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installation.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>DIPLOMAT - Installation</title>
<style>
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</style>
</head>
<body>
<header>
<h1 id="logo">DIPLOMAT</h1>
<p>Deep Learning-Based Identity Preserving Labeled-Object Multi-Animal Tracking</p>
</header>
<nav>
<a href="index.html">Home</a>
<a href="installation.html">Installation</a>
<a href="supplementary.html">Supplementary Information</a>
</nav>
<div class="container">
<section>
<h2>Installation Guide</h2>
<p>This guide will walk you through the steps to set up DIPLOMAT on your system using <a href="https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html" target="_blank">mamba</a>, which can be installed on Windows, Linux, or MacOS using the <a href="https://github.com/conda-forge/miniforge" target="_blank">Miniforge</a> installer.</p>
</section>
<div class="divider"></div>
<section>
<h3>1. Environment Setup</h3>
<p>To create an environment using mamba, run one of these commands based on your requirements:</p>
<div class="commands">
<pre># Create the environment for using DIPLOMAT with DeepLabCut
# GPU:
mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT.yaml
# CPU only:
mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml
# OR Create an environment for using DIPLOMAT with SLEAP instead...
# GPU:
mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP.yaml
# CPU only:
mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP-CPU.yaml</pre>
</div>
</section>
<div class="divider"></div>
<section>
<h3>2. Activating the Environment</h3>
<p>After creating the environment, activate it using one of the following commands:</p>
<div class="commands">
<pre># Activate the DeepLabCut/DIPLOMAT environment...
mamba activate DIPLOMAT-DEEPLABCUT
# Activate the SLEAP/DIPLOMAT environment...
mamba activate DIPLOMAT-SLEAP</pre>
</div>
</section>
<div class="divider"></div>
<section>
<h3>3. Documentation and Additional Help</h3>
<p>For a more thorough explanation of the installation process and alternative installation methods, see the <a href="https://diplomat.readthedocs.io/en/latest/installation.html" target="_blank">official documentation</a>.</p>
<p>All DIPLOMAT commands are documented via help strings. To get more information about a DIPLOMAT subcommand or command, simply run it with the <code>-h</code> or <code>--help</code> flag. For example:</p>
<div class="commands">
<pre># Help for all of DIPLOMAT (lists subcommands of DIPLOMAT):
diplomat --help
# Help for the track subcommand:
diplomat track --help
# Help for the predictors subcommand space:
diplomat predictors --help</pre>
</div>
</section>
<div class="divider"></div>
<section>
<h3>4. Common Commands</h3>
<p>Below are some common commands you might find useful once DIPLOMAT is installed:</p>
<div class="commands">
<pre># Run DIPLOMAT with no UI...
diplomat track -c path/to/config -v path/to/video
# Run DIPLOMAT with UI...
diplomat track_and_interact -c path/to/config -v path/to/video
# Annotate video with labels...
diplomat annotate -c path/to/config -v path/to/video
# Reopen the UI for further modifications...
diplomat interact -s path/to/ui_state.dipui
# Make minor modifications after tracking...
diplomat tweak -c path/to/config -v path/to/video</pre>
</div>
</section>
</div>
<footer>
<p>© 2024 DIPLOMAT Project</p>
<p>See <code>LICENSE</code> for details.</p>
</footer>
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