User's Guide - Visualization Techniques

## A.2 Visualization Techniques

Now we have our data in a Field Object inside Data Explorer. What can we do with it? This section discusses some common visualization techniques and the Data Explorer modules associated with them:

- "Animation"
- "Annotation"
- "Color Mapping"
- "Contours and Isosurfaces"
- "Mapping"
- "Normals and Shading"
- "Plots and Histograms"
- "Rubbersheet"
- "Transformations and Structuring"
- "Vector Fields"
- "Volume Rendering".

### Animation

The Sequencer tool is the primary device used in Data Explorer to produce animation or motion control. There are two basic types of animation: show a series of steps one after another, or, cause an object to move or rotate or change scale in order to study it from different points of view.

Since many data sets are measured at a series of different times, your data may have a "time value" associated with each measurement set. There are two ways to read in these time step data files in order to study the dynamic process you have measured.

In one scheme, you can collect all your data files into a Series, a special Group of Fields understood by Data Explorer. Each Series member can represent a data collection event at a certain time. Series do not have to be based on time; you may have a set of experimental measurements made at different voltages (e.g., a voltage series). Each series member is assumed to have the same type (scalar, vector, etc.) and the same dimensionality (2-D, 3-D, etc.), but the data and even the grid size or number of connections and positions may be different for each Series member. The Series Field is described in detail in "Series Groups". Series "values" do not have to be continuous but may represent useful information like the actual voltage setting for that Series entry (0.04, 2.3, 13.4). Series members are accessed by their ordinal position, starting at 0, regardless of their "value."

Another way to organize a collection of associated data files is to create individual files for each time step (or voltage measurement, etc.). Give each file a filename containing an ordinal number so you can access them easily with a computer program (e.g., myfield.001.dx, myfield.002.dx, and so on). Each file will contain the Field to be imported at each time step.

In either case (Series Field or separately numbered files), you can control when a particular time step is visualized in a visual program using the Sequencer tool. This tool emits a series of integers. You set the minimum, maximum, and increment, as well as choosing to start at a specific number (so you can jump ahead in the series if you like). The Sequencer can be connected to the Import module to specify which Series member to read in from the specified input file at the next iteration. Alternately, you could Import the Series Group file with Import, then use the Select module. Select takes an integer input (from Sequencer, for example) to choose the appropriate series member.

If you choose to use separate files for separate data samples, you would likely want to use the Sequencer as an input to a Format module. The Format module could construct the filename with a format string like `%s%03d%s` along with three inputs, "myfield.", the output of the Sequencer, and ".dx". Then, when the Sequencer emits the integer "2", the output string from Format becomes "myfield.002.dx". This can be fed into Import as the name of the .dx file to read. The result is that you can use the Sequencer to specify either any specific file or a whole series of files to import and image one after another.

Another common type of animation is to use the Sequencer to control object motion. Usually, this requires that you run the output of Sequencer through at least one Compute module. For instance, you can rotate an object around the Y-axis one full revolution by employing the Rotate module. The smaller the angular increment, the smoother the animation will appear, but there is a trade-off in apparent motion rate if your graphics workstation is not very fast. So you may have to adjust the incremental angular amount to your liking.

You will find the technique of wiring Interactors to Compute modules useful for converting the output of Sequencer to arbitrary floating-point values. If you wanted to vary the Scale of your object using the Scale module, it might be more convenient to adjust the scale in increments of 0.01. With a little thought, you can extend this idea so that the same (one and only) Sequencer integer series can be converted into several different series of numbers that can simultaneously rotate, scale, and read in different time steps of data. Just a caution, though: too much changing at the same time will probably not help you visualize your data, but instead will cause confusion. Is the object getting bigger because the data values are increasing, or because you are changing the scale, or because you are moving the object closer to you with Translate? When you start out, keep your animations simple and they will be much more effective.

### Annotation

It is imperative that good visualizations contain sufficient annotation for a viewer to derive appropriate information from the imagery. A colored height field or streamline set with no supporting labeling can make perfectly beautiful, utterly meaningless computer graphics.

Annotating a scene can be done in several ways using Data Explorer modules. You can, for example, provide a ColorBar with numeric values automatically labeled next to the related colors, show Text or Caption information to provide textual descriptions of objects, or turn on AutoAxes to show neatly labeled and numbered axes around the perimeter of your data space.

Using the Format module, it is possible to create "clocks" or other "meters." Format creates a formatted string of text suitable for Caption or Text modules to display. Format takes a "template" and text strings and/or numbers as `value` inputs and assembles an informative text string as output. For example, inputting the minimum value of your data to the first `value` input (the second input tab) of a Format module, you could create a Caption that reads:

    Minimum temperature = 0.0 deg.

To do this, the "template" inside the Format module would read:

    Minimum temperature = %1.1f deg.

In this template, the "%1.1f" serves as a place holder for the first value (which must be floating point) provided to Format; consequently, the minimum value argument is substituted into the string when the visual program is executed. The "1.1" means that the floating-point number should display at least one number to the left of the decimal point but should round off to only one decimal place to the right of the decimal. By tying the data Field to Statistics (Transformation category), you can easily extract the minimum value of the data; use this as the second input to Format. If you later input a different data set with a different minimum, Caption will automatically change to reflect the new minimum value.

One trick for showing text together with numbers that are changing is to use a "fixed width" font instead of a "variable" or "proportional" font. Variable text looks better when making Captions that do not include changing values, but fixed width text maintains the same width regardless of the numeric characters currently being displayed. Try both ways and you will see that the variable text has an annoying shrinking-expanding effect as your clock or time step meter changes value. To get the fixed text clock to behave correctly, you must use a Format template like "%03.2f" that allows for enough numbers to the left of the decimal point. In this example, we have predetermined that we will never create a number greater than 999.99 (note that if we do go over 1000, the text will expand to show the whole number, causing the Caption string to expand: the very thing we are trying to avoid!). The "%03.2f" format makes floating-point numbers with 3 numerals before the decimal, including left side zero padding, and 2 numerals after the decimal.

### Color Mapping

Data Explorer provides an automatically generated color map (AutoColor), an automatically generated grayscale (AutoGrayScale), and a user-definable color map (the Colormap module that attaches to the Color module). A color map represents a relationship between a continuous range of floating point numeric data values and a set of color values. Frequently, you will encounter color maps with continuous ("spectral") color tones like a rainbow, but there is no requirement that color maps appear continuous. Each color map has associated with it a minimum and a maximum scalar value. You can either specify the minimum and maximum or connect the data Field to the Colormap module and have these values automatically extracted.

We can describe "color" to a computer in a number of ways. One of the more intuitive is the "hue-saturation-value" model used by Data Explorer's Colormap tool. Hue is the color's "name", like blue, red, and so on. Hue is considered to form a circle from red through yellow, green, cyan, blue, magenta, and back to red; think of Hue as an "angle" around this color wheel (scaled from 0.0 to 1.0). Saturation is the "richness" of a color. Decreasing the Saturation of a color from 1.0 to 0.0 makes the color progressively more pastel, so for example, bright red becomes light red, then pink, finally turning white. You can think of decreasing the Saturation as adding "white paint" to paint of a pure hue. At Saturation 0.0, any color becomes white (assuming Value is held at 1.0). Similarly, Value is a measure of the amount of "black paint" mixed with a color. As you decrease the color's Value from 1.0 to 0.0, you add more "black", so bright red becomes progressively darker red, and finally black. Any color becomes black at a Value of 0.0. All three of these parameters interact, so you can adjust Hue and decrease Saturation and Value to get a "dark pastel blue."

Another scheme for describing color is RGB (Red-Green-Blue). As in the HSV model just described, you specify a color as a triplet (a 3-vector). Each component can have a value from 0.0 to 1.0. If all three are 0.0, the resulting color is black; if all three are 1.0, you get white. Given Red = 1.0, Green = 0.0, Blue = 0.0, the color is fully saturated bright red. You can observe a graph of RGB lines at the far left of the Colormap tool as you manipulate the colors using the Hue-Saturation-Value (HSV) controls. You can specify an RGB vector in the Color module in place of connecting a Colormap if you want the output object to have a single color (or you can specify one of the X Window System color names). And you can convert from RGB to HSV or back using the Convert module. See Color and Colormap in IBM Visualization Data Explorer User's Reference for more details about these different specification schemes.

Let us assume that we have set the Colormap minimum and maximum to equal the minimum and maximum of the temperature data we collected in the atmosphere (this is done automatically if you connect the data Field to the input on Colormap). Recall that we collected position-dependent data, one temperature value at each grid position. For this example, assume the minimum temperature measured was 0 degrees Centigrade and the maximum 20. What color is 10? That depends entirely on the color map used. If we have a standard spectral (rainbow) map with blue at 0 and red at 20, then 10 would have a color halfway between blue and red. On the default color map, this would be green. When we ask Data Explorer to color-map our data, it examines each data value, performs a linear interpolation between the minimum and maximum values to find the color associated with that interpolated value in the color map and "colorizes" the object at all points containing that data value with that color.

If we change the maximum value in the color map to 30, the measured data value of 10 (taken from the same data set as above) will now map to a cyan color, part way between blue and green. On the other hand, we could keep our same extreme values but manipulate the color map's color distribution in such a way that any value has any color we like. You can learn the details about this capability in 6.3 , "Using the Colormap Editor".

The best way to learn about the power of color mapping is to take some sample data, color-map it, then manipulate the settings in the Colormap Editor you have connected to the Color module your data Field passes through.

Note: Choose `Execute on Change` from the Colormap Editor `Execute` menu and you will see the data change colors as soon as you make a change in the Colormap Editor.)

For instance, you can create sharp color discontinuities by placing two control points close together vertically on the Hue control line, then dragging one horizontally away from the other. This can be used to indicate a sharp edge transition in your data. It is sometimes useful to place a special contrasting color in the middle of an otherwise continuous color map. For example, to highlight the value of 12 degrees C in our temperature data, we could insert a sharply defined red notch or band into the middle of our smooth rainbow color map. This would highlight that particular value or range for someone examining the scene. You can automatically generate a number of control point patterns by choosing `Generate Waveforms...` from the `Edit` menu in the Colormap window. To make a notch, choose one of the "S" shaped curves from the pop-up menu in the `Generate Waveforms` dialog box. Set the number of Steps to 4 to make a single notch, or 3 to make a single step. Click `Apply` to place control points on the currently chosen curve (Hue, Saturation, Value, or Opacity). You can then drag the new control points where you like.

If you use a red color notch in the middle of your data range, you probably will not want to use red elsewhere in your color map or it will be difficult for a viewer to tell the 12-degree specially highlighted red area from the 20-degree red maximum values (assuming 20 is the maximum). In fact, it might be safer to use a white or gray color to mark the special value of 12 degrees. Do this by creating a notch on the Saturation or Value curves instead of on the Hue curve.

Similarly, you can change the opacity of objects. Opacity is the inverse of transparency: that is, the more opaque the object, the less transparent. You can set opacity to a value between 0.0 and 1.0. Opacities less than 1.0 allow you to see through an object to reveal objects inside or behind the transparent object. For all objects except volumes, an Opacity of 0.0 will make the object disappear completely. Since Data Explorer uses an emissive volume rendering technique, you must set the color of a volume to "black" (RGB of [0, 0, 0]), as well as setting the Opacity to 0.0, to make the volume disappear. You will notice that when you view slightly transparent objects through each other, the colors of each object combine, making it very difficult to accurately assess the color of any one object. Used sparingly, opacity is a very powerful tool for examining the insides of objects or volumes and gauging the physical relationships between intersecting objects.

You can create a variable opacity on an object by manipulating the opacity curve in Colormap. This can make parts of an object trail off to transparency, useful if some data values are not of interest. Be aware that "hiding" data in this way may mislead someone viewing your results. But in some data sets, there may be a large number of "noisy" data values that you would like to exclude in order to see the "signal" data values of interest. In that case, setting an Opacity notch to hide the noisy values may be the best visualization technique.

When you lower opacity below 1.0, you will see two stripes, one white and one black, or a checkerboard pattern of black and white behind the sample color strip in the Colormap Editor. These are useful when you manipulate Opacity to check the apparent color against both a light and dark background. As with the color tools, you can turn on `Execute On Change` and interactively play with the Opacity of the selected object until you get the effect you want.

### Contours and Isosurfaces

Given a set of samples taken over a presumably continuous region, it is meaningful to consider drawing smooth lines connecting together the locations on the grid containing the same data values. You are probably familiar with topographic maps that show contour lines connecting together the same values of elevation of the Earth's surface features, such as hills and valleys. These lines are called "contour lines" or "isolines" (iso means "same" or "equal"). In most cases, the places on the surface of the sample grid that have identical data values will not coincide with the grid sample points. This is another case where the "connections" component is required for Data Explorer to determine where on the grid the same value occurs (say the value 5.2) in order to create lines connecting together all these locations.

To return to our 3-dimensional data set taken from the atmosphere. Since we have collected data throughout a 3-dimensional space, we can identify volumetric elements defined by connecting adjacent grid sample points in three dimensions using a "connections" component like cubes. It now becomes possible to draw "isosurfaces" rather than "isolines." An isosurface is that surface cutting through a volume on which all data values are equal to a specified value. Depending on the actual distribution of the data, isosurfaces may look more or less like flat sheets (the isosurface of "sea level" in a data set of elevations would look like this); it might enclose a portion of our space or appear as a whole set of small disconnected surfaces or enclosed spaces.

To create an isosurface, we pick a value of interest. Suppose that according to our knowledge of meteorology, we know that the dew point (at which water condenses from vapor to liquid) is 12 degrees C in our sample. Although we measured temperatures at only a fixed number of grid points, we are interested in seeing where rain formation may begin throughout the atmosphere. We could show only the sample points highlighted by themselves, but once again, we make a reasonable assumption that we have taken discrete samples from a continuous natural volume. In other words, rain formation will not simply occur at the limited set of discrete points where we have sampled temperatures of 12 degrees C, but at all the points in between that are also at 12 degrees. How do we find all those in-between points? By interpolating through the volumetric elements between adjacent sample points. And in fact, the Isosurface module will do this automatically.

The resulting isosurface will represent all values of 12 degrees C throughout our volume of sampled space. The actual image depends on the distribution of the data, of course. If the outside of a rain cloud were at exactly 12 degrees C, we would see a shape resembling a cloud in the sky. But if rain formed at an altitude where the temperature was 12 degrees C, we would instead expect to see a flat sheet. Or we may not know what to expect: that is one of the uses of visualization, as well--for discovery, not just for verification.

Generally, the vertices that describe the mesh positions of an isosurface will not coincide with the original grid points. It is important to realize that an Isosurface is a new and valid Data Explorer Field with positions and connections and a data component (in which all data values are identical). You can treat this Field just like any data Field you have imported. Color mapping such a Field is not particularly useful since all the data values are identical, so you will get the same color for every point.

To draw contour lines on a 2-dimensional grid, you also use the Isosurface module. Data Explorer figures out the dimensionality of the visualization by looking at the input data. Thus, a biologist's 2-D grid can be easily contour-mapped with the same tool as a meteorologist's 3-D volume, but the visual output will be appropriately different for the different inputs. Similar to Isosurface's contour lines is the output of the Band module. This yields filled regions between contours; these bands can be colored by a color map or AutoColor to yield the kind of image frequently used to show temperature distributions on a weather map.

### Mapping

There is a very useful module called Map in Data Explorer that permits you to "map" one data set onto a Field defined by another data set. For example, in our rain cloud data, we have measured temperature and cloud-water density throughout a volume. We learned earlier how to make an isosurface of temperature equal to 12 degrees C. Now it may be instructive to observe the cloud-water density associated with this temperature isosurface.

The operation we wish to perform is to use our temperature isosurface with its arbitrary (data-defined) shape as a sampling surface to pick out the values of cloudwater density as they occur throughout the volume. That is, conceptually, we will dip the temperature isosurface into the cloudwater volume. Wherever the isosurface comes in contact with the cloudwater volume, the values that stick to the isosurface represent the values of cloudwater density that occur at that intersection. But remember that the isosurface was created using temperature data. The isosurface of temperature (the input Field to Map in this example) had only one data value (12 degrees C) at every position, but the mapped isosurface (the output of Map) will contain arbitrary patches of data corresponding to the distribution of cloudwater density. If we AutoColor this output isosurface, we will see an arbitrary geometric surface with a patchy color scheme. The surface is the location of all 12 degree temperatures, and the patchy color corresponds to the distribution of different cloudwater densities sampled on that surface. (Of course, if cloudwater density happened to have the same value at all points on the 12-degree temperature surface, we would see only one color.)

Naturally, you can do the opposite! First, make an isosurface of cloudwater density, say at the mean value of density. The mean value of a Field is taken as the default value by the Isosurface module: this is convenient when you start exploring a new data set and do not know what the extreme values are. Now map the temperature data onto the cloudwater isosurface. Run the output through AutoColor. The result will look very different. This time, you have "dipped" the cloudwater isosurface into a "bucket" of temperature data. Once again, this serves as a reminder that you must indicate to an observer exactly what kind of operation you performed if your visualization is to bear any meaning.

You can also dip the cloudwater isosurface into the temperature colors. To do this, first AutoColor the temperature data set. Then use Mark to "mark" the colors as data (this temporarily renames the colors component to data, while saving the original data component). Then use Map to map this marked Field into the cloudwater isosurface colors component. (It is necessary to mark the colors as data before mapping because Map always maps from the data component). An example visual program that performs each of these mapping operations can be found in `/usr/local/dx/samples/programs/UsingMap.net`.

Note that we changed the order of the modules slightly in the third example. In the second case, we Mapped data values from the "map" Field (cloudwater density) onto the "input" Field (the temperature isosurface), then AutoColored the resulting Field. In the third case, we AutoColored the "map" Field (temperature), then mapped color values onto the "input" Field (cloudwater density). This illustrates some of the flexibility of both the Map module itself and Data Explorer in general. In this case, the output image would be similar whether you colored by temperature then mapped, or mapped temperature first, then colored by temperature. There will be color differences if the range of values that mapped onto the isosurface is different from the entire data range used to AutoColor the entire temperature Field. You could avoid this problem by substituting a Color and Colormap pair in place of AutoColor, then connecting the original temperature Field to the input of the Colormap. This would automatically lock the minimum and maximum to the entire range of temperature, not just to the range of values that happened to fall on the isosurface.

But there are other cases in which commutative ordering of modules will yield a quite different visual output. For example, suppose we have a volumetric Field containing both vector data and a scalar data set. We can generate a series of Streamlines through the vector Field, Map the scalar data from the volume through which the Streamlines pass onto these lines, then AutoColor the lines according to the scalar data. To make the lines easier to see, we employ the Tube module to create cylinders along the path of each streamline. The radius of the Tubes can be adjusted until we get the look we like. By performing the operations in that order, the original colors are carried from the lines out to the outside of the cylinders, resulting in distinct circumferential bands of color on the Tube surfaces.

Now, change the order: create Streamlines, then Tube the lines. This yields uncolored cylinders. At this point, we Map the scalar data values from the volumetric Field in which the cylinders are embedded onto the surfaces of the cylinders, then AutoColor. This time, we will have patches of color on the cylinders, since it is highly unlikely that the volumetric data would lie in perfect rings around the outside of the tubes.

Which of the above two representations is "correct"? Both are accurate. Which you choose to show depends on the point you are trying to make. In the first case, you are illustrating the values of data precisely as they occur along the Streamlines: the Tubes are used to make these very thin lines more visible. In the second case, you wish to sample the data volume at a specified radius away from a given Streamline. By varying the radius of the Tubes, you can investigate phenomena such as the rate of change of the data Field as you move further away from the Streamline itself.

### Normals and Shading

Another Field component used in Data Explorer is the "normals" component. normals are unit vectors that tell the computer graphics program and the image renderer which direction is "up" or "out." Several tools, like Isosurface, automatically create a normals component so you do not have to calculate these numbers yourself.

There are two types of normals provided in Data Explorer, "connections normals" and "positions normals". Connection-based normals are vectors perpendicular to each connection element on the surface. They are created by the Normals module when you set the `method` input to "connections". The resulting surface reveals the underlying polygonal grid structure of your sample grid. Frequently, this is a valuable way to show your data, as any observer can then see the grid resolution directly. At the same time, this surface can be colored or color mapped either by connection-dependent or position-dependent data.

The other type of normals are created by the Normals module when you enter "positions" as the `method` (this is the default method, in fact). In this case, the surface will be much smoother in appearance yielding a more aesthetically pleasing surface at the expense of being able to directly perceive the grid resolution. It is sometimes less confusing to use position normals in place of connection normals because the object is less "busy" looking. You must be the judge of what is the appropriate way to observe your own data. You can also show your data first with connection normals, to illustrate the sample resolution, then switch to position normals in order to better show some other aspect of your data.

Normals are used by various modules in Data Explorer. One use of this information is that it is required by the image renderer (the Image, Render, and Display modules all incorporate the image renderer) to calculate the amount and direction of light falling on an object's surface (we will discuss this in more detail below). Rubbersheet assumes that the input grid or line is flat (if there is no "normals" component in the input Field) and projects the values in a perpendicular direction. However, you may wish to create your own normals or modify an existing "normals" component (using the Compute module, for example) and Rubbersheet will then use the modified normals to control the direction of projection of the surface or line. After performing the Rubbersheet projection, you may want to insert another Normals module. This will take the projected object and generate real surface normals before rendering, resulting in better-looking shading on you projected surface. See RubberSheet in IBM Visualization Data Explorer User's Reference for a full description.

Isosurface will also generate normals automatically; to do so, Isosurface either calculates or reads the previously calculated Field gradient (depending on the setting of the `gradient` input flag). Therefore, the normals generated by Isosurface are not necessarily perpendicular to the connection elements generated by the Isosurface module, but better indicate the actual Field direction than simple perpendicular normals.

If you wish to understand Normals better, you can use the Glyph module to visualize them. First use Mark to mark the "normals" component. This makes Data Explorer treat the "normals" component as if it were the "data" component. Then, Glyph the Field. Finally, Unmark the `normals` to restore the previous `data` component to its proper place. By showing the normals as vector glyphs in conjunction with a surface, you should be able to see how different modules, like Rubbersheet and Isosurface, deal with these vectors.

Normals are also useful in helping you determine the "inside" and "outside" of an object. In addition to a "colors" component, which holds the color-mapped information for each data point in a Field, you can specify a "front colors" and a "back colors" component. Which is front and which is back is determined by the direction of the normal for that vertex (position normals) or polygon (connection normals). By setting different colors for the inside and outside of a complicated object, you may be able to understand its shape better. This technique can also be helpful when you are trying to convert a connection list like a finite element mesh into Data Explorer form. If you accidentally describe the "winding" (rhymes with "binding") of a polygonal face in the wrong order, the normal for that face will point in the wrong direction. Setting "back colors" to red and "front colors" to white will clearly indicate which faces are pointing the wrong way.

The Shade module employs the "normals" component; it will make a "normals" component if it does not already exist. Shade allows you to set up the lighting of your objects to make them more "realistic" in appearance. That is to say, when we observe a 3-dimensional object, the way light falls on the object is an important cue to our eyes that helps us understand the shape of the object. We expect the surfaces of the object that are generally facing a light source to be brighter than those that face away. Data Explorer, like other computer graphics rendering programs, takes the normal directions of the object surfaces into account when calculating the angle between the object, the light(s) in the scene, and the viewer's eye point (the camera in the scene).

In the real world, different materials react to incident light differently. For example, many metals scatter light causing the "specular" reflection to be more spread out than it is on shiny plastic surfaces. The specular highlight is the highlight (many types of cloth and other dull surfaces have no specular brightest spot on a shiny surface. Think of how the sun sometimes bounces off the hood of your car at just the right angle and makes a bright sharp reflection. By adjusting the "specular" and "shininess" inputs to the Shade module, you can make your object appear more metallic or more plastic. If you turn the specular value all the way to 0.0, you eliminate the specular reflection). This can be important if you are trying to make sense of color-mapped data, since the specular highlight will be a bright white area on the surface of the object (assuming the incident light color is white). This white spot or area could confuse a viewer who is trying to interpret the color mapping of the data.

Two other inputs in the Shade module (`diffuse` and `ambient`) are also used by Data Explorer when it lights an object. Diffuse light is light emanating from a direct light source, like the default Light in any Data Explorer network, or from Light modules you place in your network. Think of diffuse light as the light coming from a light bulb and falling on an object surface, like a light in your office shining directly on your desk. This property is called "diffuse" because it represents the way light bounces off a surface, depending on the "roughness" of the surface. The rougher the surface, the more the light rays are scattered ("diffused"). An extremely smooth surface tends to bounce light more uniformly to the eye. Ambient light is light that is indirect: for example, daylight coming through a window, bouncing off white walls and then impinging on your desk. Data Explorer automatically places an AmbientLight value in any scene, or you can override this value by placing your own AmbientLight module in a network. Ambient light is best thought of as a sort of "glow" emanating from a non-point source of light and therefore illuminating even the parts of objects that face away from the point light sources in a scene. If you remove the ambient light, the apparent "shadows" on an object lit only by a point source of light are much harsher.

Like Normals, the Shade module can light an object in two fundamentally different ways. If you enter "smooth" in the `how` input to Shade, the surface will appear smoothly rounded (assuming it is not completely flat to start with). This is equivalent to setting "positions" in a Normals module. Shade will, if necessary, create position normals, then light the object accordingly. Any point on a connection between positions will be lit by calculating an interpolated normal value between the position normals. If you choose `faceted` in Shade, the effect is the same as selecting "connections" in the Normals module. In this case, each connection element has one normal direction over the entire face. As a result, every point on a connection element reflects light exactly the same way. The image that you see will thus show faceted polygons. Once again, while this may make the object look less "realistic," it does more accurately reflect the sampling resolution of your data and may therefore be a more desirable image to show other viewers.

### Plots and Histograms

Data Explorer provides a Plot module that will give you a simple 2-D graphics plot of your data. This can be convenient for showing one parameter plotted "traditionally" while you show a colored 3-D height Field illustrating the same or other parameters, in the same scene.

Histogram regroups your data into a specified number of bins (it acts like a form of filter on your data). The output of Histogram is a new Field with connection-dependent data. The connections are the bars on the histogram (which can be plotted). The height of each histogram bar is proportional to the number of samples of original data that occur in the range covered by that bar. You can feed the output of Histogram through AutoColor then Plot to get a colored plot of the data distribution.

If the aspect ratio of the Plot is distorted, you can correct it in the Plot module. This will stretch the Plot out in either the X or the Y direction until you achieve the look you want. Visual designers recommend an aspect ratio of approximately 4 units wide to 3 units high; since this is also the aspect ratio of television, your image will be ready both for video and for print.

Be aware that "binning" your data with Histogram can sometimes create rather arbitrary distributions. It is important to make this clear to the viewer of your visualization. For example, by carefully selecting bin size, you may turn a unimodal distribution into a bimodal one. Which distribution is correct for the phenomenon under study must be determined by the underlying science, not by the arbitrary picture you create.

On the other hand, if you wish to actually redistribute your data rather than just show a histogram of its distribution, you can use the Equalize module. The output of this module is essentially the same scalar Field you fed into it, but the data values have been changed to fit the specified distribution. By default, the data values are changed to approximate a uniform distribution, but you can create your own custom distribution, like a normal Gaussian curve. Equalize is useful to reduce extreme values back to a range similar to the majority of data values. You may also wish to experiment with other data "compression" and "expansion" techniques by connecting your data Field to Compute and applying a function like "ln(a)" or "a^2", where "a" is the input Field.

### Rubbersheet

Another technique used to visualize data collected on a 2-dimensional grid is sometimes called a "height map." In Data Explorer, the Rubbersheet module will generate this for you. Conceptually, a height map is drawn by elevating the 2-D grid into the third dimension. Call it the Z dimension, with our original grid lying in the X-Y plane. The height or Z-value given to each vertex of the original grid is proportional to the specified scalar data value at that vertex. If the data were vector data, you could elevate the grid by the magnitude of the vector, since magnitude is a scalar value. The result usually resembles something akin to a relief map of the surface of the Earth with hills and valleys.

However, this brings up an important point that will occur elsewhere in Data Explorer (and visualization in general). Remember that the original data were collected on the X-Y plane (for example, our grass-counting botanist's data). It is one thing to indicate the different distributions of grass species by showing a 3-D plot of the numbers using a height map. But it is not correct to say, then, that the data values so shown were collected from these 3-dimensional positions: that would imply the botanist counted grass species growing in mid-air! This might be true in the Amazon, but not in Kansas.

That is, we may have counted 2 species at the grid point [x=0, y=0]. If we Rubbersheet using the species count as the Z deflection value, our 3-D height map will now have a point at [x=0,y=0, z=2] (if the Rubbersheet "scale" is 1.0 and the minimum count in our data set is 0). The data was not collected at that point but rather at [x=0,y=0, (z=0)]. For our convenience, Data Explorer maintains the original data values as if they were attached to the original grid. It is your responsibility to remember and, if necessary, make it clear to other viewers that the representation of the data in 3-D is not a "realistic" image of the original 2-D sampling space. Rather, Rubbersheet is used to visualize the "ups and downs" in the data Field as actual differences in height. This is a very powerful visualization technique because of our familiarity with actual heights in everyday experience. One simple way to show viewers the difference is to make two copies of the Field by taking two wires from the output tab of the Import module you use to import the data Field. Connect one wire to a Color module with a Colormap attached, but leave the Field 2-dimensional. Arrange the 2-D colored grid such that the viewer is looking straight down on it. Connect the second wire from Import to Rubbersheet and then use a second Color module, but run wires from the same Colormap as you used to color the first copy. The second copy, a 3-D colored "height Field", can then be rotated into a "perspective" view. The result will be a Field both colorized according to the data values and also elevated into the third dimension according the same data values. This redundancy is often more instructive than either visualization technique used alone.

### Transformations and Structuring

Rotate, Scale, Translate, and Transform are all special types of operations that change the location, orientation, or size of objects in your scene. These operations can be performed anywhere in a visual program. You can create "hierarchical" motion by attaching Rotates and Translates to individual objects, then Collect these objects together and attach another Rotate and Translate to the Group (output of Collect). In this fashion, you can individually rotate members of the group independently of each other, or you can rotate the entire group as one.

By default, many modules operate on the "data" component. We have been treating "data" as a special kind of numeric Array, separate from "positions" and "connections". We mentioned earlier that you can have several different "data" components, but each must have a unique name; for example, your input data file can contain "positions", "connections", "temperature" (data), and "wind" (data). For this example, assume that "wind" is a 3-D vector.

Using the Structuring category tools Mark and Unmark, you can convert any Field component into the "data" component. When you Mark "wind" for example, the old "data" component (if any) is moved into a safe place called "saved data" and the "wind" values are copied into the "data" component. Since "wind" is a 3-D vector, the new (current) data component becomes a 3-D vector also. The Compute module is used to make changes in the data component of a Field. So by multiplying the first (x) component of our 3-D "data" we are, in effect, scaling in X. For example, the Compute expression in this case would be "[a.x * 2.0, a.y, a.z]" to double the size of each x component of each "data" point while leaving the y and z components the same. Any module connected to the output of Compute will see the scaled "wind" values as the "data" component of the Field. However, the old unscaled "wind" values are still kept in memory, also. By connecting other modules to the originally imported "wind" values, you still have access to those original values, at the same time. To operate on the "temperature" data, first use Unmark to return the "data" to the "wind" component. The result will be to place the scaled "wind" values into the "wind" component for all modules connected to the output of Unmark. Unmark also copies back all values from "saved data" into the "data" component. Then, you can Mark "temperature" as "data" and perform operations on it, if you like.

Since "positions" are also 2-D or 3-D vectors, you can Mark "positions", perform operations on the grid itself, then Unmark "positions" to perform operations on the "data". With a little knowledge of the correct matrix operations, it is possible to simulate the effects of rotations, translations, and scalings using this Mark technique. You can warp flat grids into cylinders or polar coordinate systems or create more complex objects like cones. In fact, there are already many macros available in the Data Explorer Repository that handle these types of operations using this technique, which you may wish to download and use yourself. (For the Data Explorer Repository, see "Other sources of information".)

### Vector Fields

Vector-valued data sets occur very frequently in visualization. Data Explorer offers three ways to visualize vector Fields: vector glyphs, streamlines, and streaklines. For this example, assume that we acquired data on wind velocity and direction in the atmosphere.

Recall that a "glyph" is a visual object; a Field of glyphs is made by copying a generic object, positioning each copy appropriately, and scaling or coloring each copy according to the data associated with that sample point. Vector glyphs resemble arrows or rockets and are generated for you by the Glyph or AutoGlyph modules. A vector Field, like any Field, must have a positions component to identify where the vector-valued data was sampled (even if the data is connection-dependent, it still requires positions). For Glyph realizations, a "connections" component is not required, but it may exist if the Field contained it for other purposes. Of course, a data component containing a vector quantity is needed. Each vector glyph will point in the direction of the vector given by the datum at that point, with the base of the vector fixed at the vertex position (sample point) for position-dependent data. The base of the vector is located at the center of the connection element for connection-dependent data. The length of each vector glyph is scaled based on the vector "magnitude", relative to all the other vectors in the data Field. Glyph and AutoGlyph offer a number of modifications you can make to achieve the appearance you desire. The effect of glyphing a vector Field is to create a "porcupine" plot with lots of arrows sticking out in various directions. This can become hard to interpret if there are many vector data points or, if one area of your data has very large values, the vectors may intersect or occlude each other. You can use the Reduce module (in the Import and Export category) to downsample the original data Field and thereby decrease the number of vectors in the image. Picking a reasonable reduction factor will permit the viewer to see the overall vector Field direction(s) while reducing the visual clutter.

You can also use the Sample module to extract a subset of points of the data Field. For example, you can select a subset of points lying on an isosurface; these data points can then be fed to Glyph. The effect in this case is to show the vector Field direction and magnitude sampled at the surface of constant value. This is another technique to reduce the number of vectors glyphed at the same time and may make it easier to perceive the structure of the vector Field.

Another technique for visualizing a vector Field relies on the concept that there exists a potential flow direction through the Field. Imagine releasing some very light styrofoam balls into our wind Field; each ball has a streamer attached to it. (Gravity and friction are ignored by the visualization tool; of course, you may have accounted for these forces in the simulation that modeled the vector Field, if these forces are relevant to your science.) We release the balls at one instant on one side of our Field and after they have passed through the Field, we take a snapshot of the streamers. This type of image is essentially what you get with the Streamline module. Streamline is used to visualize a flow Field at an instant in time; it assumes that you have a particular measure of a vector Field and wish to study the "shape" of that static Field.

Streamline produces a set of lines that show the flight path of each "ball and streamer." You can indicate the starting positions of these paths in a number of ways: essentially, any kind of object with positions can be the designated start point or points for Streamline. For example, you can use the Sample module to extract an arbitrary subset of positions from an isosurface, then treat this subset of positions as valid starting points for Streamline. You would see a set of streamlines that began on an isosurface and then traversed your vector Field. If you want to visualize the streamers' associated "twist," use the Ribbon module and use the curl and flag parameters of Streamline to force computation of the vorticity field. Streamlines can also start from a Grid, a list of positions, or a Probe. The Probe is a handy way to interactively investigate a vector Field; Probe tools are selected from the Special category. They are manipulated in the Image window; select `View Control...` from the Image window's `Options` menu, then choose `Cursors` from the `Mode` pop-up menu. Any Probes that you have placed in your visual program will be listed in another pop-up menu, so you can pick the one you wish to interactively manipulate. By dragging the probe through the vector Field, the Streamline starting point will follow the mouse pointer (again use `Execute on Change` to see this happen interactively).

Streakline is used to study a dynamic vector Field. Streakline is equivalent to taking a series of snapshots as our styrofoam balls and streamers (or just the balls without streamers if you like) fly through the vector Field, but with the additional fact that each time we take a snapshot, we import the next time step of our Field. That is, at each moment, we provide new data for vector direction and intensity at each sample point. As a result, you would expect the direction and speed of the balls and streamers to change as their flight is affected by the changing Field. This technique is often referred to as "particle advection."

Note that both Streamline and Streakline perform interpolation, so both modules require that your input vector Field has positions, data, and a "connections" component.

### Volume Rendering

Another way to examine data collected throughout a volume of space is called volume rendering. Imagine a glass bowl full of lemon gelatin. Holding it up to a light, you can see through the gelatin because it is somewhat translucent. Now imagine that you have added strawberries to the bowl of gelatin before it set up. You can see the strawberries embedded in the gelatin. What is really happening, visually? Light shines through the mass of gelatin "accumulating" color. If you look through the top corner, it will appear somewhat less yellow than if you look through the thickest part. If the light strikes a strawberry as it passes through the gelatin, your eyes will detect an orange object with a distinct outline, which of course enables us to find the location of the strawberries in the volume of gelatin. The strawberry appears orange because its red color is partly occluded by the yellow gelatin: nevertheless, our brains convert the strawberry color back to red because it is a familiar object. If someone has added a fruit unfamiliar to you, you will have a hard time identifying the true color of the fruit, since our brains are not good at performing subtractive color calculations.

Volume rendering a data space yields an image something like our bowl of gelatin. By default, a volume rendering appears somewhat transparent. As light passes through from behind the volume toward your eye, it is absorbed more in areas of densely concentrated values. These areas will appear to be more "opaque." If you color-map your volume according to the data component, you will see indistinct colored areas in their relation to each other. For more detail on the "dense emitter" model used by Data Explorer, see "Opacities Component".

If we are looking for those areas of rain formation within a rain cloud data volume, we do not have a built-in conception of the "correct" color for such an area. The colors assigned will come from the color map we construct. If we map the 12 degree C area to red, as in the example above, the red-colored rain-forming areas seen through a yellow cloud will, in fact, be perceived as orange areas. We can temporarily hide the yellow cloud (by changing its opacity to 0.0 and its color to black) and entrain ourselves to see the red regions by themselves.

This is a fine point of perception, but it is important to be aware of. Perception of natural objects is greatly modified by psychological memories and judgements about their "correctness" in size, color, mass, and relationship to each other. Once we move into the abstract world of visualization, we have no firm psychological constructs on which to base our perceptions. While this may imply that we are working with a "clean slate"--no preconceptions, and an unbiased scientific viewpoint--just the opposite happens: we seek to impose interpretation on the scene and may ascribe invalid attributes to objects as we try to derive "meaning" from the scene. On one hand, this is precisely why we imaged the volume in the first place! We want to derive patterns or shape and then figure out why they exist. On the other hand, we can be fooled by our own eyes if we are not very careful to comprehend and explain to others exactly the assumptions we make as we convert our sample numbers into colored images.

By the way, you won't find a specific module named VolumeRendering. As it happens, any volumetric Field can be directly rendered by the Image module or the Render or Display modules. So if you simply Import your volumetric data, run it through AutoColor, and attach it to Image, you will get a colored volume rendering of your data space.

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