Running the Segmentation Tool
Each time you want to run a classification on new imagery follow these steps.
Open Anaconda Prompt
Open anaconda prompt by searching “Anaconda Prompt” in search tool bar.
Change Environments
The default environment is called (base)
which will appear in brackets before each
line of text.
To change to the new environment that you created in Part 1,
type: conda activate KelpSegmentation
and press enter.
In this command, "KelpSegmentation" was the name that you chose for your new
environment.
Now you will see that the environment has changed from (base)
to (KelpSegmentation)
as KelpSegmentation is now appearing in brackets.
Note
If you used a different name for your environment, be sure to replace
conda activate KelpSegmentation
with conda activate <your-environment-name-here>
You can see a list of all installed environments by typing and entering the
command: conda env list
.
Run Segmentation Tool
Type kom find-kelp
and copy and paste the location of the image in which you would
like to detect kelp. Add a space
and then type or paste the location you would like the output file to be saved on your
computer with the name of the
output file.
In this example the orthomosaic to be classified is named “Kelp_Bed_Orthomosaic_2022.tif” and its location is in the C drive, documents folder, Drone_Images subfolder.
C:\Users\sbs33.DESKTOP-K0SDD1B\Documents\Drone_Images\Kelp_Bed_Orthomosaic_2022.tif
The output results will be sent to the same Drone_Images folder and will have the name “Kelp_Bed_Orthomosiac_2022_output.tif”, where .tif is the file type.
C:\Users\sbs33.DESKTOP-K0SDD1B\Documents\Drone_Images\Kelp_Bed_Orthomosaic_2022_output.tif
So, the entire command in the Anaconda prompt is:
kom find-kelp C:\Users\sbs33.DESKTOP-K0SDD1B\Documents\Drone_Images\Kelp_Bed_Orthomosaic_2022.tif C:\Users\sbs33.DESKTOP-K0SDD1B\Documents\Drone_Images\Kelp_Bed_Orthomosaic_2022_output.tif
Press Enter and wait for the segmentation to run; the time may vary depending on the size of the image.
Note
You can always get help documentation for the kom find-kelp
tool by typing into
the prompt kom find-kelp --help
.
This help documentation is the same as what is shown under
the :doc:Command Line Reference <./cli>
.
Tip
If you manually type in the path to your file, use the <tab>
key to have your
operating system autocomplete the paths for you.
e.g., if you type kom find-kelp C:\\Desk
, then press the <tab>
key, your
operating system should complete the command for you so it
reads: kom find-kelp C:\\Desktop
.
If the partial path is ambiguous, tapping <tab>
multiple times will cycle through
the possible path options.
You can continue doing this as you type in the location to autocomplete the text for long path names. It is faster, and less error prone than typing the whole path yourself.
Once the processing bar is at 100%, you can open the results in an image processing or spatial analysis software such as QGIS or ArcGIS. Review the results for errors and edit as needed.
Part 2 Kelp Segmentation is now complete!
Continue to Part 3 to learn how to post-process the results.
Authors: Sarah Schroeder and Taylor Denouden