SCIENTIFIC VISUALIZATION

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SCIENTIFIC VISUALIZATION
CS521 Computational Sciences Spring 2001

• Chirwa, Ji, Padilla

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Definition

• The technique to explore numerical data by means
  of visual, graphical objects.
• Results of complex numerical computations and
  measurements become intuitively understandable.
• Interaction methods allow investigation of
  relevant aspects of a data set

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History

• Three phases of multidimensional multivariate
  visualization (mdmv) development
• Searching stage
• Awakening stage
• Discovery stage
• Elaboration

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Searching stage

• From about 1782 to 1976
• Statisticians and psychologists were first to
  study mdmv long before Computer Science
• Mostly 2D xy displays

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Awakening stage

• From 1977 to 1985
• Exploratory data analysis methods (Tukey)
• Not just a tool but a way of thinking how to
  decode data
• 2D and 3D spatial data most commonly studied

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Discovery stage

• From 1987 to 1991
• NSF workshop in 1987 declared need for 2D/3D
  spatial object visualization
• Moved away from exploratory data analysis to
  colorful high-D visualization requiring
  high-speed computations.
• User interaction started including virtual reality

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Elaboration stage

• From 1992 to now
• Not many new techniques but improvements
  (elaboration) of existing methods
• Latest research issues are evaluation of
  correctness, effectiveness, and usefulness of
  mdmv visualization techniques

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Definition

• Dimension independent variable dimension
• Variate dependent variable dimension
• y f(x)
• x is independent y is dependent

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Immersive Investigation of scientific data

• Requirements

• Input devices tracking devices, gloves, flying
  joysticks, Spaceball, speech
• Acoustic output synthesizers
• Visual output desktop display, large projection
  screen, head bound systems (helmet)

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Software for virtual environments

• Real-time rendering and shading of realistic
  images
• Hierarchical data structures/viewing culling
• Level of detail
• Successive refinement
• Rendering caches
• Multiprocessing
• Collision detect
• Textures, shadows

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Numerical Grid Generation methodologies
Two grid types

• Structured grids generated by a combination of
  transfinite interpolation (TFI) and solving
  elliptic systems of PDEs
• Unstructured grids generated by a
  triangulation/tesselation algorithm or advancing
  front approach

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Structured grid
Hierarchical grid
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Unstructured grid
Unstructured-tetrahedral grid around wing
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Scientific Visualization

• Frameworks and Methodologies

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Three areas that visualization tools are being
used

• 1. Data entry and data integrity
• 2. Code debugging and code performance analysis
• 3. Interpretation and display of final results

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Visualization to be done correctly can act as and
end user on Unix

• 1. Produce a graphics file containing the results
  to be viewed.
• 2. Operate an appropriate visualization software
  package.
• 3. Navigate the operating system and user
  interface of a selected workstation.

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Data entry and integrity

• A Graphics screen provide most the efficient form
  of data entry.(manipulate graphics objects on the
  screen or modify data sets.)
• Visualization software allows a modeler to
• 1. pan- screen over larger data sets.
• 2. stack- one screen behind another.
• These tools allow researchers to put millions of
  data values by simply painting the screen.
• Also before running a model,you can query the
  data base in a graphical manner.This permits us
  to see errors or inconsistencies in massive data
  sets.

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Code debugging and performance analysis

• If you display color a map of some section of a
  models region each step of execution. This will
  us to gain important information about the
  behavior of the model.
• If an error shows up during computation. Then
  the program can be hauled right there, instead of
  waiting for the program to finish its
  computation. This will save valuable times for
  the computer and researcher.
• An example is if you use a raster map during
  a simulation, the modeler can find the cause of a
  problem such as computational instability or
  problems with the boundaries.

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Cont. code debugging and performance Analysis

• Code performance analysis and tuning
• - subroutine histogram gives us relative
  importance of various subroutines.
• - total area under represents is total
  execution
• - total area under subroutines gives us the
  percentage of time spent on executing a certain
  subroutine.
• This type of histogram can also be used to
  represent a network.
• -This would be done by having the
  subroutines represent different nodes in you
  network.

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Interpretation and presentation of Results

• Human brain can taken and process visual aspects
  better than numerical models.
• You can use color,texture,translucency to display
  large scale complicated models in a form that can
  be understood easily by people.
• Example the most common method of showing 2-D
  data is to produce a raster image of that data.
• Also, most visual packages allow the color
  palette to be manipulated. This results in being
  able to interactively and nearly instantaneously
  change data representation.
• Prepare photo-realistic images on sever, add
  texture to pictures, overlay color contour.

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Other methodologies

• Environmental Modeling
• -Air quality and deposition, water
  quality and sedimentation, air and water model
  linkages(cross-media), subsurface water,
  Molecular modeling, Environment Management
  framework.
• Framework Environment
• 1. This allows local industry,s state and
  local government, special interest groups, and
  people in community to evaluate numerous
  strategies for meeting community environment
  goals.
• 2. Enable a collection of environmental data
  models, and analysis tools to operate as a
  cohesive unit to assist all members of a
  community to take part in environmental decision
  making.
• 3. Initial implementation support urban and
  regional air quality assessments.

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Environmental Modeling

• Major leader in this field is the EPAs
  scientific Visualization Center
• Designed an Air quality Modeling system(models-3)
• Also, addressed critical health and welfare
  issues related to ozone, acid deposition, and
  fire particles.
• EPA works with Environmental Supercomputing
  Center(NESC)
• Both of these organization are located in
  Research triangle Park (RTP) in North Carolina
• Data is presented in many different forms. Like
  videotape and online formats.(MPEG, QuickTime,
  Gif and Jpeg)

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Air Quality and Deposition Modeling

• Studies have shown particles less than 2.5
  micrometers are potentially harmful to human
  health as well as causing wide spread reduction
  in visual range.
• Research to study air quality is happening at
  EPAs National Exposure Research
  Laboratory(NERL). This project involves
  scientists from NERL,MCNC,University of
  Delaware,California Institute of technology.
• Two types of Models
• -First uses sectional approach,
  predicts aerosol mass and chemical specialization
  as a set of size sections.
• -Second uses a model approach. Uses a
  explicit formula for particle size.
• Regional Particulate Model(RPM) uses the second
  approach.
• -examines the effect of emissions
  reductions of sulfur,hydrocarbons and nitrogen
  oxides.

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Techniques
and
Examples
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In scientific computation, the position of
objects is very important, so we states the
general steps to visualize the position of
objects. Techniques to visualize an object from
different viewpoints are introduced.
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To visualize an object, we should

• Establish the model to describe the object
• Got equations according to the model
• Solve these equations to get the data (such as
  coordinates of the object)
• Display the object on the screen (visualization)

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Establish Model and Equations

• Analyze your subject and gather information from
  literature - According to the
  literature, what theory was used by other
  scientist in the related area. It maybe
  helpful - What theory could be applied
  to your subject
• Establish equations - Determine the
  initial conditions and boundary
  conditions

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Solve the equations and get raw data

• Get the analytical solution - In general, it
  is difficult to get analytical solution
• Or...
• Get the numerical solution - For most
  problems, numerical solution is good enough

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Visualize data

• Display the objects by their coordinates
• View these objects from different angle

For example, to view
ion, we should have the coordinates of
its 8 atoms
C 19.9350 45.5278 19.6960 C 21.0809
45.5375 20.3937 C 22.4128 45.5364 19.6938 H
19.0095 45.5288 20.1928 H 22.9698
46.4312 19.9745 H 22.2784 45.5245 18.6113 H
22.9782 44.6531 19.9931 H 21.0490
45.5460 21.4449 C stands for carbon atom, H
stands for hydrogen atom
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The picture according to its coordinates is
Figure 1 Front view
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If we view it from top (rotate the ion about x
axis by 90 degree), it looks like this
Figure 2 Top View
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View the ion from the right (rotate about z axis
by 90 degree)
Figure 3 Right view
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To view and display the objects from different
orientation, we need to change our viewpoint. We
need two frames of reference.

• World frame a fixed coordinate system for
  representing objects in
  the world. The reference is the
  earth.
• View frame a coordinate system fixed on the
  observer. The reference
  is the observer itself.

x
Z
P
z
y
Y
X
View frame
World frame
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Point Ps coordinate has different values in
world frame and view frame. If we know the Ps
coordinate in world frame, we could get its
coordinate in view frame by rotation and
translation. Suppose than the translation vector
is T, the rotation matrix is R, Ps coordinate in
world frame is Pw, then Ps coordinate in view
frame Pv is
where
iv jv and kv are the unit vectors of view
frame iw jw and kw are the unit vectors of world
frame
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The Rotation matrix for rotations about all three
axes

• Rotation about x axis

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• Rotation about y axis

• Rotation about z axis

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Apply the rotation matrix to rotate the ion about
x axis by 45 degree
For the first carbon atom, its vector in the
world frame is
Its vector in the view frame (after rotation) is
So, the new coordinate is x19.9350, y18.2658,
z46.1202
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Then, calculate the new coordinate for other
atoms, well get the new coordinate list for the
ion after rotation
C 19.935 18.2658 46.1202 C 21.0809 17.7793
46.6205 C 22.1428 18.2735 46.1246 H 19.0095
17.9152 46.4721 H 22.9698 18.0006 47.663 H
22.2784 19.0305 45.3509 H 22.9782 17.4373
45.7118 H 21.0491 17.0421 47.3697
Figure 4 Rotate by 45 degree
According to the new coordinates, the ion after
rotation is shown in figure 4.
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Some visualization softwares

• Xmol It allows researchers to view 3D
  molecular models produced by other
  software packages It is only for unix
  (AIX, IRIX). http//www.chimie.fundp.ac.
  be/cms/cmsinfo/xmol.htm
• RasMol It also could visualize 3D
  molecular models. It is for Windows.
  http//www.umass.edu/microbio/rasmol/getra
  s.htm
• Jmol It is similar to Xmol. This
  software is written in Java. Its
  source code is open.
  http//www.openscience.org/jmol/