Methods for Post-Processing Kelp-O-Matic Output1
This document describes the methods used for generating analysis ready data on species-level kelp extent from outputs from the Kelp-O-Matic tool. Final outputs consist of polygon features (.shp) that contain species-level classification of emergent canopy kelp present in drone imagery.
These instructions assume a basic level of experience with the ArcMAP GIS interface. For questions, please contact Luba Reshitnyk at the Hakai Institute.
Workflow Overview
graph TB
A[/"Raw KoM output (.tif)"/]-- Open in ArcGIS -->B["Convert to polygon feature (raster to polygon)"];
B-->edit
subgraph edit [Edit]
direction TB
C[Remove polygons < 0.2m<sup>2</sup>]-->D[Manually remove non-kelp polygons];
D-->E[Manually digitize kelp canopy that was missed];
E-->F[Fix any misclassified species];
end
edit-- Have secondary analyst review, time permitting -->G[/"Final output (.shp)"/]
Detailed Workflow
This section assumes that you have obtained output from the Kelp-O-Matic (.tif) and have a new instance of ArcMap (version 10.8). These same steps can be done using other GIS software (e.g. QGIS)
Tip: ArcMap Keyboard Shortcuts
Keyboard shortcuts can make the editing process much faster. To enable some, go
to Customize > Customize Mode > Keyboard…
.
Some useful shortcuts include:
- Edit tool (set to Ctrl+E)
- This lets you toggle to the editor tool.
- Delete (set to Ctrl+D)
- Delete selected polygon features.
- Freehand tool (set to Ctrl+R)
- Toggle to freehand tool to manually digitize kelp feature polygons.
- Clip (set to Ctrl+W)
- Quickly draw a polygon then click ctrl+W to delete the polygon features within the newly drawn polygon. Then delete that polygon.
Load Kelp-O-Matic Raster
Load the output .tif
file from Kelp-O-Matic into ArcMap. The raster will have the
following
attributes:
Output value (gridcode) | Class |
---|---|
0 | Background |
1 | Kelp (presence mode) |
2 | Macrocystis (species mode) |
3 | Nereocystis (species mode) |
Convert to Polygons
Convert this raster into polygons using the Raster to Polygon
tool in ArcMap.
- Uncheck "simplify polygons"
- Leave the other defaults as they are
Add New Attributes to Polygons
- Add a new "area" field
- Right click layer in the table of contents
- Select
Open attribute table > Table options > Add field
- Name = "area"
- Type = "float"
- Click
OK
- Calculate the area for each polygon
- Right-click the "area" header in the attribute table,
select
Calculate Geometry...
- Property = "area"
- Units = "square meters"
- Coordinate system = choose an appropriate projection that preserves area ( e.g. NAD83 BC Albers Equal Area EPSG = 3005)
- Click "OK"
- Right-click the "area" header in the attribute table,
select
- Add a new "species" field
- Right click layer in the table of contents
- Select
Open attribute table > Table options > Add field
- Name = "species"
- Type = "text"
- Click
OK
Editing and Data Cleaning
Delete small polygons that are unlikely to be kelp
- Start editing this feature polygon layer
- In the Editor toolbar click
Editor > start editing
. Select the feature layer you will be editing
- In the Editor toolbar click
- Right click layer in the table of contents, Select
Open attribute table
. ClickSelect by attribute
- Select features < 0.2 m2 by typing:
"area" < 0.2
- Right click highlighted features in attribute table and click
Delete Selected
- Save edits
Manually delete non-kelp polygons
There may be areas where KoM classifier falsely detected kelp and these polygons need to be removed manually.
- Select using the edit tool or “Select by Lasso” tool
- Delete the selected polygon(s)
- Save edits.
Add kelp not detected by KoM
If there are locations where emergent canopy kelp was missed by the KoM classifier ( example in figure below) manually digitize these features using the Freehand Tool. You will need to manually classify these new regions to species (change value in the attribute table). A 1:100 scale is recommended.
Review Species Attributes
There may be some areas where the KoM classifier misclassified the species in a given area. These polygons can be edited manually. If you're just interested in presence/absence don't worry about this step.
- Select all polygon features classified as giant kelp by opening the attribute table
and “select
by attribute”. Select features representing giant kelp by typing:
"gridcode" = 2
. At the bottom of the attribute table click on the "Show selected records" tab. - Right-click the "species" field you created earlier. Select "Field Calculator".
- In the text box enter "Macrocystis pyrifera" (with quotes included) and click OK. This will fill out that attribute for all the selected polygons.
Repeat steps 1 - 3 for bull kelp by using "gridcode" = 3
and "Nereocystis luetkeana".
- Review all the polygon species classification and manually change ones that the KoM classifier misclassified by changing the text in the "species" field for that polygon feature.
- Save edits.
- Delete the "gridcode" attribute once you are done.
- Save edits.
Export Data
That's it! You can now export your data a shapefile and give it an appropriate name.
Authors: Luba Reshitnyk and Taylor Denouden
-
Created by Luba Reshitnyk, February 2023 ↩