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Copy file name to clipboardexpand all lines: docs/beginner_guide/execution.md
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@@ -23,7 +23,7 @@ It is typical of many CLI tools to also have a `--help` option that can be used
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To get help documentation for the `kom` tool, you can type `kom --help` into your terminal.
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??? tip "Shorthand flags"
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You can also use the shorthand flags `-h` to get help, e.g. `kom -h`. This is common for many CLI tools.
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You can also use the shorthand flags `-h` to get help, e.g. `kom -h`. This is common for many CLI tools.
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Options will be shown in the help documentation with both the long form (`--help`) and the shorthand form (`-h`).
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```console
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### Processing an Image
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??? note "A note on mussel detection"
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The Kelp-O-Matic tool is designed to detect both kelp and mussels. The following information was written for kelp
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detection, but the same information applies for mussels. All you have to do to find mussels instead of kelp is use
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The Kelp-O-Matic tool is designed to detect both kelp and mussels. The following information was written for kelp
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detection, but the same information applies for mussels. All you have to do to find mussels instead of kelp is use
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the `kom find-mussels` subcommand instead of `kom find-kelp` in the following steps.
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#### Subcommands and Options
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To process an image, you will need to use the `kom find-kelp` subcommand. This subcommand is used to detect kelp in an
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To process an image, you will need to use the `kom find-kelp` subcommand. This subcommand is used to detect kelp in an
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image. Like we did for `kom`, we can also get help for subcommands:
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```console
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The options are flags that can be used to enable or disable certain features of the tool, or they can take arguments to customize the behavior of the tool.
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!!! example "An Example Command"
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=== "Windows"
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```console
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kom find-kelp --species --crop-size 2048 .\some\image_with_kelp.tif .\some\output.tif
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```
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In this example, we are running the `find-kelp` subcommand with the `--species` option and a
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`--crop-size` of 2048. The input image is located at `.\some\image_with_kelp.tif`.
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In this example, we are running the `find-kelp` subcommand with the `--species` option and a
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`--crop-size` of 2048. The input image is located at `.\some\image_with_kelp.tif`.
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The output will be saved to `.\some\output.tif`.
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=== "MacOS/Linux"
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```console
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kom find-kelp --species --crop-size 2048 ./some/image_with_kelp.tif ./some/output.tif
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```
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In this example, we are running the `find-kelp` subcommand with the `--species` option and a
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`--crop-size` of 2048. The input image is located at `./some/image_with_kelp.tif`.
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In this example, we are running the `find-kelp` subcommand with the `--species` option and a
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`--crop-size` of 2048. The input image is located at `./some/image_with_kelp.tif`.
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The output will be saved to `./some/output.tif`.
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##### Executing the Command
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Once you have constructed your command, execute it by pressing ++enter++.
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Once you have constructed your command, execute it by pressing ++enter++.
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Wait for the progress bar to reach 100%, then open the results in an image processing or spatial analysis software such as QGIS or ArcGIS.
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Wait for the progress bar to reach 100%, then open the results in an image processing or spatial analysis software such as QGIS or ArcGIS.
Copy file name to clipboardexpand all lines: docs/beginner_guide/terminal_crash_course.md
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application that appears.
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=== "MacOS/Linux"
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On MacOS and Linux, the default terminal is called Terminal. To open Terminal, search for "Terminal" in the search bar
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On MacOS and Linux, the default terminal is called Terminal. To open Terminal, search for "Terminal" in the search bar
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and click on the application that appears.
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### Nagivating around
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| ------- | ----------- |
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| `cd [some path]` | Change directory |
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| `ls [some path]` | List files and folders in the current directory |
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#### Specifying Paths
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- Using `..` is interpreted as "the parent directory" of my current location.
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- Using `.` is interpreted as "the current directory".
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- Using `~` is interpreted as the user's home directory. (e.g. `C:\Users\McLovin`, if that is your username)
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- You can use relative paths to navigate to folders in relation to your current location, like ` cd .\Documents`
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- You can use relative paths to navigate to folders in relation to your current location, like ` cd .\Documents`
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- You can also use absolute paths to navigate, like `cd C:\Users\McLovin\Documents`.
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- Use ++tab++ to autocomplete file and folder names. It is **very strongly** recommended to use this to avoid typos and save time typing long paths.
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- e.g. `cd C:\Users\McLovin\Docu` then press ++tab++ to autocomplete to `cd C:\Users\McLovin\Documents`. Pressing ++tab++ again will cycle through all possible completions.
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- Using `..` is interpreted as "the parent directory" of my current location.
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- Using `.` is interpreted as "the current directory".
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- Using `~` is interpreted as the user's home directory. (e.g. `/home/mclovin`, if that is your username)
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- You can use relative paths to navigate to folders in relation to your current location, like ` cd ./documents`
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- You can use relative paths to navigate to folders in relation to your current location, like ` cd ./documents`
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- You can also use absolute paths to navigate, like `cd /home/mclovin/documents`. Absolute paths start from the root directory `/`.
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- Use ++tab++ to autocomplete file and folder names. It is **very strongly** recommended to use this to avoid typos and save time typing long paths.
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- e.g. `cd /home/mclovin/docu` then press ++tab++ to autocomplete to `cd /home/mclovin/documents`. Pressing ++tab++ again will cycle through all possible completions.
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| `cd /home/mclovin/documents` | Move to a folder called `documents` inside the `mclovin` home directory |
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!!! warning "Spaces in Paths"
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If a folder or file name has a space in it, you need to enclose the path in quotes.
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For example, if you have a folder called `My Documents`, you would need to use `cd "My Documents"`.
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It's a good idea to avoid spaces in folder and file names to make your life easier. Many people use
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If a folder or file name has a space in it, you need to enclose the path in quotes.
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For example, if you have a folder called `My Documents`, you would need to use `cd "My Documents"`.
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It's a good idea to avoid spaces in folder and file names to make your life easier. Many people use
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underscores `_` or hyphens `-` instead of spaces.
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You did it! You now know enough to navigate around the terminal. There are many commands you can use
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in the terminal, but these are the most important ones to get you started. You're now going to copy and paste some
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commands to set up the Kelp-O-Matic tool, detailed in the next section. This is going to add a new command to your
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You did it! You now know enough to navigate around the terminal. There are many commands you can use
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in the terminal, but these are the most important ones to get you started. You're now going to copy and paste some
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commands to set up the Kelp-O-Matic tool, detailed in the next section. This is going to add a new command to your
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terminal that you can use to run the Kelp-O-Matic tool.
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