Update CLI docs

HakaiInstitute · Jan 31, 2025 · 5171c59 · 5171c59
1 parent a4e3f5a
commit 5171c59
Showing 1 changed file with 13 additions and 28 deletions.
diff --git a/docs/cli.md b/docs/cli.md
@@ -7,29 +7,30 @@ that the `kelp-o-matic` package is installed to.
 ```
 $ kom --help
 
- Usage: python -m kelp_o_matic.cli [OPTIONS] COMMAND [ARGS]...
+ Usage: kom [OPTIONS] COMMAND [ARGS]...
 
    Options
-  --version             -v
-  --help                -h                                       Show this message and exit.
+  --version   -v        Show version and exit.
+  --gpu-test            Test if GPU is detected and exit.
+  --help      -h        Show this message and exit.
 
    Commands
-  find-kelp           Detect kelp in image at path SOURCE and output the resulting classification raster to file at path DEST.
-  find-mussels        Detect mussels in image at path SOURCE and output the resulting classification raster to file at path DEST.
+  find-kelp      Detect kelp in image at path SOURCE and output the resulting classification raster to file at path DEST.
+  find-mussels   Detect mussels in image at path SOURCE and output the resulting classification raster to file at path DEST.
 ```
 
 ## find-kelp
 
 ```
 $ kom find-kelp --help
 
- Usage: python -m kelp_o_matic.cli find-kelp [OPTIONS] SOURCE DEST
+ Usage: kom find-kelp [OPTIONS] SOURCE DEST
 
  Detect kelp in image at path SOURCE and output the resulting classification raster to file at path DEST.
 
    Arguments
-  *    source      TEXT  Input image with Byte data type. [default: None] [required]
-  *    dest        TEXT  File path location to save output to. [default: None] [required]
+  *    source      FILE  Input image with Byte data type. [default: None] [required]
+  *    dest        FILE  File path location to save output to. [default: None] [required]
 
    Options
   --species        --presence             Segment to species or presence/absence level. [default: presence]
@@ -76,38 +77,22 @@ $ kom find-kelp --help
     Also worth noting is that the `crop_size` parameter will change the outputs.
     If you need to reproduce a result, make sure to use the same `crop_size` as the original run.
 
-[//]: # (??? info "Info: Misclassifications over land")
-
-[//]: # ()
-
-[//]: # (    Currently, Kelp-O-Matic is mostly optimized to differentiate between canopy-forming kelp, water, and)
-
-[//]: # (    near-shore land. It is a known issue that inland vegetation is sometimes misclassified as)
-
-[//]: # (    kelp. )
-
-[//]: # ()
-
-[//]: # (    Please check out our [post-process documentation]&#40;post_process.md&#41; for our recommendations on)
-
-[//]: # (    cleaning up the output classification mask.)
-
 ## find-mussels
 
 ```
 $ kom find-mussels --help
 
- Usage: python -m kelp_o_matic.cli find-mussels [OPTIONS] SOURCE DEST
+ Usage: kom find-mussels [OPTIONS] SOURCE DEST
 
  Detect mussels in image at path SOURCE and output the resulting classification raster to file at path DEST.
 
    Arguments
-  *    source      TEXT  Input image with Byte data type. [default: None] [required]
-  *    dest        TEXT  File path location to save output to. [default: None] [required]
+  *    source      FILE  Input image with Byte data type. [default: None] [required]
+  *    dest        FILE  File path location to save output to. [default: None] [required]
 
    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]
+               -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]
   --tta            --no-tta             Use test time augmentation to improve accuracy at the cost of processing time. [default: no-tta]
   --help       -h                       Show this message and exit.