Explore multidimensional soil data

First, you'll access an ArcGIS Pro project package from ArcGIS Online and download it to your computer. Once you have the project, you will explore a multidimensional voxel layer that contains geological data from the Netherlands.

Download the data

The project that you will use is on ArcGIS Online. You'll download it locally and work with it from your computer.

  1. Go the GeologicVoxels item on ArcGIS Online.
  2. Click Download and download the project package to a location on your computer you can easily remember.
  3. In the folder to which you downloaded the project package, double-click GeologicVoxels to open it in ArcGIS Pro. If prompted, sign in to your ArcGIS organizational account.
    Note:

    If you don't have ArcGIS Pro or an ArcGIS account, you can sign up for an ArcGIS free trial.

    This lesson was most recently tested for ArcGIS Pro 2.7. If you're using a different version of ArcGIS Pro, you may encounter different functionality and results.

    The scene displays a geological voxel layer and also contains a layer for buildings in Kamerik, a village in the Netherlands that you'll explore.

    Geologic voxel layer in scene

    Note:

    In this project, the voxel layer was added for you ahead of time. You can add your own multidimensional voxel layers, as a Net CDF file, from the ribbon, by going to the Map tab, in the Layer section, Add Data button, and by choosing Add Multidimensional Voxel Layer.

    In the Contents pane, the layer is symbolized discretely using a variable named meest waarschijnlijke lithoklasse, or soil or rock class description.

    Legend for geotop layer

    The layer is symbolized using unique values for each soil class, and one class for all other values.

Add descriptive symbology

The legend is not useful without a description of the color that is used for a category in the voxel layer. Next, you'll add descriptive information to the legend so you can tell which color is associated with each geological type. First, you'll visualize lithological categories with discrete voxel cubes, and see how the unique lithological classes are distributed in the region—most importantly, peat.

  1. In the Contents pane, right-click geotop and choose Symbology.

    The Symbology pane appears, showing the layer's symbology. Currently, the labels for each category aren't meaningful. You'll provide meaningful labels by editing each row in the Label column.

    No labels displayed

  2. In the Label column, double-click 0 in the first row to make it editable.
  3. Type Anthropogenic deposit and press Enter.

    First label edited

    Note:

    You can also double-click the next label to edit, rather than pressing Enter after each entry.

  4. For each remaining Value, edit the Label and replace the current value with the matching description:
    • 0Anthropogenic deposit
    • 1Peat
    • 2Clay
    • 3Sandy clay and clayey sand
    • 5Fine Sand
    • 6Medium grained sand
    • 7Coarse sand
    • 8Gravel

    The labels are updated in the Symbology and Contents panes.

    Geotop legend updated.

    While the labels provide a better description than a numeric value, the colors do not accurately represent the lithology. Next, you'll modify the color scheme of the layer to be more geologically relevant.

  5. In the Symbology pane, for Color scheme, click the menu and check Show names and Show all.

    Show names and Show all color schemes

  6. Scroll down and click Terra Tones.

    Terra Tones color scheme

    Once you assign the Terra Tones color scheme, the colors update in the Symbology pane.

    Terra Tones in Symbology pane

    Note:

    Colors from the color scheme are randomly assigned to each category. Your results may be different from the example images.

    The Contents pane also displays the updated legend.

    Terra Tones in Contents pane

    In the scene, the voxel layer symbology is also updated.

    Terra Tones symbology in map

    Note:

    You can modify the symbology of the individual unique values for a greater contrast by clicking the color symbol in the Symbology pane.

    Next, you'll display the voxel layer using a vertical exaggeration. It's common to apply a vertical exaggeration to subsurface data to visualize it better. If a 3D voxel layer occupies a large horizontal area, it might appear flat if no vertical exaggeration is applied. Using vertical exaggeration pronounces the dimensionality of your voxel data and can enhance its appearance and visualization.

  7. In the Contents pane, click geotop to select the layer.

    Selected geotop layer in Contents pane

  8. On the ribbon, on the Appearance tab, in the Elevation section, for Vertical Exaggeration, type 250 and press Enter.

    Vertical Exaggeration set to 250

  9. In the scene, click the wheel button on the mouse and move your pointer up and down to tilt the scene so you can visualize the vertical exaggeration.

    Scene tilted to view vertical exaggeration

    Now that you have the lithology symbolized correctly, you'll explore individual types. Each of the lithological classes have a unique value that can be explored by turning their visibility on or off. You'll turn off all values and then explore some values independently.

  10. In the Symbology pane, under Values, uncheck Visible.

    Visible check box

  11. In the Visible column, check the box for Peat to turn it on.

    Peat check box

    On the scene, only peat voxels display.

    Scene with only peat voxels being displayed

    Next, you'll use a bookmark to navigate to an area to explore its soils.

  12. On the Map tab, in the Navigate section, click Bookmarks and choose Green Heart.

    Select the Green Heart bookmark.

    Green Heart, the rural area between the major cities of Amsterdam, The Hague, Rotterdam, and Utrecht, contains many brown peat voxel cubes at land surface. This peat is currently at risk of oxidization, so this area is prone to land subsidence. To visualize the concentration of the voxels, you'll set a transparency.

  13. In the Symbology pane, click the color patch for Peat.

    Peat color patch

  14. Click Color Properties and set the Transparency to 80 percent.

    Transparency set to 80 percent

  15. Click OK.

    There is a dense concentration of peat in the Green Heart area.

    Dense peat in Green Heart area

    A signature example of a thick layer of peat underneath a building can be seen for the village of Kamerik. You'ill zoom to a bookmark of the village and explore its underlying peat.

  16. In the Contents pane, turn off geotop.
  17. On the Map tab, in the Navigate section, click Bookmarks and choose Kamerik.

    Village of Kamerik shown in scene.

    Peat is causing land subsidence and damage to the houses and the dairy farms around the village. The thin blue lines in the basemap are ditches used to drain the peat. Drainage is necessary to keep the meadows dry so cows from the dairy farms can walk around and eat from the grass. The water board/water authority keeps the area dry by lowering the phreatic groundwater level by pumping water out of the area through the network of ditches. As a result, the peat is exposed to air and oxidizes. Oxidizing means that the peat, which consists of dead plant material originally formed in swamps, is decomposed in CO2 and H2O. Oxidization of peat contributes considerably to the Dutch national CO2 emissions. In addition, the land surface is lowered. This means the groundwater table must be lowered even more, more peat is exposed to air, and the land subsides even farther, and so on.

  18. On the Quick Access Toolbar, click the Save button.

Next, you'll explore the underground lithology for the Kamerik area by creating an area of interest by slicing the voxels to view a subsection that exists under the village.


Analyze and animate voxel data

Viewing all the voxels at once provides great visualization for an entire area. To get a better idea of a specific area, you can slice the voxels to create an area of interest. The area of interest allows you to cut into the voxels to see exactly what is occurring in the area, whether it be above ground or underground. In this example, you can tell that peat is prevalent in Kamerik village, however, by viewing the entire voxel layer or just the peat, you cannot tell where the peat is below the ground. For example, if a developer wants to build in the Kamerik area, they would want to know about the peat because it can adversely affect the project.

Create an area of interest

You'll focus your analysis on Kamerik village so that you can visualize the lithology beneath it and determine whether it's suitable for development. To focus your analysis, you'll slice the voxel layer like a cake to eliminate all voxels around Kamerik, thus allowing you to see a clearer picture of the lithology for the area of interest. First, you'll turn off all basemaps and the ground surface so that these layers do not obstruct the voxels. You'll also offset the voxels so that they display directly under Kamerik village.

  1. If necessary, open your project in ArcGIS Pro.
  2. In the Contents pane, turn off World Topographic Map, World Hillshade, and WorldElevation3D/Terrain3D.

    2D Layers and Ground layers turned off

  3. In the Contents pane, click geotop, and on the ribbon, click the Appearance tab.

    You'll set a negative Offset to move the voxels below ground, rather than view it above ground. The voxel layer measures data up to approximately 50 meters, and you set a 250-meter Vertical Exaggeration value, so you'll set the Offset to ~50x250 = ~12,500 so that the top layer of the voxel appears on the basemap. The value varies slightly because of elevation variances in the area. For Kamerik, an offset of -12,080 makes it appear on the surface of the voxel layer.

  4. On the Appearance tab, in the Elevation section, for Offset, type -12080 and press Enter.

    Offset of -12080

    The Kamerik buildings now display close to the surface of the voxel layer, which will make creating the area of interest easier.

  5. In the Symbology pane, for Visible, click the check box to turn off all categories and click it again to turn on all categories.

    All categories visible

    All soil categories display in the scene.

    Buildings on top of voxels

    Note:

    Depending on the tilt angle, the voxels may not be visible at ground level. Zoom out to see them appear.

  6. On the scene, zoom out so you are not so close to the voxel layer.

    Zoomed out from Kamerik

    It is easier to slide the voxels when you are zoomed out from it. If you are too close to the voxel layer, it is like trying to cut a cake from within it. Zooming out provides more space to visualize the slices. In the Contents pane, the voxel layer has multiple components, such as Volume, Surfaces, and Slices.

  7. In the Contents pane, right-click Slices and choose Create Slice.

    Create Slice option

    When you click Create Slice, the Slice and Section toolbar opens near the bottom of the scene.

    Slice and Section toolbar

    From the Slice and Section toolbar, you can create slices, and modify them using the other tools. You'll create vertical slices to view the soil under Kamerik village. The Vertical Slice tool is active by default.

    You'll create four slices that designate the perimeter of Kamerik village, using the buildings as a guide.

    Note:

    The screen shots are to be used as a reference to show you where to click for the slices. However, exactly where you click does not matter when you are creating a perimeter around the buildings.

  8. On the scene, click one time near the following location to start the slice.

    Slice start point

    Once you click to start the slice, you'll see the voxel slice preview.

    First slice added

  9. Click a second time to complete the slice, making a vertical line to the west of the village.
    Note:

    Be sure to click within the voxels, not in the white space.

    Southwest corner of the slice

  10. In the Contents pane, right-click Slices and choose Create Slice.
  11. On the scene, click the voxels on the other side of Kamerik village.

    Second vertical slice

  12. Click a second time to complete the slice.

    Second vertical slice completed

    The voxels are on the other side of Kamerik. You want to view the voxels beneath Kamerik, so you'll flip it.

  13. From the Slice and Section toolbar, click the Flip button.

    Flip button

    Now the visible voxels are under Kamerik village.

    Voxels under Kamerik village

    Next, you'ill create two more slices to clip out only the area under Kamerik village.

  14. In the Contents pane, right-click Slices and choose Create Slice.
  15. On the scene, create a slice to the north of Kamerik village by clicking one time within the voxels on each side.
  16. From the Slice and Section toolbar, click Flip.

    Three slices completed

  17. In the Contents pane, right-click Slices and choose Create Slice.
  18. Create another slice for the south side of Kamerik village.
  19. Click anywhere in the scene to deselect the slices.
  20. On the Map tab, click the Explore tool and tilt the scene to view the voxels beneath Kamerik village.

    Area of interest completed

    After creating the area of interest, you can see the entire lithology under Kamerik village. You can turn off all categories and view them separately to see the prevalence of each lithological class. At a glance, there is a dense concentration of peat near the surface.

  21. In the Contents pane, right-click geotop and choose Symbology.
  22. Uncheck Visible and turn on Peat.

    Peat beneath Kamerik village

    There is a dense concentration of peat at the surface, which has caused the land in Kamerik to subside by up to four meters in the past 1,000 years. Developers and city planners in the area must prioritize this actively.

  23. Turn on and off the various lithology categories to view their voxels. When finished, make all categories visible.
  24. In the Contents pane, turn off Slices.

    Slices turned off

    You've created an area of interest for Kamerik village by slicing the voxel layer to explore the soil concentrations beneath the village. Slicing the voxel layer and viewing the area of interest gives you more insight into a specific area to help you make data-driven decisions.

Create an animation of the coastal lithology

The main line of defense against the rising sea level is the range of sandy beaches and coastal dunes. Next, you'll explore the unique coastal geology of the area. You'll view bookmarks for several places of interest and explore the lithology along the coast. The bookmarks were set up in the project for use in the animation that you are about to create.

  1. In the Contents pane, turn on World Topographic Map, World Hillshade, and WorldElevation3D/Terrain3D.
  2. On the Map tab, in the Navigate section, click Bookmarks and choose Coastal Geography - 1.

    Coastal Geography - 1 bookmark

    The scene zooms to the coast.

    Lithology of coastal areas

    The coastal dunes display as mountains of medium-grained sand voxels. In areas where the dunes are small, low, or even absent, the coastline is being reinforced by dikes. You'll explore these areas using bookmarks.

  3. On the Map tab, in the Navigate section, click Bookmarks.
  4. One by one, click each of the Coastal Geography bookmarks to view them.
    Note:

    You must click the Bookmarks button each time you want to view a different bookmark.

  5. On the Map tab, in the Navigate section, click Bookmarks and choose Zuiderzee Works.

    Zuiderzee Works area

    The last bookmark is the Zuiderzee Works area, declared as one of the seven wonders of the modern world. This area was a series of dams, land reclamation, and water drainage projects. At first, some dams or dikes were built to separate the Zuiderzee (South Sea) from the North Sea. The biggest dam was the Afsluitdijk (closure dike). As a result, the South Sea was completely cut off and became a lake called the IJsselmeer.

  6. In the Contents pane, turn off the geotop layer.

    Shut-off dike on basemap

    Once the voxel layer is off, you can see the Afsluitdijk (shut-off dike) as a thin strip on the basemap.

  7. In the Contents pane, turn the geotop layer on and click it to select it.

    You'll adjust the lighting of the voxel layer to achieve better contrast. Values are suggested, but you can adjust them to what you think looks good.

  8. On the Appearance tab, in the Lighting section, set Diffuse to 72 percent and Specular to 8 percent.

    Adjusted lighting

    Next, you'll create more bookmarks for your animation.

  9. Pan along the coastline and locate other visually appealing areas. From the Map tab, in the Navigate section, click Bookmarks and choose New Bookmark.
  10. Name each bookmark accordingly, based on what is being shown.

    Next, you'll create the animation.

  11. On the View tab, in the Animation group, click Add.

    Add button

    The Animation Tab becomes visible on the ribbon and the Animation Timeline pane appears.

  12. On the Animation tab, in the Create section, click Import and choose Bookmarks to Fly-Through.

    Bookmarks to Fly-Through option

    All the bookmarks are added as frames in the animation timeline.

    Bookmarks in Animation Timeline

    Note:

    Your bookmarks may be different based on where you zoomed to and how many you added.

  13. In the Animation Timeline pane, click Play.

    Play button

    The animation flies through the bookmarks in the order in which they appear in the Bookmarks pane.

    Note:

    You can change the order of bookmarks in the Bookmarks pane by dragging them up or down in the list. You can also change the order in the Animation Timeline, Keyframe Gallery, by dragging the keyframes to a different place in the animation.

    At the end of the animation, you can choose to add a circle around the animation to focus on an area of interest and show it from different views.

  14. On the Animation tab, in the Create section, click Import and choose Circle Right Around Center.

    Circle Right Around Center option

  15. On the Animation Timeline, click Play.

    When the animation reaches the final keyframe, it circles to the right around it to provide views from every direction. Next, you'll export your animation as a movie.

  16. On the Animation tab, in the Export section, click Movie.

    Movie button

  17. In the Export Movie pane, for Movie Export Presets, click HD720.

    Export movie settings with HD720 selected

    Note:

    A higher resolution will take longer to complete, but you can choose a smaller resolution to expedite the process. You can also customize the export options for a faster or higher-quality export.

  18. For File Name, accept the default path of ..\Documents\ArcGIS\Media to store the video there.
  19. Click Export.
  20. When the movie has finished exporting, browse to the folder where you stored it and watch it.

You can now share this video. When many stakeholders are involved, animations can help you tell a story with a map or a scene and then export it as a video to share. This makes your analysis accessible.

You've worked with complex subsurface data that has been interpreted into discrete categorical values that you visualized and analyzed using a voxel layer. Through the process of visualizing the lithological classes in the Netherlands, you can now estimate the importance of peat in the Netherlands' geology, as it has shaped much of the country’s history, policy, and environmental reality. By using the Netherlands' geological categories visualized with voxel layer functionalities, you created slices, areas of interest, and exported various views of the voxel layer as a movie for effective storytelling.

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