scientific visualization using vtk
DESCRIPTION
Scientific Visualization Using VTK. Robert Putnam [email protected]. Scientific Visualization Using VTK – Fall 2011. Outline. Introduction VTK overview VTK data geometry/topology Case study Interactive session. Scientific Visualization Using VTK – Fall 2011. Introduction. - PowerPoint PPT PresentationTRANSCRIPT
Scientific Visualization Using VTKScientific Visualization Using VTK
Robert Putnam
Scientific Visualization Using VTK – Fall 2011
OutlineOutline
• Introduction• VTK overview• VTK data geometry/topology• Case study• Interactive session
Scientific Visualization Using VTK – Fall 2011
IntroductionIntroduction
Scientific Visualization Using VTK – Fall 2011
*Adapted from The ParaView Tutorial, Moreland
• Visualization: converting raw data to a form that is viewable and understandable to humans.
• Scientific visualization: specifically concerned with data that has a well-defined representation in 2D or 3D space (e.g., from simulation mesh or scanner).
VTKVTK
Visualization Toolkit– Inception at GE in 1993; since 1998 spun off to “Kitware”, supported by
Sandia Labs.
– Open source
– Set of object-oriented class libraries for visualization and data analysis
– Several language interfaces• C++
• Tcl
• Java
• Python
– Portable (MS Windows, Linux, OSX)
– Active developer community
– Good documentation available, free and otherwise
– Professional support services available from Kitware
Scientific Visualization Using VTK – Fall 2011
Generic visualization pipelineGeneric visualization pipeline
Scientific Visualization Using VTK – Fall 2011
Source(s) Filters(s) Output - - - - - - - - - - - - - - - - - - - - -
data/geometry/topology graphics
VTK terminology/modelVTK terminology/model
Scientific Visualization Using VTK – Fall 2011
Source Filter Renderer
- - - - - - - - - - - - - - - - - - - - -
data/geometry/topology graphics
Mapper
VTK terminology/modelVTK terminology/model
Scientific Visualization Using VTK – Fall 2011
Source/ Reader
Filter Renderer
- - - - - - - - - - - - - - - - - - - - -
data/geometry/topology graphics
Mapper
“Scene"
Lights, Camera
DataObject ProcessObject
Actor
RenderWindow
vtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("density.vtk");
reader->Update();
vtkContourFilter *iso = vtkContourFilter::New();
iso->SetInputConnection(reader->GetOutputPort());
iso->SetValue(0,0.26);
vtkPolyDataMapper *isoMapper = vtkPolyDataMapper::New();
isoMapper->SetInputConnection(iso->GetOutputPort());
vtkActor *isoActor = vtkActor::New();
isoActor->SetMapper(isoMapper);
vtkRenderer *ren1 = vtkRenderer::New();
ren1->AddActor(isoActor);
vtkRenderWindow *renWin = vtkRenderWindow::New();
renWin->SetSize(500,500);
renWin->AddRenderer(ren1);
Pipeline -> Sample CodePipeline -> Sample Code
Scientific Visualization Using VTK – Fall 2011
Reader
Filter
Mapper
Actor
Renderer
RenderWindow
C++ v. TclC++ v. Tcl
• C++
• Tcl
Scientific Visualization Using VTK – Fall 2011
vtkStructuredGridReader reader
reader SetFileName "density.vtk"
reader Update
vtkContourFilter iso
iso SetInputConnection [reader GetOutputPort]
iso SetValue 0 .26
vtkStructuredGridReader *reader = vtkStructuredGridReader::New();reader->SetFileName("density.vtk");reader->Update();
vtkContourFilter *iso = vtkCountourFilter::New();iso->SetInputConnection(reader->GetOutputPort());iso->SetValue(0, .26);
Coding tip of the day!Coding tip of the day!
• Google “VTK class list”, or• Go to:
http://www.vtk.org/doc/nightly/html/annotated.html
Scientific Visualization Using VTK – Fall 2011
VTK – Geometry v. TopologyVTK – Geometry v. Topology
Geometry of a dataset ~= points
Scientific Visualization Using VTK – Fall 2011
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
Topology ~= connections among points, which define cells
So, what’s the topology here?
VTK – Geometry v. TopologyVTK – Geometry v. Topology
Scientific Visualization Using VTK – Fall 2011
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
VTK – Geometry v. TopologyVTK – Geometry v. Topology
Scientific Visualization Using VTK – Fall 2011
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
or
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
VTK – Geometry v. TopologyVTK – Geometry v. Topology
Scientific Visualization Using VTK – Fall 2011
or
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
or
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
VTK – Geometry v. TopologyVTK – Geometry v. Topology
Scientific Visualization Using VTK – Fall 2011
or
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
or
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
or
0,1 1,1 2,1 3,1
0,0 1,0 2,0 3,0
Geometry/Topology StructureGeometry/Topology Structure
Geometry/topology 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
Scientific Visualization Using VTK – Fall 2011
Characteristics of DataCharacteristics of Data
Data is organized into datasets for visualization– Datasets consist of two pieces
• organizing structure– points (geometry)
– cells (topology)
• data attributes associated with the structure
– File format derived from organizing structure
Scientific Visualization Using VTK – Fall 2011
Data is discrete– Interpolation functions generate data values in between known points
Examples of Dataset TypesExamples of Dataset Types
Structured Points (Image Data)– 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 (Curvilinear)– regular topology and irregular geometry
– applications: fluid flow, heat transfer
Scientific Visualization Using VTK – Fall 2011
Examples of Dataset Types (cont)Examples of Dataset Types (cont)
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
Scientific Visualization Using VTK – Fall 2011
Examples of Cell TypesExamples of Cell Types
Scientific Visualization Using VTK – Fall 2011
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 • 3x3 only
• examples: stress, strain
Scientific Visualization Using VTK – Fall 2011
File Format – Structured PointsFile Format – Structured Points
Scientific Visualization Using VTK – Fall 2011
Editor structured-points.vtk:
# vtk DataFile Version 3.0
first dataset
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 3 4 5
ORIGIN 0 0 0
SPACING 1 1 2
POINT_DATA 60
SCALARS temp-point float
LOOKUP_TABLE default
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
File Format – Structured PointsFile Format – Structured Points
Scientific Visualization Using VTK – Fall 2011
Editor structured-points.vtk:
# vtk DataFile Version 3.0
first dataset
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 3 4 5
ORIGIN 0 0 0
SPACING 1 1 2
POINT_DATA 60
SCALARS temp-point float
LOOKUP_TABLE default
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
0 0 0 1 1 1 1 1 1 0 0 0
File Format – Structured PointsFile Format – Structured Points
Scientific Visualization Using VTK – Fall 2011
Editor structured-points2.vtk:
# vtk DataFile Version 3.0
first dataset
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 3 4 5
ORIGIN 0 0 0
SPACING 1 1 2
CELL_DATA 24
SCALARS temp-cell float
LOOKUP_TABLE default
0 0 1 1 0 0
0 0 1 1 0 0
0 0 1 1 0 0
0 0 1 1 0 0
File Format – Structured PointsFile Format – Structured Points
Scientific Visualization Using VTK – Fall 2011
Editor structured-points2.vtk:
# vtk DataFile Version 3.0
first dataset
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 3 4 5
ORIGIN 0 0 0
SPACING 1 1 2
CELL_DATA 24
SCALARS temp-cell float
LOOKUP_TABLE default
0 0 1 1 0 0
0 0 1 1 0 0
0 0 1 1 0 0
0 0 1 1 0 0
Structured Points – C++ codeStructured Points – C++ code
Scientific Visualization Using VTK – Fall 2011
Editor structured-points.cxx:vtkStructuredPointsReader *reader = vtkStructuredPointsReader::New();
reader->SetFileName("structured-points.vtk");
reader->Update();
vtkLookupTable *lut = vtkLookupTable::New();
lut->SetNumberOfColors(2);
lut->SetTableValue(0, 0.0, 0.0, 1.0, 1);
lut->SetTableValue(1, 1.0, 0.0, 0.0, 1);
vtkDataSetMapper *mapper = vtkDataSetMapper::New();
mapper->SetInputConnection(reader->GetOutputPort());
mapper->SetLookupTable(lut);
vtkActor *actor = vtkActor::New();
actor->SetMapper(mapper);
actor->GetProperty()->EdgeVisibilityOn();
actor->GetProperty()->SetLineWidth(2);
Structured Points – C++ code (cont.)Structured Points – C++ code (cont.)
Scientific Visualization Using VTK – Fall 2011
Editor structured-points.cxx:vtkRenderer *ren1 = vtkRenderer::New();
ren1->AddActor(actor);
ren1->SetBackground(0.5,0.5,0.5);
vtkRenderWindow *renWin = vtkRenderWindow::New();
renWin->AddRenderer(ren1);
renWin->SetSize(500,500);
vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
iren->SetRenderWindow(renWin);
iren->Initialize();
iren->Start();
Work flow – Case StudyWork flow – Case Study
BU Space Physics simulation Meteor trails in the ionosphere Data wrangling:
Consolidate datafiles (from parallel code), create single binary datafile
Add VTK header:
Scientific Visualization Using VTK – Fall 2011
# vtk DataFile Version 3.0output of reassemble.cBINARYDATASET STRUCTURED_POINTSORIGIN 0.0 0.0 0.0SPACING 1.0 1.0 1.0DIMENSIONS 512 64 128POINT_DATA 4194304SCALARS plasma floatLOOKUP_TABLE default
Work flow – Case StudyWork flow – Case Study
Use Tcl for fast development/testing:
Scientific Visualization Using VTK – Fall 2011
vtkStructuredPointsReader reader reader SetFileName "opp.vtk" reader Update
vtkContourFilter iso iso SetInputConnection [reader GetOutputPort] iso SetValue 0 0.1
. . .
Work flow – Case StudyWork flow – Case Study
Add gaussian filter :
Scientific Visualization Using VTK – Fall 2011
vtkImageGaussianSmooth gaussian gaussian SetInputConnection [reader GetOutputPort] gaussian SetDimensionality 3 gaussian SetRadiusFactor 1 vtkContourFilter iso iso SetInputConnection [gaussian GetOutputPort] iso SetValue 0 0.1
. . .
Work flow – Case StudyWork flow – Case Study
Add more isosurfaces :
Scientific Visualization Using VTK – Fall 2011
vtkContourFilter iso iso SetInputConnection [gaussian GetOutputPort] iso SetValue 0 1.0 iso SetValue 1 0.5 iso SetValue 2 0.1
Work flow – Case StudyWork flow – Case Study
Port to C++, add cutplane, transparency :
Scientific Visualization Using VTK – Fall 2011
vtkPlane *plane = vtkPlane::New(); plane->SetOrigin(256,2,63.5); plane->SetNormal(0,1,0);
vtkCutter *planeCut = vtkCutter::New(); planeCut->SetInputConnection(reader>GetOutputPort()); planeCut->SetCutFunction(plane);
vtkActor *isoActor = vtkActor::New(); isoActor->SetMapper(isoMapper); isoActor->GetProperty()->SetOpacity(iv_opacity);
Work flow – Case StudyWork flow – Case Study
Change color map, use script to loop over *.vtk, generate multiple jpegs, read into Adobe Premiere, produce animation:
Scientific Visualization Using VTK – Fall 2011
VTK – Getting Started - UIVTK – Getting Started - UI
Scientific Visualization Using VTK – Fall 2011
Unix Shell:
katana:% cone2
Keyboard shortcutsKeyboard shortcuts
Scientific Visualization Using VTK – Fall 2011
j – joystick (continuous) modet – trackball mode
c –camera move modea –actor move mode
left mouse – rotate x,yctrl - left mouse – rotate zmiddle mouse –panright mouse –zoom
r –reset cameras/w –surface/wireframee (or q) –exit
Code – simple.cxxCode – simple.cxx
Scientific Visualization Using VTK – Fall 2011
Editor: simple.cxx
#include <stdio.h>
#include <stdlib.h>
#include "vtk-include.h"
int main(int argc, char *argv[]) {
vtkRenderer *ren1 = vtkRenderer::New();
ren1->SetBackground(0.0,0.0,0.0);
vtkRenderWindow *renWin = vtkRenderWindow::New();
renWin->SetSize(500,500);
renWin->AddRenderer(ren1);
renWin->Render();
sleep(2);
}
ExerciseExercise
Scientific Visualization Using VTK – Fall 2011
Editor: simple2.cxx
Change background color to gray (or fuchsia, etc.)
Code – ExerciseCode – Exercise
Scientific Visualization Using VTK – Fall 2011
Editor: simple2.cxx
int main(int argc, char *argv[]) {
vtkRenderer *ren1 = vtkRenderer::New();
ren1->SetBackground(0.5,0.5,0.5);
vtkRenderWindow *renWin = vtkRenderWindow::New();
renWin->SetSize(500,500);
renWin->AddRenderer(ren1);
renWin->Render();
sleep(2);
}
Code – cone2.cxxCode – cone2.cxx
Scientific Visualization Using VTK – Fall 2011
Editor cone2.cxx:vtkConeSource *cone = vtkConeSource::New();
cone->SetResolution(100);
vtkPolyDataMapper *coneMapper = vtkPolyDataMapper::New();
coneMapper->SetInputConnection(cone->GetOutputPort());
vtkActor *coneActor = vtkActor::New();
coneActor->SetMapper(coneMapper);
coneActor->GetProperty()->SetColor(1.0, 0.0, 0.0);
vtkRenderer *ren1 = vtkRenderer::New();
ren1->SetBackground(0.0,0.0,0.0);
ren1->AddActor(coneActor);
vtkRenderWindow *renWin = vtkRenderWindow::New();
renWin->SetSize(500,500);
renWin->AddRenderer(ren1);
vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
iren->SetRenderWindow(renWin);
iren->Initialize();
iren->Start();
ExerciseExercise
Scientific Visualization Using VTK – Fall 2011
Editor: cone3.cxx
Add coneActor2, and color it green. (Copy
coneActor, and make appropriate changes.
Remember to add the new actor to the render
window [near the end of the “pipeline”].)
Optional: to rotate, scale and set the position away
from the origin, use the following:
coneActor2->RotateZ(90);
coneActor2->SetScale(0.5,0.5,0.5);
coneActor2->SetPosition(-1.0,0.0,0.0);
Otherwise, use ‘a’ to use mouse to separate the
green and red cones.
Code – ExerciseCode – Exercise
Scientific Visualization Using VTK – Fall 2011
Editor: cone3.cxx
. . .
vtkActor *coneActor2 = vtkActor::New();
coneActor2->SetMapper(coneMapper);
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(coneActor);
ren1->AddActor(coneActor2);
. . .
VTK - ReadersVTK - Readers Image and Volume Readers
– 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– vtkStructuredGridReader - read VTK structured grid data files
– vtkPLOT3DReader - read structured grid PLOT3D files
Rectilinear Grid Readers– vtkRectilinearGridReader - read VTK rectilinear grid data files
Unstructured Grid Readers– vtkUnstructuredGridReader - read VTK unstructured grid data files
Scientific Visualization Using VTK – Fall 2011
VTK - ReadersVTK - Readers Polygonal Data Readers
– vtkPolyDataReader - read VTK polygonal data files
– vtkBYUReader - read MOVIE.BYU files
– vtkMCubesReader - read binary marching cubes files
– vtkOBJReader - read Wavefront (Maya) .obj files
– vtkPLYReader - read Stanford University PLY polygonal data files
– vtkSTLReader - read stereo-lithography files
– vtkUGFacetReader - read EDS Unigraphic facet files
Image and Volume Readers (add’l)– 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
Scientific Visualization Using VTK – Fall 2011
File Format – Structured GridFile Format – Structured Grid
Scientific Visualization Using VTK – Fall 2011
Editor density.vtk:# vtk DataFile Version 3.0
vtk sample data
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
0.639897 0.239841 0.252319 0.255393 0.252118 0.246661 0.240134 0.234116 0.229199
0.225886 0.224268 0.224647 0.231496 0.246895 0.26417 0.27585 0.278987 0.274621
. . .
VECTORS Momentum float
0 0 0 13.753 -5.32483 -19.964 42.3106 -15.57 -43.0034
64.2447 -13.3958 -46.2281 73.7861 -4.83205 -36.3829 88.3374 6.23797 -22.8846
. . .
Clipping, Cutting, SubsamplingClipping, Cutting, Subsampling
Selection 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
Scientific Visualization Using VTK – Fall 2011
Code – ClippingCode – Clipping
Scientific Visualization Using VTK – Fall 2011
Editor: clipping.cxxvtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("density.vtk");
reader->Update();
vtkPlane *plane = vtkPlane::New();
plane->SetOrigin(reader->GetOutput()->GetCenter());
plane->SetNormal(-0.287, 0, 0.9579);
vtkClipDataSet *clip = vtkClipDataSet::New();
clip->SetInputConnection(reader->GetOutputPort());
clip->SetClipFunction(plane);
clip->InsideOutOn();
vtkDataSetMapper *clipMapper = vtkDataSetMapper::New();
clipMapper->SetInputConnection(clip->GetOutputPort());
clipMapper->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *clipActor = vtkActor::New();
clipActor->SetMapper(clipMapper);
Code – Cutplane/SlicingCode – Cutplane/Slicing
Scientific Visualization Using VTK – Fall 2011
Editor: cutplane.cxxvtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("density.vtk");
reader->Update();
vtkPlane *plane = vtkPlane::New();
plane->SetOrigin(reader->GetOutput()->GetCenter());
plane->SetNormal(-0.287, 0, 0.9579);
vtkCutter *planeCut = vtkCutter::New();
planeCut->SetInputConnection(reader->GetOutputPort());
planeCut->SetCutFunction(plane);
vtkPolyDataMapper *cutMapper = vtkPolyDataMapper::New();
cutMapper->SetInputConnection(planeCut->GetOutputPort());
cutMapper->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *cutActor = vtkActor::New();
cutActor->SetMapper(cutMapper);*To see the cutplane with a colorbar guide, try ‘cutplane-with-colorbar’.
Code – ExtractGridCode – ExtractGrid
Scientific Visualization Using VTK – Fall 2011
Editor: extract.cxxvtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("density.vtk");
reader->Update();
vtkExtractGrid *extract = vtkExtractGrid::New();
extract->SetInputConnection(reader->GetOutputPort());
extract->SetVOI(-1000,1000,-1000,1000,7,10);
vtkDataSetMapper *extractMapper = vtkDataSetMapper::New();
extractMapper->SetInputConnection(extract->GetOutputPort());
extractMapper->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *extractActor = vtkActor::New();
extractActor->SetMapper(extractMapper);
*Optional: enable EdgeVisibility inExtractActor.
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
– VTK • vtkLookupTable
• vtkDataSetMapper
Scientific Visualization Using VTK – Fall 2011
Code – Color MappingCode – Color Mapping
Scientific Visualization Using VTK – Fall 2011
Editor: colormap.numcolors.cxx
. . .
vtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("subset.vtk");
reader->Update();
vtkLookupTable *lut = vtkLookupTable::New();
lut->SetNumberOfColors(16);
lut->SetHueRange(0.0, 0.667);
vtkDataSetMapper *mapper = vtkDataSetMapper::New();
mapper->SetInputConnection(reader->GetOutputPort());
mapper->SetLookupTable(lut);
mapper->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *actor = vtkActor::New();
actor->SetMapper(mapper);
ExerciseExercise
Scientific Visualization Using VTK – Fall 2011
* Change the number of colors in colormap
* Reverse the Hue Range
* Change the Scalar Range [or see what happens if you don’t set it]
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
Scientific Visualization Using VTK – Fall 2011
Code – Contour (isoline)Code – Contour (isoline)
Scientific Visualization Using VTK – Fall 2011
Editor: contour.single.cxx
. . .
vtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("subset.vtk");
reader->Update();
vtkContourFilter *iso = vtkContourFilter::New();
iso->SetInputConnection(reader->GetOutputPort());
iso->SetValue(0,0.26);
vtkPolyDataMapper *isoMapper = vtkPolyDataMapper::New();
isoMapper->SetInputConnection(iso->GetOutputPort());
isoMapper->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *isoActor = vtkActor::New();
isoActor->SetMapper(isoMapper);
. . .
Code – Contour (isosurface)Code – Contour (isosurface)
Scientific Visualization Using VTK – Fall 2011
Editor: isosurface.cxx
. . .
vtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName(“density.vtk");
reader->Update();
vtkContourFilter *iso = vtkContourFilter::New();
iso->SetInputConnection(reader->GetOutputPort());
iso->SetValue(0,0.26);
vtkPolyDataMapper *isoMapper = vtkPolyDataMapper::New();
isoMapper->SetInputConnection(iso->GetOutputPort());
isoMapper->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *isoActor = vtkActor::New();
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
Scientific Visualization Using VTK – Fall 2011
Code – Scalar GenerationCode – Scalar Generation
Scientific Visualization Using VTK – Fall 2011
Editor: hawaii.color.cxxvtkPolyDataReader *hawaii = vtkPolyDataReader::New();
hawaii->SetFileName("honolulu.vtk");
hawaii->Update();
hawaii->GetOutput()->GetBounds(bounds);
vtkElevationFilter *elevation = vtkElevationFilter::New();
elevation->SetInputConnection(hawaii->GetOutputPort());
elevation->SetLowPoint(0,0,bounds[4]);
elevation->SetHighPoint(0,0,bounds[5]);
vtkLookupTable *lut = vtkLookupTable::New();
lut->SetHueRange(0.7,0);
vtkDataSetMapper *hawaiiMapper = vtkDataSetMapper::New();
hawaiiMapper->SetInputConnection(elevation->GetOutputPort());
hawaiiMapper->SetLookupTable(lut);
vtkActor *hawaiiActor = vtkActor::New();
hawaiiActor->SetMapper(hawaiiMapper);
Scalar generation – Color MapScalar generation – Color Map
Scientific Visualization Using VTK – Fall 2011
Editor: hawaii.color2.cxxvtkLookupTable *lut = vtkLookupTable::New();
lut->SetNumberOfColors(9);
lut->SetTableValue(0, 0.0, 0.40, 0.8, 1);
lut->SetTableValue(1, 0.0, 0.75, 0.2, 1);
lut->SetTableValue(2, 0.25, 0.625, 0.5, 1);
lut->SetTableValue(3, 0.0, 0.5, 0.25, 1);
lut->SetTableValue(4, 0.5, 0.365, 0.0, 1);
lut->SetTableValue(5, 0.75, 0.625, 0.25, 1);
lut->SetTableValue(6, 1.0, 0.75, 0.625, 1);
lut->SetTableValue(7, 1.0, 0.75, 0.5, 1);
lut->SetTableValue(8, 1.0, 1, 1, 1);
HedgehogsHedgehogs
Vector Algorithms– Hedgehogs
• oriented scaled line for each vector
• scale indicates magnitude
• color indicates magnitude, pressure, temperature, or any variable
– VTK• vtkHedgeHog
Scientific Visualization Using VTK – Fall 2011
Code – HedgeHogsCode – HedgeHogs
Scientific Visualization Using VTK – Fall 2011
Editor: hedgehog.cxxvtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("density.vtk");
reader->Update();
vtkHedgeHog *hhog = vtkHedgeHog::New();
hhog->SetInputConnection(reader->GetOutputPort());
hhog->SetScaleFactor(0.001);
vtkPolyDataMapper *hhogMapper = vtkPolyDataMapper::New();
hhogMapper->SetInputConnection(hhog->GetOutputPort());
hhogMapper->SetLookupTable(lut);
hhogMapper->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *hhogActor = vtkActor::New();
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
Scientific Visualization Using VTK – Fall 2011
Code – Oriented GlyphsCode – Oriented Glyphs
Scientific Visualization Using VTK – Fall 2011
Editor: glyph.cxxvtkArrowSource *arrow = vtkArrowSource::New();
arrow->SetTipResolution(6);
arrow->SetTipRadius(0.1);
arrow->SetTipLength(0.35);
arrow->SetShaftResolution(6);
arrow->SetShaftRadius(0.03);
vtkGlyph3D *glyph = vtkGlyph3D::New();
glyph->SetInputConnection(extract->GetOutputPort());
glyph->SetSource(arrow->GetOutput());
glyph->SetVectorModeToUseVector();
glyph->SetColorModeToColorByScalar();
glyph->SetScaleModeToDataScalingOff();
glyph->OrientOn();
glyph->SetScaleFactor(0.25);
vtkPolyDataMapper *glyphMapper = vtkPolyDataMapper::New();
glyphMapper->SetInputConnection(glyph->GetOutputPort());
glyphMapper->SetLookupTable(lut);
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
Scientific Visualization Using VTK – Fall 2011
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
Scientific Visualization Using VTK – Fall 2011
Code – StreamlinesCode – Streamlines
Scientific Visualization Using VTK – Fall 2011
Editor: streamLines.cxxvtkPointSource *seeds = vtkPointSource::New();
seeds->SetRadius(3.0);
seeds->SetCenter(reader->GetOutput()->GetCenter());
seeds->SetNumberOfPoints(100);
vtkRungeKutta4 *integ = vtkRungeKutta4::New();
vtkStreamTracer *streamer = vtkStreamTracer::New();
streamer->SetInputConnection(reader->GetOutputPort());
streamer->SetSourceConnection(seeds->GetOutputPort());
streamer->SetMaximumPropagation(100);
streamer->SetIntegrationDirectionToBoth();
streamer->SetIntegrator(integ);
vtkPolyDataMapper *mapStreamLines = vtkPolyDataMapper::New();
mapStreamLines->SetInputConnection(streamer->GetOutputPort());
mapStreamLines->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *streamLineActor = vtkActor::New();
streamLineActor->SetMapper(mapStreamLines);
Code – StreamtubesCode – Streamtubes
Scientific Visualization Using VTK – Fall 2011
Editor: streamTubes.varyRadius.cxxvtkPointSource *seeds = vtkPointSource::New();
seeds->SetRadius(1.0);
seeds->SetCenter(1.5, 0.01, 27);
seeds->SetNumberOfPoints(50);
vtkRungeKutta4 *integ = vtkRungeKutta4::New();
vtkStreamTracer *streamer = vtkStreamTracer::New();
streamer->SetInputConnection(reader->GetOutputPort());
streamer->SetSourceConnection(seeds->GetOutputPort());
…
vtkTubeFilter *streamTube = vtkTubeFilter::New();
streamTube->SetInputConnection(streamer->GetOutputPort());
streamTube->SetRadius(0.01);
streamTube->SetNumberOfSides(6);
streamTube->SetVaryRadiusToVaryRadiusByScalar();
vtkPolyDataMapper *mapStreamTube = vtkPolyDataMapper::New();
mapStreamTube->SetInputConnection(streamTube->GetOutputPort());
mapStreamTube->SetScalarRange(reader->GetOutput()->GetScalarRange());
vtkActor *streamTubeActor = vtkActor::New();
streamTubeActor->SetMapper(mapStreamTube);
AnnotationAnnotation
Annotation– used for annotating visualization
– VTK• vtkScalarBarActor
• vtkTextMapper
• vtkScaledTextActor
Scientific Visualization Using VTK – Fall 2011
Code – colorBarCode – colorBar
Scientific Visualization Using VTK – Fall 2011
Editor: colorBar.cxxvtkStructuredGridReader *reader = vtkStructuredGridReader::New();
reader->SetFileName("density.vtk");
reader->Update();
vtkScalarBarActor *scalarBar = vtkScalarBarActor::New();
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 = vtkRenderer::New();
ren1->SetBackground(0.5,0.5,0.5);
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
Scientific Visualization Using VTK – Fall 2011
Saving ImagesSaving Images
Saving Images– common formats:
• jpeg (lossy)
• png (lossless)
• postscript
• tiff (lossless)
– VTK•vtkWindowToImageFilter
•vtkRenderLargeImage
Scientific Visualization Using VTK – Fall 2011
Code – Saving ImagesCode – Saving Images
Scientific Visualization Using VTK – Fall 2011
Editor: output.cxxvtkRenderer *ren1 = vtkRenderer::New();
ren1->AddActor(streamTubeActor);
ren1->ResetCamera();
ren1->GetActiveCamera()->Dolly(1.25);
ren1->ResetCameraClippingRange();
vtkRenderWindow *renWin = vtkRenderWindow::New();
renWin->PointSmoothingOn();
renWin->LineSmoothingOn();
renWin->PolygonSmoothingOn();
renWin->AddRenderer(ren1);
renWin->SetSize(500,500);
renWin->Render();
vtkWindowToImageFilter *w2if = vtkWindowToImageFilter::New();
w2if->SetInput(renWin);
vtkTIFFWriter *writer = vtkTIFFWriter::New();
writer->SetInputConnection(w2if->GetOutputPort());
writer->SetFileName("image.tif");
writer->Write();
vtkRenderLargeImage *renderLarge = vtkRenderLargeImage::New();
renderLarge->SetInput(ren1);
renderLarge->SetMagnification(4);
vtkTIFFWriter *lwriter = vtkTIFFWriter::New();
lwriter->SetInputConnection(renderLarge->GetOutputPort());
lwriter->SetFileName("./largeimage.tif");
lwriter->Write();
VTK - ResourcesVTK - Resources
Scientific Visualization Using VTK – Fall 2011
IS&T tutorials– Scientific Visualization Using VTK
www.bu.edu/tech/research/training/tutorials/vtk/
– VTK Examples
www.bu.edu/tech/research/training/scv-software-packages/vtk/vtk_examples/
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
Questions?Questions?
Tutorial survey:
- http://scv.bu.edu/survey/tutorial_evaluation.html
Scientific Visualization Using VTK – Fall 2011