scientific visualization using vtk ray gasser [email protected] is&t scientific visualization tutorial...

Scientific Visualization using VTKScientific Visualization using VTK

Ray Gasser

[email protected]

IS&T Scientific Visualization Tutorial – Spring 2010

VTKVTK

Visualization Toolkit– Set of object oriented class libraries for visualization

– Several language interfaces• Python

• Tcl

• C++

• Java

• Visual Basic

– Open source

– Standards based

– Portable

– Active developer community

– Good documentation available

– Professional support services available from Kitware


VTK – Getting StartedVTK – Getting Started


Unix Shell:

katana:% cp -r scivis_workshop/VTK/materials/ .

katana:% cd materials/Demos/Simple

katana:% vtk cone2.tcl

VTK - Graphics ModelVTK - Graphics Model

Graphics Model – Transforms graphical data into pictures

– Class names adapted from movie industry: lights, camera, actor, props

– Consists of the following core objects:• vtkActor - object in scene

• vtkLight - illumination of scene

• vtkCamera - view of scene

• vtkProperty - appearance of actor

• vtkMapper - geometry of actor

• vtkTransform - positioning of actor, camera, lights

• vtkLookupTable - defines color tables used in scene

• vtkRenderer - manages rendering of scene

• vtkRenderWindow - manages graphics window

• vtkRenderWindowInteractor - manages keyboard and mouse


Code – simple.tclCode – simple.tcl


Editor:

package require vtk

vtkRenderWindow renWin

renWin SetSize 500 500

vtkRenderer ren1

ren1 SetBackground 0.0 0.0 0.0

renWin AddRenderer ren1

renWin Render

Unix Shell:

katana:% vtk simple.tcl

Exercise1Exercise1


Editor: simple2.tcl

Change background color to gray

Code – Exercise1Code – Exercise1


Editor: simple2.tcl

package require vtk



vtkRenderer ren1



renWin Render

Code – cone.tclCode – cone.tcl


Editor:package require vtk

vtkConeSource cone

cone SetResolution 100

vtkPolyDataMapper coneMapper

coneMapper SetInput [cone GetOutput]

vtkActor coneActor

coneActor SetMapper coneMapper

[coneActor GetProperty] SetColor 1.0 0.0 0.0



vtkRenderer ren1


ren1 AddActor coneActor


renWin Render

Code – cone2.tclCode – cone2.tcl


Editor:package require vtk

vtkConeSource cone

cone SetResolution 100

vtkPolyDataMapper coneMapper

coneMapper SetInput [cone GetOutput]

vtkActor coneActor

coneActor SetMapper coneMapper

[coneActor GetProperty] SetColor 1.0 0.0 0.0

vtkRenderWindowInteractor iren



vtkRenderer ren1




iren SetRenderWindow renWin

iren Initialize

Exercise2Exercise2


Editor: cone3.tcl

Add a green cone

will need to use:coneActor2 RotateZ 90

coneActor2 SetScale 0.5 0.5 0.5

coneActor2 GetProperty3D SetPosition 1.0 0.0 0.0

Code – Exercise 2Code – Exercise 2


Editor: cone3.tcl

. . .

vtkConeSource cone2

cone2 SetResolution 100

vtkPolyDataMapper coneMapper2

coneMapper2 SetInput [cone2 GetOutput]

vtkActor coneActor2

coneActor2 SetMapper coneMapper2

[coneActor2 GetProperty] SetColor 0.0 1.0 0.0

coneActor2 RotateZ 90

coneActor2 SetScale 0.5 0.5 0.5

coneActor2 SetPosition 1.0 0.0 0.0


ren1 AddActor coneActor2

. . .

VTK - Visualization ModelVTK - Visualization Model

Visualization Model– Transforms information into graphical data

– Uses a data flow approach

– Two basic types of objects involved• vtkDataObject

– represents data of various types

– consist of geometry and topology (points and cells) and attribute data

• vtkProcessObject– filters which operate on data objects to produce new data objects

– represent visualization algorithms

– Data Objects and Process Objects are connected together to form a visualization pipeline

Source -> Reader -> Filter -> Mapper -> Actor


VTK - Sample CodeVTK - Sample CodevtkStructuredGridReader reader

reader SetFileName "Data/density.vtk"

reader Update

vtkContourFilter iso

iso SetInputConnection [reader GetOutputPort]

iso SetValue 0 .26

vtkPolyDataMapper isoMapper

isoMapper SetInputConnection [iso GetOutputPort]

isoMapper ScalarVisibilityOn

vtkActor isoActor

isoActor SetMapper isoMapper

vtkRenderer ren1





ren1 AddActor isoActor


renWin Render


Reader

Filter

Mapper

Actor

VTK - ReadersVTK - Readers Polygonal Data Readers

– vtkBYUReader - read MOVIE.BYU files

– vtkMCubesReader - read binary marching cubes files

– vtkOBJReader - read Wavefront (Maya) .obj files

– vtkPolyDataReader - read VTK polygonal data files

– vtkPLYReader - read Standford University PLY polygonal data files

– vtkSTLReader - read stereo-lithography files

– vtkUGFacetReader - read EDS Unigraphic facet files

Image and Volume Readers– vtkBMPReader - read PC bitmap files

– vtkDEMReader - read digital elevation model files

– vtkJPEGReader - read JPEG files

– vtkImageReader - read various image files

– vtkPNMReader - read PNM (ppm, pgm, pbm) files

– vtkPNGRReader - read Portable Network Graphic files


VTK - ReadersVTK - Readers Image and Volume Readers (cont)

– vtkStructuredPointsReader - read VTK structured points data files

– vtkSLCReader - read SLC structured points files

– vtkTIFFReader - read files in TIFF format

– vtkVolumeReader - read image (volume) files

– vtkVolume16Reader - read 16-bit image (volume) files

Structured Grid Readers– vtkPLOT3DReader - read structured grid PLOT3D files

– vtkStructuredGridReader - read VTK structured grid data files

Rectilinear Grid Readers– vtkRectilinearGridReader - read VTK rectilinear grid data files

Unstructured Grid Readers– vtkUnstructuredGridReader - read VTK unstructured grid data files


Characteristics of DataCharacteristics of Data

Data is discrete– Interpolation functions generate data values in between known points

Structure may be regular or irregular– Regular (structured)

• need to store only beginning position, spacing, number of points

• smaller memory footprint per cell (topology can be generated on the fly)

• examples: image data, rectilinear grid, structured grid

– Irregular (unstructured)• information can be represented more densely where it changes quickly

• higher memory footprint (topology must be explicitly written) but more freedom

• examples: polygonal data, unstructured grid


Characteristics of DataCharacteristics of Data

Data has a topological dimension– determines methods for visualization

– determines data representation

– examples:• 0D - points

• 1D - lines/Curves

• 2D - surfaces

• 3D - volumes

Data is organized into datasets for visualization– Datasets consist of two pieces

• organizing structure– cells (topology)

– points (geometry)

• data attributes associated with the structure

– File format derived from organizing structure


Organizing Structure (Topology)Organizing Structure (Topology) Topology

– the way in which constituent parts are interrelated or arranged

– specified by one or more cells (types vary with visualization packages)• vertex - (0D) point

• polyvertex - (0D) arbitrarily ordered list of points

• line - (1D) defined by two points

• polyline - (1D) ordered list of one or more connected lines

• triangle - (2D) ordered list of three points

• triangle strip - (2D) ordered list of n + 2 points (n is the number of triangles)

• polygon - (2D) ordered list of three or more points lying in a plane

• pixel - (2D) ordered list of four points with geometric constraints

• quadrilateral - (2D) - ordered list of four points lying in a plane

• tetrahedron - (3D) ordered list of four nonplanar points

• voxel - (3D) ordered list of eight nonplanar points with geometric constraints

• hexahedron - (3D) ordered list of eight nonplanar points


VTK Example Cell TypesVTK Example Cell Types


Organizing Structure (Geometry)Organizing Structure (Geometry) Geometry

– point coordinates assigned to a topology in 3D space

– represented by points

– example: (0 0 0), (0 1 0), (1 0 0) would be the geometry for a triangle


Dataset Types (VTK)Dataset Types (VTK)

Image Data (Structured Points)– regular in both topology and geometry

– examples: lines, pixels, voxels

– applications: imaging CT, MRI

Rectilinear Grid– regular topology but geometry only partially

regular

– examples: pixels, voxels

Structured Grid– regular topology and irregular geometry

– examples: quadrilaterals, hexahedron

– applications: fluid flow, heat transfer


Dataset Types (cont)Dataset Types (cont)

Unstructured Points– no topology and irregular geometry

– examples: vertex, polyvertex

– applications: data with no inherent structure

Polygonal Data– irregular in both topology and geometry

– examples: vertices, polyvertices, lines, polylines, polygons, triangle strips

Unstructured Grid – irregular in both topology and geometry

– examples: any combination of cells

– applications: finite element analysis, structural design, vibration


Dataset Types (cont)Dataset Types (cont)

XML – much more complicated than the dataset

types described above, but supports many more features

– provides the user with the ability to extend a file format with application specific tags

– in VTK the XML dataset has support for compression, portable binary encoding, random access, byte ordering, and multiple file representation of piece data


Data AttributesData Attributes

Data attributes associated with the organizing structure– Scalars

• single valued

• examples: temperature, pressure, density, elevation

– Vectors• magnitude and direction

• examples: velocity, momentum

– Normals • direction vectors (magnitude of 1) used for shading

– Texture Coordinates• used to map a point in Cartesian space into 1, 2, or 3D texture space

• used for texture mapping

– Tensors (generalizations of scalars, vectors and matrices)• rank 0 ( scalar), rank 1 (vector), rank 2 (matrix), rank3 (3D rectangular array)

• examples: stress, strain


File Format – Structured GridFile Format – Structured Grid


Editor density.vtk:# vtk DataFile Version 3.0

vtk output

ASCII

DATASET STRUCTURED_GRID

DIMENSIONS 57 33 25

POINTS 47025 float

2.667 -3.77476 23.8329 2.94346 -3.74825 23.6656 3.21986 -3.72175 23.4982

3.50007 -3.70204 23.3738 3.9116 -3.72708 23.5319 4.1656 -3.69529 23.3312

. . .

POINT_DATA 47025

SCALARS Density float

LOOKUP_TABLE default

0.498983 0.376668 0.333115 0.311612 0.267114 0.639897 0.479756 0.477011 0.461867

0.428373 0.639897 0.608989 0.570884 0.510595 0.443823 0.407467 0.376066 0.34614

. . .

VECTORS Momentum float

0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 64.5673 0 0

0 0 0 0 0 0 0 0 0

. . .

Color MappingColor Mapping

Scalar Algorithms– Color Mapping

• maps scalar data to colors

• implemented by using scalar values as an index into a color lookup table

• specify a HSVA (Hue-Saturation-Value-Alpha) ramp and then generate the colors in the table by using linear interpolation into the HSVA space.

– VTK • vtkLookupTable

• vtkDataSetMapper


Code – Color MappingCode – Color Mapping


Editor: colormap.numcolors.tcl

. . .

vtkLookupTable lut

lut SetNumberofColors 16

lut SetHueRange 0.0 0.667

lut Build

vtkStructuredGridReader reader

reader SetFileName “Data/subset.vtk”

reader Update

vtkDataSetMapper mapper

mapper SetInputConnection [reader GetOutputPort]

mapper SetLookupTable lut

eval mapper SetScalarRange [[reader GetOutput] GetScalarRange]

vtkActor actor

actor SetMapper mapper

. . .

Exercise3Exercise3


* Change the number of colors in colormap

* Reverse the Hue Range

* Change the Scalar Range

mapper SetScalarRange 0.0 0.7

ContouringContouring

Scalar Algorithms (cont)– Contouring

• construct a boundary between distinct regions, two steps:– explore space to find points near contour

– connect points into contour (2D) or surface (3D)

• 2D contour map (isoline):– applications: elevation contours from topography, pressure contours

(weather maps) from meteorology3D isosurface:

• 3D isosurface:– applications: tissue surfaces from tomography, constant pressure or

temperature in fluid flow, implicit surfaces from math and CAD

– VTK• vtkContourFilter


Code – Contour (isoline)Code – Contour (isoline)


Editor: contour.single.tcl

. . .


reader SetFileName “Data/subset.vtk”

reader Update

vtkContourFilter contour

contour SetInputConnection [reader GetOutputPort]

contour SetValue 0 0.26

vtkPolyDataMapper contourMapper

contourMapper SetInputConnection [contour GetOutputPort]

eval contourMapper SetScalarRange

[[reader GetOutput] GetScalarRange]

vtkActor contourActor

contourActor SetMapper contourMapper

. . .

Code – Contour (isosurface)Code – Contour (isosurface)


Editor: isosurface.tcl

. . .


reader SetFileName “Data/density.vtk”

reader Update

vtkContourFilter iso

iso SetInputConnection [reader GetOutputPort]

iso SetValue 0 0.26

vtkPolyDataMapper isoMapper

isoMapper SetInputConnection [iso GetOutputPort]

eval isoMapper SetScalarRange [[reader GetOutput] GetScalarRange]

vtkActor isoActor

isoActor SetMapper isoMapper

. . .

Scalar GenerationScalar Generation

Scalar Algorithms (cont)– Scalar Generation

• extract scalars from part of data

• example: extracting z coordinate (elevation) from terrain data to create scalar values

– VTK• vtkElevationFilter


Code – Scalar GenerationCode – Scalar Generation


Editor: hawaii.color.tclvtkPolyDataReader hawaii

hawaii SetFileName "Data/honolulu.vtk"

hawaii Update

vtkElevationFilter elevation

elevation SetInput [hawaii GetOutput]

elevation SetLowPoint 0 0 0

elevation SetHighPoint 0 0 1000

elevation SetScalarRange 0 1000

vtkLookupTable lut

lut SetHueRange 0.7 0

vtkDataSetMapper hawaiiMapper

hawaiiMapper SetInput [elevation GetOutput]

hawaiiMapper SetScalarRange 0 1000

hawaiiMapper SetLookupTable lut

vtkActor hawaiiActor

hawaiiActor SetMapper hawaiiMapper

HedgehogsHedgehogs

Vector Algorithms– Hedgehogs

• oriented scaled line for each vector

• scale indicates magnitude

• color indicates magnitude, pressure, temperature, or any variable

– VTK• vtkHedgeHog


Code – HedgeHogsCode – HedgeHogs


Editor: hedgehog.tclvtkStructuredGridReader reader


reader Update

vtkHedgeHog hhog

hhog SetInput [reader GetOutput]

hhog SetScaleFactor 0.001

vtkPolyDataMapper hhogMapper

hhogMapper SetInput [hhog GetOutput]

hhogMapper SetLookupTable lut

hhogMapper ScalarVisibilityOn

eval hhogMapper SetScalarRange [[reader GetOutput] GetScalarRange]

vtkActor hhogActor

hhogActor SetMapper hhogMapper

Oriented GlyphsOriented Glyphs

Vector Algorithms (cont)– Oriented Glyphs

• orientation indicates direction

• scale indicates magnitude

• color indicates magnitude, pressure, temperature, or any variable

– VTK• vtkGlyph3D


Code – Oriented GlyphsCode – Oriented Glyphs


Editor: glyph.tclvtkArrowSource arrow

arrow SetTipResolution 6

arrow SetTipRadius 0.1

arrow SetTipLength 0.35

arrow SetShaftResolution 6

arrow SetShaftRadius 0.03

vtkGlyph3D glyph

glyph SetInput [reader GetOutputPort]

glyph SetSource [arrow GetOutputPort]

glyph SetVectorModeToUseVector

glyph SetColorModeToColorByScalar

glyph SetScaleModeToDataScalingOff

glyph OrientOn

glyph SetScaleFactor 0.2

vtkPolyDataMapper glyphMapper

glyphMapper SetInput [glyph GetOutput]

glyphMapper SetLookupTable lut

glyphMapper ScalarVisibilityOn

eval glyphMapper SetScalarRange [[reader GetOutput] GetScalarRange]

Field LinesField Lines

Vector Algorithms (cont)– Field Lines

• Fluid flow is described by a vector field in three dimensions for steady (fixed time) flows or four dimensions for unsteady (time varying) flows

• Three techniques for determining flow– Pathline (Trace)

• tracks particle through unsteady (time-varying) flow

• shows particle trajectories over time

• rake releases particles from multiple positions at the same time instant

• reveals compression, vorticity

– Streamline

• tracks particle through steady (fixed-time) flow

• holds flow steady at a fixed time

• snapshot of flow at a given time instant

– Streakline

• particles released from the same position over a time interval (time-varying)

• snapshot of the variation of flow over time

• example: dye steadily injected into fluid at a fixed point


Field LinesField LinesStreamlines

• Lines show particle flow

• VTK – vtkStreamTracer

Streamlets• half way between streamlines and glyphs

• VTK - vtkStreamTracer, vtkGlyph3D

Streamribbon• rake of two particles to create a ribbon

• VTK - vtkStreamTracer, vtkRuledSurfaceFilter

Streamtube• circular rake of particles to create a tube

• VTK - vtkStreamTracer, vtkTubeFilter


Code – StreamlinesCode – Streamlines


Editor: streamLines.tclvtkPointSource seeds

seeds SetRadius 3.0

eval seeds SetCenter [[reader GetOutput] GetCenter]

seeds SetNumberOfPoints 100

vtkRungeKutta4 integ

vtkStreamTracer streamer

streamer SetInputConnection [reader GetOutputPort]

streamer SetSourceConnection [seeds GetOutputPort]

streamer SetMaximumPropagation 100

streamer SetMaximumPropagationUnitToTimeUnit

streamer SetInitialIntegrationStepUnitToCellLengthUnit

streamer SetInitialIntegrationStep 0.1

streamer SetIntegrationDirectionToBoth

streamer SetIntegrator integ

vtkPolyDataMapper mapStreamLines

mapStreamLines SetInputConnection [streamer GetOutputPort]

eval mapStreamLines SetScalarRange [[reader GetOutput] GetScalarRange]

vtkActor streamLineActor

streamLineActor SetMapper mapStreamLines

Code – StreamtubesCode – Streamtubes


Editor: streamTubes.varyRadius.tclvtkPointSource seeds

seeds SetRadius 1.0

eval seeds SetCenter 1.5 0.01 27

seeds SetNumberOfPoints 50

vtkRungeKutta4 integ

vtkStreamTracer streamer

streamer SetInputConnection [reader GetOutputPort]

streamer SetSourceConnection [seeds GetOutputPort]

. . .

vtkTubeFilter streamTube

streamTube SetInputConnection [streamer GetOutputPort]

streamTube SetRadius 0.01

streamTube SetNumberOfSides 6

# streamTube SetVaryRadiusToVaryRadiusOff

streamTube SetVaryRadiusToVaryRadiusByScalar

vtkPolyDataMapper mapStreamTube

mapStreamTube SetInputConnection [streamTube GetOutputPort]

mapStreamTube SetLookupTable lut

eval mapStreamTube SetScalarRange [[[[reader GetOutput] GetPointData] GetScalars] GetRange]

vtkActor streamTubeActor

streamTubeActor SetMapper mapStreamTube

[streamTubeActor GetProperty] BackfaceCullingOn

Clipping, Cutting, SubsamplingClipping, Cutting, Subsampling

Modeling Algorithms - Clipping

• can reveal internal details of surface

• VTK - vtkClipDataSet

- Cutting/Slicing• cutting through a dataset with a surface

• VTK - vtkCutter

- Subsampling• reduces data size by selecting a subset of

the original data

• VTK - vtkExtractGrid


Code – ClippingCode – Clipping


Editor: clipping.tclvtkStructuredGridReader reader


reader Update

vtkPlane plane

eval plane SetOrigin [[reader GetOutput] GetCenter]

plane SetNormal -0.287 0 0.9579

vtkClipDataSet clip

clip SetInputConnection [reader GetOutputPort]

clip SetClipFunction plane

clip InsideOutOn

vtkDataSetMapper clipMapper

clipMapper SetInputConnection [clip GetOutputPort]

eval clipMapper SetScalarRange [[reader GetOutput] GetScalarRange]

vtkActor clipActor

clipActor SetMapper clipMapper

Code – Cutplane/SlicingCode – Cutplane/Slicing


Editor: cutplane.tclvtkStructuredGridReader reader


reader Update

vtkPlane plane

eval plane SetOrigin [[reader GetOutput] GetCenter]

plane SetNormal -0.287 0 0.9579

vtkCutter planeCut

planeCut SetInputConnection

[reader GetOutputPort] planeCut SetCutFunction plane

vtkPolyDataMapper cutMapper

cutMapper SetInputConnection [planeCut GetOutputPort]

eval cutMapper SetScalarRange [[reader GetOutput] GetScalarRange]

vtkActor cutActor

cutActor SetMapper cutMapper

AnnotationAnnotation

Annotation– used for annotating visualization

– VTK• vtkScalarBarActor

• vtkTextMapper

• vtkScaledTextActor


Code – colorBarCode – colorBar


Editor: colorBar.tclvtkStructuredGridReader reader


reader Update

vtkScalarBarActor scalarBar

scalarBar SetLookupTable lut

scalarBar SetTitle "Combustor Density Magnitude"

scalarBar SetNumberOfLabels 2

[scalarBar GetPositionCoordinate] SetValue 0.1 0.01

scalarBar SetOrientationToHorizontal

scalarBar SetWidth 0.8

scalarBar SetHeight 0.09

vtkRenderer ren1





ren1 AddActor streamTubeActor

ren1 AddActor outlineActor

ren1 AddActor scalarBar


VTK - WritersVTK - Writers Polygonal Data Writers

– vtkBYUWriter - write MOVIE.BYU files

– vtkCGMWriter - write 2D polygonal data as a CGM file

– vtkIVWriter - write Inventor files

– vtkMCubesWriter - write triangles in marching cubes format

– vtkPolyDataWriter - write VTK polygonal data files

– vtkPLYWriter - write Standford University PLY polygonal data files

– vtkSTLWriter - write stereo-lithography files

Image and Volume writers– vtkBMPwriter - write PC bitmap files

– vtkJPEGwriter - write images in JPEG format

– vtkPostscriptWriter – write image files in Postscript format

– vtkPNMwriter - write PNM (ppm, pgm, pbm) image files

– vtkPNGwriter - write image file in Portable Network Graphic format

– vtkTIFFWriter – write image files in TIFF format

– vtkStructuredPointsWriter – write a vtkStructuredPoints file


Saving ImagesSaving Images

Saving Images– common formats:

• jpeg (lossy)

• png (lossless)

• postscript

• tiff (lossless)

– VTK•vtkWindowToImageFilter

•vtkRenderLargeImage


Code – Saving ImagesCode – Saving Images


Editor: output.tclrenWin Render

vtkWindowToImageFilter w2if

w2if SetInput renWin

w2if Update

vtkRenderLargeImage renderLarge

renderLarge SetInput ren1

renderLarge SetMagnification 4

#vtkJPEGWriter writer

# writer SetInputConnection [w2if GetOutputPort]

# writer SetFileName "image.jpg"

# writer SetQuality 100

# writer Write

#vtkPNGWriter writer


# writer SetFileName "image.png"

# writer Write

#vtkPostScriptWriter writer


# writer SetFileName "image.ps"

# writer Write

#vtkTIFFWriter writer


# writer SetFileName "image.tif"

# writer Write

vtkTIFFWriter writer

writer SetInputConnection [renderLarge GetOutputPort]

writer SetFileName "largeimage.tif"

writer Write

VTK - ResourcesVTK - Resources


IS&T tutorials– Using VTK to Visualize Scientific Data

http://scv.bu.edu/documentation/tutorials/VTK/

– VTK Examples http://scv.bu.edu/documentation/software-help/scivis/vtk_examples/index.html

Texts– The Visualization Toolkit, 4th Edition, Kitware, Inc, 2006.

– The VTK User’s Guide, 5th Edition, Kitware, Inc, 2006.

Websites– www.vtk.org

– www.kitware.com

– www.vtk.org/doc/release/5.4/html/classes.html

Wiki– www.vtk.org/Wiki/VTK

Mailing Lists– www.vtk.org/VTK/help/mailing.html

SourcesSources

The Visualization Toolkit, 3rd Edition, Will Schroeder, Pearson Education, Inc, 2002.

The VTK User’s Guide, 4.2 Edition, Kitware, 2003.

Kitware: www.vtk.org


scientific visualization using vtk ray gasser [email protected] is&t scientific visualization tutorial...

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