"Candle in a Box"
NOESYS INSTRUCTIONS

(Long Version)

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In this experiment, you will use software (Noesys) to visualize data in 3 dimensions.
[NOTE: For your convenience, PLEASE print these instructions]

Noesys Instructions - Part 1 (longer form):

  1. Find and open Noesys on the Power Macs (BioIm3 and BioIm4) in lab room 158.
  2. Under File go to New.
  3. You get a Dialogue Box that shows you 2 folders; leave those in place.
  4. Now go back up to the Menu and go to Data and choose New Data Set. A new Dialogue Box appears; give it a name. It is already highlighted for you. (See Fig. 1)
  5. Notice where it says Dimension 1. Click on Dimension 1. (Double-click on it.)
  6. Name Dimension 1 "X-axis". (under Dimension 1 type in the name "X-axis")
  7. Under Dimension Size put 2 (because you are only going to put 2 values in it).
  8. Name Dimension 2 "Y-axis". And under Dimension Size put 2 (because you are only going to put 2 values in it).
  9. Under Add (click on Add), and set Dimension 3 - it’s going to become the Z- axis - and you’re going to type in 2, because you will only put in 2 data values.
  10. Then click "OK".
  11. You should have X-axis, Y-axis, Z-axis with 2, 2, 2. Then click "OK".
  12. You have now a 2-dimensional array that you might recognize as a spreadsheet. What you don’t realize is that you are looking at a 3-dimensional array.
  13. Notice on the screen that "X-axis" is Dimension number 1 and "Y-axis" is Dimension number 2 and Dimension number 3 should be the "Z-axis" for the Glider Box. (See Fig 2.)
  14. Find a small Glider Bar with "Z-axis" written below it down in the lower right-hand corner. If the Glider Box is all the way to the left on the Glider Bar you are in Z-1. If the Glider Box is all the way to the right on the Glider Bar you are in Z-2. If you are in the box # 1 under X-axis, you are in 1:X; If you are in the box # 2 under Y- axis, then you are in 2:Y. So by clicking on the spread sheet and by moving the Glider Box, you are actually in three different planes of data.
  15. Leave the orientation on 3:Z, that is, put the Glider Box all the way to the left. The spreadsheet should also be in 1:X and 2:Y as well.
  16. Now, use your temperature data from your Lab Worksheet in part a) "baseline temperatures" under part 1"Temperature Data". Enter your temperature value for X1, Y1, Z1 in the spreadsheet section for X1, Y1, Z1 by double-clicking on the "0" and typing in your value.
  17. Now move to the box in the spreadsheet for be X2, Y1, Z1 and enter your data from X2, Y1, Z1.
  18. Now do the same for the X1, Y2, Z1 box. And the same for the X2, Y2, Z1.
  19. Now click the Glider Box and put it into Z2. You should now see a new box full of "zeroes" because you are at a different plane of data.
  20. So now you are going to enter values for X1 Y1 Z2 and for the rest of the the Z2’s.
  21. At the end you should have filled in a 3-dimensional matrix, which is a 3-D spreadsheet.
  22. Now you have to save your entries.
  23. Go over to File, then to Save. Notice it ends with the extension term "hdf". The "hdf" is a file structure that this software works with, so it automatically adds the ".hdf" to the filename.
  24. You should save your file to the Desktop and give it a unique name. It is important to use a unique name so you are not using a name that already exists on another file. 25) When you have finished saving your file, you should see it appear on the Desktop.

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Noesys Instructions - Part 2:

  1. Now go back to the Noesys folder and open up T3D. (You are going to open up the software called T3D. It is in the Noesys folder. It is in the same place that you got Noesys 1.2 - it is part of a suite.)
  2. When it opens, go up to File and open the folder that you just saved. The software will now render your data and will display a 3-D graph of your data. You will be able to control and manipulate this 3-Dimensional image.
  3. If the displayed image is too small, then you can resize it. Look on the left side of the window; you should see a stack of icons. Find and click on the 6th icon down in this stack. It is the one with the arrow pointing back and forth next to a cube. A box should appear at the bottom of your window. Beside (to the right of) "Zoom", enter 0.75, and to the right of "Width" and "Height", enter 300 instead of 200 in each of the boxes. These are pixel values. Then click on the icon with the back-and-forth arrow. This will Rerender (redraw) the 3-D graph. You can also locate "Render" by looking in the drop-down menu under View.
    [note:     The rerendering process takes a while, so you have to be patient -- it shows you the progress of the rerendering process by displaying a box with a black bar that increases in height as the process proceeds.]
  4. To interpolate the graph, go up to Options, at the top of the window. Choose Rendering Options, and a box should appear in the lower left, below the window. In that box you should see "Interpolate". Click on that small box to the left of "Interpolate" and an "x" should appear in the box. Then move the cursor to the icon just above the box and click on it. This will interpolate the data and Rerender the graph. So instead of a "patchwork quilt" look, it will show a smooth gradient between different values.
  5. To change back to the uninterpolated graph, remove the "x" from the small box to the left of "Interpolate" by double-clicking on it. Then click on the icon just above the box, and it will Rerender the graph.
  6. To see a histogram of the range of values, go to, click on and hold down the View bar at the top of the window. Then move the cursor down the drop-down menu to "Range" and release. This will display a histogram of the range of values. The histogram spikes you see show you the values at those points. It should display the gradient of temperature change you have entered in the spreadsheet. Click on the small box in the upper left of that window to remove it.
  7. If you want to rotate the graph, look in the stack of icons on the left of the window. Find the 5th icon down, which has a cube with a curved arrow around it. You can click on that icon and then click on the cube, and it will change it to a cube with coordinates on it.
  8. You can change the orientation of the cube-graph and look at the image from the other side. Click on the image and drag it around. Now click on the icon with the curved arrow around the cube. This will Rerender the graph and display a graph with the new orientation.
  9. You can save a particular view of the image you have created as a Pic File. Click on File and select Save Image As on the drop-down menu. Type in a unique file name. Then click OK (or Save).
  10. If you have a color printer, you can send the file information to the printer and use the image for further analysis. You can also send the information to a black and white printer.


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