Improve the quality of water features using a Waterbody Mask

[dozer]

Overview 

The waterbody mask feature is available as of Site Scan’s latest release v4.210. This offers an important improvement to processing quality in the Reality Engine for projects that contain water areas like coastlines, lakes, and rivers.

Background

Water is notoriously difficult in photogrammetry. Its homogenous appearance makes it difficult to find unique keypoints to match between images. Furthermore, the sun can create severe glare effects that confuse photogrammetry engines, especially because the location of the glare is always relative to the sensor’s location (which is changing constantly throughout the drone’s mapping mission). Finally, water is often in motion which makes it even more challenging to map.

As a result, areas of water are susceptible to interpolation artifacts and in severe cases, holes in the output data.

The waterbody mask feature involves a user-defined polygon to designate where water is supposed to be. When the Reality Engine knows this information, it will apply a different algorithm to more reliably reconstruct the water’s surface. 

When using a waterbody mask, you can expect the quality of the water features for all data products to improve.

Procedure

Create a waterbody mask by using a copying the geometry of a volume measurement that has been pinned to the project, or by drawing a polygon directly. This is somewhat like using a Mission Area polygon.

Add a waterbody mask from project measurement 

The main advantage to using a project measurement as your waterbody mask is that you can use the exact same polygon for multiple missions in your project. This is helpful if there is a static body of water on your site that you need to apply the same water correction feature for each survey mission in your project. 

1. Open your mission that contains water features on the site.
   
   Tip: If you don’t know where the water features are, process the mission first without using a waterbody mask to generate a True Ortho. Then, use the True Ortho to trace water features.
   
   
2.  Click on the Volume tool.
    
3. Draw a volume measurement that outlines the approximate water area.
   
   Tip: It is generally better to overestimate than to underestimate the water area. Site Scan always uses the Coarse waterbody option from the Reality Engine, which means that the polygon that you draw does not need to precisely follow the water’s edge. Non-water features within the polygon should be retained.
   Comparison between different waterbody inputs. Site Scan always uses the "Coarse" water body correction, which automatically detects and excludes non-water objects.
   
4. Rename the volume measurement if desired.
   Rename the polygon so that you and other project members can recognize it as the water correction feature.
   
5. Pin the volume measurement to the project.
   Click the star icon to pin to the project. It must be pinned to the project to select it as a waterbody mask.
   
   
6. Click the Layers tab. 
7. Expand the Boundaries section, if it’s not yet expanded already. 
8. Under Waterbody Mask, click Add polygon. 
9. From the list, click the project measurement you created.
   All pinned project measurements will be available to select.
   Tip: If adding multiple project measurements, repeat steps 8-9 for each polygon.
   
   
10. In the upper right corner, click Save.
    All changes must be saved before processing.
    

Now that a waterbody mask has been saved to the mission, it will be used each time you process.

Draw a waterbody mask for one mission

If you do not use a project measurement, you can still add one or multiple waterbody masks for a single mission. These polygons will be saved to the mission but cannot be used for other missions in the project.

1. Open your mission that contains water features on the site. 
    
   Tip: Same as above, if you don’t know where the water features are, process the mission first without using a waterbody mask to generate a True Ortho. Then, use the True Ortho to trace water features. 
   
   
2. Expand the Boundaries section, if it’s not yet expanded already. 
3. Under Waterbody Mask, click Add polygon.  
4. Click Draw new mask.
   Draw a new waterbody mask polygon to use for the current mission only.
   
5. Draw a volume measurement that outlines the approximate water area. Double click to finish drawing. 
    
   Tip: Same as above, it is generally better to overestimate than to underestimate the water area. Site Scan always uses the Coarse waterbody option from the Reality Engine, which means that the polygon that you draw does not need to precisely follow the water’s edge. Non-water features within the polygon should be retained.
   
   
6. If your site has multiple water features, add another by clicking Add in the upper left and repeating step 5.
   If needed you can draw multiple polygons.
   
7. In the upper right corner, click Save. 

After saving your waterbody polygons, process the mission to generate outputs with waterbody corrections applied. 

The output quality of the coastline is improved after using the waterbody correction.
The waterbody correction applies to all output layers including the 3D mesh. Textured features within the waterbody polygon, such as the rock outcrops, are reasonably preserved, while the rest of the water area is flat.

Another example showing the waterbody mask polygon traced from the processed True Ortho (no water correction).
The water area is complete and smooth after reprocessing with the waterbody mask.

Delete waterbody masks 

You can delete waterbody masks saved to the mission if you change your mind and do not want to use the mask during processing. 

1. Under Waterbody Mask, click the options menu (ellipses). 
2. Click Remove all.
   Remove all waterbody mask polygons that are currently saved to the mission. Original project measurements will be unaffected.
   
3. Click Delete all. Deleting the waterbody mask will not delete the original project measurements.

If you only want to delete some polygons but not all, you can delete them by selecting the polygons on the map and clicking Delete in the upper left corner. You must be in "Edit" mode to select polygons on the map. To choose more than one polygon, use shift-click on the polygons you want to delete.
Delete individual polygons that you have selected from the map.

A few tips to using the waterbody mask feature

• While in “Edit” mode, you can add multiple polygons by either drawing them or by choosing them from the project measurements. Remember that if you draw a waterbody polygon with the draw function and not with the project measurement, it can only be used for the current mission. 
• All changes made in “Edit” mode must be saved by clicking Save in the upper right corner. 
• Polygons can overlap each other. 
• Polygons can extend beyond the mission area, but the processed outputs will only extend to the mission area. 
• A polygon cannot have self-intersecting geometry. You will be unable to save in this case. The invalid polygon should be edited or deleted to allow saving. 
• If tracing the waterbody polygon off of the basemap, note that the polygon may not  align with the actual water areas of your surveyed mission. That is why it can often help to process an initial True Ortho and trace the polygon based on that imagery.
• There is currently no option to use a shapefile as the waterbody polygon. If you have a water shapefile, you may upload it in the Files section and then trace a new polygon over the shapefile polygon. 

New in v4.213

We added additional editing options for configuring your waterbody polygons: Subtract and Combine.

You can now create ring-shaped polygons, which is helpful to mask water areas around an island. Trace two or more polygons, select the polygon that cover the area you want to subtract, and click the Subtract button. Make sure to save your changes.

The Subtract option removes all areas covered by the selected polygon.

You can also combine multiple waterbody polygons into one. This is helpful if you have a large, complicated water feature on your site that you want to trace using multiple polygons and merge later. Select multiple overlapping polygons using shift-click, then click Combine.

A bug was also fixed in v4.213 that caused the waterbody mask polygon to not properly apply in some missions with oblique images.

Thanks to those who have sent feedback already; we are open to additional feedback so that we can further improve on the feature.