Set-up and Installation

Before you can run the Kelp-O-Matic tool, you will need to set up some programs which will allow the tool to run. Once set-up is complete the tool can be run very easily from ones terminal.

Install Anaconda

If not already installed, download Anaconda on your computer from the Anaconda download website. Follow the prompts to install the most recent version of Anaconda for your operating system.

Install Anaconda

Open Anaconda Prompt

Open Prompt

Open anaconda prompt by searching “Anaconda Prompt” in search tool bar.

Create New Environment

In the prompt window, create a new Anaconda environment by typing the following command:

conda create -n KelpSegmentation python=3.10

This will create an isolated Python environment for packages and their dependencies to be installed in. The name of the environment is KelpSegmentation in this example, but you can choose any name you like. This command also installs Python version 3.10 into your new environment.

Why do we use a new environment?

Using a new Conda environment is a good practice to get into when installing Python packages. It ensures that the software you install does not conflict with other software on your computer, as well as makes it easy to remove when you don't want it anymore.

Change Environments

Now, we're going to activate the environment we just created. By default, the Anaconda Prompt always starts in the (base) environment. You can tell this is the case, because (base) will appear in brackets before each line of text.

Change Environments 1

Let's change into the environment we just created. To do this, type into the prompt:

conda activate KelpSegmentation

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.

Change Environments 2

You should see that the environment has changed from (base) to (KelpSegmentation) in the prompt.

Install packages

Now that we're in the new environment, we can install the packages that the Kelp-O-Matic tool needs to run, followed by Kelp-O-Matic itself.

At this stage, you can directly reference the installation instructions if you find that easier, or continue with the following instructions.

Install PyTorch

Kelp-O-Matic relies on PyTorch to run. PyTorch is a machine learning library for Python. PyTorch can be installed to use your CPU only, or can make use of an NVIDIA GPUs you may have in your machine to accelerate processing.

The most up-to-date and reliable instructions for installing PyTorch can be found on the PyTorch website. Typically, the installation commands are:

GPU

conda install pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia

CPU

conda install pytorch torchvision cpuonly -c pytorch

Install Kelp-O-Matic

Now that PyTorch is installed, we can install Kelp-O-Matic itself. To do so, run the command:

conda install -c conda-forge kelp-o-matic

Part 1 set-up is now complete!

You are now ready to run the Kelp-O-Matic tool. Now that the setup steps are completed, you will not have to repeat them again unless installing on a different computer.

Continue to Part 2: Running the Segmentation tool

Authors: Sarah Schroeder and Taylor Denouden