensorsMEG / Diffusion Tensors

SCIRun

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Photorealism for Sci Vis: RTRTPhotorealism for Sci Vis: RTRT

SCIRun

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CSAFE: Fire-spreadCSAFE: Fire-spread

SCIRun

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Nuclear Fusion: TokamakNuclear Fusion: Tokamak

SCIRun

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SCIRun

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Integration and InteractionIntegration and Interaction

Modeling

Simulation

Visualization

userguides

What If?

SCIRun

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Elements of SCIRunElements of SCIRun

Visual programming Environment

SCIRun

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PSE RelationshipsPSE Relationships

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ExtensibilityExtensibility

• Leverage existing utilities• Extensibility through bridges

SCIRun

Matlab

mpeg

libimage

Teem

GENESIS

liblib

liblibsocketsocket

liblib

SQLSQL

SCIRun

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Documentation: The Central SourceDocumentation: The Central Source

http://internal.sci.utah.edu/developer/doc/

SCIRun

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Documentation: User SupportDocumentation: User Support

On-line Documentation• Tutorial• User’s Manual• FAQ Lists

Printed Documentation• User’s Manuals

Mailing List• [email protected]

Direct Contact• Email and Bugzilla• Phone

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System Specs and RequirementsSystem Specs and Requirements

Required OS and Build ToolsRequired OS and Build Tools• SGISGI• IRIX 6.5IRIX 6.5• MIPSPro Compilers (CC) 7.3.1.1mMIPSPro Compilers (CC) 7.3.1.1m

• LinuxLinux• Kernel 2.2.17Kernel 2.2.17• GCC 2.95.3GCC 2.95.3

• BothBoth• GNU Make 3.79.1GNU Make 3.79.1

http://software.sci.utah.edu/doc/TechnicalGuide/p1c1.htmlhttp://software.sci.utah.edu/doc/TechnicalGuide/p1c1.html

SCIRun

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Minimum System RequirementsMinimum System Requirements

Tested Systems: Gateway, Micron, Dell.Tested Systems: Gateway, Micron, Dell.http://software.sci.utah.edu/tested_systems/tested_systems.htmlhttp://software.sci.utah.edu/tested_systems/tested_systems.html

Processor(s)Processor(s) Main MemoryMain Memory Other HW/SWOther HW/SW

SGISGI250 MHz250 MHz

R10KR10K256 MB256 MB Texture Mapping Texture Mapping

Hardware/MemoryHardware/Memory

LinuxLinux700 MHz700 MHz

Pentium IIIPentium III256 MB256 MB

NVIDIA GeForce3 Graphics NVIDIA GeForce3 Graphics Card, XFree86 drivers Card, XFree86 drivers

version 1.0-1541version 1.0-1541

http://software.sci.utah.edu/doc/TechnicalGuide/p1c2.htmlhttp://software.sci.utah.edu/doc/TechnicalGuide/p1c2.html

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Documentation: TutorialDocumentation: Tutorial

SCIRun

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Network DesignNetwork Design• Dataflow Vocabulary• Module• Dataport• Datapipe• UI

• Send and Get• GuiVars• Scheduler• Dependencies• loops: send_intermediate

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PackagesPackages

• Encapsulated project• External code resides in Thirdparty• Packages enabled via “configure”

options% configure ‘--enable-package=BioPSE mypackage’

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Module CategoriesModule Categories

• …/Dataflow/Modules/{Fields,Math,…}

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FieldsFields

Data

int, float, double, …

Vector, Tensor, …

Data

int, float, double, …

Vector, Tensor, …

Geometry

Regular

Irregular

Geometry

Regular

Irregular

Properties

Data_at (center)

Properties

Data_at (center)

PointCloudField

ScanlineField CurveField

ImageField QuadSurfField TriSurfField

LatVolField HexVolField TetVolField

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On-the-fly CompilationOn-the-fly Compilation

•Combinatorial Explosion!•Geometry•Data type•Data_at

•Build source, compile, link – all at run time

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Error MessagesError Messages

•Run-time messages are sent to the module’s “log”

Startup messagesStartup messages

Log message indicatorGray: no messagesRed: errorBlue: warning/remark

Log message indicatorGray: no messagesRed: errorBlue: warning/remark

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Tikhonov RegularizationTikhonov Regularization

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How To Build A ModuleHow To Build A Module

•Before You Start

• Structure of a Module

• Ports and Datatypes

•Component Wizard

•GUI’s

•Dynamic Compilation Algorithm

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Before You StartBefore You Start

Design Your Function• A Module is a Function• Inputs and Outputs• User Input (GUI Variables)• Dataflow

Coding Standard• Standards• Advice• SCIRun/doc/Developer/Guide/coding_standard.html

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Module StructureModule Structure

Support Files• .cc file• sub.mk• .xml file• .tcl file• sub.mk• .h file (optional)

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Ports and DatatypesPorts and Datatypes

Ports• LockingHandles• Generation number• Memory Management• Sending Data• Cache Results

Datatypes• Fields, Matrix, SceneGraph• Detach (Dataflow)• Properties

SCIRun

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Component WizardComponent Wizard

Adding a Module

SCIRun

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SCIRun

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Edit a Port• Name• Namespace

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Component WizardComponent Wizard• Package• Category• Path

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Component WizardComponent Wizard• New Package?• New Category?• Reconfiguring.

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After Compiling

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Your Skeleton GUI

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GUI’sGUI’s

TCL• itcl

• blt

•Use Simple GUI as a Pattern

•GuiVars

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GUI’sGUI’s itcl_class SCIRun_Fields_SelectField {

inherit Module constructor {config} { set name SelectField

global $this-stampvalue global $this-runmode

set_defaults }

method set_defaults {} {set $this-stampvalue 100set $this-runmode 0# 0 nothing 1 accumulate 2 replace

}

method replace {} {set $this-runmode 2$this-c needexecute

}

method accumulate {} {set $this-runmode 1$this-c needexecute

}

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GUI’sGUI’s method ui {} {

set w .ui[modname] if {[winfo exists $w]} { raise $w return } toplevel $w

frame $w.row1frame $w.row3frame $w.row4

pack $w.row1 $w.row3 $w.row4 -side top -e y -f both -padx 5 -pady 5

label $w.row1.value_label -text "Selection Value"entry $w.row1.value -textvariable $this-stampvaluepack $w.row1.value_label $w.row1.value -side left

button $w.row3.execute -text "Replace" -command "$this replace"pack $w.row3.execute -side top -e n -f both

button $w.row4.execute -text "Accumulate" -command "$this accumulate"

pack $w.row4.execute -side top -e n -f both }

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GUI’sGUI’s

GuiVars• Values to from C side– Initialize

C++ side constructor synchs with tcl name tcl side sets the initial value

–my_var.reset()

–my_var.get()

• tcl_command(...)– $this-c “needexecute”

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Algorithm StructureAlgorithm StructureAlgorithm Base Class

• Inherits from common base class• Defines the pure virtual interface needed by a module• Provides a static CompileInfo

Templated Algorithm• Implements the pure virtual interface in the base class• Potentially specialized for specific field type

Algorithm Base Class• Inherits from common base class• Defines the pure virtual interface needed by a module• Provides a static CompileInfo

Templated Algorithm• Implements the pure virtual interface in the base class• Potentially specialized for specific field type

RenderFieldBase

RenderField<TetVol<double> >

RenderField<TetVol<Vector> >

RenderField<LatticeVol<double> >

RenderField<LatticeVol<Vector> >

etc...

virtual void render(FieldBase&)=0;virtual void render(FieldBase&)=0;

template<class Field> RenderField : public RenderFieldBasetemplate<class Field> RenderField : public RenderFieldBase

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TypeDescriptionTypeDescription

TypeDescription object augments RTTIHolds:

• Strings that describe object’s exact type• Namespace string• Path to the .h file that declares the object

Has a recursive structure

Example: foo<bar, foobar<int> >;

TypeDescription object augments RTTIHolds:

• Strings that describe object’s exact type• Namespace string• Path to the .h file that declares the object

Has a recursive structure

Example: foo<bar, foobar<int> >;

foo

int

foobarbar

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CompileInfoCompileInfo

Similar info as a TypeDescriptionAlgorithm is not instantiated, so cannot yet be

queriedStart with a CompileInfo from Algorithm base classAugmented with information from all pertinent

TypeDescription objects for the specific types involved

Passed to DynamicLoader, which creates the proper type

Similar info as a TypeDescriptionAlgorithm is not instantiated, so cannot yet be

queriedStart with a CompileInfo from Algorithm base classAugmented with information from all pertinent

TypeDescription objects for the specific types involved

Passed to DynamicLoader, which creates the proper type

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DynamicLoaderDynamicLoader

Returns Requested Algorithm• Writes C++ instantiation code• Compile shared library, using SCIRun makefiles• Load shared library (dlopen)• Return Instance of Algorithm (Cached for next use)

Synchronization code such that• Only 1 thread can compile at a time per algorithm• Multiple algorithms can compile and load at the same time

Returns Requested Algorithm• Writes C++ instantiation code• Compile shared library, using SCIRun makefiles• Load shared library (dlopen)• Return Instance of Algorithm (Cached for next use)

Synchronization code such that• Only 1 thread can compile at a time per algorithm• Multiple algorithms can compile and load at the same time

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Calling ModuleCalling Module void ShowField::execute()

{ // Get a Field from input field port. field = (FieldIPort *)get_iport("Field"); field->get(field_handle); // Get the input field's type info. const TypeDescription *td = field_handle->get_type_description();

// Get the Algorithm. CompileInfo *ci = RenderFieldBase::get_compile_info(td); if (! DynamicLoader::scirun_loader().get(*ci, rend_algo)) { error("Could not compile algorithm for ShowField -");

return; } RenderFieldBase *rf = dynamic_cast<RenderFieldBase*>(rend_algo); // Let the templated algorithm render this field. rf->render(field_handle, /* any other parameters from gui */);

// Send results downstream...}

No template instantiations for the exact algorithm typeNo template instantiations for the exact algorithm type

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ExampleExample

//! ConvertTetBase supports the dynamically loadable algorithm concept.//! when dynamically loaded the user will dynamically cast to a //! ConvertTetBase from the DynamicAlgoBase they will have a pointer to.class ConvertTetBase : public DynamicAlgoBase{public: virtual FieldHandle convert_quadratic(FieldHandle in) = 0; virtual ~ConvertTetBase();

static const string& get_h_file_path(); static string dyn_file_name(const TypeDescription *td) { // add no extension. return template_class_name() + "." + td->get_filename() + "."; }

static const string base_class_name() { static string name("ConvertTetBase"); return name; }

static const string template_class_name() { static string name("ConvertTet"); return name; }

//! support the dynamically compiled algorithm concept static CompileInfo *get_compile_info(const TypeDescription *td);};

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ExampleExample

template <class Fld>class ConvertTet : public ConvertTetBase{public: //! virtual interface. virtual FieldHandle convert_quadratic(FieldHandle in);};

template <class Fld>FieldHandleConvertTet<Fld>::convert_quadratic(FieldHandle ifh){ Fld *fld = dynamic_cast<Fld*>(ifh.get_rep()); ASSERT(fld != 0); typedef typename Fld::value_type val_t; FieldHandle fh(QuadraticTetVolField<val_t>::create_from(*fld)); return fh;}

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SummarySummary

Concepts• Ports and Datatypes

•Modules (Component Wizard)

• Templated Algorithms

•Dynamic Loading

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On the Horizon (BioPSE 2.0)On the Horizon (BioPSE 2.0)

GUI Separation: Event/State Managers•Detachable interface•Reproducibility•Collaboration•Remote vis•Custom UI• Scripting•Regression testing

BioPSEGUI

StateManager

GUI

GUI

scientific visualization in scirun

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