Scientific Visualization Workshop Series ScientificVisualization with ParaView William Sherman 9/5/18 1 1 AVL Visualization Workshop Series – Fall 2018 Wednesdays @ 4:00pm – Luddy Hall Vis Lab (IQ-Wall) Date Topic Pre se nte r Aug. 29 Introduction to Scientific Visualization Bill Sherman Sep. 5 Scientific Visualization with ParaView (on RED) Bill Sherman Sep. 12 3 D Di gi ti zati on Jeff Rogers Sep. 19 Virtual Reality for Visualization Bill Sherman Sep. 26 Augmented Reality for Visualization Chauncey Frend Oct. 3 Vi sual i zi ng l i dar datasets using QGIS on RED Justin Peters Oct. 10 Augmented Reality & I oT Vi sual i zati ons Andreas Bueckle Oct. 17 Volume Rendering Visualizations Bill Sherman Oct. 24 InfoVis with Vega & D3.js Dav i d Reagan Oct. 31 Advanced Media & Ultra-Res Displays for Research Chris Eller Nov. 7 VTK VTK.js Bill Sherman Nov. 14 Data Vi sual i zati on Li teracy and Mak e-A-Vi s UI Katy Borner & Bruce Herr II Nov. 21 (no talk – Thanksgiving Eve) N/A Nov. 28 Molecular visualization with VMD (on RED) Bill Sherman Dec. 5 Brain Diffusion Imaging with DIPY Dav i d Reagan 5 Scientific Visualization with ParaView (on the IU Research Desktop system) Bill Sherman Advanced Visualization Lab Indiana University September 5, 2018 6 The Visualization Process 7 ParaView’s role in the Visualization Process 8 But first … Using the IU Research Desktop 9 IU HPC Desktop System(s) • Research Desktop (aka RED) on Carbonate ØRequires Carbonate Account vhttps://access.iu.edu/Accounts ØRequires “ThinLinc” software vhttps://k b.iu.edu/d/aput vAvailable for: ✧MS-Windows ✧Apple OSX ✧Linux ØProvides vReady-to-use software vDesktop interface to HPC system
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AVL Visualization Workshop Series – Fall 2018Wednesdays @ 4:00pm – Luddy Hall Vis Lab (IQ-Wall)Date Topic PresenterAug. 29 Introduction to Scienti fic Vi sual i zation Bi l l ShermanS ep. 5 S cienti fic Visualization with ParaView (on RE D) Bil l S herman
Sep. 12 3D Digi ti zation Jeff RogersSep. 19 Vi rtual Real i ty for Vi sual i zation Bi l l Sherman
Sep. 26 Augmented Real i ty for Vi sual i zation Chauncey Frend
Oct. 3 Vi sual i zi ng l idar datasets using QGIS on RED Justin Peters
Oct. 10 Augmented Real i ty & IoT Vi sual i zations Andreas Bueck leOct. 17 Volume Rendering Vi sual i zations Bi l l ShermanOct. 24 InfoVi s wi th Vega & D3.j s David ReaganOct. 31 Advanced Media & Ul tra-Res Di splays for Research Chri s E l lerNov. 7 VTK VTK.j s Bi l l ShermanNov. 14 Data Vi sual i zation Li teracy and Mak e-A-Vi s UI Katy Borner & Bruce Herr I INov. 21 (no tal k – Thank sgiv ing Eve) N/ANov. 28 Molecular v i sual i zation wi th VMD (on RED) Bi l l ShermanDec. 5 Brain Di ffusion Imaging wi th DIPY David Reagan
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Scientific Visualization with ParaView(on the IU Research Desktop system)
Bill ShermanAdvanced Visualization Lab
Indiana Univers ity
September 5, 2018
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The Visualization Process
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ParaView’s role in the Visualization Process
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But first … Using the IU Research Desktop
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IU HPC Desktop System(s)
• Research Desktop (aka RED) on CarbonateØRequires Carbonate Account
• An open-source, scalable, multi-platform visualization application.• Support for distributed computation models to process large data sets.• An open, flexible, and intuitive user interface.• An extensible, modular architecture based on open standards.• A flexible BSD-2 license.• Commercial maintenance and support.
Jer r y Clar ke, US Ar m y Resear ch Labor at or y
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ParaView Application Architecture
MPIOpenGL IceT Etc.
VTK
ParaView Server
ParaView Client pvpython Custom App
UI (Qt Widgets, Python Wrappings)
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ParaView & VTK
• General Purpose visualization tools from Kitware:
• VTK: Ø Program your own tool with standard techniquesØ Can be scripted
vPython, TCL, Java Ø Can be integrated into web notebooks
• ParaView:Ø Typical Desktop User InterfaceØ Can be integrated into Web interfacesØ ParallelizableØ Uses the VTK libraryØ Can be scripted
Ø AVL large format displaysØ Consumer-grade HMD displays
• CustomizableØ C++ extensionsØ Python scriptingØ Web interface
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ParaView Development
• Started in 2000 as collaborative effort between Los Alamos National Laboratories and KitwareInc. (lead by James Ahrens).• ParaView 0.6 released October 2002.• ParaView 1.0 released in November 2003.• ParaView 2.0 released in March 2005.
• September 2005: collaborative effort between Sandia National Laboratories, Kitware Inc. and CSimSoft to rewrite user interface to be more user friendly and develop quantitative analysis framework.• ParaView 3.0 released in May 2007.• ParaView 4.0 released in June 2013.• ParaView 5.0 released in January 2016.• ParaView 5.5 released in April 2018.
• M iranda (.mir, .raw)• Mu lti level 3 d P lasma (.m3 d , .h5 )• NASTRAN (.n as, .f06 )• Nek5 0 0 0 Fi les• Nrrd Raw Image (.n rrd ,.n hdr)• OpenFOAM Fi les (.foam)• PATRAN (.n eu)• P FLOTRAN (.h 5 )• P LOT2D (.p 2 d)• P LOT3D (.xyz, .q , .x, .vp3d )• P LYP o lygonal Fi leFo rmat• PNG ImageFi les• POP Ocean Fi les• P araDIS Fi les• Phasta Fi les (.p h t)• P ixieFi les (.h 5 )• P ro STAR (.cel , .vrt)• P ro tein DataBank (.p db , .en t, .pdb)• Raw ImageFi les• RawNRRD image fi les (.nrrd )• SAMRAI (.samrai )• SAR (.SAR , .sar)• SAS (.sasgeom, .sas, .sasd ata)• SESAMETab les• SLAC netCDF mesh and modedata
• SLAC netCDFp articled ata• Si lo (.si lo , .pdb)• Spheral (.spheral , .sv)• Sp yP lo tCTH• SpyP lo t (.case)• Stereo Li thography (.stl )• TFT Fi les• TIFF Image Fi les• TSu rfFi les• Tecp lo tASC II (.tec,.tp)• Tecp lo tB in ary (.p lt)• Tetrad (.h d f5 , .h 5)• UNIC (.h 5 )• VASP CHGCA (.CHG)• VASP OUT (.OUT)• VASP POSTCAR (.POS)• VP IC (.vp c)• VRML (.wrl )• Velod yne (.vld , .rst)• VizSchema (.h 5 , .vsh5)• Wavefron tP o lygonal Data (.o bj)• WindB lade (.wind )• XDMFand hdf5 (.xmf, .xdmf)• XMo l Molecu le
• Wavelets:Ø Another “dataset” that doesn’t require a fileØ Good for quickly testing volume dataset features of ParaViewØ Size/Center can be adjusted (we’ll s tick with the defaults )
• Condensed Matter Astrophysics (Nuclear Pasta) • For: Charles Horowitz, Cyclotron/Physics• Task: Produce analysis and videos for public
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Nuclear Pasta: The Data
• Data provided as locations of NeutronsØPoints can be loaded directly into ParaView, but ...ØA volume is better for the desired representationØVisualization expert transforms the data from points to density volume
vUs ing “Gauss ian Splat” to create Neutron dens ity
• Simulation evolves over timeØ temporal data
Ø each timestep is separately processedØ ParaView understands time-varying data
vs ingle filevmultiple files with numeric filenames
• Enhancing the visualization• Contour Filter (0.035)
Ø
Ø Turn off “otime_0000* ”• Connectiv ity (search)
Ø Colors:• Discretize to 12• Choose a varying colormap• Set range to 0-400
• See “Information” tabØ Play to follow changes over time
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Reset ParaView
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But wait!
• ParaView provides the ability to save the state of your visualization:• à File à Save State …
• I’ve already saved the final state, so restore to where we were:• à File à Load State ...• Select “connectivity_state.pvsm” (in “…/Data/Horowitz”)• à OK• “Use File Names From State”• à OK