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<main class="pdoc">
<section class="module-info">
<h1 class="modulename">
go_utils </h1>
<div class="docstring"><p>go_utils contains utilities for interfacing with the GLOBE Observer datasets, primarily the Mosquito Habitat Mapper and Landcover.</p>
<h2 id="main-features">Main Features</h2>
<p>Here are the major utilities provided by the package:</p>
<ul>
<li>Easy downloading of the GLOBE Observer datasets as Pandas DataFrames</li>
<li>Utilities for cleaning up Mosquito Habitat Mapper and Landcover Datasets</li>
<li>CLI Scripts for downloading data and photos for the Mosquito Habitat Mapper and Landcover Protocols.</li>
</ul>
<h2 id="example-notebooks">Example Notebooks</h2>
<p><a href="https://github.com/IGES-Geospatial/globe-observer-utils/tree/main/notebooks">Example Notebooks</a> have been made to show basic examples and applications of this library.</p>
<h2 id="cli-script-documentation">CLI Script Documentation</h2>
<p>The CLI Scripts are intended to provide fast and accessible ways of collecting cleaned GLOBE Observer data from the commandline.</p>
<h2 id="getting-globe-data-csvs">Getting GLOBE Data CSVs</h2>
<p>There are two commands that can be used to get data from Mosquito Habitat Mapper and Land Cover, respectively.
For Mosquito Habitat Mapper, there is <code>mhm-data-download</code> and for Land Cover, there is <code>lc-data-download</code>.</p>
<p>For each of these commands, there are several flags that can be specified to narrow down the data:</p>
<h3 id="general-flags">General Flags</h3>
<h4 id="output-path">Output Path</h4>
<p>You can use <code>--out</code> or <code>-o</code> followed by a file path to specify the output path of the download. If this is not specified, the script will generate diagnostic plots for you to get insight into the data that you would be downloading.</p>
<h4 id="start-and-end-dates">Start and End Dates</h4>
<p>You can use <code>--start</code> or <code>-s</code> followed by a date in YYYY-MM-DD form to specify the start date. Similarly, you can use <code>--end</code> or <code>-e</code> to specify the end date.</p>
<h4 id="countries">Countries</h4>
<p>You can use <code>--countries</code> or <code>-co</code> followed by a list of countries separated by commas to specify a download of specific country data. For example <code>-co "Brazil, Argentina"</code> would only download data from Brazil and Argentina.</p>
<h4 id="regions">Regions</h4>
<p>You can use <code>--regions</code> or <code>-r</code> followed by a list of regions separated by commas to specify a download of specific GLOBE region data. For example <code>-r "North America"</code> would download data from North America. See the region dictionary to see the countries that comprise each GLOBE Region.</p>
<h4 id="bounding-box">Bounding Box</h4>
<p>You can use <code>--box</code> or <code>-b</code> followed by the coordinates of your bounding box in this format: <code>min latitude, min longitude, max latitude, max longitude</code></p>
<h3 id="mosquito-habitat-mapper-flags">Mosquito Habitat Mapper Flags</h3>
<h4 id="genus">Genus</h4>
<p>You can use <code>--hasgenus</code> or <code>-hg</code> to only get data that has an identified genus.</p>
<h4 id="container">Container</h4>
<p>You can use <code>--iscontainer</code> or <code>-ic</code> to only get data which has a container as a watersource.</p>
<h4 id="photo">Photo</h4>
<p>You can use <code>--hasphotos</code> or <code>-hp</code> to only get data which has recorded photo entries.</p>
<h4 id="minimum-larvae-count">Minimum Larvae Count</h4>
<p>You can use <code>--minlarvae</code> or <code>-ml</code> to only get data which has a certain amount of larvae.</p>
<h4 id="example">Example</h4>
<p>The command:</p>
<div class="pdoc-code codehilite"><pre><span></span><code><span class="n">mhm</span><span class="o">-</span><span class="n">download</span> <span class="o">-</span><span class="n">s</span> <span class="s2">"2021-05-01"</span> <span class="o">-</span><span class="n">e</span> <span class="s2">"2021-05-31"</span> <span class="o">-</span><span class="n">hg</span> <span class="o">-</span><span class="n">o</span> <span class="n">MHM_Regular_Test</span><span class="o">.</span><span class="n">csv</span>
</code></pre></div>
<p>Would download all mosquito mapper data with an identified genus during May 1st, 2021 to May 31st, 2021 into a <code>MHM_Regular_Test.csv</code> file.</p>
<h3 id="land-cover-flags">Land Cover Flags</h3>
<h4 id="has-a-classification">Has a Classification</h4>
<p>You can use <code>--hasclassification</code> or <code>-hc</code> to only get data which has atleast one Land Cover Classification.</p>
<h4 id="has-photo">Has Photo</h4>
<p>You can use <code>--hasphoto</code> or <code>-hp</code> to only get data which has atleast one Photo entry.</p>
<h4 id="has-all-classifications">Has All Classifications</h4>
<p>You can use <code>--hasallclassifications</code> or <code>-hac</code> to only get data which has all classifications filled out.</p>
<h4 id="has-all-photos">Has All Photos</h4>
<p>You can use <code>--hasallphotos</code> or <code>-hap</code> to only get data which has all photos filled out.</p>
<h4 id="example-2">Example</h4>
<p>The command:</p>
<div class="pdoc-code codehilite"><pre><span></span><code><span class="n">lc</span><span class="o">-</span><span class="n">download</span> <span class="o">-</span><span class="n">s</span> <span class="s2">"2021-05-01"</span> <span class="o">-</span><span class="n">e</span> <span class="s2">"2021-05-31"</span> <span class="o">-</span><span class="n">hap</span> <span class="o">-</span><span class="n">o</span> <span class="n">LC_Regular_Test</span><span class="o">.</span><span class="n">csv</span>
</code></pre></div>
<p>Would download all landcover data with fully filled out photo observations during May 1st, 2021 to May 31st, 2021 into a <code>LC_Regular_Test.csv</code> file.</p>
<h2 id="downloading-photos">Downloading Photos</h2>
<p>There are two commands that can be used to get photos for cleaned Mosquito Habitat Mapper and Land Cover CSV files, respectively.
For Mosquito Habitat Mapper, there is <code>mhm-photo-download</code> and for Land Cover, there is <code>lc-photo-download</code>.</p>
<h3 id="general-command">General Command</h3>
<p>In order for the photo download scripts to work, you must specify an input path and output path.
For example, <code>mhm_photo_download "input csv path" "output directory"</code> will take the Mosquito Habitat Mapper data stored in the input CSV and download the photos to the output directory. If the output directory doesn't exist, it will be created.</p>
<h4 id="all-flag">All Flag</h4>
<p>You can use the <code>--all</code> or <code>-a</code> to set all the following flags.</p>
<h4 id="custom-photo-naming-flags">Custom Photo Naming Flags</h4>
<ul>
<li>Use <code>--name_additional</code> or <code>-add</code> to add custom additional information to the photo names.</li>
<li>Use <code>--nargs_include</code> or <code>-in</code> to include a field from the default photo name. Can include any of the following:
<ul>
<li>For <strong>mosquito_habitat_mapper</strong> -- Accepted Included Names include:
<ul>
<li><code>url_type</code> -- Type of photo (e.g. Watersource, Larvae, Abdomen)</li>
<li><code>watersource</code> -- Watersource for the observed mosquito habitat</li>
<li><code>latitude</code> -- GPS Latitude Coordinate (rounded to 5 decimal places)</li>
<li><code>longitude</code> -- GPS Longitude Coordinate (rounded to 5 decimal places)</li>
<li><code>date_str</code> -- Date Range expressed as a String</li>
<li><code>mhm_id</code> -- Unique ID for a MHM observation</li>
<li><code>classification</code> -- Mosquito classification (or <code>"None"</code> if no classification available)</li>
</ul></li>
<li>For <strong>land_cover</strong> -- Accepted Included Names include:
<ul>
<li><code>direction</code> -- Direction where the photo was taken (e.g. North, South, East, West, Up, Down)</li>
<li><code>latitude</code> -- GPS Latitude Coordinate (rounded to 5 decimal places)</li>
<li><code>longitude</code> -- GPS Longitude Coordinate (rounded to 5 decimal places)</li>
<li><code>date_str</code> -- Date Range expressed as a String</li>
<li><code>lc_id</code> -- Unique ID for a LC observation</li>
</ul></li>
</ul></li>
</ul>
<h3 id="mosquito-specifics">Mosquito Specifics</h3>
<h4 id="larvae-photos">Larvae Photos</h4>
<p>You can use <code>--larvae</code> or <code>-l</code> to specify the download of larvae photos.</p>
<h4 id="watersource-photos">Watersource Photos</h4>
<p>You can use <code>--watersource</code> or <code>-w</code> to specify the download of watersource photos.</p>
<h4 id="abdomen-photos">Abdomen Photos</h4>
<p>You can use <code>--abdomen</code> or "-ab" to specify the download of abdomen photos.</p>
<h4 id="example-3">Example</h4>
<p>The command</p>
<div class="pdoc-code codehilite"><pre><span></span><code><span class="n">mhm</span><span class="o">-</span><span class="n">photo</span><span class="o">-</span><span class="n">download</span> <span class="n">mhm_sample</span><span class="o">.</span><span class="n">csv</span> <span class="n">mhm_outdir</span>
</code></pre></div>
<p>Would download all mosquito mapper photos in the <code>mhm_sample.csv</code> file to a directory named <code>mhm_outdir</code></p>
<h3 id="landcover-specifics">Landcover Specifics</h3>
<h4 id="up-photos">Up Photos</h4>
<p>You can use <code>--up</code> or <code>-u</code> to specify the download of upward photos.</p>
<h4 id="down-photos">Down Photos</h4>
<p>You can use <code>--down</code> or <code>-d</code> to specify the download of downward photos.</p>
<h4 id="north-photos">North Photos</h4>
<p>You can use <code>--north</code> or <code>-n</code> to specify the download of northward photos.</p>
<h4 id="south-photos">South Photos</h4>
<p>You can use <code>--south</code> or <code>-s</code> to specify the download of southward photos.</p>
<h4 id="east-photos">East Photos</h4>
<p>You can use <code>--east</code> or <code>-e</code> to specify the download of eastward photos.</p>
<h4 id="west-photos">West Photos</h4>
<p>You can use <code>--west</code> or <code>-w</code> to specify the download of westward photos.</p>
<h4 id="example-4">Example</h4>
<p>The command:</p>
<div class="pdoc-code codehilite"><pre><span></span><code><span class="n">lc</span><span class="o">-</span><span class="n">photo</span><span class="o">-</span><span class="n">download</span> <span class="n">lc_sample</span><span class="o">.</span><span class="n">csv</span> <span class="n">lc_outdir</span> <span class="o">-</span><span class="n">a</span>
</code></pre></div>
<p>Would download all landcover photos in the <code>lc_sample.csv</code> file to a directory named <code>lc_outdir</code></p>
</div>
<input id="go_utils-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<label class="view-source-button" for="go_utils-view-source"><span>View Source</span></label>
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="c1"># flake8: noqa</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span> <span class="nn">go_utils.download</span> <span class="kn">import</span> <span class="n">get_api_data</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="n">__docformat__</span> <span class="o">=</span> <span class="s2">"restructuredtext"</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="vm">__doc__</span> <span class="o">=</span> <span class="s2">"""</span>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="s2">go_utils contains utilities for interfacing with the GLOBE Observer datasets, primarily the Mosquito Habitat Mapper and Landcover.</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a>
</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="s2">Main Features</span>
</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="s2">-------------</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="s2">Here are the major utilities provided by the package:</span>
</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a>
</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="s2">- Easy downloading of the GLOBE Observer datasets as Pandas DataFrames</span>
</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="s2">- Utilities for cleaning up Mosquito Habitat Mapper and Landcover Datasets</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="s2">- CLI Scripts for downloading data and photos for the Mosquito Habitat Mapper and Landcover Protocols.</span>
</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a>
</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="s2">Example Notebooks</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="s2">-----------------</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="s2">[Example Notebooks](https://github.com/IGES-Geospatial/globe-observer-utils/tree/main/notebooks) have been made to show basic examples and applications of this library.</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a>
</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a><span class="s2">CLI Script Documentation</span>
</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="s2">-----------</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a>
</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a><span class="s2">The CLI Scripts are intended to provide fast and accessible ways of collecting cleaned GLOBE Observer data from the commandline.</span>
</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a>
</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="s2">## Getting GLOBE Data CSVs</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a><span class="s2">There are two commands that can be used to get data from Mosquito Habitat Mapper and Land Cover, respectively.</span>
</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="s2">For Mosquito Habitat Mapper, there is `mhm-data-download` and for Land Cover, there is `lc-data-download`.</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a>
</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="s2">For each of these commands, there are several flags that can be specified to narrow down the data:</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a><span class="s2">### General Flags</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a>
</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="s2">#### Output Path</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="s2">You can use `--out` or `-o` followed by a file path to specify the output path of the download. If this is not specified, the script will generate diagnostic plots for you to get insight into the data that you would be downloading.</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a>
</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="s2">#### Start and End Dates</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="s2">You can use `--start` or `-s` followed by a date in YYYY-MM-DD form to specify the start date. Similarly, you can use `--end` or `-e` to specify the end date.</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a>
</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="s2">#### Countries</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a><span class="s2">You can use `--countries` or `-co` followed by a list of countries separated by commas to specify a download of specific country data. For example `-co "Brazil, Argentina"` would only download data from Brazil and Argentina.</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a>
</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a><span class="s2">#### Regions</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a><span class="s2">You can use `--regions` or `-r` followed by a list of regions separated by commas to specify a download of specific GLOBE region data. For example `-r "North America"` would download data from North America. See the region dictionary to see the countries that comprise each GLOBE Region.</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a>
</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a><span class="s2">#### Bounding Box</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a><span class="s2">You can use `--box` or `-b` followed by the coordinates of your bounding box in this format: `min latitude, min longitude, max latitude, max longitude`</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a>
</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a><span class="s2">### Mosquito Habitat Mapper Flags</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a>
</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a><span class="s2">#### Genus</span>
</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a><span class="s2">You can use `--hasgenus` or `-hg` to only get data that has an identified genus.</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a>
</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a><span class="s2">#### Container</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a><span class="s2">You can use `--iscontainer` or `-ic` to only get data which has a container as a watersource.</span>
</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a>
</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a><span class="s2">#### Photo</span>
</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a><span class="s2">You can use `--hasphotos` or `-hp` to only get data which has recorded photo entries.</span>
</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a>
</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a><span class="s2">#### Minimum Larvae Count</span>
</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a><span class="s2">You can use `--minlarvae` or `-ml` to only get data which has a certain amount of larvae.</span>
</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a>
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a><span class="s2">#### Example</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a><span class="s2">The command:</span>
</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="s2">```py</span>
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="s2">mhm-download -s "2021-05-01" -e "2021-05-31" -hg -o MHM_Regular_Test.csv</span>
</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a><span class="s2">```</span>
</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a>
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="s2">Would download all mosquito mapper data with an identified genus during May 1st, 2021 to May 31st, 2021 into a `MHM_Regular_Test.csv` file.</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a><span class="s2">### Land Cover Flags</span>
</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a>
</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a><span class="s2">#### Has a Classification</span>
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a><span class="s2">You can use `--hasclassification` or `-hc` to only get data which has atleast one Land Cover Classification.</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a>
</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a><span class="s2">#### Has Photo</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a><span class="s2">You can use `--hasphoto` or `-hp` to only get data which has atleast one Photo entry.</span>
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a>
</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a><span class="s2">#### Has All Classifications</span>
</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a><span class="s2">You can use `--hasallclassifications` or `-hac` to only get data which has all classifications filled out.</span>
</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a>
</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a><span class="s2">#### Has All Photos</span>
</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a><span class="s2">You can use `--hasallphotos` or `-hap` to only get data which has all photos filled out.</span>
</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a>
</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a><span class="s2">#### Example</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a><span class="s2">The command:</span>
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a><span class="s2">```py</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a><span class="s2">lc-download -s "2021-05-01" -e "2021-05-31" -hap -o LC_Regular_Test.csv</span>
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a><span class="s2">```</span>
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a>
</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a><span class="s2">Would download all landcover data with fully filled out photo observations during May 1st, 2021 to May 31st, 2021 into a `LC_Regular_Test.csv` file.</span>
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a>
</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a><span class="s2">## Downloading Photos</span>
</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a><span class="s2">There are two commands that can be used to get photos for cleaned Mosquito Habitat Mapper and Land Cover CSV files, respectively.</span>
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a><span class="s2">For Mosquito Habitat Mapper, there is `mhm-photo-download` and for Land Cover, there is `lc-photo-download`.</span>
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a>
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a><span class="s2">### General Command</span>
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a><span class="s2">In order for the photo download scripts to work, you must specify an input path and output path.</span>
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a><span class="s2">For example, `mhm_photo_download "input csv path" "output directory"` will take the Mosquito Habitat Mapper data stored in the input CSV and download the photos to the output directory. If the output directory doesn't exist, it will be created.</span>
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a>
</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a><span class="s2">#### All Flag</span>
</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a><span class="s2">You can use the `--all` or `-a` to set all the following flags.</span>
</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a>
</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="s2">#### Custom Photo Naming Flags</span>
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="s2">* Use `--name_additional` or `-add` to add custom additional information to the photo names.</span>
</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a><span class="s2">* Use `--nargs_include` or `-in` to include a field from the default photo name. Can include any of the following:</span>
</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a><span class="s2"> * For **mosquito_habitat_mapper** -- Accepted Included Names include:</span>
</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a><span class="s2"> * `url_type` -- Type of photo (e.g. Watersource, Larvae, Abdomen)</span>
</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a><span class="s2"> * `watersource` -- Watersource for the observed mosquito habitat</span>
</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a><span class="s2"> * `latitude` -- GPS Latitude Coordinate (rounded to 5 decimal places)</span>
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a><span class="s2"> * `longitude` -- GPS Longitude Coordinate (rounded to 5 decimal places)</span>
</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a><span class="s2"> * `date_str` -- Date Range expressed as a String</span>
</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a><span class="s2"> * `mhm_id` -- Unique ID for a MHM observation</span>
</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a><span class="s2"> * `classification` -- Mosquito classification (or `"None"` if no classification available)</span>
</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="s2"> * For **land_cover** -- Accepted Included Names include:</span>
</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="s2"> * `direction` -- Direction where the photo was taken (e.g. North, South, East, West, Up, Down)</span>
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a><span class="s2"> * `latitude` -- GPS Latitude Coordinate (rounded to 5 decimal places)</span>
</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a><span class="s2"> * `longitude` -- GPS Longitude Coordinate (rounded to 5 decimal places)</span>
</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a><span class="s2"> * `date_str` -- Date Range expressed as a String</span>
</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a><span class="s2"> * `lc_id` -- Unique ID for a LC observation</span>
</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a>
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a><span class="s2">### Mosquito Specifics</span>
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a>
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a><span class="s2">#### Larvae Photos</span>
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a><span class="s2">You can use `--larvae` or `-l` to specify the download of larvae photos.</span>
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a>
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a><span class="s2">#### Watersource Photos</span>
</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a><span class="s2">You can use `--watersource` or `-w` to specify the download of watersource photos.</span>
</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a>
</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a><span class="s2">#### Abdomen Photos</span>
</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a><span class="s2">You can use `--abdomen` or "-ab" to specify the download of abdomen photos.</span>
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a>
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a><span class="s2">#### Example</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a><span class="s2">The command</span>
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a><span class="s2">```py</span>
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a><span class="s2">mhm-photo-download mhm_sample.csv mhm_outdir</span>
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a><span class="s2">```</span>
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a><span class="s2">Would download all mosquito mapper photos in the `mhm_sample.csv` file to a directory named `mhm_outdir`</span>
</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a><span class="s2">### Landcover Specifics</span>
</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a>
</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a><span class="s2">#### Up Photos</span>
</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a><span class="s2">You can use `--up` or `-u` to specify the download of upward photos.</span>
</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a>
</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a><span class="s2">#### Down Photos</span>
</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a><span class="s2">You can use `--down` or `-d` to specify the download of downward photos.</span>
</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a>
</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a><span class="s2">#### North Photos</span>
</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a><span class="s2">You can use `--north` or `-n` to specify the download of northward photos.</span>
</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a>
</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a><span class="s2">#### South Photos</span>
</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a><span class="s2">You can use `--south` or `-s` to specify the download of southward photos.</span>
</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a>
</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a><span class="s2">#### East Photos</span>
</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a><span class="s2">You can use `--east` or `-e` to specify the download of eastward photos.</span>
</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a>
</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a><span class="s2">#### West Photos</span>
</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a><span class="s2">You can use `--west` or `-w` to specify the download of westward photos.</span>
</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a>
</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a><span class="s2">#### Example</span>
</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a><span class="s2">The command:</span>
</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a><span class="s2">```py</span>
</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a><span class="s2">lc-photo-download lc_sample.csv lc_outdir -a</span>
</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a><span class="s2">```</span>
</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a><span class="s2">Would download all landcover photos in the `lc_sample.csv` file to a directory named `lc_outdir`</span>
</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a><span class="s2">"""</span>
</span></pre></div>
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const originalContent = document.querySelector("main.pdoc");
let currentContent = originalContent;
function setContent(innerHTML) {
let elem;
if (innerHTML) {
elem = document.createElement("main");
elem.classList.add("pdoc");
elem.innerHTML = innerHTML;
} else {
elem = originalContent;
}
if (currentContent !== elem) {
currentContent.replaceWith(elem);
currentContent = elem;
}
}
function getSearchTerm() {
return (new URL(window.location)).searchParams.get("search");
}
const searchBox = document.querySelector(".pdoc input[type=search]");
searchBox.addEventListener("input", function () {
let url = new URL(window.location);
if (searchBox.value.trim()) {
url.hash = "";
url.searchParams.set("search", searchBox.value);
} else {
url.searchParams.delete("search");
}
history.replaceState("", "", url.toString());
onInput();
});
window.addEventListener("popstate", onInput);
let search, searchErr;
async function initialize() {
try {
search = await new Promise((resolve, reject) => {
const script = document.createElement("script");
script.type = "text/javascript";
script.async = true;
script.onload = () => resolve(window.pdocSearch);
script.onerror = (e) => reject(e);
script.src = "search.js";
document.getElementsByTagName("head")[0].appendChild(script);
});
} catch (e) {
console.error("Cannot fetch pdoc search index");
searchErr = "Cannot fetch search index.";
}
onInput();
document.querySelector("nav.pdoc").addEventListener("click", e => {
if (e.target.hash) {
searchBox.value = "";
searchBox.dispatchEvent(new Event("input"));
}
});
}
function onInput() {
setContent((() => {
const term = getSearchTerm();
if (!term) {
return null
}
if (searchErr) {
return `<h3>Error: ${searchErr}</h3>`
}
if (!search) {
return "<h3>Searching...</h3>"
}
window.scrollTo({top: 0, left: 0, behavior: 'auto'});
const results = search(term);
let html;
if (results.length === 0) {
html = `No search results for '${escapeHTML(term)}'.`
} else {
html = `<h4>${results.length} search result${results.length > 1 ? "s" : ""} for '${escapeHTML(term)}'.</h4>`;
}
for (let result of results.slice(0, 10)) {
let doc = result.doc;
let url = `${doc.modulename.replaceAll(".", "/")}.html`;
if (doc.qualname) {
url += `#${doc.qualname}`;
}
let heading;
switch (result.doc.type) {
case "function":
heading = `<span class="def">${doc.funcdef}</span> <span class="name">${doc.fullname}</span><span class="signature">${doc.signature}:</span>`;
break;
case "class":
heading = `<span class="def">class</span> <span class="name">${doc.fullname}</span>`;
if (doc.bases)
heading += `<wbr>(<span class="base">${doc.bases}</span>)`;
heading += `:`;
break;
case "variable":
heading = `<span class="name">${doc.fullname}</span>`;
if (doc.annotation)
heading += `<span class="annotation">${doc.annotation}</span>`;
if (doc.default_value)
heading += `<span class="default_value">${doc.default_value}</span>`;
break;
default:
heading = `<span class="name">${doc.fullname}</span>`;
break;
}
html += `
<section class="search-result">
<a href="${url}" class="attr ${doc.type}">${heading}</a>
<div class="docstring">${doc.doc}</div>
</section>
`;
}
return html;
})());
}
if (getSearchTerm()) {
initialize();
searchBox.value = getSearchTerm();
onInput();
} else {
searchBox.addEventListener("focus", initialize, {once: true});
}
searchBox.addEventListener("keydown", e => {
if (["ArrowDown", "ArrowUp", "Enter"].includes(e.key)) {
let focused = currentContent.querySelector(".search-result.focused");
if (!focused) {
currentContent.querySelector(".search-result").classList.add("focused");
} else if (
e.key === "ArrowDown"
&& focused.nextElementSibling
&& focused.nextElementSibling.classList.contains("search-result")
) {
focused.classList.remove("focused");
focused.nextElementSibling.classList.add("focused");
focused.nextElementSibling.scrollIntoView({
behavior: "smooth",
block: "nearest",
inline: "nearest"
});
} else if (
e.key === "ArrowUp"
&& focused.previousElementSibling
&& focused.previousElementSibling.classList.contains("search-result")
) {
focused.classList.remove("focused");
focused.previousElementSibling.classList.add("focused");
focused.previousElementSibling.scrollIntoView({
behavior: "smooth",
block: "nearest",
inline: "nearest"
});
} else if (
e.key === "Enter"
) {
focused.querySelector("a").click();
}
}
});
</script></body>
</html>