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Update post_processing.md
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changed instructions to work with ArcGIS Pro
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willhakai committed Feb 7, 2025
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Expand Up @@ -5,7 +5,7 @@ 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
These instructions assume a basic level of experience with ArcGIS Pro. For
questions,
please contact [Luba Reshitnyk](email:luba.reshitnyk@hakai.org) at
the [Hakai Institute](https://hakai.org).
Expand All @@ -20,7 +20,7 @@ the [Hakai Institute](https://hakai.org).

```mermaid
graph TB
A[/"Raw KoM output (.tif)"/]-- Open in ArcGIS -->B["Convert to polygon feature (raster to polygon)"];
A[/"Raw KoM output (.tif)"/]-- Open in ArcGIS Pro -->B["Convert to polygon feature (raster to polygon)"];
B-->edit
subgraph edit [Edit]
direction TB
Expand All @@ -35,10 +35,10 @@ graph TB

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
instance of ArcGIS Pro (3.4). These same steps can be done using other GIS
software (e.g. QGIS)

??? tip "Tip: ArcMap Keyboard Shortcuts"
??? tip "Tip: ArcGIS Pro Keyboard Shortcuts"

Keyboard shortcuts can make the editing process much faster. To enable some, go
to `Customize > Customize Mode > Keyboard…`.
Expand All @@ -57,7 +57,7 @@ software (e.g. QGIS)

### Load Kelp-O-Matic Raster

Load the output `.tif` file from Kelp-O-Matic into ArcMap. The raster will have the
Load the output `.tif` file from Kelp-O-Matic into ArcGIS Pro. The raster will have the
following
attributes:

Expand All @@ -70,56 +70,48 @@ attributes:

### Convert to Polygons

Convert this raster into polygons using the `Raster to Polygon` tool in ArcMap.
Convert this raster into polygons using the `Raster to Polygon` tool in ArcGIS Pro.

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

### Add New Attributes to Polygons

1. Add a new "area" field
1. Right click layer in the table of contents
2. Select `Open attribute table > Table options > Add field`
1. Name = "area"
2. Type = "float"
3. Click `OK`
#### Note - if you are exporting to GDB you don't need to calculate area

1. Add a new `area` and `species` field
1. Right-click the layer in the Contents pane
2. Select `Attribute Table`
3. 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
2. Calculate the area for each polygon
1. Right-click the "area" header in the attribute table,
1. Right-click the `area` header in the attribute table,
select `Calculate Geometry...`
1. Property = "area"
2. Units = "square meters"
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"
3. Add a new "species" field
1. Right click layer in the table of contents
2. Select `Open attribute table > Table options > Add field`
1. Name = "species"
2. Type = "text"
3. Click `OK`
4. Click `OK`

### Editing and Data Cleaning

#### Delete small polygons that are unlikely to be kelp

1. Start editing this feature polygon layer
1. In the Editor toolbar click `Editor > start editing`. Select the feature layer
you will be
editing
2. Right click layer in the table of contents, Select `Open attribute table`.
1. Right click layer in the table of contents, Select `Open attribute table`.
Click `Select by attribute`
3. Select features < 0.2 m2 by typing: `"area" < 0.2`
4. Right click highlighted features in attribute table and click `Delete Selected`
5. Save edits
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 KoM classifier falsely detected kelp and these polygons need to
be removed
manually.

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

Expand All @@ -144,24 +136,22 @@ 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.
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".
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 KoM
classifier
misclassified by changing the text in the "species" field for that polygon feature.
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.
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 and give it an appropriate name.
That's it! You can now export your data a shapefile or gdb feature class and give it an appropriate name.

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