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Methods for Post-Processing Habitat-Mapper Output1

This document describes the methods used for generating analysis ready data on species-level kelp extent from outputs from the Habitat-Mapper tool. Final outputs consist of polygon features (.shp) that contain species-level classification of emergent canopy kelp present in drone imagery.

These instructions use ArcGIS Pro (version 3.4+), but can also be adapted for QGIS (a free, open-source alternative). The core workflow is the same across GIS platforms.

QGIS Equivalents

If using QGIS instead of ArcGIS Pro, the equivalent tools are:

  • "Raster to Polygon" → Raster menu > Conversion > Polygonize (Raster to Vector)
  • "Field Calculator" → Open Attribute Table > Open Field Calculator (calculator icon)
  • "Calculate Geometry" → Field Calculator with expression $area
  • "Select by Attribute" → Select Features Using an Expression (toolbar button)

For questions, please contact Luba Reshitnyk at the Hakai Institute.

Overview

Workflow Overview

graph TB
    A[/"Raw Habitat-Mapper output (.tif)"/]-- Open in ArcGIS Pro -->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 Habitat-Mapper (.tif) and have a new instance of ArcGIS Pro (3.4). These same steps can be done using other GIS software (e.g. QGIS)

Tip: ArcGIS Pro Keyboard Shortcuts

Keyboard shortcuts can make the editing process much faster. To enable some, go to Customize > Customize Mode > Keyboard….

Some useful shortcuts include:

  1. Edit tool (set to Ctrl+E)
    1. This lets you toggle to the editor tool.
  2. Delete (set to Ctrl+D)
    1. Delete selected polygon features.
  3. Freehand tool (set to Ctrl+R)
    1. Toggle to freehand tool to manually digitize kelp feature polygons.
  4. Clip (set to Ctrl+W)
    1. Quickly draw a polygon then click ctrl+W to delete the polygon features within the newly drawn polygon. Then delete that polygon.

Load Habitat-Mapper Raster

Load the output .tif file from Habitat-Mapper into ArcGIS Pro. 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 ArcGIS Pro.

  1. Uncheck simplify polygons
  2. Leave the other defaults as they are

Add New Attributes to Polygons

Note - if you are exporting to GDB you don't need to calculate area

  1. Add a new area and species field
  2. Right-click the layer in the Contents pane
  3. Select Attribute Table
  4. Click the New Field button in the Fields tab of the ribbon
    1. Name = area, Type = Double
    2. Name = species, Type = Text
    3. Click Save on the fields tab of the ribbon
  5. Calculate the area for each polygon
    1. Right-click the area header in the attribute table, select Calculate Geometry...
      1. Property = area
      2. Units = square meters
      3. Coordinate system = choose an appropriate projection that preserves area ( e.g. NAD83 BC Albers Equal Area EPSG = 3005)
      4. Click OK

Editing and Data Cleaning

Delete small polygons that are unlikely to be kelp

  1. Right click layer in the table of contents, Select Open attribute table. Click Select by attribute
  2. Select features < 0.2 m2 by typing: "area" < 0.2
  3. Right click highlighted features in attribute table and click Delete Selected
  4. Save edits

Manually delete non-kelp polygons

There may be areas where the Habitat-Mapper classifier falsely detected kelp and these polygons need to be removed manually.

  1. Select using the edit tool or Select by Lasso tool
  2. Delete the selected polygon(s)
  3. Save edits.

Add kelp not detected by Habitat-Mapper

If there are locations where emergent canopy kelp was missed by the Habitat-Mapper 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.

Missed Kelp

Review Species Attributes

There may be some areas where the Habitat-Mapper 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.

  1. 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.
  2. Right-click the species field you created earlier. Select Field Calculator.
  3. 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.

  1. Review all the polygon species classification and manually change ones that the Habitat-Mapper classifier misclassified by changing the text in the species field for that polygon feature.
  2. Save edits.
  3. Delete the gridcode attribute once you are done.
  4. Save edits.

Export Data

That's it! You can now export your data a shapefile or gdb feature class and give it an appropriate name.

  1. Created by Luba Reshitnyk, February 2023 ↩