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<h1>Construct an im3d object representing 3D image data, densities etc</h1>
<small class="dont-index">Source: <a href="https://github.com/natverse/nat/blob/HEAD/R/im3d.R" class="external-link"><code>R/im3d.R</code></a></small>
<div class="hidden name"><code>im3d.Rd</code></div>
</div>
<div class="ref-description">
<p><code>im3d</code> objects consist of a data array with attributes defining the
spatial positions at which the voxels are located. There should always be a
<code>BoundingBox</code> attribute which defines the physical extent of the volume
in the same manner as the Amira 3D visualisation and analysis software. This
corresponds to the <strong>node</strong> centers option in the
<a href="http://teem.sourceforge.net/nrrd/format.html" class="external-link">NRRD format</a>.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">im3d</span><span class="op">(</span>
x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="fl">0</span><span class="op">)</span>,
dims <span class="op">=</span> <span class="cn">NULL</span>,
voxdims <span class="op">=</span> <span class="cn">NULL</span>,
origin <span class="op">=</span> <span class="cn">NULL</span>,
BoundingBox <span class="op">=</span> <span class="cn">NULL</span>,
bounds <span class="op">=</span> <span class="cn">NULL</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>The object to turn into an im3d</p></dd>
<dt>dims</dt>
<dd><p>The dimensions of the image array either as an integer vector
<em>or</em> as an im3d object, whose attributes will provide defaults for
<code>dims, origin, BoundingBox, bounds</code> arguments. The default
(<code>dims=NULL</code>) will result in <code>dims</code> being set to <code>x</code> if
<code>x</code> is an <code>im3d</code> object or <code>dim(x)</code> otherwise.</p></dd>
<dt>voxdims</dt>
<dd><p>The voxel dimensions</p></dd>
<dt>origin</dt>
<dd><p>the location (or centre) of the first voxel</p></dd>
<dt>BoundingBox, bounds</dt>
<dd><p>Physical extent of image. See the details section
of <code><a href="boundingbox.html">boundingbox</a></code>'s help for the distinction.</p></dd>
<dt>...</dt>
<dd><p>Additional attributes such as units or materials</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>An array with additional class <code>im3d</code></p>
</div>
<div id="details">
<h2>Details</h2>
<p>We follow Amira's convention of setting the bounding box equal to
voxel dimension (rather than 0) for any dimension with only 1 voxel.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p>Other im3d:
<code><a href="as.im3d.html">as.im3d</a>()</code>,
<code><a href="boundingbox.html">boundingbox</a>()</code>,
<code><a href="im3d-coords.html">im3d-coords</a></code>,
<code><a href="im3d-io.html">im3d-io</a></code>,
<code><a href="imexpand.grid.html">imexpand.grid</a>()</code>,
<code><a href="imslice.html">imslice</a>()</code>,
<code><a href="is.im3d.html">is.im3d</a>()</code>,
<code><a href="mask.html">mask</a>()</code>,
<code><a href="origin.html">origin</a>()</code>,
<code><a href="projection.html">projection</a>()</code>,
<code><a href="threshold.html">threshold</a>()</code>,
<code><a href="unmask.html">unmask</a>()</code>,
<code><a href="voxdims.html">voxdims</a>()</code></p></div>
</div>
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