Lab 7: Research Sites, Part 2 - Creating Streams and Watersheds

Introduction

In the previous lab, we learned where to acquire data and how to perform a standardized quality assurance and quality control procedure. Now that we have the data, we will prepare it for analysis by projecting the data into the same projection and coordinate system. Once this is done, we will create some additional data sets and run some basic calculations.

The key questions we are trying to ask with this lab are:

1. How many streams are there in Arcata Forest, what is there length, and what is the total length of the streams?
2. What are the watersheds in Arcata Forestry and how large are they?

Learning Outcomes

• Use the " Project " tool to project data into the same spatial reference
• Create stream networks and watersheds from a DEM
• Use Raster Calculator for simple raster math.
• Create fields (attributes) and compute length and area.
• Create maps that convey results of spatial analysis

Walk Through: Projecting Vector Data

It is important that each layer in any analysis you perform have the same spatial reference system. This will minimize uncertainty and error. Any error related to map projections will at least be uniform throughout the analysis if they all share the same spatial reference system.

In this step we will project each of our data sets into NAD83 UTM Zone 10 North. If you will recall from GSP 101, this is an international coordinate system based on the Transverse Mercator projection. It is particularly accurate for regions with a North/South orientation, such as Humboldt County. UTM always uses meters as the linear unit.

1. Let’s begin by creating our standard folder structure on the local hard drive, "1_Orignals", "2_Working", and "3_Finals".
2. Download a copy of all the data sets for this lab to your "1_Orignals" folder using these two links: Data and Wetlands. These are all the data sets downloaded in the previous lab, plus one additional dataset containing information on the cell towers. The data from the web sites you downloaded in the previous lab may have changed and we want to make sure you are successful in this lab so we've provided a set we know will work.
3. Use the 7-Zip software to extract the zipped files.
4. Launch ArcMap and open a blank map document (.mxd).
5. Open the Catalog Tree and navigate to your originals folder.
6. Drag and drop the file containing the rivers and streams onto your map. It may be called "nhd24kst_I_ca023.shp".

This first layer is already in the spatial reference system we want to use, NAD83 UTM Zone10N. However, we should check to be sure.

7. Open the layer properties for "nhd24kst_I_ca023.shp" and check the spatial reference system.
8. If the spatial reference system is correct, give the shapefile a more meaningful name. Right click on the shapefile "nhd24kst_I_ca023.shp"in the Catalog tree and select "Rename". Change the name to "rivers.shp".

Next, we will add the remaining shapefiles one at a time. You may ignore any "Geographic Coordinate Systems Warning" that may pop-up.

9. Rename the shapefile "apnhum50sp.shp" to "parcels.shp" and add it to the map by dragging and dropping it from the Catalog tree.
10. Rename the shapefile "CA_Wetlands.shp" to "wetlands.shp" and add it to the map.
11. Rename the shapefile "CNTYOUTL.shp" to "county.shp" and add it to the map.
12. Rename the shapefile "humtrans3sp_2013130417.shp" to "roads.shp" and add it to the map.
13. Rename the shapefile "humz33sp.shp" to "zones.shp" and add it to the map.
14. Rename the shapefile "nhd24kst_l_ca023.shp" to "streams.shp" and add it to the map.
15. Leave the LandSat image of Humboldt County ("LC80460322015046LGN00") alone for now. We will get to that later.

We have now loaded each one of the shapefiles. It is now time to use the "Project" tool to create copies of these files in the spatial reference system that we want, NAD83 UTM Zone 10 North.

15. Open the ArcToolbox by clicking on the red toolbox icon.
16. Navigate to "Data Management Tools", "Projections and Transformations", and select the "Batch Project" tool.

We could use the "Project" tool to create a copy of the shapefiles in the new spatial reference system one at a time. However, there is a script tool called "Batch Project" which allows us to load multiple files and project them all at once. It iterates though the list of loaded files and runs the "Project" tool for each one. To save time, we will use "Batch Project".

Remember, the rivers layer is already in the projection we want. We don't need to project this shapefile.

17. Double Click the "Batch Project" tool from ArcToolbox to open the tool.
18. Drag and Drop roads, zones, wetlands, parcels, streams, and county into the lined window of the "Batch Project" tool as shown above.
19. The "Output Workspace" wants a folder, NOT a file. Use the yellow browse button on the right to navigate to your "working" folder. Select the working folder and click add a new folder called "HumboldtCounty" and then click "Add".

20. Next to "Output Coordinate System" click on the icon to the right to choose the spatial reference system we want to use.
21. Expand the "Layers Folder". This folder contains a list of all of the spatial reference systems currently in use by ArcMap. Since our "Rivers" shapefile has the spatial reference system we want and it is currently loaded on the map, "NAD 1983 UTM Zone 10N" will appear on the list. Select "NAD_1983_UTM_Zone_10N" and click OK. See the image below.

22. Keep the remaining default settings and click OK.

Some of the files are rather large. It may take a few minutes to project them all. Please be patient.

Once the batch project tool is complete, you should see a copy of each of these layers in your "2_Working" folder.

Now, repeat this process for the vector data layers for Arcata Forest from last week and place them in a folder called "ArcataForest" in your "2_Working" folder.

Walk Through: Projecting Raster Data

Now that we have our shapefiles in the correct projection, we will do the same for our raster data. You will find that most tools require a separate set for raster and vector data. In this case we will use the "Project Raster" tool.

23. Navigate to "Data Management Tools", "Projections and Transformations","Raster", and select the "Project Raster" tool.
24. Drag and drop the LandSat image into the "Input Raster" field.
25. For the "Output Raster Dataset" be sure to save to your working folder. Call the output "LandSat.img". The "img" or "Imagine" file format is the best file format for rasters when working with ArcGIS.
26. For the "Output Coordinate System", open the Spatial Reference Properties window by clicking the icon on the right. Just as before, we will use the "Layers" folder to select "NAD_1983_UTM_Zone_10N".
27. Make sure to change the "Resampling technique" to "Bilinear" or you'll have really bad artifacts (vertical and horizontal lines) in your DEM. You won't see them until you run a hillshade or direction algorithm but they will be there.
28. Leave the remaining default settings as they are and click OK. See the image below for clarification.

Repeat these steps for the DEM from last week except, make sure to select "BILINEAR" for the "Resampling Technique" or you will have artifacts in your DEM that will show up when you create direction or hillshade rasters from it.

When completed, you should have two folders in your "2_Working" folder that contain data for Humboldt County and Arcata Forest. All the data should be in the same spatial reference and ready for us to do some Spatial Analysis!

Streams Data

Streams data is very important to natural resource research but it is also very challenging to find a "good" stream layer, especially at high resolution. In this step, we'll take a look at some existing stream layers and then create one of our own.

Clipping The Wetlands Data

One of the layers we want to look at are the wetlands for Californio but the data set is huge! Let's cut it down to just Humboldt County. In ArcGIS:

1. From the "Geoprocessing" menu, select "Clip"
2. For the "Input Features" use the "CA_Wetlands" shapefile.
3. For the "Clip Features" use the Humboldt County Boundary.
4. Set the "Output Feature Class" to "Humboldt_WetLands.shp" and save it in the "Humboldt_County" "Working" folder.
5. When you click "OK", ArcMap will take a few minutes and then should display a wetlands shapefile for just Humboldt County that will load and redraw much faster than the one for all of California.
6. 

Comparing Water Body Layers

1. In ArcMap, load the data sets for:
   1. Arcata Forest Boundary
   2. Arcata Forest Creeks
   3. Humboldt County Streams
   4. California Wetlands that were clipped to Humboldt County
2. Zoom in to the layers and take a minute to examine the layers.

Question 1: for your final report, create a map for each of the water body layers and mention the problems you see that might impact research in the forest.

Clipping Rasters to an Area

The bottom line is that none of the water body layers we have are going to work for the research we want to do in Arcata Forest. Because of this, we need to create a new stream layer. I recommend walking through these steps rather carefully as a wrong turn can cause your computer to crash or take a really long time to finish processing.

First, to make the stream network processes move really fast, we need to clip the DEM to just the area around Arcata Forest.

1. If the "Draw" tool bar is not visible, right click in the blank area of the menu bar in the top-right area of ArcMap and select "Draw".
2. Draw a "box" around Arcata Forest with plenty of room on the sides. The box should be about four times as large as the forest.
3. In the "Draw" toolbar, select "Convert Graphics To Features" in the "Drawing" menu. This feature allows us to convert a drawn element into a feature in a shapefile which is really handy.
4. Set the "Output shapefile" to be a file called "ClippingBoundary.shp" and store it in your "Arcata Forest" folder in your working folder.
5. When you click "OK" you'll see the boundary added as a layer.
6. Click on the original box you draw and then click the "Delete" key on the keyboard. This will delete the box you draw but the feature in the shapefile should still be visible.
7. Clipping rasters is different from clipping vectors so open the search box and type in "Clip Raster"
8. The first item should be "Clip" in "Data Management". Select this tool.
9. Select the DEM as the "Input Raster" and the "ClippingBoundary" as the "Output Extent". Then, set the "Output Raster" to "DEM_Clipped.img" in your Arcata Forest working folder.
10. The clipped DEM should appear around your Arcata Forest boundary.

Checking for Artifacts and Creating Hillshades

Before continuing, we want to make sure our DEM does not have any artifacts that could cause problems (this happens a lot with DEMs). A handy tool for this, and making backgrounds on maps is the "Hillshade" tool.

1. In the ArcToolbox, navigate to "Spatial Analyst -> Surface -> Hillshade".
2. Select our clipped DEM for the "input raster"
3. Give the "Output raster" a good name like "Hillshade" and save it in the Arcata Forest working folder.
4. For now, we'll leave the "Azimuth" and "Altitude" values at the defaults as these are also the default for most western maps.
5. When you click "OK", you should see a simulation of light reflecting from the topography as if the sun were to the north west. If you see any lines running through the hillshade that should not be there then you have "artifacts" in the image from processing or the original data collection and you'll run into problems down the road.
6. Hillshades are very commonly used for backgrounds on maps as well. As long as we're here, let's make on.
7. Right click on your DEM and select "Properties".
8. Select the "Symbology" tab and change the "Color Ramp" to something more interesting.
9. Right click on your Hillshade layer and set the "Transparency" to 50%.
10. When you have a chance, come back to these steps and play with the color ramps and other settings to make nice backgrounds for this report and future ones.
11. Note: Change the "Brightness" in the "Display" tab of both rasters to make the hillshade fade into the background.

Creating a Stream Network

Creating a stream network requires a number of steps but should work out if you are careful (or are ready to go through the process several times).

1. Load the DEM that is clipped around Arcata Forest from the previous section.
2. Open the "ArcToolbox" and "Spatial Analyst Tools" -> Hydrology". If you receive an error that you do not have a license for these tools, go to "Customize -> Extensions" and select "Spatial Analyst".
3. Before we work with a DEM we have to "Fill" any "Holes" in the DEM. These are pixels that have very low values and will cause a stream to disappear during processing (take a look at your existing streams layers and see if you can find the one that was done with a DEM without the holes filled). Select the "Fill" tool.
4. Select our clipped DEM for the "Input surface raster"
5. Name the "Output surface raster" "Filled.img" and save it into the Arcata Forest working folder. When you click OK, you should see a new DEM that looks just like the old one.
6. The next step is to create a raster that shows the direction that water will flow downhill. Select the "Flow Direction" tool.
7. Use our filled DEM for the "Input surface raster"
8. Set the "Output flow direction raster" to "Direction.img" and save it into the Arcata Forest working folder. you should see a very brightly colored image where the pixels have been given "codes" for the cardinal direction (N, NW, W, SW, S, etc.) for the direction that water would flow from this pixel.
9. We'll now use the Direction raster to create a raster where each pixel represent the number of pixels that "flow" or "accumulate" into it. Select the "Flow Accumulation" tool.
10. Select the "Direction" raster for the "Input flow direction raster" and give the output raster a name like "Accumulation.img" and save it in the "Arcata Forest" working folder.
11. After you click "OK", you should see a few lines that are the ends of the streams that appear in the DEM. To see these better, right click on the "Accumulation" layer and select "Properties".
12. Click on the "Symbology" tab and make sure "Show" is set to "Stretched".
13. Change the "Color Ramp" to something more interesting and set the "Type" to "Standard Deviations". This should make it easier to see the streams.
14. Next, we need to create a raster that contains 1's where we want the steams to be and 0's elsewhere. In the ArcToolbox, navigate to "Spatial Analyst -> Map Algebra" and open the "Raster Calculator". This is a powerful tool that lets you do mathematical and other operations on entire rasters. Double click no the "Accumulation" raster and then type ">1000".
15. Name the output file "Accumulation_GreaterThan_100.img".
16. 
17. When you click "OK", you should see a raster with 1's where the pixels along the streams have "accumulated" the water from over 1000 other pixels.
18. Try one at 1000 pixels and some other values. Note that this tool is handy for making streams at different levels of detail for research and for cartography.
19. Our last step is to convert these rasters to polylines that represent a stream network. Open the "Search" tool and enter "Raster to Polyline".
20. Use your Accumulation_GreaterThan_100" raster for the "Input rater" and name the output "Streams_Over_100.shp".

Clean up

You may have noticed some little squares where the conversion to polyline followed multiple paths for your streams. These are not desired so we'll need to remove them.

1. Clip the streams to just the boundary of the forest and use the new shapefile for this section.
2. Open the attribute table.
3. Start and edit session.
4. Zoom in to one of the areas with the extra polylines.
5. Select some of the extra polylines.
6. At the bottom of the attribute table window, select the icon to "Show selected records". This will allow you to view just the selected records and you should now see the rows for the features you selected.
7. 
8. Right click on one of the rows and select "Delete Selected".
9. The rows should disappear and the extra polylines with them.
10. Repeat this process until all the extra polylines are gone and then, stop the edit session.
11. You also may have noticed that the stream reaches are broken into far more segments than needed. Run the "Unsplit" tool to join the streams into their correct reaches.

When completed, you should have a stream network that is a visible improvement over some of the other layers and, even more critically, it matches your DEM exactly for future analysis!

Comparing Results

Load your other water body layers into ArcMap and compare them with your new stream layer. Add a map for this new layer to your report and make sure to mention the advantages and disadvantages of it. While it also had issues, it will work much better for our purposes.

Finding the Watershed

First, we need to create a point file that contains "pour points". These are the points where the water will "flow" through the streams. ArcGIS uses these as a starting point and will then backtrack using our direction raster until it reaches the ridges that define our watersheds.

1. Create a point shapefile as we have done before (right click on the folder in ArcCatalog, select "New Shapefile", etc.).
2. Name the file "PourPoints.shp".
3. When you create the file, make sure to set the spatial reference to match your existing layers. A short cut is to "Import" the spatial reference from one of your existing files.
4. 
5. When digitizing your points, make sure to zoom in and the tool should "snap" to your polyline for your stream.
6. 
7. Your selection of points is also important. Try to find areas of stream reaches that are away from tributaries and low in the watershed. This will reduce the number of points you need.
8. Make sure to "Stop Editing" when you feel you have a good set of points.
9. Before creating the watershed, we need to make sure our points are actually on the accumulation raster pixels that the stream flows through.
10. Open the "Hydrology" toolset in Spatial Analyst and select "Snap Pour Point". This feature will create a raster with pixels that are in exactly the location we need.
11. Select your pour point shape file fro the first input.
12. Select the "FID" as the "Pour point field" so we have a unique value for each pixel in the watershed.
13. Select the accumulation raster you made above for the "Input accumulation raster".
14. Give the raster a good name and save it in your working folder.
15. The "Snap distance" is how far ArcGIS should look for the highest value (our stream course) in map units (i.e. meters). Enter a value that is a few pixels across (if you've forgotten the resolution of our rasters, you can check in "Properties -> Source".
16. Zoom into one of your pour points and you should see a pixel nearby. Grab the "Info" tool and check that the pixel value matches the FID of the point nearby.
17. 
18. Finally, select the "Watershed" tool from the ArcToolbox.
19. Select our direction raster for the first input.
20. Select the "pour point" raster you just created for the second input.
21. Give the watershed output a good name and save it in the working folder.
22. When done, you should see watersheds for Arcata Forest. However, don't be surprised if this does not work the first time. You will probably have to go back to step 7 and add pour points or move them to be on top of the right accumulation pixel to catch all the water sheds

Arcata Forest drains into two main watersheds, the Mad River and Arcata Bay! Depending on the pour points you selected, you may see many more "watersheds" or fewer depending on where you placed your pour points.

The last step is to convert this into a polygon shapefile which will be much easier to work with and will be easier on the eyes!

1. In the search box, enter "Raster to polygon".
2. At this point, we're going to be giving you fewer instructions in the labs as you're begining to master running ArcGIS. For this tool, just make sure to uncheck the "Simplify polygons" option as we want our polygon and exactly match our raster and we can always simplify it later if desired.

For your report, include a map of the watersheds, pour points, and streams. Use a nice hillshade but make sure to make the contract low or make it relatively transparent so it does not interfere with your key message. The one below is just to give an idea of the final map. Yours should include the required elements, labels, and look nicer!

 

Computing geometries

For our report, we need to include the number of streams, their length, and the number of watersheds, and their area. For the report, we'll be using the streams that drain at least 100 pixels (include the area of these headwaters in your report).

1. Open the attribute table (right click on the layer and select "Open Attribute Table".
2. Click on the little arrow in the upper left of the attribute table and select "Add Field".
3. 
4. Name the field "Length". Note that the names of fields in ArcGIS are only allowed to be 10 characters long.
5. Set the "Type" to "Double".
6. Don't worry about the "Field Properties" now or even in the future. I never change these.
7. When you click "OK" the new field should appear.
8. Right click on the field heading and select "Calculate Geometry...". This will open a tool you can use to compute the length of polylines, the area of polygons, and to get the coordinate values for points.
9. 
10. You may get an error at this point that you are outside an editing session. That is OK and just keep going.
11. Compute the "Length" of the streams

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