system overview cibc scirun / biopse system overview
TRANSCRIPT
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System Overview
CIBCCIBC
SCIRun / BioPSESystem OverviewSCIRun / BioPSESystem Overview
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System Overview
CIBCCIBC
Problem Solving Environments (PSEs)Problem Solving Environments (PSEs)
CoreMemory MgmtProcess Mgmt
FrameworkLibraries
Modeling
Simulation AnalysisCore
PSEPSE
Chemistry Physics
Medicine
Biology
Astronomy
Geoscience
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System Overview
CIBCCIBC
Integration and InteractionIntegration and Interaction
Modeling
Simulation
Visualization
userguides
What If?
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System Overview
CIBCCIBC
SCIRun GoalsSCIRun Goals
Integration Extensibility
UsabilityInteractivity
Portability Utility
Modeling
Simulation AnalysisCore
SCIRunSCIRun
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System Overview
CIBCCIBC
SCIRun and BioPSESCIRun and BioPSE
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System Overview
CIBCCIBC
OverviewOverview• Computational Science• Problem Solving Environments• Dataflow• Datatypes• Software Organization• Extensibility• PowerApps
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System Overview
CIBCCIBC
Elements of SCIRunElements of SCIRun
Visual programming Environment
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
MODULE
void execute() { // get data from ports // get data from UI // … do work … // set data on UI // send data out ports}
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System Overview
CIBCCIBC
Module StatusModule Status
• 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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System Overview
CIBCCIBC
Example Module: CastMatrixExample Module: CastMatrix
SCIRun/src/Dataflow/ Modules/Math/CastMatrix.cc
GUI/CastMatrix.xml
XML/CastMatrix.xml
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
….sendget……
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI Matrix
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI Matrix
Field
ColorMapGeometry
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System Overview
CIBCCIBC
Network ElementsNetwork Elements• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
– GuiVars
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System Overview
CIBCCIBC
Network DesignNetwork Design• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
• Send and Get• GuiVars• Scheduler
• Dependencies• loops: send_intermediate
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System Overview
CIBCCIBC
Network DesignNetwork Design• Dataflow Vocabulary
• Module• Dataport• Datapipe• UI
• Send and Get• GuiVars• Scheduler
• Dependencies• loops: send_intermediate
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System Overview
CIBCCIBC
Packages and CategoriesPackages and Categories
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System Overview
CIBCCIBC
Managing Complexity: SubnetsManaging Complexity: Subnets
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System Overview
CIBCCIBC
Managing Complexity: SubnetsManaging Complexity: Subnets
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System Overview
CIBCCIBC
Managing Complexity: SubnetsManaging Complexity: Subnets
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System Overview
CIBCCIBC
Managing Complexity: SubnetsManaging Complexity: Subnets
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System Overview
CIBCCIBC
Managing Complexity: SubnetsManaging Complexity: Subnets
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System Overview
CIBCCIBC
Managing Complexity: SubnetsManaging Complexity: Subnets
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System Overview
CIBCCIBC
Managing Complexity: SubnetsManaging Complexity: Subnets
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System Overview
CIBCCIBC
Managing Complexity: AnnotationsManaging Complexity: Annotations
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System Overview
CIBCCIBC
build-fem-elem-leadfield.netbuild-fem-elem-leadfield.net
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System Overview
CIBCCIBC
dipole-localization-leadfield-vis.netdipole-localization-leadfield-vis.net
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System Overview
CIBCCIBC
build-misfit-and-localize.netbuild-misfit-and-localize.net
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System Overview
CIBCCIBC
showmatrix.netshowmatrix.net
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System Overview
CIBCCIBC
show-text.netshow-text.net
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System Overview
CIBCCIBC
Dataflow Datatypes RevisitedDataflow Datatypes Revisited
Matrix
Field
ColorMap
Geometry
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System Overview
CIBCCIBC
Matrices: Class HierarchyMatrices: Class Hierarchy• Matrix: base class
• get, put, [ ], nrows, ncols, get_row, get_col, get_val, zero, mult, mult_transpose, print, {is_,as_,}{sparse,dense,column}, cg_solve, bicg_solve, scalar_multiply
• SparseRowMatrix• int *rows, int *cols, double *a, int nnz;
• ColumnMatrix• double *data;
• DenseMatrix• double **data;
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System Overview
CIBCCIBC
Matrices: External LibrariesMatrices: External Libraries
• PETSc• Preconditioners: jacobi, bijacobi, sor,
eisenstat, icc, ilu, asm, sles, lu, mg, spai, milu, nn, cholesky, ramg
• Solvers: KSRICHARDSON, PSPCHEBYCHEV, KSPGG, KSPGMRES, KSPTCQMR, KSPBCGS, KSPBGS, KSPTFQMR, KSPCR, KSPLSQR, KSPBICG, KSPPREONLY
• BLAS and Atlas• Faster linear-algebra via loop unrolling
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System Overview
CIBCCIBC
Fields: Mesh + DataFields: Mesh + Data
Data
int, float, double, …
Vector, Tensor, …
basis
Data
int, float, double, …
Vector, Tensor, …
basis
Geometry
Regular
Irregular (basis)
Geometry
Regular
Irregular (basis)
PropertiesProperties
PointCloudField
ScanlineField CurveField
ImageField QuadSurfField TriSurfField
LatVolField HexVolField TetVolField
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System Overview
CIBCCIBC
PersistencePersistence• Networks• Serialize data for disk I/O• Architecture independent
• Smart pointers• Byte swapping
• Data files are (somewhat) human readable, but should ~not~ be generated / edited by anything other than SCIRun• Use “convert” programs
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System Overview
CIBCCIBC
PersistentPersistentvoidMatrix::io(Piostream& stream){ /* int version = */ stream.begin_class("Matrix", MATRIX_VERSION); PropertyManager::io(stream); stream.end_class();}
void ColumnMatrix::io(Piostream& stream){ /* int version = */stream.begin_class("ColumnMatrix", COLUMNMATRIX_VERSION); Matrix::io(stream);
stream.io(rows); if(stream.reading()) { data=scinew double[rows]; } int i; for(i=0;i<rows;i++) stream.io(data[i]); stream.end_class();}
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System Overview
CIBCCIBC
Example DatasetsExample Datasets
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System Overview
CIBCCIBC
OverviewOverview• Computational Science• Problem Solving Environments• Dataflow• Datatypes• Software Organization• Extensibility• PowerApps
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System Overview
CIBCCIBC
Source Tree OrganizationSource Tree Organization
SCIRunSCIRun
BioPSE MatlabInterfaceBioPSE MatlabInterface
Core Dataflow StandAlone
Packages linux src docsPackages linux src docs
Core: algorithms, datatypes, math, threadsDataflow: network, modules, ports, schedulerStandAlone: converters, utilities
Core: algorithms, datatypes, math, threadsDataflow: network, modules, ports, schedulerStandAlone: converters, utilities
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System Overview
CIBCCIBC
SCIRun CategoriesSCIRun CategoriesFields
• FieldsCreate– “sources” for new Fields– e.g. SampleLattice, FieldBoundary, ClipByFunction
• FieldsData– Just change data for an existing Field (Mesh untouched)– TransformFieldData, ManageFieldData, DirectMapping /
ApplyMappingMatrix• FieldsGeometry
– Just change geometry for an existing Field (Data untouched)– Unstructure, HexToTet, QuadToTri– TransformField
• FieldsOther– Miscellaneous (FieldInfo, ChooseField, FieldMeasures, …)
Visualization• ColorMaps• Isosurfaces
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System Overview
CIBCCIBC
ExtensibilityExtensibility
• Leverage existing utilities• Extensibility through bridges
SCIRun
Matlab
mpeg
libimage
Teem
GENESIS
liblib
liblibsocketsocket
liblib
SQLSQL
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System Overview
CIBCCIBC
Three ApproachesThree Approaches
• Data Level• Command line tools to convert files• Communicating data across sockets
• Library Level• Teem, BLAS, ITK
• Application Level• Rewrite algorithms natively in SCIRun
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System Overview
CIBCCIBC
ConvertersConverters
• Convert between human-editable text (e.g. CVRTI .pts, .dat files) and SCIRun Persistent objects
• See examples in SCIRunData/convert-examples/• Each converter gives you usage info if invoked without
arguments: dmw stitch% TextToHexVolField
Usage: TextToHexVolField pts hexes HexVolMesh [-noPtsCount] [-noElementsCount] [-oneBasedIndexing] [-binOutput] [debug]
This program will read in a .pts (specifying the x/y/z coords of each point, one per line, entries separated by white space, file can have an optional one line header specifying number of points... and if it doesn't, you have to use the -noPtsCount command-line argument) and a .hex file (specifying i/j/k/l/m/n/o/p indices for each hex, also one per line, again with an optional one line header (use -noElementsCount if it's not there). The hex entries are assumed to be zero-based, unless you specify -oneBasedIndexing. And the SCIRun output file is written in ASCII, unless you specify -binOutput.
• Plug-ins for Readers / Writers
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System Overview
CIBCCIBC
Data Import / ExportData Import / Export
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System Overview
CIBCCIBC
MatlabInterfaceMatlabInterface
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System Overview
CIBCCIBC
Three ApproachesThree Approaches
• Data Level• Command line tools to convert files
• Library Level• Teem, BLAS, ITK
• Application Level• Rewrite algorithms natively in SCIRun
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System Overview
CIBCCIBC
ITK IntegrationITK Integration
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System Overview
CIBCCIBC
TeemTeem
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System Overview
CIBCCIBC
OverviewOverview• Computational Science• Problem Solving Environments• Dataflow• Datatypes• Software Organization• Extensibility• PowerApps
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System Overview
CIBCCIBC
Managing Complexity: UIsManaging Complexity: UIs
Subnets
Annotations
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System Overview
CIBCCIBC
All Modules are “Generic”All Modules are “Generic”
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System Overview
CIBCCIBC
PowerApps: User-Friendly, Domain-SpecificPowerApps: User-Friendly, Domain-Specific
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System Overview
CIBCCIBC
Power AppsPower Apps
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System Overview
CIBCCIBC
Power AppsPower Apps
Problem specific applications
•Hide the complexities of dataflow
•Provide a simplified graphical
user interface
•Focus on a specific
Problem specific applications
•Hide the complexities of dataflow
•Provide a simplified graphical
user interface
•Focus on a specifictasktask
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System Overview
CIBCCIBC
Power AppsPower Apps
Guide the user through specific processing stepsGuide the user through specific processing steps
Processing PaneProcessing Pane
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System Overview
CIBCCIBC
Power AppsPower Apps
Provide different visualization optionsProvide different visualization options
Visualization PaneVisualization Pane
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System Overview
CIBCCIBC
BioFEM BioFEM
Encapsulation of the forward-fem network Encapsulation of the forward-fem network
http://software.sci.utah.edu/doc/User/Tutorials/BioFEM/BioFEM.htmlhttp://software.sci.utah.edu/doc/User/Tutorials/BioFEM/BioFEM.html
• Change datasets
• Streamlines
• Isosurfaces
• Electrodes
• Change datasets
• Streamlines
• Isosurfaces
• Electrodes
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System Overview
CIBCCIBC
BioTensorBioTensor
Diffusion Tensor Imaging Processing Steps
•Data Acquisition
•Registration
•Building Tensors
Visualization Options
Diffusion Tensor Imaging Processing Steps
•Data Acquisition
•Registration
•Building Tensors
Visualization Options•Planes
•Isosurfaces
•Planes
•Isosurfaces
•Glyphs
•Fibers
•Glyphs
•Fibers
http://software.sci.utah.edu/doc/User/Tutorials/BioTensor/BioTensor.htmlhttp://software.sci.utah.edu/doc/User/Tutorials/BioTensor/BioTensor.html
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System Overview
CIBCCIBC
BioImageBioImage
Volume Rendering Processing Steps
•Crop
•Resample
•Histogram Eq
Visualization Options
Volume Rendering Processing Steps
•Crop
•Resample
•Histogram Eq
Visualization Options•Slices
•MIPs
•Slices
•MIPs
•Window Width / Level
•Multi-dimensional Transfer Functions
•Window Width / Level
•Multi-dimensional Transfer Functions
http://software.sci.utah.edu/doc/User/Tutorials/BioImage/BioImage.htmlhttp://software.sci.utah.edu/doc/User/Tutorials/BioImage/BioImage.html