Visualization Visualization ToolsTools

SDSC Summer Institute 2007SDSC Summer Institute 2007Dr. Steve CutchinDr. Steve Cutchin

Visservices.sdsc.edu

Web SitesWeb Sites visservices.sdsc.edu/software/visservices.sdsc.edu/software/

installed.phpinstalled.php visservices.sdsc.eduvisservices.sdsc.edu www.sdsc.eduwww.sdsc.edu www.syncenter.orgwww.syncenter.org

Interactive Viz on Interactive Viz on DatastarDatastar

Use X-Windows and SShUse X-Windows and SSh From xterm – From xterm – ssh –X dsloginssh –X dslogin

Use ssh and winscpUse ssh and winscp Generate images on Datastar, transfer to local host.Generate images on Datastar, transfer to local host.

Use a client/server visualization toolUse a client/server visualization tool Paraview in client/server mode.Paraview in client/server mode. VISIT in client/server mode.VISIT in client/server mode.

Other Options – VNC, Batch.Other Options – VNC, Batch.

Most Difficult Viz Most Difficult Viz Activity Is?Activity Is?

File Format Conversion!

Installed Visualization Installed Visualization Tools -HPC Tools -HPC

/usr/local/apps{32}/usr/local/apps{32} GIMP – Open Source Photoshop with batch.GIMP – Open Source Photoshop with batch. GnuPlot – command line plotting tool.GnuPlot – command line plotting tool. ImageMagick – image processing commands.ImageMagick – image processing commands. ParaView – Client/Server Scientific ParaView – Client/Server Scientific

Visualization Application.Visualization Application. VISIT – LLNL Scientific Visualization VISIT – LLNL Scientific Visualization

Application.Application. VTK – Visualization Toolkit – library of VTK – Visualization Toolkit – library of

visualization tools.visualization tools. VISTA – Volume visualization tool from SDSC.VISTA – Volume visualization tool from SDSC. Tecplot – Commercial CFD Plotting Tool.Tecplot – Commercial CFD Plotting Tool. XV – an excellent image viewing tool.XV – an excellent image viewing tool.

Configure X-WindowsConfigure X-Windows Set up X-Windows on your desktopSet up X-Windows on your desktop

Windows users – Cygwin/X Windows users – Cygwin/X http://x.cygwin.comhttp://x.cygwin.com

Then ssh to dslogin with X-Then ssh to dslogin with X-Forwarding enabled.Forwarding enabled. ssh –X dsloginssh –X dslogin

Add all Vistools to your path:Add all Vistools to your path: source /gpfs/projects/vis/cutchin/pathssource /gpfs/projects/vis/cutchin/paths

Tool 1: Image MagickTool 1: Image Magick Great command line Great command line

image tools.image tools. Well documented, well Well documented, well

supported.supported. Great for piping, Great for piping,

scripting, easily scripting, easily extensible.extensible.

www.imagemagick.org

Tool 1: Image MagickTool 1: Image Magick Current version in: Current version in:

/usr/local/apps32/imagemagick-6.2.8/bin/usr/local/apps32/imagemagick-6.2.8/bin Add to your path.Add to your path. Type %convert to testType %convert to test Web site: Web site: www.imagemagick.org Formats: Formats:

www.imagemagick.org/script/formats.php Bug: /opt/freeware/bin/display,animate, Bug: /opt/freeware/bin/display,animate,

importimport Also use ‘xv’Also use ‘xv’

Tool 1: ImageMagick Tool 1: ImageMagick CommandsCommands

Ex: convert magick:rose rose.jpgEx: convert magick:rose rose.jpg Convert: change formats, change various Convert: change formats, change various

params.params. Composite: combine images together.Composite: combine images together. Animate: animate series*.jpgAnimate: animate series*.jpg Display: display images*.jpg…Display: display images*.jpg… Montage: creates a thumbnail sheet.Montage: creates a thumbnail sheet. conjure: …..script engine . Magic scripting conjure: …..script engine . Magic scripting

language.language. Others: compare, identify, import, mogrify…Others: compare, identify, import, mogrify…

Tool 1: ImageMagick Tool 1: ImageMagick CommandsCommands

animate animates an image sequence on any X server.animates an image sequence on any X server. compare mathematically and visually annotate the difference between an mathematically and visually annotate the difference between an

image and its reconstruction.image and its reconstruction. composite overlaps one image over another.overlaps one image over another. conjure interprets and executes scripts written in the Magick Scripting interprets and executes scripts written in the Magick Scripting

Language (MSL).Language (MSL). convert convert between image formats.convert between image formats. displaydisplay displays an image or image sequence on any X server. displays an image or image sequence on any X server. identifyidentify describes the format and characteristics of one or more image describes the format and characteristics of one or more image

files.files. importimport saves any visible window on an X server and outputs it as an saves any visible window on an X server and outputs it as an

image file.image file. mogrifymogrify resize an image, blur, crop, despeckle, dither, draw on, flip, join, resize an image, blur, crop, despeckle, dither, draw on, flip, join,

re-sample, and much more.re-sample, and much more. montage montage create a composite image by combining several separate create a composite image by combining several separate

images.images.

Tool 2: GnuPlotTool 2: GnuPlot www.gnuplot.infowww.gnuplot.info A free GNU tool.A free GNU tool. Supports 2D & 3D Supports 2D & 3D

Plotting.Plotting. Very feature rich.Very feature rich. Command line usage.Command line usage. Great for quick and Great for quick and

dirty plots and text.dirty plots and text.

Tool 2: GnuPlotTool 2: GnuPlot Path: /usr/local/apps/gnuplot-4.0.0/ Path: /usr/local/apps/gnuplot-4.0.0/ Interactive visualization:Interactive visualization:

Ex: gnuplot Ex: gnuplot gnuplot> load “simple.gpl”gnuplot> load “simple.gpl”

Write image to a file:Write image to a file: Change the terminal: set terminal postscriptChange the terminal: set terminal postscript gnuplot> set terminal postscript color solidgnuplot> set terminal postscript color solid gnuplot> set output “outfile.ps“gnuplot> set output “outfile.ps“ gnuplot> load ‘simple.gpl’gnuplot> load ‘simple.gpl’ gnuplot> set outputgnuplot> set output gnuplot> set terminal pop gnuplot> set terminal pop

Or use /opt/freeware/bin/importOr use /opt/freeware/bin/import

Tool 2: GnuPlotTool 2: GnuPlot EX:/gpfs/projects/vis/cutchin/EX:/gpfs/projects/vis/cutchin/

gnuplot/demosgnuplot/demos Simple 2D Plot: simple.demSimple 2D Plot: simple.dem Basic 3D Plot: scatter.demBasic 3D Plot: scatter.dem Coloring Text: textcolor.demColoring Text: textcolor.dem Rotating Text: textrotate.demRotating Text: textrotate.dem Parsing data files: multimesh.demParsing data files: multimesh.dem More web help: www.gnuplot.infoMore web help: www.gnuplot.info

Tool 3: VISTATool 3: VISTA SDSC BuiltSDSC Built Volume RendererVolume Renderer Command line Command line

driven.driven. Lots of options.Lots of options. visservices.sdsc.edvisservices.sdsc.ed

u/software/vista/u/software/vista/ Supports HDR Supports HDR

output.output.http://visservices.sdsc.edu/software/vista

Tool 3: VISTATool 3: VISTA /gpfs/projects/vis/vistools/bin/gpfs/projects/vis/vistools/bin %vista –help for list of options.%vista –help for list of options. %vista –raw 512 512 512 %vista –raw 512 512 512

monkey_512by3.raw monkey_512by3.raw %vista –raw 512 512 512 –minmax -%vista –raw 512 512 512 –minmax -

33553920.0 33554688.0 33553920.0 33554688.0 monkey_512by3.raw monkey_512by3.raw

%/opt/freeware/bin/display %/opt/freeware/bin/display img_00000.ppmimg_00000.ppm

Tool 3: VISTA TerashakeTool 3: VISTA Terashake %vista –lsb –raw 40 150 300 –rawtype float –%vista –lsb –raw 40 150 300 –rawtype float –

minmax -0.1 0.1 tshake/tshake.05800.rawminmax -0.1 0.1 tshake/tshake.05800.raw Recolor: vista … --bigspect…Recolor: vista … --bigspect… Cameras: vista … -left –right –front –cam Cameras: vista … -left –right –front –cam

camfile…camfile… Sizing: vista … -r 0.2 0.45 0.8 ….Sizing: vista … -r 0.2 0.45 0.8 …. Custom cam: vista –cam tshake/tshake.camCustom cam: vista –cam tshake/tshake.cam Colormaps: vista …. –tmapfile …Colormaps: vista …. –tmapfile … Format types: %vista –rawtype float | int | Format types: %vista –rawtype float | int |

short | byte…short | byte…

Tool 4: ParaviewTool 4: Paraview OpenSource tool.OpenSource tool. Well supported.Well supported. Common in HPCCommon in HPC Uses VTKUses VTK Mostly designed Mostly designed

for programmers for programmers by programmers.by programmers.

www.paraview.orgwww.paraview.org

http://www.paraview.org

Tool 4: ParaviewTool 4: Paraview Path: /usr/local/apps32/paraview-Path: /usr/local/apps32/paraview-

2.2.1/ 2.2.1/ Interactive %paraviewInteractive %paraview Can load a variety of data formats Can load a variety of data formats

including unstructured and point including unstructured and point clouds.clouds.

Supports client/server mode: pserverSupports client/server mode: pserver Run client locally.Run client locally.http://visservices.sdsc.edu/tools/paraview/paraview.html

Tool 4: ParaviewTool 4: Paraview Local mode:Local mode:

Simply use paraviewSimply use paraview Then load your data.Then load your data.

Tutorial at: Tutorial at: http://visservices.sdsc.edu/threads/paraview/paraview.htmlhttp://visservices.sdsc.edu/threads/paraview/paraview.html

Tutorial at: Tutorial at: http://visservices.sdsc.edu/tools/paraview/paraview.htmlhttp://visservices.sdsc.edu/tools/paraview/paraview.html

Client/Server Mode Client/Server Mode Start up pserver on Datastar – how can they do that?Start up pserver on Datastar – how can they do that? pvserver –sp=use your own unique port number.pvserver –sp=use your own unique port number. Start up pclient on local hostStart up pclient on local host Pvclient –sh=dslogin –sp=remote port number.Pvclient –sh=dslogin –sp=remote port number. Select remote data and render.Select remote data and render. Manipulate the data transfer level.Manipulate the data transfer level. Play with several filters.Play with several filters.

Tool 5: TecplotTool 5: Tecplot Commercial product.Commercial product. Our users can use it.Our users can use it. Excellent tool.Excellent tool. GUI based.GUI based. Very popular and Very popular and

effective.effective. Takes a bit to get Takes a bit to get

started.started. Supports command Supports command

line processing.line processing.

Tool 5: TecplotTool 5: Tecplot In path: /usr/local/apps/tecplot/bin In path: /usr/local/apps/tecplot/bin %setenv TECHOME /usr/local/apps/tecplot%setenv TECHOME /usr/local/apps/tecplot % setenv TLMHOST dmv.sdsc.edu% setenv TLMHOST dmv.sdsc.edu %tecplot%tecplot Run simple example in tecplot.Run simple example in tecplot. Batch mode:Batch mode: Tecplot batchscript….Tecplot batchscript…. Display output imageDisplay output image www.tecplot.com for lots and lots of support.www.tecplot.com for lots and lots of support.

More Help?More Help? www.sdsc.eduwww.sdsc.edu E-mail: consult@sdsc.eduE-mail: consult@sdsc.edu E-mail: cutchin@sdsc.eduE-mail: cutchin@sdsc.edu