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		<H2><A NAME="HDRVIS" ></A>Chapter 2. Introduction to Visualization
		</H2>
		
<P><A NAME="PToC5" HREF="../usrguide.htm">Partial Table-of-Contents</A> 
<MENU>
<LI><A NAME="PToC_41" HREF="#Header_41">2.1 Terminology</A>
<MENU>
<LI><A NAME="PToC_42" HREF="#Header_42">Rendering</A>
<LI><A NAME="PToC_43" HREF="#Header_43">Positions and Connections Dependence</A>
<LI><A NAME="PToC_44" HREF="#Header_44">Connections and Interpolation</A>
<LI><A NAME="PToC_45" HREF="#Header_45">Identifying Connections</A>
<LI><A NAME="PToC_46" HREF="#HDRINVDAT">Invalid Data</A>
<LI><A NAME="PToC_47" HREF="#HDRFIELDS">Fields</A>
</MENU>
<LI><A NAME="PToC_48" HREF="usrgu023.htm#Header_48">2.2 Visual Programming: The
Basics</A>
</MENU><HR><P>
This chapter is not a substitute for the detailed information in the
rest of this Guide, but it does summarize some important terms
and concepts that may be new to you if you have not used
a scientific visualization application before.
So we suggest the following:
<UL COMPACT>
<LI>Read this section first, concentrating on topics that are unfamiliar.
<LI>Follow the tutorials in <I>IBM Visualization Data Explorer QuickStart
Guide</I>.
<LI>Start using Data Explorer.
A good place to begin is the set of example "networks" (or
"visual programs") in the directory
<TT><STRONG>/usr/share/dx/samples/programs</STRONG></TT>.
You can open up any visual program file and study how the different modules are
interconnected and then run the visual programs to observe the visual
output.
<LI>Use the online Help system to get more information about these
example visual programs and Data Explorer tools.
This system also contains hypertext references to additional
information.
<P>
The printed documentation contains detailed information, including
graphics, sample code, and data examples.
</UL>
<HR>
<H2><A NAME="Header_41" ></A>2.1 Terminology</H2>
<P>
Many of the terms used in Data Explorer are borrowed from traditional scientific
disciplines, others come from computer graphics, and a few have been
coined by the Data Explorer software developers for lack of
any widely accepted term.
Important Data Explorer terms are defined in the Glossary.
<P>
<H3><A NAME="Header_42" ></A>Rendering</H3>
<P>
The process of <I>rendering</I> an image involves a computer
calculation of the amount of light falling on each visible
surface of the objects in the "scene,"
as seen from the point of view of the
computer "camera" (the
viewer&#39;s eye point).
During the rendering process, surface properties of objects are taken
into account as are the colors of both the objects and the
"lights" shining on them.
In other words, a computer graphics renderer samples the scene in front
of the camera at the resolution of the computer monitor on which
the scene is to be displayed.
Its sample space is the 3-dimensional "world" containing the
objects.
But the image renderer does not create a 3-dimensional picture; it only
calculates the colors of the dots that can be seen on the
2-dimensional monitor screen from the chosen point of
view.
Any parts of objects that cannot be seen from that point of view are
neither sampled nor rendered, nor are they stored in the image
file or displayed on the monitor.
This 2-dimensional image may appear 3-dimensional to our eyes because
of shading, occlusion of distant objects by closer ones, and other
visual cues that, in the real world, indicate dimensionality.
Like any image, it is a representation, however real it may appear.
<P>
<H3><A NAME="Header_43" ></A>Positions and Connections Dependence
</H3>
<A NAME="IDX476"></A>
<A NAME="IDX477"></A>
<A NAME="IDX478"></A>
<P>
The concept of sampling should be familiar to anyone who has ever
collected data on some kind of grid.
For example, a botanist may lay down a series of square grid markers
over an area of interest then count the numbers of species of
grasses growing inside each grid square.
The number so collected becomes a sample value or datum associated with
that grid marker.
A single number like this, whether floating point or integer, is called
a <I>scalar</I>.
If the wind velocity and direction at, say, the center of each grid
square is also measured, the botanist would record a
<I>vector</I> quantity as a second datum
sampled at the same place.
A vector encodes both direction and magnitude with two or more numeric
"vector components."
<P>
In this example, the locations of the corners of each grid marker are
recorded as an array of 2-dimensional coordinates that define
the sampling area dimensions and the sampling resolution.
In computer graphics terms, these spatial location points are called
<I>vertices</I> (singular: vertex); in Data Explorer, they are
referred to as "positions".
Loosely, everyone calls them "points."
<P>
Four coordinate positions can be connected by a quadrilateral to define
a grid <I>element</I>.
The quadrilateral itself is called a <I>connection</I> in Data Explorer
(we will discuss other connection types in a moment).
Since the botanist collected one set of data per grid element, such
data are termed <I>connection-dependent data</I>.
This implies that the data value is assumed by Data Explorer to be constant
within that element.
<P>
Consider another technique for data sampling:
on a larger scale, remote-sensing satellites can resolve various
features of the Earth down to some finite level of resolution.
In this case, the grid positions are identified by a latitude-longitude
coordinate pair, and the data values may encode such things as
surface reflectance in the ultraviolet.
By associating each data value with a latitude-longitude position, we
produce <I>position-dependent data</I>.
<P>
This implies that data values should be interpolated between positions,
using  the connections (grid) if one is present.
Data Explorer works equally well with position-dependent and
connection-dependent data (see <A HREF="#FIGCPDPND">Figure 1</A>).
<P><B><A NAME="FIGCPDPND" HREF="../usrguide.htm#FT_FIGCPDPND">Figure 1. Examples of
Data Dependency</A></B><BR>
<B><BR><CENTER><IMG SRC="../images/datdpnd.gif" ALT="Figure datdpnd not
displayed."></CENTER><BR></B><BR>
Generally, the decision about which dependency the data has is made by
you at the time of data collection or simulation.
(There is a simple way in Data Explorer to convert either dependency to the
other.
See
<A HREF="refgu105.htm#HDRPOST">Post</A> in <I>IBM Visualization Data Explorer
User&#39;s Reference</I>.)
<P>
We can extend our data sampling into three dimensions
where appropriate.
In that case, we identify each grid position with three coordinates.
These coordinates form the corners of "volumetric" elements and the
entire sample space is called a <I>volume</I>.
A volumetric element may be a rectangular prism (like a <I>cube</I>)
or a <I>tetrahedron</I> (a solid with four triangular faces, not
necessarily equilateral).
<P>
<H3><A NAME="Header_44" ></A>Connections and Interpolation</H3>
<A NAME="IDX479"></A>
<A NAME="IDX480"></A>
<P>
In the cases just discussed, we made the implicit assumption that there
is a logical connectivity between adjacent members of our
2-dimensional or 3-dimensional grid positions.
The path connecting grid positions is called a <I>connection</I> in
Data Explorer.
For a surface (2- or 3-dimensional positions connected by 2-dimensional
connections),
we could choose to make triangular or quadrilateral connections
(i.e., <I>triangles</I> or <I>quads</I>).
Quads require four positions for each connection and triangles three.
Data Explorer supports these <I>element types</I> as well as cubes,
tetrahedra, and lines.
<P>
Suppose we first choose to link adjacent positions in the
botanist&#39;s sample area with <I>line</I> connections.
The grid markers were 1 meter on a side.
Given a sampling area of 5 meters by 3 meters, the entire sample would
be 15 meters square; there would be 24 positions (6 in X, and
4 in Y).
On such a plot, we see that a position located at &#91;x=0,y=0&#93;
is connected to its neighbor at &#91;x=1,y=0&#93;.
We can imagine that it is meaningful to draw associations between data
values at adjacent grid positions considering that so many natural
phenomena are continuous rather than discrete.
We assume that the grasses are free to spread across the area and the
wind is free to blow in any direction over the area.
<P>
Previously, we assumed that samples were measured at the center of each
grid square; that is, the botanist used <I>quad</I> connections
to associate sets of four positions into 4-sided elements, then
measured data values at the center of each connection element,
yielding connection-dependent data.
Now, assume that the botanist measures temperature values at
each grid <I>position</I>.
Temperature would then be position-dependent data.
It&#39;s perfectly acceptable to have both kinds of data in the same
data set.
We will see how this works when we discuss <I>Fields</I>.
<P>
Assume that the first grid position (sampling point) lies
precisely at the position coordinate
&#91;x=0,y=0&#93;.
We take a measurement and record the value.
Then we measure the temperature at &#91;x=1,y=0&#93;.
Later, we ask, what was the temperature at &#91;x=0.5,y=0&#93;?
Quite honestly, we do not know, because our sampling resolution was not
fine enough for us to give a definitive answer.
However, if we make the assumption (very often, a perfectly reasonable
assumption, but not always!) that our grid overlaid a continuous
set of values, we can derive the expected data value by
interpolation between known values.
If we use <I>line</I> connections to connect adjacent points, we
realize by looking at our mesh that a straight line connects the
grid point &#91;x=0,y=0&#93; and &#91;x=1,y=0&#93; and that
halfway along this line lies the grid point
&#91;x=0.5,y=0&#93;.
We can further assume that the data value at this midpoint is the
average of the data values at known sample points bordering
this location.
By linear interpolation, we calculate a reasonable value for the
temperature at &#91;x=0.5,y=0&#93;.
<P>
We need to define polygonal connections over the 2-D grid if we wish to
find the value at the point &#91;x=0.2,y=0.7&#93;.
With <I>line</I> connections between adjacent pairs of grid points,
we can only reasonably perform interpolations along those linear
boundaries but not into the middle of our grid elements.
By defining areas bounded by three or more points, we can perform
interpolation across the area (the polygon surface) using
weighting functions that take into account the data
values at all points surrounding the area.
In fact, this is the same process used by an image-rendering program:
it interpolates from known values (at the vertices) across the
faces of polygons and computes the appropriate color at all
visible points on the surface, at the resolution allowed
by the output device (digital file, computer
monitor, etc.).
<P>
<H3><A NAME="Header_45" ></A>Identifying Connections</H3>
<P>
In Data Explorer, we identify connections in the following way.
List the sample point location vertices in any order: that list is
called the "positions" as we discussed above.
Consider each point in the positions list to have an ordinal number,
starting at 0 for the first point in the list (these ordinal
numbers are not explicitly listed in a Data Explorer file).
A connection is denoted by a "list of lists" of numbers in which
each entry represents the ordinal values of the points that are to
be connected, listed in the order they are to be
connected.
So for example, if the first point in the positions list is
"0.0 0.0" and the second point is "1.0 0.0",
we denote a <I>line</I> connection between these
two points by "0 1", indicating that a line
joins point 0 (first point in the positions
list) to point 1 (the second point in the
list).
<P>
As mentioned above, a <I>triangle</I> connection must reference
three positions and a <I>quad</I> references four positions.
For complete examples of position and connection lists, see
<A HREF="usrgu024.htm#HDRDATMOD">Chapter 3. "Understanding the Data Model"</A>.
<P>
As a direct extension of this concept, when we define volumetric
elements like <I>cubes</I> and <I>tetrahedra</I>,
we can perform 3-dimensional interpolation and
derive a reasonable data value for any point
in a sample volume.
The good news about all of this interpolation is that Data Explorer already
knows how to do the necessary calculations.
As a researcher, your job is to define your data space to
Data Explorer--its positions, connections, and
data-dependency--but you do not
have to worry about the details of how
the interpolation is actually
performed.
<P>
The connections list is optional if it makes no sense to connect your
sample points; for example, if you are studying gas molecules, there
may be no meaningful interconnecting lines between separate
molecules.
Nevertheless, you may wish to define "line" connections linking the
atoms within each molecule, in order to visualize interatomic bonds
or protein backbones;
or you may define cubic volumetric elements in the space around the
nucleus if you wish to visualize electronic potential fields, for
instance.
<P>
In any case, you must define a set of connections before you can
perform interpolation operations between sampled
data values.
This is true both for position-dependent data and for
connection-dependent data.
Once again, positions are discrete points in space, and connections are
logical paths between those points representing reasonable
interpolation paths between the sampled data values.
If you do not have connection information available, you can use the
Connect or Regrid modules to create connections for scattered
point data.
<P>
If you work with regular grids, the "connections" can be defined
in a simple way by Data Explorer regardless of the import format you are
using.
See <A HREF="usrgu024.htm#HDRDATMOD">Chapter 3. "Understanding the Data
Model"</A> in this Guide and <A HREF="qikgu027.htm">Chapter 5.
"Importing Data"</A>
in <I>IBM Visualization Data Explorer QuickStart Guide</I>.
<P>
If your work requires irregular grids, you will need to carefully read
the section of this manual that describes the format of Data Explorer
element types.
You may need to write a filter program to convert the connection list
output from your finite element program to the format required by
Data Explorer before you can import and visualize data sampled
on arbitrary structures.
<P>
<H3><A NAME="HDRINVDAT" ></A>Invalid Data</H3>
<P>
Sometimes in the process of collecting or analyzing data, certain
regions or positions have no data value associated with them.
For example, an instrument may have a "data drop-out" or a
simulation may (for whatever reason) produce an invalid entry.
Of course, if you are explicitly listing your positions or connections,
you can simply leave those positions out when you create your
data file.
However, if you have a regular grid (for which you simply list the
origin of the grid and the delta in each dimension), this is
not convenient.
Data Explorer has a way to easily handle this situation, using "invalid
positions" and "invalid connections" components.
These components are discussed in <A HREF="usrgu024.htm#HDRDATMOD">Chapter 3.
"Understanding the Data Model"</A>, but
briefly, when present in a Field, they instruct any module
processing that Field to completely ignore any position
or connection identified in that component.
For example, an "invalid positions" component may list the
integers 0, 15, and 23.
This instructs Data Explorer to ignore the positions 0, 15, and 23 (and the
data associated with those positions).
<P>
You can create these components in a Data Explorer format file (see
<A HREF="usrgu067.htm#HDRIMD">Appendix B. "Importing Data: File Formats"</A>)
or, often more easily, using the Include
module.
For example, suppose in your data file drop-outs are indicated with a
data value of 9999, while all valid data lies in the range
0-100.
Then set the <TT><STRONG>max</STRONG></TT> parameter of Include
to 9998.
Include will then remove or invalidate all of the positions with the
value 9999.
Note that it is usually preferable to set the <TT><STRONG>cull</STRONG></TT>
flag of Include to 0 so that the data values are
invalidated rather than actually removed (see Include
in <I>IBM Visualization Data Explorer User&#39;s Reference</I>).
<P>
All Data Explorer modules know to ignore invalid data.
For example, Streamlines will stop when they reach an invalid element,
and Statistics will ignore data values associated with invalid
elements.
<P>
<H3><A NAME="HDRFIELDS" ></A>Fields</H3>
<A NAME="IDX481"></A>
<P>
Given the sets of numbers, "positions,"
"connections," and "data", we can define a
<I>Field</I>, as it is called in Data Explorer.
The positions identify locations in space, the (optional) connections
define logical continuities (interpolation paths) between positions,
and the data are the values measured either at each position or
within each connection element.
Data Explorer calls each of these sets of numbers (positions, connections, data)
a Field <I>component</I>.
Components are represented as arrays of numbers with some auxiliary
information specifying <I>attributes</I> (e.g., type of
dependency).
In addition, there are many other types of Field components.
The Field is the basic unit of information in Data Explorer, so it is important
to understand how to express your data in these terms.
<P>
A Field can only have one "positions" and one "connections"
component.
A Field can have only one component actually named "data", but you
may assign names of your choosing to additional components
representing other data sets that are also mapped to
the same grid.
So you can name a "data" component "temperature" and another
"wind velocity", or you can just use the default name
"data" if you only have one "data" component.
<P>
The ".dx" file format provides the most flexibility for describing
data sets to Data Explorer.
But many researchers produce fairly straightforward arrays of numbers
mapped onto regular or deformed regular grids.
If your data are already written out in such a form, you may not need to
convert your data files into the native ".dx" file format.
Instead, Data Explorer&#39;s General Array Importer can read your data directly,
given a small "header" file that you create to tell the General
Array Importer the name of your data file and
its dimensions (see <A HREF="qikgu027.htm">Chapter 5. "Importing
Data"</A> in <I>IBM Visualization Data Explorer QuickStart Guide</I>).
<P>
This shorthand description is enough for Data Explorer to convert your data
structure into a Field when it reads your raw data file.
You will still find it valuable to understand the components of a
Field, because once you begin using the Data Explorer visual programming
language, you will have direct access to these components.
Much of the power and flexibility of the visual programming language is
derived from our ability to access and manipulate Field components
in a variety of ways.

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