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Update CLI docs
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tayden committed Dec 13, 2023
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# Command Line Reference

The `kelp-o-matic` package includes one command line tool, `kom`. It will be registered in the same Conda environment
The `kelp-o-matic` package includes one command line tool, `kom`. It will be registered
in the same Conda environment
that the `kelp-o-matic` package is installed to.

```
Expand Down Expand Up @@ -35,16 +36,26 @@ $ kom find-kelp --help
Options
--species --presence Segment to species or presence/absence level. [default: presence]
--crop-size INTEGER The data window size to run through the segmentation model. [default: 1024]
--rgbi --rgb Use RGB and NIR bands for classification. Assumes RGBI ordering. [default: rgb]
-b INTEGER GDAL-style band re-ordering flag. Defaults to RGB or RGBI order. To e.g., reorder a BGRI image at runtime, pass flags `-b 3 -b 2 -b 1 -b 4`. [default: None]
--gpu --no-gpu Enable or disable GPU, if available. [default: gpu]
--help -h Show this message and exit.
```

!!! Example

Classify kelp species in an RGB image:

```bash
kom find-kelp --species --crop-size=1024 ./some/image_with_kelp.tif ./some/place_to_write_output.tif
```

Classify kelp presence/absence in an BGRI image:

```bash
kom find-kelp --rgbi -b 3 -b 2 -b 1 -b 4 --crop-size=1024 ./some/image_with_kelp.tif ./some/place_to_write_output.tif
```

???+ tip "Tip: Reduce windowed processing artifacts"

To reduce artifacts caused by Kelp-O-Matic's moving window classification, use the largest `crop_size` that you can.
Expand Down Expand Up @@ -97,6 +108,7 @@ $ kom find-mussels --help
Options
--crop-size INTEGER The data window size to run through the segmentation model. [default: 1024]
-b INTEGER GDAL-style band re-ordering flag. Defaults to RGB order. To e.g., reorder a BGR image at runtime, pass flags `-b 3 -b 2 -b 1`. [default: None]
--gpu --no-gpu Enable or disable GPU, if available. [default: gpu]
--help -h Show this message and exit.
```
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