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docs/beginner_guide/execution.md

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!!! note
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If you used a different name for your environment, be sure to replace
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If you used a different name for your environment, be sure to replace
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`conda activate KelpSegmentation` with `conda activate <your-environment-name-here>`
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You can see a list of all installed environments by typing and entering the
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You can see a list of all installed environments by typing and entering the
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command: `conda env list`.
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***
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!!! note
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You can always get help documentation for the `kom find-kelp` tool by typing into
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You can always get help documentation for the `kom find-kelp` tool by typing into
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the prompt `kom find-kelp --help`.
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This help documentation is the same as what is shown under
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This help documentation is the same as what is shown under
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the :doc:`Command Line Reference <./cli>`.
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!!! tip
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If you manually type in the path to your file, use the `<tab>` key to have your
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If you manually type in the path to your file, use the `<tab>` key to have your
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operating system autocomplete the paths for you.
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*e.g.*, if you type `kom find-kelp C:\\Desk`, then press the `<tab>` key, your
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operating system should complete the command for you so it
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*e.g.*, if you type `kom find-kelp C:\\Desk`, then press the `<tab>` key, your
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operating system should complete the command for you so it
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reads: `kom find-kelp C:\\Desktop`.
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If the partial path is ambiguous, tapping `<tab>` multiple times will cycle through
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If the partial path is ambiguous, tapping `<tab>` multiple times will cycle through
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the possible path options.
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You can continue doing this as you type in the location to autocomplete the text
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for long path names. It is faster, and less error prone than typing the whole
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You can continue doing this as you type in the location to autocomplete the text
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for long path names. It is faster, and less error prone than typing the whole
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path yourself.
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![Complete Segmentation](images/complete_segmentation.png)

docs/beginner_guide/post_processing.md

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# Methods for Post-Processing Kelp-O-Matic Output[^1]
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This document describes the methods used for generating analysis ready data on
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species-level kelp extent from outputs from the Kelp-O-Matic tool. Final outputs
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consist of polygon features (.shp) that contain species-level classification of
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species-level kelp extent from outputs from the Kelp-O-Matic tool. Final outputs
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consist of polygon features (.shp) that contain species-level classification of
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emergent canopy kelp present in drone imagery.
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These instructions assume a basic level of experience with the ArcMAP GIS interface. For
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??? tip "Tip: ArcMap Keyboard Shortcuts"
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Keyboard shortcuts can make the editing process much faster. To enable some, go
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Keyboard shortcuts can make the editing process much faster. To enable some, go
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to `Customize > Customize Mode > Keyboard…`.
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Some useful shortcuts include:
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3. Freehand tool (set to ++ctrl+r++)
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1. Toggle to freehand tool to manually digitize kelp feature polygons.
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4. Clip (set to ++ctrl+w++)
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1. Quickly draw a polygon then click ctrl+W to delete the polygon features
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1. Quickly draw a polygon then click ctrl+W to delete the polygon features
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within the newly drawn polygon. Then delete that polygon.
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### Load Kelp-O-Matic Raster

docs/beginner_guide/setup.md

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??? question "Why do we use a new environment?"
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Using a new Conda environment is a good practice to get into when installing Python
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packages. It ensures that the software you install does not conflict with other
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software on your computer, as well as makes it easy to remove when you don't want
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Using a new Conda environment is a good practice to get into when installing Python
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packages. It ensures that the software you install does not conflict with other
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software on your computer, as well as makes it easy to remove when you don't want
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it anymore.
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## Change Environments
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!!! note
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If you used a different name for your environment, be sure to replace
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If you used a different name for your environment, be sure to replace
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`conda activate KelpSegmentation` with `conda activate <your-environment-name-here>`
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You can see a list of all installed environments by typing and entering the
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You can see a list of all installed environments by typing and entering the
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command: `conda env list`.
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![Change Environments 2](images/change_environments2.png)
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Now that we're in the new environment, we can install the packages that the Kelp-O-Matic
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tool needs to run, followed by Kelp-O-Matic itself.
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At this stage, you can directly reference
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At this stage, you can directly reference
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the [installation instructions](../installation.md) if you find that easier, or continue
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with the following instructions.
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docs/installation.md

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will be added when possible.
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New versions of the tool are occasionally released to improve segmentation performance,
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speed, and the user interface of the tool. Changes are published to the PyPI and
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Anaconda repositories using [semantic versioning](https://semver.org/). You may want to
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occasionally run the update commands to ensure that you're using the most up-to-date
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speed, and the user interface of the tool. Changes are published to the PyPI and
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Anaconda repositories using [semantic versioning](https://semver.org/). You may want to
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occasionally run the update commands to ensure that you're using the most up-to-date
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version of `kelp-o-matic`.
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## Commands
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!!! help "Need more help?"
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If you are unfamiliar with the command line or installing Python packages, you may
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If you are unfamiliar with the command line or installing Python packages, you may
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find our [Beginner Guide](beginner_guide/index.md) helpful.
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### Pre-requisites

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