scientific visualization workshop series 9/5/18 scientific...

ScientificVisualizationWorkshopSeriesScientificVisualizationwithParaViewWilliamSherman

9/5/18

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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

vhttps://access.iu.edu/AccountsØRequires “ThinLinc” software

vhttps://kb.iu.edu/d/aputvAvailable for:

✧MS-Windows✧Apple OSX✧Linux

ØProvidesvReady-to-use softwarevDesktop interface to HPC system


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Start ThinLinc and login

• Logging onto RED:Ø Start ThinLincØ Server: red.uits .iu.edØ Username: <your IU ADS name>Ø Password: <Your Passphrase>

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ThinLinc connects to Duo login

• RED uses the Duo two-factor loginØ Provide one of the confirmation options

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Now connected to RED (IU Research Desktop)

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Two ways to start ParaView on RED

• 1) Using the Applications menu:Øà Aplications à Visualization à paraview

• 2) Using the command line terminal shell:Ø % load module paraviewØ % paraview

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ParaView running

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A Word about ParaView


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What is ParaView?

• 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

vPythonØ MPI & CUDA available

vMostly CPU-based (for now)

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What Can ParaView Do?

• Interactive Desktop Exploration• Parallel computation using HPC systems• Batch Big-Iron (HPC) rendering• Interactive & Immersive Interfaces

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.

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Basic Usage


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User InterfaceMenu BarToolbars

Pipeline Browser

Object Inspector

3D View

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Controlling GUI Components

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Creating a Cylinder Source

1. Go to the Source menu and select Cylinder. 2. Click the Apply button to accept the default

parameters.

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Simple Camera Manipulation

• Drag left, middle, right buttons for rotate, pan, zoom.• Also use Shift, Ctrl modifiers.

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parameters.3. Increase the Resolution parameter.

4. Click the Apply button again.

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Pipeline Object Controls


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Undo Redo

RedoUndo

CameraRedo

CameraUndo

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Object Properties panel

Advanced SettingsProperty saving

{Properties

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Object Properties saving

Copy PropertiesPaste Properties

Restore Properties to DefaultMake Current Properties the Default

OS/X Iconography

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“Display” (representation) Properties

Primary representationparameters repeated on toolbar

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Information Tab

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parameters.3. Increase the Resolution parameter.

4. Click the Apply button again.

5. Delete the Cylinder.


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Real Data

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• Par aView Dat a ( . pvd)

• VTK ( . vt p, . vt u, . vt i, . vt s , . vt r )

• VTK Legacy ( . vt k)• VTK Mult i Block

( . vt m, . vt mb, . vt mg, . vt hd, . vt hb)

• Par t it ioned VTK ( . pvt u, . pvt i, . pvt s , . pvt r )

• ADAPT ( . nc, . cdf , . elev, . ncd)

• ANALYZE ( . img, . hdr )

• ANSYS ( . inp)• AVS UC D ( . inp)

• BOV ( . bov)• BYU ( . g)

• C C SM MTSD ( . nc, . cdf , . elev, . ncd)

• C C SM STSD ( . nc, . cdf , . elev, . ncd)

• C EAucd ( . ucd, . inp)

• C MAT ( . cmat )• C TRL ( . ct r l)

• C hombo ( . hdf 5, . h5)

• C law ( . claw )• C omma Separ at ed Values ( . csv)

• C osmology Files ( . cosmo, . gadget 2)

• C ur ve2D ( . cur ve, . ult r a, . ult , . u)

• DDC MD ( . ddcmd)

• Digit al Elevat ion Map ( . dem)

• Dyna3D( . dyn)

• EnSight ( . case, . sos)

• Enzo boundar y and hier ar chy• Exodus II ( . g, . e, . exe, . ex2, . ex2v. . ,

et c)

• Ext r udedVol ( . exvol)• FVC OM (MTMD, MTSD, Par t icle,

STSD)

• Facet Polygonal Dat a

• Flash mult iblock f iles• Fluent C ase Files ( . cas)

• GGC M ( . 3df , . mer )• GTC ( . h5)

• GULP ( . t r g)

• Gadget ( . gadget )• Gauss ian C ube File ( . cube)

• JPG Image ( . jpg, . jpeg)• LAMPPS Dump ( . dump)

• LAMPPS St r uct ur e Files

• LODI ( . nc, . cdf , . elev, . ncd)• LODI Par t icle ( . nc, . cdf , . elev, . ncd)

• LS- DYNA ( . k, . lsdyna, . d3plot , d3plot )• M3DC l ( . h5)

• MFIX Unst r uct r ed Gr id ( . RES)

• MM5 ( . mm5)• MPAS Net C DF ( . nc)

• Met a Image ( . mhd, . mha)

• 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

Supported Data Types

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Data Types

vtkImageData vtkRectilinearGrid vtkStructuredGrid vtkPolyData vtkUnstructuredGrid

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Data Types (not limited to 2D)

Uniform Rectilinear(vtkImageData)

Non-Uniform Rectilinear(vtkRectilinearGrid)

Curvilinear(vtkStructuredGrid)

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Pseudo Data

• 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 )

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Geometry Representations

Points

WireframeSurface w/ Edges Volume

Outline

Surface

Point Gaussian Slice


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Threshold

Extract Subset

Glyph

Stream Tracer

Common Filters

Warp (vector)

Group Datasets

Extract Level

Calculator

Contour

Clip

Slice

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Apply a Filter

1. Make sure that Wavelet1 is selected in the pipeline browser.

2. Select the contour filter.

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Apply a Filter

3. Parameters (default)Ø Data: RTDataØ Value: 157.09…

v (i.e. middle of the Range)

Ø Enable “Compute Scalars”RTData

Isosurface value

�Scalars, yes

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Apply a Filter

1. Make sure that disk_out_ref.ex2 is selected in the pipeline browser.

2. Select the contour filter.3. Change parameters to create an isosurface at

Temp = 400K.4. Click5. Color by “Pres”

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Apply a Filter

• Why no color?

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Apply a Filter

• Why no color?• A: because “white” is at the

center of this color map. (and we contoured in the center)


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Apply a Filter: Clip

• Now clip away to see inside:• Select Wavelet1• Click on “Clip” icon

• When “Clip1” is selected, can move the clipping plane

• Click after making adjustments

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Apply a Filter: Clip

• Now clip away to see inside:• Disable the “eye” icon on

“Contour1” to see only the clip• To change the clip to another

orthogonal, use:• ctrl/cmd-X ctrl/cmd-Y ctrl/cmd-Z

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Reset ParaView

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Real World Examples

(from Indiana University researcher)

AVL Visualization: Nuclear Pasta

• 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


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Nuclear Pasta: The Data

• Load Nuclear Pasta dataØà File à OpenØBrowse to (or type):

v/N/soft/rhel7/paraview/Data/Horowitzvà Navigatevà 51200_40 …và otime_..vtk

✧NOTE: the “..” is the time sequencevà OKvà

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Basic representations

• Basic visualization techniques:• Points

• NOTE: only shows the outer surface• “Point Gaussian”

• New features of ParaView 5.0• Not the same as splatting – more like sized points

• Slice• Wireframe• Surface• Surface w/ Edges• Volume

• à Adjust color maps (opacity)

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Animating through time• Simple animation:

• Press the “play arrow”: !

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Regional Connectivity

• Enhancing the visualization• Contour Filter (0.035)

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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


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Reset ParaViewAVL Visualizations: Globular Clusters

• Globular Cluster Evolution• For: Enrico Vesperini• Task: Produce analysis and videos for public

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Globular Clusters: The Data

• Vesperini Particle location data• Original data

• Columns of ASCII encoded numbers• Output from Starlab N-Body simulation

Ø Converted to VTK format• Data set: (BCollision_05/jhdata)

• Point dataØ with identification (“id”)

• Multi-time step• JH (Jongsuk Hong data)

Ø binary/trinary star collis ions

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Particles in Motion

• Partic le data (Simulation1/evdata)v locationv idv massv typev velocityv vphi

• RepresentationØ Color by “id”Ø Represent: 3D Glyphs

• arrows by defaultØ Set to spheres

• can set the resolution

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Particles in Motion

• Where are they?• Center the data with the “Camera Reset” button

• (or “Zoom to Data”)

• Animate!

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Particles in Motion

• What happened?• How did the stars interact?

• Trace their paths:Ø Add: TemporalPartic lesToPathlines• NOTE: creates two new entries in the pipeline• Partic les:

Ø Mask Points à 1Ø Max Track Length à 100Ø Rep: 3D Glyphs

Ø Glyph Type: SphereØ Coloring: id


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Particles/Paths in Motion

• Partic les:• Paths:

Ø Make them visible!Ø Select “Pathlines”Ø Add filter à “Tube”Ø Radius: 0.15Ø Vary Radius: off (default)

• Animate!

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Particles/Paths in Motion

• Animate!• Jump in time?

Ø No pathØ Path is calculated on-the-fly

• Longer path?Ø Set Max Track Length: 1000Ø Reanimate from the beginning

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ParaView Sample Data: Bluntfin

• à File à Open à “Data/ParaViewData/Data/bluntfin.v ts

• Data:Ø DensityØ MomentumØ StagnationEnergy

• Comparing variables

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• Comparing variables?• Multi-view layout:

Ø Split HorizontalØ Choose new “Render View”

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• Can independently adjust parameters and visibility

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• Can independently adjust parameters and visibility• Can connect the camera between views

Ø (NOTE: mouse required for right-click over ThinLinc on OS/X)


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• Can independently adjust parameters and visibility• Can connect the camera between views

Ø (NOTE: mouse required for right-click over ThinLinc on OS/X)

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More Information

• Help Menu

• The ParaView User’s Guide• http://paraview.org/Wiki/ParaView/Us ers_ Guide /Tabl e_Of _Cont ents

• The ParaView web page• www.paraview.org

• ParaView mailing lis t• [email protected]

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Future Steps

• Color Map opacity:Ø Transfer functions (we will talk about this later)

• Enhanced animating:Ø Camera movesØ Parameter controlsØ Batch rendering

• Python scripting:Ø Creating objectsØ Manipulating dataØ Batch mode processing

• Data queries & selection:Ø Select data based on parametersØ Manipulate/inspect particular data

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Questions?

(or perhaps a video)

Fin

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