1. Scientific Visualization Using ParaView – Fall 2014
Robert Putnam
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2. Scientific Visualization Using ParaView – Fall 2014
Outline
Introduction
ParaView overview
ParaView/VTK data geometry/topology
Case study
Interactive session
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3. Scientific Visualization Using ParaView – Fall 2014
Introduction
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).
*Adapted from The ParaView Tutorial, Moreland
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4. Scientific Visualization Using ParaView – Fall 2014
Introduction
ParaView – open-source application designed for visualizing two- and three-dimensional data sets.
Begun in 2000 as a collaboration between Kitware, Inc. and LANL (funded by DOE)
Built on VTK (“Visualization Tool Kit”)
Graphics user interface
Python scripting
Architecture extensible by plugins
Available for MS Windows, OSX, Linux
Support for large dataset / distributed architecture (client/server model)
Online and printed documentation from Kitware
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5. Scientific Visualization Using ParaView – Fall 2014
Generic visualization pipeline
Source(s)
Filters(s)
Output (Rendering)
data/geometry/topology
graphics
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Slice display
heat.vtk
(3D dataset)
Slice
(2D)
Display
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Paraview user interface
Menu bar
Toolbars
Pipeline Browser
Object Inspector
3D View
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Combined filters to file
heat.vtk
(3D dataset)
Slice Filter
heat2.jpg
Stream Tracer
Tube Filter
Glyph Filter
scalar data
Vectordata
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Combined filters to file
heat.vtk
Slice
Stream
Tube
Glyph
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ParaView – Pipeline Browser
Pipeline Browser
located in the upper left corner of the user interface
allows you to build a visualization pipeline
allows you to interact with the current visualization pipeline
top of the pipeline browser is the name of the server to which ParaView is connected
below the server name is a tree structure representing each of the reader, source, and filter objects that are in the visualization pipeline.
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11. Scientific Visualization Using ParaView – Fall 2014
ParaView - Object Inspector
Object Inspector
located beneath the Pipeline Browser in the user interface
contains controls and information for the reader, source, or filter object selected in the Pipeline Browser
allows you to interact with the current visualization pipeline
content changes based upon the specific object selected
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Object Inspector - Properties
Object Inspector Tabs
There are three tabs in the Object Inspector:
Properties
Display
Information
The Properties Tab contains controls for specifying various parameters of the object selected in the Pipeline Browser.
Here is an example of what is shown in the Properties Tab for a Slice filter.
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Object Inspector - Display
Object Inspector Tabs
The Display Tab contains controls for setting the appearance of the object selected in the Pipeline Browser.
grouped into several sections: View, Color, Slice, Style, Edge Style, Annotation, Lighting, and Transformation.
Here is an example of what is shown in the Display Tab for a Slice filter.
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Object Inspector - Information
Object Inspector Tabs
The Information Tab contains statistical information about the output of the object selected in the Pipeline Browser.
Here is an example of what is shown in the Information Tab for a Slice filter.
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15. Scientific Visualization Using ParaView – Fall 2014
ParaView - Menus
File menu
handles various tasks such as opening data files, saving data files, loading state files, saving state files, saving screenshots, saving animations, and fileserver connections.
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ParaView - Menus
View menu
allows you to modify the camera and center of rotation for the 3D view. The view menu also allows you to toggle the visibility of the toolbars, inspectors, and views.
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ParaView - Menus
Filters menu
provides a list of available filters you can use to process data sets.
organized by recent, common, data analysis, temporal, and alphabetical.
The most commonly used filters, located under the Common subdirectory, are also located on the Common Filters Toolbar.
The filters are context sensitive and will only be available for selection if an appropriate data set has been loaded first and selected in the Pipeline Browser.
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ParaView - Menus
Help menu
provides information on the ParaView version, information on client server connections, and provides access to the online manual.
You can also visit the online version of the ParaView User’s Guide:
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ParaView - Help
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20. Scientific Visualization Using ParaView – Fall 2014
ParaView – Geometry v. Topology
Geometry of a dataset ~= points
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Topology ~= connections among points, which define cells
So, what’s the topology here?
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ParaView – Geometry v. Topology
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ParaView – Geometry v. Topology
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ParaView – Geometry v. Topology or
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ParaView – Geometry v. Topology or
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Geometry/Topology Structure
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
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Characteristics 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
Data is discrete
Interpolation functions generate data values in between known points
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Examples 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
examples: quadrilaterals, hexahedron
applications: fluid flow, heat transfer
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Examples of Dataset Types (cont)
Polygonal Data
irregular in both topology and geometry
examples: vertices, polyvertices, lines, polylines, polygons, triangle strips
Unstructured Grid
examples: any combination of cells
applications: finite element analysis, structural design, vibration
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Examples of Cell Types
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Data 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
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File Format – Structured Points
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
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File Format – Structured Points
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
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File Format – Structured Points
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
CELL_DATA 24
SCALARS temp-cell float
LOOKUP_TABLE default
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File Format – Structured Points
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
CELL_DATA 24
SCALARS temp-cell float
LOOKUP_TABLE default
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Work flow – Case Study
Student Fall project: visualize MRI lung imagery
10 slices of 256x256
MATLAB
Read in data
Noise removal, isolation of lung
Some visualization
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Work flow – Case Study
MATLAB -> VTK file
Write 256x256x10 float array to ASCII
file:
Add header , save with ‘.vtk’ extension:
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Work flow – Case Study
Read VTK file into Paraview, choose “Volume Visualization” display option, add Clip Filter:
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Work flow – Case Study
Change color map, use Paraview animation feature to move clipping plane through volume:
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Work flow – Case Study
Produce movie
Save animation from Paraview, which produces image files (jpegs).
Read image files into Adobe Premiere Pro
Save as movie (.mov, .wmv, .avi. , etc.)
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Starting out - create sphere
ParaView:
1. Choose Sources -> Sphere
2. Click Apply in Object Inspector
3. User Interface:
- Undo
- Color
- Lighting
- Camera Movement
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Example – Loading data
ParaView:
1. Disconnect from Server
File -> Disconnect
which clears the pipeline
2. Open data file
File -> Open (cylinder.vtk)
3. Click Apply in Object Inspector
4. In Toolbar area (or Object Inspector /
Display), color by Pres. Show Legend.
5. Try Multi-view option (above upper right-hand corner of 3D window).
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Clipping, Cutting, Subsampling
Selection Algorithms
- Clipping
can reveal internal details of surface
ParaView - Clip Filter
- Cutting/Slicing
cutting through a dataset with a surface
ParaView - Slice Filter
- Subsampling
reduces data size by selecting a subset of the original data
ParaView - ExtractSubset Filter
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File Format – Structured Grid
Editor density.vtk:
# vtk DataFile Version 3.0
vtk output
ASCII
DATASET STRUCTURED_GRID
DIMENSIONS
POINTS float
. . .
POINT_DATA 47025
SCALARS Density float
LOOKUP_TABLE default
VECTORS Momentum float
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Example – Clipping
ParaView:
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (density.vtk)
3. Apply Clip filter to density.vtk
Click on density.vtk in pipeline
Filter -> Clip
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Example – Cutting/Slicing
ParaView:
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (density.vtk)
3. Apply Slice filter to density.vtk
Click on density.vtk in pipeline
Filter -> Slice
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Example – Subsampling
ParaView:
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (density.vtk)
3. Apply Extract Subset filter to density.vtk
Click on density.vtk in pipeline
Filter -> Extract Subset
4. Apply Threshold filter to ExtractSubset
Click on ExtractSubset filter
Filter -> Threshold
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Color Mapping
Scalar Algorithms
Color Mapping
maps scalar data to colors
implemented by using scalar values as an index into a color lookup table
ParaView
Color panel in Display tab of Object Inspector
Color by
Edit Color Map
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Example – Color Mapping
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (subset.vtk)
3. Go to the the color section in the Display Tab in the Object Inspector
The "Color by" menu lists the names of the attribute arrays. Selecting an array name causes the dataset’s coloring to be based on the underlying scalar values in that array.
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Example – Color Mapping (cont)
ParaView:
1. The color map may be edited in the Color Scale Editor window which appears when you click the Edit Color Map button in the Color section of the Display Tab.
2. Another way to change the mapping of data values to colors is by setting the Data Range.
-- The default Data Range is set from the minimum data value in the data set to the maximum data value.
-- Click on the Rescale Range button to explicitly set these values. The values between the minimum and maximum are then linearly interpolated into the color table.
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Contouring
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
ParaView
Contour Filter
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Example – Isoline / 2D Contours
ParaView:
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (subset.vtk)
3. Apply Contour filter to subset.vtk
click on subset.vtk in pipeline
Filter -> Contour
4. To color the contour line based upon its
scalar value and the current color map,
make sure the Compute Scalars
checkbox in the Contour section of the
Properties tab is selected
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Example – Isosurface / 3D Contours
ParaView:
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (density.vtk)
3. Apply Contour filter to density.vtk
click on density.vtk in pipeline
Filter -> Contour
4. Optional: apply Clip filter to output of Contour filter
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Scalar Generation
Scalar Algorithms (cont)
Scalar Generation
extract scalars from part of data
example: extracting z coordinate (elevation) from terrain data to create scalar values
ParaView
Elevation Filter
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Example – Scalar Generation
ParaView:
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (honolulu.vtk)
3. Apply Elevation filter to density.vtk
Click on honolulu.vtk in pipeline
Filter -> Elevation
4. Import ‘elevation.xml’ in color map
editor.
5. Animate high point(2) to simulate
changing sea level (e.g., [rising:
] or [falling: )].
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Oriented Glyphs
Vector Algorithms
Oriented Glyphs
Orientation indicates direction
Length / color indicate magnitude, pressure, temperature, etc.
ParaView
Glyph Filter
Set type to arrow
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Example – Oriented Glyphs
ParaView:
1. Disconnect from Server
File -> Disconnect
2. Open data file
File -> Open (density.vtk)
3. Apply Glyph filter to density.vtk
click on density.vtk in pipeline
Filter -> Glyph
4. In the Object Inspector (Properties Tab)
set the “Scalars” menu to Density
set the “Vectors” menu to Momentum
set the “Glyph Type” to Arrow
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Field 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
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Field Lines
Streamlines
Lines show particle flow
ParaView - StreamTracer Filter
Streamlets
half way between streamlines and glyphs
ParaView - StreamTracer and Glyph Filters
Streamribbon
rake of two particles to create a ribbon
ParaView - StreamTracer and Ribbon Filters
Streamtube
circular rake of particles to create a tube
ParaView - StreamTracer and Tube Filters
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Stream Tracer Filter
StreamTracer Filter
generates streamlines in vector field from collection of seed points
first need to set up the integrator to do the numerical integration
next need to specify the seeds points
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Example – Streamlines
ParaView:
1. Open data file
File -> Open (density.vtk)
2. Apply StreamTracer filter to density.vtk
Click on density.vtk in pipeline
Filter -> Stream Tracer
3. In the Object Inspector (Properties Tab)
Set “Vectors” menu to Momentum
Set “Max Propagation” to Time 100
Set “Initial Step Length” to Cell Length 0.1
Set “Integration Direction” to Both
Set “Max Steps” to 1000
Set “Integrator Type” to Runge-Kutta 4
Set “Seed Type” to Point Source,
Center on Bounds
Set “Number of Points” to 100
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Annotation
Annotation
used for annotating visualizations
ParaView
Text Source
Source -> Text
Color Legend
“Edit Color Map” button in Display tab
“Show Color Legend” box in color legend tab of the Color Scale Editor
Axes
Edit -> View Settings
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Example – Annotation
ParaView:
1. Open data file
File -> Open (density.vtk)
2. Apply Clip filter to density.vtk
Click on density.vtk in pipeline
Filter -> Clip
3. Create a Text source
Sources -> Text
4. Turn on Color Legend
Edit Color Map for Clip in Display Tab
Color Legend tab in Color Scale Editor
Select “Show Color Legend” check box
5. Turn on orientation axis
Edit -> View Settings
Select “Orientation Axes” check box
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Saving Images
Saving Images
common formats:
jpg (lossy)
png (lossless)
pdf
tiff (lossless)
ParaView
File -> Save Screenshot
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Example – Saving Images
ParaView:
1. Open data file
File -> Open (density.vtk)
2. Apply Clip filter to density.vtk
click on density.vtk in pipeline
Filter -> Clip
3. Save Screenshot
File -> Save Screenshot
4. Set Resolution
5. Set File Type to JPG
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ParaView - Resources
Tutorials
Using ParaView to Visualize Scientific Data
scv.bu.edu/documentation/tutorials/ParaView/
ParaView Examples
scv.bu.edu/documentation/software-help/scivis/paraview_examples/index.html
-- “The Tutorial”
Texts
The ParaView Guide, v3 Edition, Kitware, Inc, 2006.
The Visualization Toolkit, 4th Edition, Will Schroeder, Ken Martin, Bill Lorensen, Kitware ,
Websites
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Questions?
Tutorial survey: -
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