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System Overview CIBC SCIRun / BioPSE System Overview
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System Overview CIBC Problem Solving Environments (PSEs) Core Memory Mgmt Process Mgmt Framework Libraries Modeling SimulationAnalysis Core PSE Chemistry Physics Medicine Biology Astronomy Geoscience
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System Overview CIBC Integration and Interaction Modeling Simulation Visualization user guides What If?
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System Overview CIBC SCIRun Goals Integration Extensibility Usability Interactivity Portability Utility Modeling SimulationAnalysis Core SCIRun
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System Overview CIBC SCIRun and BioPSE
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System Overview CIBC Overview Computational Science Problem Solving Environments Dataflow Datatypes Software Organization Extensibility PowerApps
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System Overview CIBC Elements of SCIRun Visual programming Environment
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI
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System Overview CIBC Network 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 CIBC Module Status Run-time messages are sent to the module’s “log” Startup messages Log message indicator Gray: no messages Red: error Blue: warning/remark Log message indicator Gray: no messages Red: error Blue: warning/remark
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System Overview CIBC Example Module: CastMatrix SCIRun/src/Dataflow/ Modules/Math/CastMatrix.cc GUI/CastMatrix.xml XML/CastMatrix.xml
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI ….send get……
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI Matrix
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI Matrix Field ColorMap Geometry
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System Overview CIBC Network Elements Dataflow Vocabulary Module Dataport Datapipe UI –GuiVars
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System Overview CIBC Network Design Dataflow Vocabulary Module Dataport Datapipe UI Send and Get GuiVars Scheduler Dependencies loops: send_intermediate
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System Overview CIBC Network Design Dataflow Vocabulary Module Dataport Datapipe UI Send and Get GuiVars Scheduler Dependencies loops: send_intermediate
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System Overview CIBC Packages and Categories
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System Overview CIBC Managing Complexity: Subnets
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System Overview CIBC Managing Complexity: Subnets
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System Overview CIBC Managing Complexity: Subnets
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System Overview CIBC Managing Complexity: Subnets
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System Overview CIBC Managing Complexity: Subnets
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System Overview CIBC Managing Complexity: Subnets
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System Overview CIBC Managing Complexity: Subnets
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System Overview CIBC Managing Complexity: Annotations
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System Overview CIBC build-fem-elem-leadfield.net
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System Overview CIBC dipole-localization-leadfield-vis.net
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System Overview CIBC build-misfit-and-localize.net
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System Overview CIBC showmatrix.net
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System Overview CIBC show-text.net
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System Overview CIBC Dataflow Datatypes Revisited Matrix Field ColorMap Geometry
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System Overview CIBC Matrices: 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;
![System Overview CIBC Matrices: 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;](http://images.slideplayer.com/24/7108053/slides/slide_36.jpg "System Overview CIBC Matrices: 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 CIBC Matrices: 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 CIBC Fields: Mesh + Data Data int, float, double, … Vector, Tensor, … basis Data int, float, double, … Vector, Tensor, … basis Geometry Regular Irregular (basis) Geometry Regular Irregular (basis) Properties PointCloudField ScanlineFieldCurveField ImageField QuadSurfFieldTriSurfField LatVolFieldHexVolField TetVolField
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System Overview CIBC Persistence 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 CIBC Persistent void Matrix::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(); }
![System Overview CIBC Persistent void Matrix::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(); }](http://images.slideplayer.com/24/7108053/slides/slide_40.jpg "System Overview CIBC Persistent void Matrix::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 CIBC Example Datasets
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System Overview CIBC Overview Computational Science Problem Solving Environments Dataflow Datatypes Software Organization Extensibility PowerApps
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System Overview CIBC Source Tree Organization SCIRun BioPSE MatlabInterface Core Dataflow StandAlone Packages linux src docs Core: algorithms, datatypes, math, threads Dataflow: network, modules, ports, scheduler StandAlone: converters, utilities Core: algorithms, datatypes, math, threads Dataflow: network, modules, ports, scheduler StandAlone: converters, utilities
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System Overview CIBC SCIRun Categories Fields 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 CIBC Extensibility Leverage existing utilities Extensibility through bridges SCIRun Matlab mpeg libimage Teem GENESIS lib socket lib SQL
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System Overview CIBC Three 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 CIBC Converters 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 CIBC Data Import / Export
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System Overview CIBC MatlabInterface
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System Overview CIBC Three 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 CIBC ITK Integration
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System Overview CIBC Teem
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System Overview CIBC Overview Computational Science Problem Solving Environments Dataflow Datatypes Software Organization Extensibility PowerApps
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System Overview CIBC Managing Complexity: UIs Subnets Annotations
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System Overview CIBC All Modules are “Generic”
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System Overview CIBC PowerApps: User-Friendly, Domain-Specific
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System Overview CIBC Power Apps
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System Overview CIBC Power 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 specific task
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System Overview CIBC Power Apps Guide the user through specific processing steps Processing Pane
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System Overview CIBC Power Apps Provide different visualization options Visualization Pane
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System Overview CIBC BioFEM Encapsulation of the forward-fem network http://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 CIBC BioTensor 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.html
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System Overview CIBC BioImage 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.html
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