Definitions and terminology
A D V E R T I S E M E N T
Classification of techniques
Classification of visualization techniques is often based on the
dimension of the domain of the quantity that is visualized, i.e. the number
of independent variables of the domain on which the quantity acts, and on
the type of the quantity, i.e. scalar, vector, or tensor .
In MHD, two scalar quantities occur, viz. temperature (or pressure) and
density, and two vector quantities viz. magnetic field and velocity field.
These quantities are defined on a four-dimensional domain which is spanned
up by the space and time coordinates. The time dependence is treated
different than other dependencies. In particular, animation is used to
visualize this dependency (see below).
Visualization techniques can also be divided into surface rendering
techniques, and (direct) volume rendering techniques . Surface
rendering is an indirect geometry based technique which is used to visualize
structures in 3D scalar or vector fields by converting these structures into
surface representations first and then using conventional computer graphics
techniques to render these surfaces. Direct volume rendering is a technique
for the visualization of 3D scalar data sets without a conversion to surface
representations.
Scientific Visualization Glossary
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- animation techniques
- These techniques simulate continuous motion by rapidly displaying
images. The viewer is given the impression that he is watching a continuous
motion. To achieve this, the graphical hardware needs image display rates of
at least 25 images per second, otherwise motion will look shaky. Most
graphical hardware can not reach that display rate for moderate sized
images, so one uses video hardware.
- animation script
- An animation script is used to determine which image will be the next
one to be displayed and how long it will be displayed.
- back-to-front order
- Compositing can also be done in front-to-back order without altering the
final result.
- camera and object movement
- A camera is a means to view data in a viewport. An object
represents the result of a visualization or annotation tool, e.g. an
isosurface, a cutting plane, a bounding box, etc.
-
- CGM
- A general image file format. The Computer Graphics Metafile, has been an
ISO standard since 1987. It has the capability to encompass both graphical
and image data.
-
- color coding
- IThe use of colors (usually from red to blue), in most visualization
techniques, to reveal transitions in some quantity.
-
- computational steering
- To interactively change the simulation parameters and immediately see
the effect of this change through the new data.
-
- 'compute' modules
- One could of course, write these modules oneself. However, writing an
interpreter, as used in the Compute module, requires great expertise.
- Cutting planes
- This technique makes it possible to view scalar data on a cross-section
of the data volume with a cutting plane. One defines a regular, Cartesian
grid on the plane and the data values on this grid are found by
interpolation of the original data. A convenient colormap is used to make
the data visible.
- data browsing
- The use of visualization techniques to allow one to easily browse and
understand enormous quantities of data.
-
- data manipulation or selection
- It is possible to sample a volume of interest (VOI), but this VOI must
be defined within the data file format.
-
- data size
- We assume one floating point number to occupy 4 bytes.
-
- data value
- This was done considering video limitations. Full saturated colors
cannot be represented well on video. Hence we have taken less than full
Saturation (90 %).
-
- distributive processing
- As applied to scientific visualization, this is when the computation is
distributed over a set of high-performance computers and the actual
visualization is done on a graphical workstation.
-
- flipbook animation
- This is a well known animation technique. The generated images are
displayed one after the other. Its name is attached to the thumbing or
flipping through a series of images.
-
- GIF
- GIF, the Graphical Interchange Format , is quite widespread and can
encode a number of separate images of different sizes and colors.
- the HDF format
- The Hierarchical Data Format was developed by NCSA, University of
Illinois, at Urbana-Champaign. It is a multi-object file format for the
transfer of graphical and floating-point data between different hardware
platforms. Data Visualizer only supports HDF on Silicon Graphics
workstations.
-
- high-performance computers
- These can be high-performance workstations or supercomputers depending
on what is available and what is needed for the simulation.
- images in memory
- It is clear that the number of images that can be cached in physical
memory is limited. Increasing the number of images will eventually lead to
paging and hence to a slower display rate.
- keyframe animation
- For this technique one only has to generate so-called keyframes.
Keyframes mark changes in the characteristics of the motion, for example the
sudden change in the direction of motion of an electron due to a collision
with an ion. Interpolation techniques are used to generate a set of images
between two keyframes. The larger the interpolated set of images the
smoother the conversion from one keyframe to the other will appear to the
viewer.
-
- Isosurfaces
- This technique produces surfaces in the domain of the scalar quantity on
which the scalar quantity has the same value, the so-called isosurface
value.
-
- Lossless methods
- Lossless compression methods are methods for which the original,
uncompressed data can be recovered exactly. Examples of this category are
the Run Length Encoding, and the Lempel-Ziv Welch algorithm.
- lossy methods
- In contrast to lossless compression, the original data cannot be
recovered exactly after a lossy compression of the data. An example of this
category is the Color Cell Compression method.Lossy compression techniques
can reach reduction rates of 0.9, whereas lossless compression techniques
normally have a maximum reduction rate of 0.5
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- necessary information
- This information consists of connections, connection element type,
vertex (node) normals, and vertex (node) colors.
-
- the netCDF format
- The network Common Data Form is a data abstraction for storing and
retrieval of scientific data, in particular multi-dimensional data. It is a
distributed, machine independent software library based on this data
abstraction which allows the creation, access and sharing of data in a
self-describing and network transparent form. It is defined by Unidata.
-
- reading netCDF format
- There are some restrictions. If the coordinate grid is irregularly
spaced some modifications in the netCDF file have to be made.
- Orthogonal slicers
- Often one wants to focus on the influence of only two independent
variables (i.e. coordinates). Thus, the other independent variables are kept
constant. This is what the orthogonal slicer method does.
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- parameter function editing in AVS
- The Compute module of DX can perform the same actions.
-
- particle advection or streamlines
- A method for outlining the topology, i.e. the field lines, of a vector
field. One takes a set of starting points, finds the vectors at these points
by interpolation, if necessary, and integrates the points along the
direction of the vector. At the new positions the vector values are found by
interpolation and one integrates again. This process stops if a
predetermined number of integration steps has been reached or if the points
end up outside the data volume. The calculated points are connected by
lines. The particle advection method places little spheres at the starting
points representing massless particles. The particles are also integrated
along the field lines. After every integration step each particle is drawn
together with a line or ribbon tail indicating the direction in which the
particle is moving.
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- the PLOT3D format
- The PLOT3D format, defined by NASA, is a commonly used data format in
the computational fluid dynamics world.
-
- PostScript
- PostScript or more specifically Encapsulated PostScript Format (EPSF),
is a page description language with sophisticated text facilities . For
graphics, as compared to CGM, it tends to be expensive in terms of storage.
-
- PPM, PGM, PBM
- PPPM, the Portable Pixmap Format (24 bits per pixel), PGM, the Portable
Greyscale Format (8 bits per pixel), and PBM, the Portable Bitmap Format (1
bit per pixel) formats are pixel based and are distributed with the the
X-Window system.
- property editor
- The property editor is used to set the material properties of a
geometrical object, like transparency, diffusion coefficient, specular
coefficient, specular color, etc.
- Ray casting
- For every pixel in the output image a ray is shot into the data volume.
At a predetermined number of evenly spaced locations along the ray the color
and opacity values are obtained by interpolation. The interpolated colors
and opacities are merged with each other and with the background by
compositing in back-to-front order to yield the color of the pixel.
These compositing calculations are simply linear transformations. Performing
this in a back-to-front order, i.e. starting at the background and moving
towards the image plane, will produce the pixel color. The opacity acts as a
data selector. Sample points with opacity values close to 1 (opaque) hide
almost all information along the ray between the background and opacity
values close to 0 (transparent) transfer information almost unaltered.
- RGB
- RGB, the Red Green Blue format, is used by most visualization software
packages as the internal image format. The format consist of a header
containing the dimensions of the image, followed by the actual image data.
The image data is stored as a 2D array of tupels. Each tupel is a vector
with 3 components: R, G, and B. The RGB components determine the color of
every pixel (picture element) in the image.
- Scalar glyph
- Scalar glyphs is a technique which puts a sphere or a diamond on every
data point.
- scene
- A scene is an arrangement of objects, generated by
visualization techniques, geometries, and annotations in 3D space that can
be rendered.
- sequence number
- The sequence number of the first image in the sequence is 0000, the
second is 0001, and so on. This format of the sequence numbers has the
considerable advantage of producing the correct ordering of the sequence
with the UNIX ls command. For example, the ordering of ls is used
by a command that can write the sequence to laser disk.
- splatting
- This technique was developed to improve the speed of calculation of
volume rendering techniques like ray casting, at the price of less accurate
rendering. It differs from ray casting in the projection method. Splatting
projects voxels, i.e. volume elements, on the 2D viewing plane. It
approximates this projection by a Gaussian splat, which depends on
the opacity and on the color of the voxel (other splat types, like linear
splats can also be used ). A projection is made for every voxel and the
resulting splats are composited on top of each other in back-to-front order
to produce the final image.
-
- surface rendering techniques
- We will stick to the names used in sections 2.3 and 2.4. The names of
the actual techniques in the visualization packages may differ from them.
- streaklines
- A method for outlining the topology, i.e. the field lines, of a vector
field. One takes a set of starting points, finds the vectors at these points
by interpolation, if necessary, and integrates the points along the
direction of the vector. At the new positions the vector values are found by
interpolation and one integrates again. This process stops if a
predetermined number of integration steps has been reached or if the points
end up outside the data volume. The calculated points are connected by
lines. The streaklines technique considers the vector field to be time
dependent. Hence, the streakline technique interpolates not only in the
spatial direction, but also in the time direction.
- streamlines
- A method for outlining the topology, i.e. the field lines, of a vector
field. One takes a set of starting points, finds the vectors at these points
by interpolation, if necessary, and integrates the points along the
direction of the vector. At the new positions the vector values are found by
interpolation and one integrates again. This process stops if a
predetermined number of integration steps has been reached or if the points
end up outside the data volume. The calculated points are connected by
lines. The streamlines technique considers the vector field to be static.
- textures
- This is a technique to color arbitrary surfaces, e.g. those generated by
the isosurface techniques, according to a 3D scalar field. An interpolation
scheme is used to determine the values of the scalar field on the surface. A
colormap is used to assign the color.
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- 3-dimensional dependences
- As we need the full 4D data sets with four variables per grid point (v
and OD) we have split the data set into parts containing 100 time
steps each.
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- turnkey application
- This kind of application allows the user to supply data and select from
a fixed set of operations, hence functional extension is not supported. This
is one of the most severe drawbacks of turnkey systems. If none of the
operations suits the user's needs, the user can not develop a desired
operation himself and plug it into the application, so that it would be
accessible from within the graphical user interface mode or the command
language mode.
-
- vector glyphs
- This technique uses needle or arrow glyphs to represent vectors at each
data point. The direction of the glyph corresponds to the direction of the
vector and its magnitude corresponds to the magnitude of the vector.
-
-
- vector quantities
- Unless otherwise stated, it is implicitly assumed that a vector has
three components. So a vector is often written (x, y, z), and x, y, and z
are typically floating points (scalar quantities).
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- velocity components
- The individual components of the velocity vector.
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- widgets
- A widget is a graphical representation of a logical input device. There
is a loose definition of a widget as a term used to describe any abstract
device.
- wireframe
- Wireframe rendering is a fast method in which objects are drawn as if
they have been made of wires, with only their edges showing. All edges are
drawn because hidden-edge removal is not performed.
- XBM
- XBM is the X-Window one Bit image file format, which has been
standardized by the MIT X-consortium.A major constraint on the use of the
large data volume which has to be dealt with. Large sets of image data can
have severe implications for storage, memory, and transmission costs.
Therefore, compression techniques are very important. There are two
categories, lossless and lossy methods, based on whether or not it is
possible to reconstruct the initial picture after compression.
General image file formats
There is a great variety of data formats in which to store images. They can
be divided into two types: one which describes the contents of every pixel and
another which describes how to draw the objects in an image by means of
graphical semantics.
In the absence of an image format converter, like the image toolkit imtools
of the San Diego Supercomputer Center, it is important that the visualization
software is capable of understanding the formats most used. Below, we have
summarized some of these formats. The first two are based on a graphical
language but the others are pixel based.
CGM
CGM, the Computer Graphics Metafile, has been an ISO standard since 1987. It has
the capability to encompass both graphical and image data.
PostScript
PostScript or more specifically Encapsulated PostScript Format (EPSF), is a page
description language with sophisticated text facilities . For graphics, as
compared to CGM, it tends to be expensive in terms of storage.
TIFF
TIFF, the Tagged Image File Format, encompasses a range of different formats,
originally designed for interchange between electronic publishing packages.
GIF
GIF, the Graphical Interchange Format , is quite widespread and can encode a
number of separate images of different sizes and colors.
RGB
RGB, the Red Green Blue format of Silicon Graphics, is used by most
visualization software packages as the internal image format. The format consist
of a header containing the dimensions of the image, followed by the actual image
data. The image data is stored as a 2D array of tupels. Each tupel is a vector
with 3 components: R, G, and B. The RGB components determine the color of every
pixel (picture element) in the image.
PPM, PGM, PBM
PPM, the Portable Pixmap Format (24 bits per pixel), PGM, the Portable Greyscale
Format (8 bits per pixel), and PBM, the Portable Bitmap Format (1 bit per pixel)
formats are pixel based and are distributed with the the X-Window system
(version 11.4).
XBM
XBM is the X-Window one Bit image file format, which has been standardized by
the MIT X-consortium.A major constraint on the use of images is the large data
volume which has to be dealt with. Large sets of image data can have severe
implications for storage, memory, and transmission costs. Therefore, compression
techniques are very important. There are two categories based on whether or not
it is possible to reconstruct the initial picture after compression. They are:
Lossless methods
Lossless compression methods are methods for which the original, uncompressed
data can be recovered exactly. Examples of this category are the Run Length
Encoding, and the Lempel-Ziv Welch algorithm.
Lossy methods
In contrast to lossless compression, the original data cannot be recovered
exactly after a lossy compression of the data. An example of this category is
the Color Cell Compression method.Lossy compression techniques can reach
reduction rates of 0.9, whereas lossless compression techniques normally have a
maximum reduction rate of 0.5.
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