Exercise 3: Visualizing soil contamination and thyroid cancer rates

Complexity: Beginner Data Requirement: Installed with software Data Path: See Copying the tutorial data Goal: Use ArcScene and geoprocessing tools to compare two surface created from point data

In 1986, after the catastrophic accident at the Chernobyl nuclear power plant in Ukraine, a large amount of radioactive dust fell on Belarus. Since then, scientists have studied the aftermath of the accident. One tool for exploring the data is 3D visualization. In this exercise, you will create two surfaces from point data collected in Belarus. One set of points contains measurements of soil CS137 concentrations. CS137 is one of several radioactive isotopes released by the accident. The other set of points shows the rates of thyroid cancer, aggregated by district, with the sample point placed near the district centers.

The CS137 contamination and thyroid cancer data was supplied courtesy of the International Sakharov Environmental University.

Viewing the point data

First, you will open the Chernobyl scene and view the point data.

Steps:

1. Start ArcScene by clicking Start > All Programs > ArcGIS > ArcScene 10.
2. On the ArcScene - Getting Started dialog box, click Existing Scenes --> Browse for more.
If you already have ArcScene open from the previous exercise, simply click File and click Open.

3. Navigate to Exercise3 and click the Chernobyl ArcScene document.

4. Click Open.

   The CS137 soil measurements are shown with small point symbols, using a graduated color ramp to show the intensity of the contamination. The districts’ thyroid cancer rates are shown with larger symbols, using a different color ramp.

Creating 3D point features

The soil CS137 samples are 2D points with some attributes. One way to view 2D points in 3D is by setting an extrusion expression, or a base height. You can also incorporate a z-value into a feature's geometry to allow it to be directly viewed in 3D without the need to set a base height from a surface or an attribute.

This exercise requires the use of 3D Analyst geoprocessing tools, so make sure the 3D Analyst extension is enabled so that you can access the full suite of tools available. You will use the Search window to quickly search for individual tools by their name or by function keyword.

Steps:

1. On the right side of the ArcScene window, move your pointer over the Search tab or click the Search tab to bring it into view.
2. Click Tools to set the search filter on the Search window.
3. Click inside the Search combo box and type feature to 3d by attribute and press ENTER or click the Search tool.

The search will return exact and relative keywords of tools. The hammer symbol left of the search results also indicates the item is a tool.
Using the tool search results, now you will create 3D point features from the soil CS137 points.
4. Click Feature To 3D By Attribute from the search results.
5. In the tool dialog box, click the Input Features drop-down list and click Subsample_1994_CS137.

6. Click Browse and set the Output Feature Class location to the 3D_Default geodatabase for the 3D Analyst tutorial data. Then type the output feature name to CS137_3D.
7. Click the Height Field drop-down list and click CS137_CI_K
8. Click OK.
You'll see a progress bar at the bottom of your document displaying the name of the currently executing tool. When the tool finishes executing, a pop-up notification will appear on the system tray. This is called background geoprocessing, which, by default, is turned on when the software is installed and opened. To disable background geoprocessing, use the Geoprocessing Options dialog box from the Geoprocessing main menu in ArcScene.

The features are converted to 3D point features; however, they still seem to be resting on a flat plane, because the CS137 concentration values range from 0 to 208.68, which is small relative to the horizontal extent of the data.

Increasing the vertical exaggeration

You will exaggerate the scene to show the new points with their height embedded in the feature geometry.

Steps:

1. Click View and click Scene Properties.

2. Click the General tab.
3. Click Calculate From Extent.

4. Click OK.
5. Click the Full Extent button.
Now that you can see the new 3D points in the scene, you can turn off the original CS137 sample point layer.
6. Uncheck the box in the table of contents beside Subsample_1994_CS137 and click the minus sign beside the box to hide the classification.

Extruding columns

Viewing points in 3D space is one way to investigate data. Another way is to extrude points into columns. You will extrude the thyroid cancer points into columns to compare them to the contamination data.

Steps:

1. Right-click ThyroidCancerRates and click Properties.

2. Click the Extrusion tab.
3. Check to enable Extrude features in layer and click the Calculate Extrusion Expression button.

4. Click INCID1000 (the rate of cases per 1,000 persons).
Because the z-values of the phenomena that you are comparing have different ranges, you will multiply the cancer rate by 100 to bring the values into a range similar to that of the CS137 measurements.
5. Type *100.

6. Click OK on the Expression Builder dialog box.
7. Click OK on the Layer Properties dialog box.
Now the district centroid points are shown with columns proportionate to the thyroid cancer rates. If you navigate the scene, you will see that the areas with the highest contamination levels also tend to have high thyroid cancer rates, although there are areas with lower CS137 contamination levels that also have high cancer rates.

Creating a surface from point sample data

You know what the soil concentrations of CS137 are at the sample point locations, but you do not know what they are at the locations between sample points. One way to derive the information for locations between sample points is to interpolate a raster surface from the point data. There are many ways to interpolate such surfaces, which result in different models of varying accuracy. In this exercise, you will interpolate a surface from the samples using the Inverse Distance Weighted (IDW) interpolation technique. IDW interpolation calculates a value for each cell in the output raster from the values of the data points, with closer points given more influence and distant points less influence.

Steps:

1. Click the Catalog tab to expand the Catalog window.
2. Scroll to find Toolboxes.
This is another way of finding tools as an alternative to using the Search window. The Catalog window also maintains all the toolboxes.
3. Expand Toolboxes, click System Toolboxes, then expand the 3D Analyst Tools toolbox.
4. Navigate to the Raster Interpolation toolset and double-click the IDW geoprocessing tool that appears in the lower window.

5. Click the Input point features drop-down list and click Subsample_1994_CS137.
6. Click the Z value field drop-down list and click CS137_CI_K.

7. Verify that the Output raster location is set to the default geodatabase (3D_Default.gdb),then change the output raster name to CS137_IDW.
Otherwise, click the Browse button to set the output raster location and click Save.
8. Click inside the Output cell size box and increase the value to 5000.
9. Click OK.

   ArcScene interpolates the surface and adds it to the scene.

Viewing the interpolated surface

Now that the surface has been added to the scene, you can see that there are two areas with very high concentrations of CS137. You will view the surface in perspective, with a new color ramp, to better see its shape.

Steps:

1. Right-click CS137_IDW and click Properties.

2. Click the Symbology tab and select Stretched from the Show category.
3. Click the Color Ramp drop-down arrow and click a new color ramp.

4. Click the Base Heights tab.
5. Click Floating on a custom surface.
Confirm that the IDW surface is listed as the custom surface.

6. Click OK.
7. Uncheck CS137_3D in the table of contents.

Now you can see the interpolated surface of CS137 contamination, along with the thyroid cancer rate data.

Next, you will select the province centers with the highest rates of thyroid cancer.

Selecting features by an attribute

Sometimes it is important to focus on a specific set of data or specific features. You can select features in a scene by their location, by their attributes, or by clicking them with the Select Features tool. You will select the province centers by attribute to find the locations with the highest rates.

Steps:

1. Click Selection and click Select By Attributes.

2. Click the Layer drop-down arrow and click ThyroidCancerRates.
3. Double-click INCID1000 in the fields list.

4. Click the >= button.
5. Type 0.5.
6. Click Verify to check the selection expression you have built.
7. Click Apply.
8. Click Close.

The province centers with thyroid cancer rates greater than 0.5 cases per 1,000 are now selected in the scene. They are drawn in light blue to indicate that they are selected.

Viewing the attributes of features

You will investigate attributes of the selected locations and find out how many cases of thyroid cancer occurred in these districts.

Steps:

1. Right-click ThyroidCancerRates and click Open Attribute Table.

The Table window of the layer's attributes appears in the view.

2. Click the title bar of the Table window and drag it from its current location toward the center of the 3D view.
The guide diamond appears pointing towards the four edges of the 3D view where you can optionally dock the Table window.
3. Move the pointer toward the bottom guide arrow until it darkens to indicate the selected docking location.
A shaded outline of the window appears in the designated area.

4. Release the mouse button to dock the Table window in the bottom of 3D view space.

You can play with other arrow location on the guide diamond to see which location suits your preferences. For this exercise, we will continue having the Table window docked at the bottom of the view.
5. In the Table window, click the Selected button.

The table now shows only those features that you selected.
6. Right-click CASES and click Sort Ascending.

The selected province centers are sorted according to the number of cases.
7. Right-click CASES and click Statistics.

The total number of cases in the selected set of 11 province centers is 176.
8. Close the Selection Statistics dialog box.

9. Click the Navigate button and click on the scene.

You can work in ArcScene while the Attribute Table is open.
10. Click the Save button.

In this exercise, you have created 3D features, extruded point features, and interpolated a raster surface from a set of data points. You’ve compared the extruded vector data to the surface data and explored the attributes of the vector data.