GitHub - akpetty/icesat2-book: Interactive Jupyter Book for wrangling, visualizing, and analyzing ICESat-2 monthly gridded sea ice concentration data and other related atmospheric data products.

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Interactive Jupyter Book for wrangling, visualizing, and analyzing ICESat-2 monthly gridded sea ice concentration data and other related atmospheric data products.
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                    ICESat-2 Arctic Sea Ice State Analysis
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        <p aria-level="2" class="caption" role="heading"><span class="caption-text">ICESat-2 Arctic sea ice thickness data</span></p>
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<li class="toctree-l1"><a class="reference internal" href="content/1_is2sitmogr4_intro.html">ICESat-2 L4 Monthly Gridded Sea Ice Thickness Dataset (IS2SITMOGR4)</a></li>





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<li class="toctree-l1"><a class="reference internal" href="content/3_comparisons_with_cryosat-2_and_piomas.html">Comparisons with CryoSat-2 and PIOMAS sea ice thickness estimates</a></li>




<li class="toctree-l1"><a class="reference internal" href="content/4_comparisons_with_BGEP.html">Comparisons with BGEP ULS sea ice draft estimates</a></li>


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<li class="toctree-l1"><a class="reference internal" href="content/10b_comparisons_with_BGEP_allseason.html">Comparisons of all-season thickness data with BGEP ULS sea ice draft estimates</a></li>


<li class="toctree-l1"><a class="reference internal" href="content/10c_comparisons_with_BGEP_2024winter_multivar.html">Comparisons with BGEP ULS sea ice draft estimates updated with new data</a></li>

<li class="toctree-l1"><a class="reference internal" href="content/10d_icebird_comps.html">Comparisons with AWI IceBird 2019</a></li>

<li class="toctree-l1"><a class="reference internal" href="content/10e_mosaic_comps_simba.html">Comparisons with MOSAiC SIMBA buoys</a></li>

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<li class="toctree-l1"><a class="reference internal" href="content/9_gridded_interp_demo.html">ICESat-2 interpolation workflow</a></li>





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<div id="jb-print-docs-body" class="onlyprint">
    <h1>ICESat-2 Sea Ice State Analysis Jupyter Book</h1>
    <!-- Table of contents -->
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                <h2> Contents </h2>
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            <nav aria-label="Page">
                <ul class="visible nav section-nav flex-column">
<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">ICESat-2 Sea Ice State Analysis Jupyter Book</a><ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#contributors">Contributors</a></li>
</ul>
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<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#update-history">Update history</a></li>
<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#activating-the-conda-environment">Activating the conda environment</a></li>
<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#updating-the-jupyter-book">Updating the Jupyter Book</a></li>
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<section class="tex2jax_ignore mathjax_ignore" id="icesat-2-sea-ice-state-analysis-jupyter-book">
<h1>ICESat-2 Sea Ice State Analysis Jupyter Book<a class="headerlink" href="#icesat-2-sea-ice-state-analysis-jupyter-book" title="Permalink to this heading">#</a></h1>
<p><strong>View this Jupyter Book (including options to run the code interactively!) in our Jupyter Book:</strong> <a class="reference external" href="http://www.icesat-2-sea-ice-state.info">http://www.icesat-2-sea-ice-state.info</a></p>
<section id="contributors">
<h2>Contributors<a class="headerlink" href="#contributors" title="Permalink to this heading">#</a></h2>
<p><strong>Alek Petty (Current repository lead, summer 2022 onwards)</strong><br>
<a class="reference external" href="https://github.com/akpetty"><img alt="GitHub" src="https://badgen.net/badge/icon/github?icon=github&amp;label" /></a></p>
<p><strong>Nicole Keeney (Original repository creator)</strong><br>
<a class="reference external" href="https://github.com/nicolejkeeney"><img alt="GitHub" src="https://badgen.net/badge/icon/github?icon=github&amp;label" /></a></p>
</section>
</section>
<section class="tex2jax_ignore mathjax_ignore" id="update-history">
<h1>Update history<a class="headerlink" href="#update-history" title="Permalink to this heading">#</a></h1>
<ul class="simple">
<li><p>9/4/2020: Version 1</p></li>
<li><p>11/18/2020: Updated with version 2 ICESat-2 data product for <a class="reference external" href="https://ui.adsabs.harvard.edu/abs/2020AGUFMC014.0012K/abstract">AGU Fall 2020 poster highlighting the book</a>.</p></li>
<li><p>6/14/2021: Transitioned from Google Colab interactivity to Binder.</p></li>
<li><p>10/25/2021: Added interactive plotting using hvplot. Improved interpolation/smoothing method for ICESat-2 data and added notebook to demonstrate steps.</p></li>
<li><p>01/24/2022: Updated notebooks to reflect new data variables in ICESat-2 data v2. Added drift vectors.</p></li>
<li><p>08/15/2022: Forked to akpetty and linked to a new domain (<a class="reference external" href="http://icesat-2-sea-ice-state.info">icesat-2-sea-ice-state.info</a>). Re-designed to reflect continued analysis of both the gridded and along-track thickness data.</p></li>
<li><p>11/01/2022: included new CryoSat-2 and BGEP comparison notebooks.</p></li>
<li><p>12/01/2022: upgraded the conda environment and included a new AWS S3 bucket data link, including zarr data (no download needed)</p></li>
<li><p>12/06/2023: Added the new 2022-2023 winter analysis notebook which also describes the new Version 3 IS2SITMOGR4 dataset. Updated the read dataset function. A few other little minor bug fixes.</p></li>
<li><p>02/14/2025: Added the new 2023-2024 winter analysis notebook. More updates to the read dataset function (mainly hard-coding the zarr links). A few other little minor bug fixes.</p></li>
</ul>
<p>If you find any issues in the code or have any suggestions for the book, feel free to open an issue, which you can find by mousing over the GitHub icon at the top of each page. If you are familiar with GitHub, you can also fork the book’s repository and suggest an edit that way.</p>
</section>
<section class="tex2jax_ignore mathjax_ignore" id="activating-the-conda-environment">
<h1>Activating the conda environment<a class="headerlink" href="#activating-the-conda-environment" title="Permalink to this heading">#</a></h1>
<p>This book has an associated conda environment stored in the file environment.yml. This file can be downloaded and used to set up the environment on your local computer so that you have all the required dependencies needed to run the notebooks. You’ll need anaconda and python installed on your computer first. The environment file is also required by Binder in order to set up the computational environment for running the notebooks in the book interactively. <br><br>
To create the environment, run the following in the command line:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">env</span> <span class="n">create</span> <span class="o">-</span><span class="n">f</span> <span class="n">environment</span><span class="o">.</span><span class="n">yml</span>
</pre></div>
</div>
<p>To activate the environment, run the following in the command line:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">activate</span> <span class="n">is2book_p39_env</span>
</pre></div>
</div>
<p>Note that there was an issue with ipykernal in the 6.18.1 upgrade hence our use of ipykernel=6.17.1 in the conda environment. Users have also noted some issues with conda and the boto3/s3fs packages. I’m still working on that so either try and fix yourself with further conda installs or drop the s3 imports/read options from your cloned repository.</p>
<p>Update (02/14/25): I noticed some issues with cartopy and needed to reinstall shapely. Unsure what exactly changed, but I now also provide the complete conda environment I am currently using if that helps:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">env</span> <span class="n">create</span> <span class="o">-</span><span class="n">f</span> <span class="n">environment_021425</span><span class="o">.</span><span class="n">yml</span>
</pre></div>
</div>
<p>Will eventually transition to mamba or uv..!</p>
</section>
<section class="tex2jax_ignore mathjax_ignore" id="updating-the-jupyter-book">
<h1>Updating the Jupyter Book<a class="headerlink" href="#updating-the-jupyter-book" title="Permalink to this heading">#</a></h1>
<p>Simple instructions for how to construct/update this book are pasted below for the author’s benefit, but don’t go into detail on any of the steps. For a more detailed description on Jupyter Books and how to build one of your own, see their page: <a class="reference external" href="https://jupyterbook.org/intro.html">https://jupyterbook.org/intro.html</a>. <br></p>
<ol class="arabic simple">
<li><p>Activate virtual environment associated with book</p></li>
<li><p>Update github repository with any changes</p></li>
<li><p>cd out of local book directory into the next highest directory</p></li>
<li><p>Next you’ll need to construct the html files that make up the pages in the book. Each notebook will be executed and the outputs will be cached in the build folder. In the commmand line, run:</p></li>
</ol>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">jb</span> <span class="n">build</span> <span class="n">icesat2</span><span class="o">-</span><span class="n">book</span>
</pre></div>
</div>
<ol class="arabic simple" start="5">
<li><p>Move back cd local book directory… There must be a way to do this without changing in and out of the book directory, but if there is, it’s not very intuitive.</p></li>
</ol>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">icesat2</span><span class="o">-</span><span class="n">book</span>
</pre></div>
</div>
<ol class="arabic simple" start="7">
<li><p>Next you’ll update the github page associated with all the html files. You won’t be able to see any of the changes to the webpage hosting the book until you do this. In the command line, run:</p></li>
</ol>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">ghp</span><span class="o">-</span><span class="kn">import</span> <span class="o">-</span><span class="n">n</span> <span class="o">-</span><span class="n">p</span> <span class="o">-</span><span class="n">f</span> <span class="n">_build</span><span class="o">/</span><span class="n">html</span>
</pre></div>
</div>
<p>I’m having some issues with this so in the latest version I pip installed this package to my base environment and ran this from there.</p>
<p>Finally, if serving onto a custom domain you may need to go into the GitHub settings (Settings/Pages) and make sure it’s pointing to the right custom domain and is indicating DNS check successful.</p>
</section>

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<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">ICESat-2 Sea Ice State Analysis Jupyter Book</a><ul class="visible nav section-nav flex-column">
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About

Interactive Jupyter Book for wrangling, visualizing, and analyzing ICESat-2 monthly gridded sea ice concentration data and other related atmospheric data products.
www.icesat-2-sea-ice-state.info
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