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<div class="section" id="contributions-by-serge-x-cohen">
<h1>Contributions by Serge X. Cohen<a class="headerlink" href="#contributions-by-serge-x-cohen" title="Permalink to this headline">¶</a></h1>
<p>These filters were initially written with X-ray tomographic processing
in mind. Still they are of a general usage as long as input are image.</p>
<div class="section" id="point-based-transformation">
<h2>Point-based transformation<a class="headerlink" href="#point-based-transformation" title="Permalink to this headline">¶</a></h2>
<div class="section" id="rejecting-outliers-in-3d">
<h3>Rejecting outliers in 3D<a class="headerlink" href="#rejecting-outliers-in-3d" title="Permalink to this headline">¶</a></h3>
<dl class="class">
<dt id="med-mad-reject-med-mad-reject">
<em class="property"> class </em><code class="descname">med-mad-reject</code><a class="headerlink" href="#med-mad-reject-med-mad-reject" title="Permalink to this definition">¶</a></dt>
<dd><p>For each pixel of a frame within a stream, makes a 3x3x3 box (that
is, 3x3 box including previous, current and following frames) and
compute the median (med) and median absolute deviation (mad). If
the value of the central pixel is too far from the median
(relative to the mad) it is rejected and its value is replaced by
the median value of the box.</p>
<dl class="prop">
<dt id="med-mad-reject-threshold">
<code class="descname">"threshold"</code><span>: </span>float<a class="headerlink" href="#med-mad-reject-threshold" title="Permalink to this definition">¶</a></dt>
<dd><p>When abs(px-med) > threshold*mad the pixel value (noted px)
is replaced by med.</p>
</dd></dl>
</dd></dl>
</div>
<div class="section" id="rejecting-outliers-in-2d">
<h3>Rejecting outliers in 2D<a class="headerlink" href="#rejecting-outliers-in-2d" title="Permalink to this headline">¶</a></h3>
<dl class="class">
<dt id="med-mad-reject-2d-med-mad-reject-2d">
<em class="property"> class </em><code class="descname">med-mad-reject-2d</code><a class="headerlink" href="#med-mad-reject-2d-med-mad-reject-2d" title="Permalink to this definition">¶</a></dt>
<dd><p>For each pixel of a frame make a square box centred on the pixel and
compute the median (med) and median absolute deviation (mad). If
the value of the central pixel is too far from the median
(relative to the mad) it is rejected and its value is replaced by
the median value of the box.</p>
<dl class="prop">
<dt id="med-mad-reject-2d-box-size">
<code class="descname">"box-size"</code><span>: </span>uint<a class="headerlink" href="#med-mad-reject-2d-box-size" title="Permalink to this definition">¶</a></dt>
<dd><p>The edge size of the box to be used (in px). This should be an
even number so that it can be centred on a pixel.</p>
</dd></dl>
<dl class="prop">
<dt id="med-mad-reject-2d-threshold">
<code class="descname">"threshold"</code><span>: </span>float<a class="headerlink" href="#med-mad-reject-2d-threshold" title="Permalink to this definition">¶</a></dt>
<dd><p>When abs(px-med) > threshold*mad the pixel value (noted px)
is replaced by med.</p>
</dd></dl>
</dd></dl>
</div>
<div class="section" id="opencl-one-liner-computation">
<h3>OpenCL one-liner computation<a class="headerlink" href="#opencl-one-liner-computation" title="Permalink to this headline">¶</a></h3>
<dl class="class">
<dt id="ocl-1liner-ocl-1liner">
<em class="property"> class </em><code class="descname">ocl-1liner</code><a class="headerlink" href="#ocl-1liner-ocl-1liner" title="Permalink to this definition">¶</a></dt>
<dd><p>The aim is to enable the implementation of simple, nevertheless
multiple input, computation on the basis of one work-item per pixel
of the frame. The filter accepts arbitrary number of inputs, as
long as more than one is provided. The output has the same size as
the first input (indexed 0) and the generated OpenCL kernel is run
with one work item per pixel of the output. The user provides a
single computation line and the filter places it within a skeleton
to produce an OpenCL kernel on the fly, then compiles it and uses
it in the current workflow.</p>
<p>In the kernel the following variables are defined :
<cite>sizeX</cite> and <cite>sizeY</cite> are the size of the frame in X and Y directions;
<cite>x</cite> and <cite>y</cite> are the coordinate of the pixel corresponding to the
current work item;
<cite>in_x</cite> are the buffer holding the 0..(n-1) input frames;
<cite>out</cite> is the buffer holding the output of the computation.</p>
<p>In the computation line provided through <a class="reference internal" href="#ocl-1liner-one-line" title="ocl-1liner-one-line"><code class="xref gobj gobj-prop docutils literal"><span class="pre">one-line</span></code></a> the
pixel corresponding to the current work item is <cite>px_index</cite>. Also
reference to the pixel values can use multiple syntax :
<cite>out[px_index]</cite>, <cite>in_0[px_index]</cite>, … <cite>in_x[px_index]</cite> or as
shortcut (indeed macro of those) <cite>out_px</cite>, <cite>in_0_px</cite>,
… <cite>in_x_px</cite>. Finally if one wants to have finer control over the
pixel used in the computation (being able to use neighbouring pixel
values) one can use the <cite>IMG_VAL</cite> macro as such <cite>IMG_VAL(x,y,out)</cite>,
<cite>IMG_VAL(x,y,in_x)</cite> …</p>
<dl class="prop">
<dt id="ocl-1liner-one-line">
<code class="descname">"one-line"</code><span>: </span>string<a class="headerlink" href="#ocl-1liner-one-line" title="Permalink to this definition">¶</a></dt>
<dd><p>The computation to be performed expressed in one line of
OpenCL, no trailing semi-column (added by the skeleton). To
avoid miss-interpretation of the symbols by the line parser of
ufo-launch it is advisable to surround the line by single
quotes (on top of shell quoting). One example (invoking through
ufo-launch) would be <cite>“‘out_px = (in_0_px > 0) ? sqrt(in_0_px)
: 0.0f’”</cite> .</p>
</dd></dl>
<dl class="prop">
<dt id="ocl-1liner-num-inputs">
<code class="descname">"num-inputs"</code><span>: </span>uint<a class="headerlink" href="#ocl-1liner-num-inputs" title="Permalink to this definition">¶</a></dt>
<dd><p>The number of input streams. This is mandatory since it can not
be inferred as it is the case by the <a class="reference internal" href="../filters.html#generic-opencl-ref"><span class="std std-ref">OpenCL</span></a> task.</p>
</dd></dl>
<dl class="prop">
<dt id="ocl-1liner-quiet">
<code class="descname">"quiet"</code><span>: </span>boolean<a class="headerlink" href="#ocl-1liner-quiet" title="Permalink to this definition">¶</a></dt>
<dd><p>Default to <cite>true</cite>, when set to <cite>false</cite> the dynamically
generated kernel sources are printed to the standard output
during the task setup.</p>
</dd></dl>
</dd></dl>
</div>
</div>
<div class="section" id="auxiliary">
<h2>Auxiliary<a class="headerlink" href="#auxiliary" title="Permalink to this headline">¶</a></h2>
<div class="section" id="producing-simple-statistics-on-a-stream">
<h3>Producing simple statistics on a stream<a class="headerlink" href="#producing-simple-statistics-on-a-stream" title="Permalink to this headline">¶</a></h3>
<dl class="class">
<dt id="stat-monitor-stat-monitor">
<em class="property"> class </em><code class="descname">stat-monitor</code><a class="headerlink" href="#stat-monitor-stat-monitor" title="Permalink to this definition">¶</a></dt>
<dd><p>Inspects a data stream in a way similar to the <code class="xref gobj gobj-class docutils literal"><span class="pre">monitor</span></code>
task but also computing simple statistics on the monitored frame stream:
min, max, mean and standard deviation of each frame is computed. To limit
truncation errors the OpenCL kernel uses fp64 operations if those are
supported by the used OpenCL device, otherwise it falls back to use fp32
arithmetic which might incurs significant truncation errors on images of
large dimensions.</p>
<dl class="prop">
<dt id="stat-monitor-filename">
<code class="descname">"filename"</code><span>: </span>string<a class="headerlink" href="#stat-monitor-filename" title="Permalink to this definition">¶</a></dt>
<dd><p>When provided the tabulated statistics are output the file
with this filename rather than displayed to standard output.</p>
</dd></dl>
<dl class="prop">
<dt id="stat-monitor-trace">
<code class="descname">"trace"</code><span>: </span>boolean<a class="headerlink" href="#stat-monitor-trace" title="Permalink to this definition">¶</a></dt>
<dd><p>When set to <cite>true</cite> will print processed frame index to
standard output. This is useful if the task is placed in before
a task somehow hiding the number of processed frames (in a
complex workflow). Defaulting to <cite>false</cite></p>
</dd></dl>
<dl class="prop">
<dt id="stat-monitor-quiet">
<code class="descname">"quiet"</code><span>: </span>boolean<a class="headerlink" href="#stat-monitor-quiet" title="Permalink to this definition">¶</a></dt>
<dd><p>When set to <cite>true</cite> will not print the frame
monitoring. Defaulting to <cite>false</cite> to be as close as possible
to the output of the <code class="xref gobj gobj-class docutils literal"><span class="pre">monitor</span></code> task.</p>
</dd></dl>
<dl class="prop">
<dt id="stat-monitor-print">
<code class="descname">"print"</code><span>: </span>uint<a class="headerlink" href="#stat-monitor-print" title="Permalink to this definition">¶</a></dt>
<dd><p>If set print the given numbers of items on stdout as hexadecimally
formatted numbers (taken from <code class="xref gobj gobj-class docutils literal"><span class="pre">monitor</span></code> task).</p>
</dd></dl>
</dd></dl>
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<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Contributions by Serge X. Cohen</a><ul>
<li><a class="reference internal" href="#point-based-transformation">Point-based transformation</a><ul>
<li><a class="reference internal" href="#rejecting-outliers-in-3d">Rejecting outliers in 3D</a></li>
<li><a class="reference internal" href="#rejecting-outliers-in-2d">Rejecting outliers in 2D</a></li>
<li><a class="reference internal" href="#opencl-one-liner-computation">OpenCL one-liner computation</a></li>
</ul>
</li>
<li><a class="reference internal" href="#auxiliary">Auxiliary</a><ul>
<li><a class="reference internal" href="#producing-simple-statistics-on-a-stream">Producing simple statistics on a stream</a></li>
</ul>
</li>
</ul>
</li>
</ul>
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