ESM4714
Scientific Visual Data Analysis and Multimedia
Exercise #6: Using SpyGlass & NCSA Tools on the Macintosh

Objective:
In this exercise you will learn how to use two simple visual tools on the Macintosh: SpyGlass Dicer and Transofrm. You will also be introduced briefly to a similar public domain visual tool X-Image from NCSA.

Procedure:
Learning about Dicer.

Recall the turbine-fan CT scan data file. We will investigate the 3D gradients in density using Dicer and point out some of the major features of Dicer.

1. Open Users05 on the NT_SERVER in the Hancock Multimedia Lab

   Go to Chooser, find and highlight Multimedia Lab (HAN) & NT_SERVER

   

   Select OK button and then

   Enter the Name: multimedia and Password: given in class.

   

   In the Users05 folder find and open the ESM4714 folder.

   

2. Start Dicer:
   Double click (DC) with your mouse on folders in this exercise.

   DC on the ESM4714 folder which is located in User05 (Mac_Development, Mac_Production, Mac-Video)

   SpyGlass

   Dicer

   Spyglass Dicer 2.0

   

3. Load the file fan_64_sds.hdf in the folder "64".

   DC on SpyGlass Tools

   Examples

   Kriz

   Fan

   64

   fan_64_sds.hdf

   

   When you open the HDF file fan_64_sds.hdf the table below requests additional information before the 3D figure can be drawn. The most important item to check is the data range(minimum and maximum value). These values are typically set at -1.0 to 1.0 . Click on 'Survey' and then 'Use Survey' and watch the min. and max. change. Next click on Zoom such that the Pixels changes to 128 for Dim0, 128 for Dim1, and 124 for Dim2. Then click on 'OK' and the table will be replaced with what appears to be an empty room.

   The figure first appears empty until we click on one of the orthogonal plane icons. Move the mouse into the viewing area. Click and hold the mouse button down and move the dotted plane until the desired location is obtained. The information in the plane is drawn when the mouse button is released. The plane can be moved again by using the tongs.

   If the first three planes are located up against the two walls and the floor, we see only the shaft on the left most wall.

   Additional planes can be drawn in a similar fashion. Typically as each new plane is chosen we gain new information which affects how we choose the next plane or to modify the location of previous planes. At some point we start to lose information with too many planes. This is when we can take advantage of the transparency feature.

   Choosing three or more planes gives the viewer sufficient information to interpret, analyze and perhaps discover new information. Here we show the location of embedded flaws near the center line "rotation axis" of the turbine shaft. From a fracture mechanics view point the location and size of these flaws may or may not be significant. We can use this information as input to a finite element computer program where we can complete the anlaysis.

   

4. There are many more features, many which can be learned at this point by trial and error. We will introduce you to just a few more. After this exercise we encourage you to experiment on your own with other data sets in the example folder.

   Perhaps one of the most useful features is transparency. As previously mentioned, information is lost by having drawn too many planes. We can select a particular color representing a particular numerical value of physical significance. For example here the physically significant quantity that was removed was air. The result shown below is obvious

   Some of you have probably noticed that the turbine fan blade is not oriented the same as originally defined. This gives us the opportunity to make an interesting point, that is, the HDF file created by the FORTRAN program m_sds_hdf.f was changed by the order that the data was written to file fan_64_sds.hdf . On the other hand if we view the data stored in the file fan_64.bin (which was created by the C program from the same ASCII file fan_64.ascii) we will observe the data in yet another orientation.

   We will also take this opportunity to show you two other ways to load binary data into Dicer.

5. Start Dicer and open the file fan_64.bin in folder 64.

   

   Choose 'byte' from the Data Type box with your mouse and change dimensions on Dim0, Dim1, and Dim2 to 62, 64, and 64 respectively. Recall that the data in the file fan_64.ascii was generated in the opposite order. Also notice the short, long, and floating point binary data choices. Click on 'OK' and the same File Parameter table appears as before. Configure this table the same as was done befoe. Lets try something different. Lets fill up the entire volume instead of choosing a few planes.

   From the menu along the top bar:

   - under options: load all data

   - under Objects: Create -> Full Block
   OR you can select an arbitrary block size out of the total volume by using the Solid Fill Icon shown below

   

   - choose the solid icon and with the mouse select the far left wall to map out the desired plane dimensions. Without releasing the mouse button press "4" on the numeric key board (note: the number 4 on the regular keyboard will not work) and pull the plane to the right to define the volume. This requires some practice. When you release the mouse button the volume should fill with color: purple is the lowest density "air".

   Next, select Transparency under the Windows option on the main menu bar and erase away the "air" (purple-dark blue) by sliding the left most marker to the right..

   

   Another convenient way to load binary byte data without choosing the array dimensions is to append the filefan_64.bin with the array dimensions. That is, rename the file to fan_64.bin(62x64x64) and information in the filename is used automatically to load the dimensions of the file the user goes immediately to the File Parameter table.
   The FINAL Dicer feature we will show you is how to generate and play back an animation sequence.

   Start Dicer the same as before.

   - Open file fan_64.bin(62x64x64) in folder 64.

   - Click OK on generic file format table and the File Parmeter table apprears.

   - Configure this table the same as before.

   - Choose two horizontal planes: one at the very top and one at the bottom (see below.

   - Choose 'Select All' under Objects in the main menu and the table below appears.

   - Choose 'Save Image Sequence' -> 'Slices' under File in the main menu andthe table, shown below, appears.

   - In the 'Total number of frames:' box type in 10 frames total, choose PICS file, and click on Generate.

   

   When the sequence is completed, the table on the next page appears and requests a filename.

   

   Do not change the Output File Name and click Save. To play back this sequence return to the Dicer folder, open the Dicer Animator Folder, open Dicer Animator, choose Open from File in the main menu, and open the file fan_64.bin(62x64x64)-pics from the 64 folder. The animation should appear in the upper left corner. To play the animation select 'Forward' under 'Actions' of the main menu.

   This completes the features we will present for Dicer. There are many more features that you may want to try on your own during this exercise with the other data sources in the example folder.

You will now learn how to SpyGlass Transform for the analysis and interpretation of two-dimensional (2D) data sets. We will introduce ou to some of the many features in Transform. For this introduction we will choose the 30th plane from the hdf file fan_64_sds.hdf .

Start Tranform:
DC with your mouse on the folders in the sequence show below. DC(hard-disk: Mac_Development, Mac_Production, Mac-Video), SpyGlass Tools, Transform 3.02 (68K/PPC), Spyglass Transform 3.02 (68k/PPC)

Import the 3D file fan_64_sds.hdf from the 64 folder and selct the Y-Z plane and change the Slice Number to 30 and click on 'OK'.

A table of numbers, shown below, will appear. This table can be expanded by dragging the lower right corner to the right. Next, choose 'Generate Image' from 'Image' in the main menu. The image and expanded table are shown below.

Typically you would create a raster-image-set (ris) hdf file for your 2D data set, but here we chose to show you how to extract a 2D plane form a 3D hdf data set. You can also load the other binary data sets in the same folder. The newer version of Transform also allows you to open ASCII data type files. Also available from NCSA are two public domain software graphic tools, Image 3.0 and Datascope, which have similar features.

Notice that the highlighted numbers in the table match the rectangular box (see arrow) in the grayscale image. You can expand the table as large as you CRT can accomadate. With this tool you can recover your data quantitatively. You can also generate contour, line graph, wireframe-surface, shaded-surface, and color-bar. try each type of graphic tool. This Tile feature is consistent with Tufte's definition of good graphic practice using "small multiples".

The figure above was generated by choosing 'Line Graph' from 'Image' in the main menu. Pick a cluster of numbers in the table where there is a small gradient (continuous change) in density and you will notice that in the same grayscale region you will not be able to see any gradient. With this observation we make an interesting observation, that is, the human eye can not see all 256 shades of gray that is mapped to the CRT hence we need these other tools to reveal significant information.

Next we will contour plot from the same data. Select 'Contours' from 'Image' in the main menu and a table appears as shown below. There are a number of optins but perhaps the parameter that always needs to be changed is the number of contours levels. Change this number to 20 and choose the dashed lines for zero options and click on 'OK' and the contour image of the same data appears below. Notice that the same rectangular region appears for comparison with the other graphs and for comparison we have changed the color table from grayscale to rainboe. You can label these lines with their numerical equivalent.

Next we can create an interactive wireframe plot. Although this plot at first appears to be rather course, the trade-off here is for speed of plotting. Once you find the view point of interest you can increase the resolution as desired by chosing higher resolution in the lower right box. Below we show only two of the many choices. The figure below on the left first apperars when you hold down the mouse button and rotates with the movement of the mouse. When you let go of the mouse button the wire-frame image at the right appears.

For higher resolution we chose the 'Hi-res Framed Color Surface Plot'.

The final figure show the result of choosing the 'Tile' under 'Window' of the main menu.