Scientific Visualization Using ParaView
Robert Putnam
putnam@bu.edu
Scientific Visualization Using ParaView – Fall 2014
Outline
•
Introduction
• ParaView overview
• ParaView/VTK data geometry/topology
• Case study
• Interactive session
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
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
Scientific Visualization Using ParaView – Fall 2014
Generic visualization pipeline
Filters(s)
data/geometry/topology
Scientific Visualization Using ParaView – Fall 2014
---------------------
Source(s)
Output
(Rendering)
graphics
Slice display
heat.vtk
(3D dataset)
Slice
(2D)
Scientific Visualization Using ParaView – Fall 2014
Display
Paraview user interface
Menu bar
Toolbars
Pipeline Browser
Object Inspector
3D View
Scientific Visualization Using ParaView – Fall 2014
Combined filters to file
Slice Filter
heat2.jpg
heat.vtk
(3D dataset)
Stream
Tracer
Scientific Visualization Using ParaView – Fall 2014
Tube
Filter
Glyph
Filter
heat.vtk
Combined filters to file
Stream
Slice
Tube
Glyph
Scientific Visualization Using ParaView – Fall 2014
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.
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
Scientific Visualization Using ParaView – Fall 2014
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.
Scientific Visualization Using ParaView – Fall 2014
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.
Scientific Visualization Using ParaView – Fall 2014
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.
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.
Scientific Visualization Using ParaView – Fall 2014
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.
Scientific Visualization Using ParaView – Fall 2014
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.
Scientific Visualization Using ParaView – Fall 2014
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:
http://www.itk.org/Wiki/ParaView/Users_Guide/Table_Of_Contents
Scientific Visualization Using ParaView – Fall 2014
ParaView - Help
Scientific Visualization Using ParaView – Fall 2014
ParaView – Geometry v. Topology

Geometry of a dataset ~= points
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3

Topology ~= connections among points, which
define cells

So, what’s the topology here?
Scientific Visualization Using ParaView – Fall 2014
ParaView – Geometry v. Topology
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3
Scientific Visualization Using ParaView – Fall 2014
ParaView – Geometry v. Topology
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3
or
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3
Scientific Visualization Using ParaView – Fall 2014
ParaView – Geometry v. Topology
or
0,0
0,1
0,2
0,3
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3
1,0
1,1
1,2
1,3
or
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3
Scientific Visualization Using ParaView – Fall 2014
ParaView – Geometry v. Topology
or
0,0
0,1
0,2
0,3
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3
1,0
1,1
1,2
1,3
or
or
0,0
0,1
0,2
0,3
0,0
0,1
0,2
0,3
1,0
1,1
1,2
1,3
1,0
1,1
1,2
1,3
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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 ParaView – Fall 2014
Examples of Cell Types
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
000111111000
000111111000
000111111000
000111111000
000111111000
Scientific Visualization Using ParaView – Fall 2014
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
000111111000
000111111000
000111111000
000111111000
000111111000
Scientific Visualization Using ParaView – Fall 2014
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
001100
001100
001100
001100
Scientific Visualization Using ParaView – Fall 2014
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
001100
001100
001100
001100
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
Work flow – Case Study

MATLAB -> VTK file
 Write 256x256x10 float array to ASCII
file:

Add header , save with ‘.vtk’ extension:
Scientific Visualization Using ParaView – Fall 2014
Work flow – Case Study

Read VTK file into Paraview, choose “Volume Visualization” display option,
add Clip Filter:
Scientific Visualization Using ParaView – Fall 2014
Work flow – Case Study

Change color map,
use Paraview
animation feature to
move clipping plane
through volume:
Scientific Visualization Using ParaView – Fall 2014
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.)
Scientific Visualization Using ParaView – Fall 2014
Starting out - create sphere
ParaView:
1. Choose Sources -> Sphere
2. Click Apply in Object Inspector
3. User Interface:
- Undo
- Color
- Lighting
- Camera Movement
Scientific Visualization Using ParaView – Fall 2014
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).
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
File 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
0.639897 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
...
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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.
Scientific Visualization Using ParaView – Fall 2014
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.
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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:
1050-5000] or [falling:1050-200)].
Scientific Visualization Using ParaView – Fall 2014
Oriented Glyphs

Vector Algorithms
– Oriented Glyphs
• Orientation indicates direction
• Length / color indicate magnitude, pressure,
temperature, etc.
– ParaView
• Glyph Filter
– Set type to arrow
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
*Bonus: load state ‘streamline-glyph.pvsm’
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
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
Saving Images
Saving Images
– common formats:
• jpg (lossy)
• png (lossless)
• pdf
• tiff (lossless)
– ParaView
• File -> Save Screenshot
Scientific Visualization Using ParaView – Fall 2014
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
Scientific Visualization Using ParaView – Fall 2014
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”
--
www.paraview.org/Wiki/The_ParaView_Tutorial


Texts
–
The ParaView Guide, v3 Edition, Kitware, Inc, 2006.
–
The Visualization Toolkit, 4th Edition, Will Schroeder, Ken Martin, Bill Lorensen, Kitware ,
2006.
Websites
–
www.paraview.org
–
www.paraview.org/OnlineHelpCurrent/
–
www.paraview.org/Wiki/ParaView
–
www.kitware.com
Scientific Visualization Using ParaView – Fall 2014
Questions?

Tutorial survey:
- http://scv.bu.edu/survey/tutorial_evaluation.html
Scientific Visualization Using ParaView – Fall 2014