IBM Visualization Data Explorer QuickStart Guide

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3.7 Visualizing 3-Dimensional Data

The following examples illustrate several ways of visualizing 3-dimensional data.

Isosurfaces

This example uses cloud-water density data for a severe storm.

  1. Open and execute visual program .../Isosurface3D.net.

    The "isovalue" used for generating the isosurface that appears is, by default, the average of all the data values. (The default isovalue can be found by selecting Open Message Window in the Windows pull-down menu.)

  2. Change the isovalue:
    1. Open the configuration dialog box for Isosurface.
    2. In the value parameter field, set the value to "0.3."
    3. Click on OK and reexecute the visual program. The new isosurface is significantly smaller.

See Isosurface in IBM Visualization Data Explorer User's Reference.

Slices

Following are a few examples of how to generate and process data slices.

For 3-dimensional data on any type of grid or for non-orthogonal slices, use the MapToPlane tool. If the data set is on a regular grid, use the Slab tool to take slices along connection elements. You can use other tools (e.g., AutoColor or RubberSheet) on data slices just as you can on any 2-dimensional object.

  1. Open and execute visual program .../MapToPlane.net. The image is a colored plane through a 3-dimensional data field. By default, MapToPlane maps onto a plane at the center of the data. To change the orientation of this plane:
  2. Open the configuration dialog box for MapToPlane, change the value in the normal parameter field to [1 1 1] and click on OK. The change of orientation will appear when the program is reexecuted.
  3. Reexecute the visual program. MapToPlane performs the necessary interpolation for a data slice of any orientation in a 3-dimensional field.

    See MapToPlane in IBM Visualization Data Explorer User's Reference.

To visualize an orthogonal slice without interpolation, use Slab:

  1. Open and execute visual program .../Slab.net. The image is a translucent isosurface with a colored slice (or slab) cutting through it. To visualize a slice through another part of the isosurface:
  2. Open the configuration dialog box for Slab and change the position parameter value to "10."
  3. Click on OK or Apply.
  4. Reexecute the visual program. The position of the new slice is changed.

    See Slab in IBM Visualization Data Explorer User's Reference.

To create an animation that generates different slices of the data:

  1. Select Special in the categories palette and then Sequencer in the tools palette.
  2. Position the cursor to the right of Slab in the VPE.
  3. Open the Slab configuration dialog box.
  4. Click on the position toggle (unsetting the parameter value). The parameter field now reads "(all)" and the third input tab on the Slab icon (counting from the left) projects outward from the icon (instead of into it).
  5. Click on OK.
  6. Connect the output tab of Sequencer to this third input tab (i.e., "position") of Slab.
  7. Double click on the Sequencer icon to display the Sequence Control panel.
  8. Click on the frame button (...) to display the Frame Control panel.
  9. Reset the limits:
    1. Click on the min field, type "0," and press Enter.
    2. Click on the max field, type "20," and press Enter.
  10. Click on the Forward (>) button to play the sequence.

    See "Using the Sequencer" in this Guide and Sequencer in IBM Visualization Data Explorer User's Reference.

Streamlines

The Streamline module traces the path of a massless particle through a static velocity field.

  1. Open and execute visual program .../Streamlines3D.net. The image is a translucent isosurface with a single streamline starting from the point [25000 5000 25000] (as specified in the Streamline module's configuration dialog box). This streamline can be transformed into a ribbon:
  2. Select Annotation in the categories palette and then Ribbon in the tools palette.
  3. Position the Ribbon icon below Streamline in the VPE canvas.
  4. Disconnect Streamline output from Collect input and reconnect it to Ribbon input.
  5. Connect Ribbon output to Collect input.
  6. Reexecute the visual program. The streamline changes to a ribbon.

If you want the twist of the ribbon to represent the vorticity of the wind field:

  1. Open the Streamline configuration dialog box.
  2. Change the flag parameter value from "(input dependent)" to "1" and click on OK. Streamline computes the degree of twist from the vorticity of the wind field.
  3. Reexecute the visual program. The twist is greater in regions of higher wind vorticity.

To make the color of the ribbon correspond to wind velocity:

  1. Select Transformation and then AutoColor in the palettes.
  2. Position the AutoColor icon between Ribbon and Collect in the VPE canvas.
  3. Disconnect the Ribbon output from the Collect input and reconnect it to the first (leftmost) input of AutoColor.

    Note: Both input tabs can accept a connection, but the semi-highlighting indicates required input (i.e., the module cannot function without it).

  4. Connect the first (leftmost) output of AutoColor to the available input of Collect.
  5. Reexecute the visual program. Note the variation of color in the ribbon.

    See Ribbon and Streamline in IBM Visualization Data Explorer User's Reference.

3-D Scalar Glyphs

Scalar glyphs can represent 3-dimensional as well as 2-dimensional data.

  1. Open and execute visual program .../AutoGlyph3DScalar.net. The spherical glyphs on the isosurface represent a subset of the data elements.
  2. To visualize the entire data set:
    1. Disconnect the Map output from AutoGlyph.
    2. Connect the output of the left-hand Import module to the first ("data") input tab of AutoGlyph.
    3. Reexecute the visual program. The number of glyphs is greatly increased.

You can also create your own glyphs (both scalar and vector). For example:

3-D Vector Glyphs

Vector glyphs can represent 3-dimensional as well as 2-dimensional data.

  1. Open and execute visual program .../AutoGlyph3DVector.net. The image is a set of 3-dimensional arrow glyphs on an isosurface.
  2. To visualize the entire data set:
    1. Disconnect Map output from AutoGlyph.
    2. Connect the output of the left-hand Import module to the first ("data") input tab of AutoGlyph.
    3. Reexecute the visual program. The number of glyphs is greatly increased.

Volume Rendering

Volume rendering is a technique for using color and opacity to visualize the data in a 3-dimensional data set. (In contrast, surface techniques use tools like Isosurface and MapToPlane to display a 2-dimensional surface, although in 3-dimensional space.) The following are some simple examples.

  1. Open and execute visual program .../VolumeRendering.net. As the network in the canvas shows, the color of the volume is determined by AutoColor. The data set contains relatively few high values (red) and relatively many low values (blue). No structure is apparent in the image.
  2. Select Transformation and then Equalize in the palettes.
  3. Position the Equalize icon between Import and AutoColorin the VPE canvas.
  4. Disconnect Import output from AutoColor input and reconnect it to the first input tab ("data") of Equalize.
  5. Connect Equalize output to the first input tab ("data") of AutoColor.
  6. Reexecute the visual program. Equalize redistributes the data values more or less uniformly between the minimum and maximum of the data. Although the resulting image is somewhat diffuse, the structure of the data (the electron density of an imide molecule) is now visible.

AutoColor parameters can be used to add definition to the structure.

  1. Delete the Equalize module: Click on the icon and select Delete in the Edit pull-down menu. The connections to Import and AutoColor are automatically deleted along with the icon.
  2. Reconnect the Import output to the first input tab ("data") of AutoColor.
  3. Open the AutoColor configuration dialog box.
  4. Set the value of the min parameter to ".1" and click on OK.
  5. Reexecute the visual program. All data values smaller than 0.1 are rendered invisible (black). The image is much darker, but still visible.
  6. To increase the visibility of the data, increase the value of the intensity parameter in the AutoColor configuration dialog box to "5."
  7. Click on OK and reexecute the visual program. The structure of image is now fairly distinct.

A color map gives you much greater control over the appearance of the image:

  1. Disconnect AutoColor from Image and connect the Color output to the Image input.
  2. Reexecute the visual program.
  3. Bring up the Colormap Editor by double clicking on the Colormap icon. The color-bar, Hue, and Opacity settings are clearly reflected in the image: regions of low data values (green) and smaller regions of higher data values (red). All other data values have been rendered invisible.

    Note: To make a region or volume invisible, it is necessary to set both its intrinsic opacity and its color value to zero. The reason is that the volume rendering model assumes that regions emit light as well as absorb it. So even if its opacity is zero (no absorption), a region will still emit light unless its color is black ([0 0 0]).

It is interesting to contrast the volume rendering of previous images with a surface technique. For example:

  1. Disconnect Color from Image and connect the Isosurface output to the Image input.
  2. Reexecute the visual program. The resulting image is an isosurface representation of the structure of an imide molecule.

You can also combine surface techniques with volume rendering. For example:

  1. Select Structuring and then Collect in the palettes.
  2. Position the Collect icon above Image in the VPE canvas.
  3. Disconnect Isosurface from Image.
  4. Connect the first output tab ("mapped") of AutoColor to either of the Collect input tabs.
  5. Connect the Isosurface output to the other Collect input tab.
  6. Connect the Collect output to the Image input.
  7. Reexecute the visual program. The result is a combination of the volume-rendering and isosurface images of the imide molecule.
  8. To make the isosurfaces translucent, insert a new Color module (from the Transformation category) into the network between Isosurface and Collect. (Use the first, or "input," tab of the Color icon.)
  9. Open the Color configuration dialog box and set the opacity parameter to ".3." (You can try other values as well.)
  10. Click on OK and reexecute the visual program. The isosurfaces are now translucent.

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