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<meta property="og:title" content="Parse bits — parse.bits" />
<meta property="og:description" content="Returns specified bit value based on integer input
Data such as MODIS the QC band are stored in bits. This function returns the 
value(s) for specified bit. For example, the MODIS QC flag are bits 0-1 with 
the bit value 00 representing the &quot;LST produced, good quality&quot; flag. When 
exported from HDF the QC bands are often in an 8 bit integer range (0-255). 
With this function you can parse the values for each bit to assign the 
flag values." />




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    <h1>Parse bits</h1>
    <small class="dont-index">Source: <a href='https://github.com/jeffreyevans/spatialEco/blob/master/R/parse.bits.R'><code>R/parse.bits.R</code></a></small>
    <div class="hidden name"><code>parse.bits.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Returns specified bit value based on integer input</p>
<p>Data such as MODIS the QC band are stored in bits. This function returns the 
value(s) for specified bit. For example, the MODIS QC flag are bits 0-1 with 
the bit value 00 representing the "LST produced, good quality" flag. When 
exported from HDF the QC bands are often in an 8 bit integer range (0-255). 
With this function you can parse the values for each bit to assign the 
flag values.</p>
    </div>

    <pre class="usage"><span class='fu'>parse.bits</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>bit</span>, depth <span class='op'>=</span> <span class='fl'>8</span>, order <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"reverse"</span>, <span class='st'>"none"</span><span class='op'>)</span><span class='op'>)</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
      <td><p>Integer value</p></td>
    </tr>
    <tr>
      <th>bit</th>
      <td><p>A single or vector of bits to return</p></td>
    </tr>
    <tr>
      <th>depth</th>
      <td><p>The depth (length) of the bit range, default is 8</p></td>
    </tr>
    <tr>
      <th>order</th>
      <td><p>c("reverse", "none") sort order for the bits</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>

    <p>Jeffrey S. Evans  &lt;jeffrey_evans@tnc.org&gt;</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>
 <span class='co'># Return value for bit 5 for integer value 100</span>
 <span class='fu'>parse.bits</span><span class='op'>(</span><span class='fl'>100</span>, <span class='fl'>5</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] 1</div><div class='input'> 
 <span class='co'># Return value(s) for bits 0 and 1 for integer value 100</span>
 <span class='fu'>parse.bits</span><span class='op'>(</span><span class='fl'>100</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>,<span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] "0 0"</div><div class='input'>
 <span class='co'># Return value(s) for bits 0 and 1 for integer values 0-255</span>
 <span class='kw'>for</span><span class='op'>(</span><span class='va'>i</span> <span class='kw'>in</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>255</span><span class='op'>)</span> <span class='op'>{</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='fu'>parse.bits</span><span class='op'>(</span><span class='va'>i</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>,<span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>}</span>
</div><div class='output co'>#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"
#&gt; [1] "0 0"
#&gt; [1] "1 0"
#&gt; [1] "0 1"
#&gt; [1] "1 1"</div><div class='input'> 
<span class='kw'>if</span> <span class='op'>(</span><span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'>#### Applied Example using Harmonized Landsat Sentinel-2 QC </span>

<span class='co'># Create dummy data and qc band</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://rspatial.org/raster'>raster</a></span><span class='op'>)</span>
 <span class='va'>r</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/raster/man/raster.html'>raster</a></span><span class='op'>(</span>nrow<span class='op'>=</span><span class='fl'>100</span>, ncol<span class='op'>=</span><span class='fl'>100</span><span class='op'>)</span>
   <span class='va'>r</span><span class='op'>[</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/ncell.html'>ncell</a></span><span class='op'>(</span><span class='va'>r</span><span class='op'>)</span>, <span class='fl'>0</span>,<span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> 
 <span class='va'>qc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/raster/man/raster.html'>raster</a></span><span class='op'>(</span>nrow<span class='op'>=</span><span class='fl'>100</span>, ncol<span class='op'>=</span><span class='fl'>100</span><span class='op'>)</span>
   <span class='va'>qc</span><span class='op'>[</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/ncell.html'>ncell</a></span><span class='op'>(</span><span class='va'>qc</span><span class='op'>)</span>, <span class='fl'>64</span>,<span class='fl'>234</span><span class='op'>)</span><span class='op'>)</span> 
 
 <span class='co'># Calculate bit values from QC table</span>
 <span class='op'>(</span> <span class='va'>qc_bits</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>int<span class='op'>=</span><span class='fl'>0</span><span class='op'>:</span><span class='fl'>255</span>, 
   cloud <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/unlist.html'>unlist</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>:</span><span class='fl'>255</span>, FUN<span class='op'>=</span><span class='va'>parse.bits</span>, bit<span class='op'>=</span><span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span>,
   shadow <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/unlist.html'>unlist</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>:</span><span class='fl'>255</span>, FUN<span class='op'>=</span><span class='va'>parse.bits</span>, bit<span class='op'>=</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span>,
   acloud <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/unlist.html'>unlist</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>:</span><span class='fl'>255</span>, FUN<span class='op'>=</span><span class='va'>parse.bits</span>, bit<span class='op'>=</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span>,
   cirrus <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/unlist.html'>unlist</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>:</span><span class='fl'>255</span>, FUN<span class='op'>=</span><span class='va'>parse.bits</span>, bit<span class='op'>=</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span>,
   aerosol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/unlist.html'>unlist</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>:</span><span class='fl'>255</span>, FUN<span class='op'>=</span><span class='va'>parse.bits</span>, bit<span class='op'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>7</span>,<span class='fl'>6</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>)</span>
     
 <span class='co'># Query the results to create a vector of integer values indicating what to mask </span>
 <span class='va'>m</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/sort.html'>sort</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/unique.html'>unique</a></span><span class='op'>(</span><span class='va'>qc_bits</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='va'>qc_bits</span><span class='op'>$</span><span class='va'>cloud</span> <span class='op'>==</span> <span class='fl'>1</span><span class='op'>)</span>,
                            <span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='va'>qc_bits</span><span class='op'>$</span><span class='va'>shadow</span> <span class='op'>==</span> <span class='fl'>1</span><span class='op'>)</span>
                <span class='op'>)</span>,<span class='op'>]</span><span class='op'>$</span><span class='va'>int</span><span class='op'>)</span><span class='op'>)</span>
 
 <span class='co'># Apply queried integer values to mask image with QA band</span>
 <span class='va'>qc</span><span class='op'>[</span><span class='va'>qc</span> <span class='op'>%in%</span> <span class='va'>m</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='cn'>NA</span>
 <span class='va'>r</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/raster/man/mask.html'>mask</a></span><span class='op'>(</span><span class='va'>r</span>, <span class='va'>qc</span><span class='op'>)</span>
<span class='op'>}</span>

</div></pre>
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