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<chapter id="user-alignment"><title>Alignment</title>

<p>Alignment compares each supplemental frame in the sequence with an intermediate
incremental rendering known as the alignment reference image.  Based on this
comparison, a transformation is assigned to the supplemental frame.  Many
different transformations can be assigned before alignment of the frame is
complete.</p>

<p>This manual page offers an overview of alignment options; see also <xref
linkend="user-tdf"/>.</p>

<s><t>Transformations</t>

<p>The variables used to adjust alignment are called transformations; they map
points from the source image coordinate system to a target coordinate system
(the rendering coordinate system).</p>

<p>ALE supports three transformation classes -- translational, euclidean, and
projective -- as well as barrel/pincushion distortion correction.  The
translational class applies only translations to the inputs, changing only the
positions of images; the Euclidean class applies translations and rotations;
and the projective class applies general projective transformations.
Additionally, barrel/pincushion distortion correction can be applied to each
frame.  The Euclidean class is most appropriate for use with scanners, or as a
first pass for projective transformations.  The projective class and
barrel/pincushion distortion correction are most appropriate for use with
cameras.  Except when capturing flat scenes, ALE does not correct perspective
changes, so movement of cameras should ideally be constrained so that no large
translations occur.</p>

<s><t>Transformation Class Options</t>

<ll>--translation     Only adjust the position of images
--euclidean       Adjust the position and orientation of images [default]
--projective      Use projective transformations.  Best quality, but slow.
</ll>

<p>For more information on barrel distortion correction, see <xref linkend="user-tdf"/>.</p>

</s><s><t>Transformation data file options</t>

<p>Transformations used in alignment can be loaded from, or saved to, a
transformation data file..  This can be useful when performing alignment in
several passes, or when refining rendering options.  A transformation data file
is required for barrel/pincushion distortion correction.  For more information, 
see <xref linkend="user-tdf"/>.</p>

<ll>--trans-load=x    Load initial transformation settings from file x
--trans-save=x    Save final transformation data in file x
</ll>

</s><s><t>Alignment following</t>

<p>The --follow option hints that frames tend to be more closely aligned with
adjacent frames in the sequence than with the original frame.  --identity 
indicates that frames tend to closely align with the original frame.  These hints can be
useful even when initial alignment information is loaded from a file.</p>

<ll>--follow          Frames align closely with their predecessor.  [default]
--identity        Frames align closely with the original frame.
</ll>

</s></s><s><t>Match statistics</t>

<p>The match statistic indicates how well a transformed frame aligns with the
alignment reference image; it is used to select or reject transformations
during alignment.  After alignment of a particular frame is complete, ALE
displays the corresponding final match statistic.  If the value is close to
100%, then the frames are well aligned; very low values can indicate
misalignment; but even frames that are very well aligned typically do not
achieve 100% alignment.  For improving image quality, ALE works most
effectively when match values are lower than 100%.</p>

<s><t>Match threshold</t>

<p>A match threshold can be specified; no images with final match statistics
falling below this threshold will contribute to the final output.</p>

<ll>--threshold=x     Min. match threshold; a perfect match is 100.  (0 is default)
</ll>

</s><s><t>Alignment failure</t>

<p>When an image fails to meet the match threshold, a transformation is still
assigned to the frame (e.g., for writing to a <link
linkend="user-tdf">transformation data file</link>).  The assigned
transformation can be either the optimal alignment found (this is default) or
the default transformation.</p>

<ll>--fail-optimal    Frames beneath threshold are aligned optimally.  [default]
--fail-default    Frames beneath threshold keep their default alignment.
</ll>

</s><s><t>Alignment error metric exponent</t>

<p>The function calculated at each pixel to determine the match statistic is of
the form <i>(a-b)<sup>x</sup></i>.  The exponent value <i>x</i>
is 2 by default.  Larger numbers give greater influence to smaller image
features.</p>

<ll>--metric=x        Set the alignment error metric exponent.       (2 is default)
</ll>

</s><s><t>Alignment Channel Options</t>

<p>In calculating the per-pixel error metric, there are three ways in which ALE
can handle color channels.  By default, ALE adds the channels before
calculating the match, but it can also be configured to rely solely on the
green color channel, or to use all three channels separately.</p>

<ll>--align-all       Align images using all color channels
--align-green     Align images using the green channel
--align-sum       Align images using a sum of channels [default]
</ll>

</s><s><t>Monte Carlo Alignment</t>

<p>As aligning large images can take a long time if all pixels are examined, it
is often desirable to examine a smaller subset of pixels.  The Monte Carlo
alignment option samples a subset of pixels, specified as a percentage of the
total pixel count, with smaller numbers providing faster, but less precise,
alignment.  For defaults, see <xref linkend="user-defaults"/>.</p>

<ll>--mc &lt;x&gt;          Align using, on average, x% of available pixels (0 &lt; x &lt; 100)
--no-mc           Align using all pixels.
</ll>

</s><s><t>Alignment weight map</t>

<p>Typically, measured differences at each pixel in the alignment reference
image contribute equally to the match statistic.  To weight pixels differently,
a weight map can be used.  The scale of the map should correspond with that of
the alignment reference image, and if the upper-left corner of the map does not
coincide with the upper-left corner of the first frame in the sequence, then a
non-zero offset should be specified to indicate the difference.  See also <xref linkend="user-exclusion"/>.</p>

<ll>--wm &lt;f&gt; &lt;x&gt; &lt;y&gt;  Use weight map image &lt;f&gt; at offset (&lt;x&gt;, &lt;y&gt;)
</ll>

</s><s><t>Frequency weighting</t>

<p>If ALE is compiled with FFTW support, then a high-pass-filtered version of
the alignment reference image can be used to weight reference image pixels'
contributions to the match statistic.  Frequency limiting can occur as a
fraction of the highest horizontal frequency, the highest vertical frequency,
or the highest average frequency.  Limit values should range between 0 (pass
all) and 1 (pass none).  If any limit is assigned a value of 1, no alignment
will occur, since all frequencies will have been excluded.  An output file can
optionally be specified for high-pass filtered data.</p>

<ll>--fl &lt;h&gt; &lt;v&gt; &lt;a&gt;  High-pass filters: horizontal &lt;h&gt;, vertical &lt;v&gt;, average &lt;a&gt;.
--flshow &lt;o&gt;      Write high-pass filtered data to file &lt;o&gt;.
</ll>

</s><s><t>Certainty weighting</t>

<p>Certainty weighting causes contributions to alignment error to be weighted
by certainty values.</p>

<ll>--cw              Weight alignment error by certainty.
--no-cw           Don't weight alignment error by certainty. [default]
</ll>

</s><s><t>Algorithmic weighting</t>

<p>This option writes the current alignment reference image and definition map
to specified files, executes a specified program with these arguments, and then
reads back alignment weights.  This option requires POSIX libraries, and
requires that ALE have been built with POSIX support enabled.</p>

<ll>--wmx &lt;e&gt; &lt;r&gt; &lt;d&gt; Write reference &lt;r&gt;, definition &lt;d&gt;, execute `&lt;e&gt; &lt;f&gt; &lt;d&gt;`,
                  read weights &lt;r&gt; back.
</ll>

</s></s><s><t>Perturbation</t>

<p>The perturbation size determines the magnitude by which alignment parameters
are changed.  The size is initially set to be large, allowing large changes in
alignment to be evaluated, and is reduced as the locally optimal alignment is
found for each size.  When this size drops below a specified lower bound, the
frame is considered to be aligned.</p>

<s><t>Perturbation bounds</t>

<p>These options determine the upper and lower bounds for perturbation size.  The
perturb-upper and perturb-lower bounds apply to rotation (in arclength),
translation (in pixels), and the movement of the boundaries of a projected
frame (in pixels).  By appending the '%' character, values may optionally be
specified as a percentage of the number of pixels in the smallest image
dimension.  The rot-upper bound disables rotational perturbation above a
certain perturbation size (in degrees).  To disable alignment, set
perturb-upper to zero.</p>

<ll>--perturb-upper=x Perturbation upper bound pixels/arclength    (14% is default)
                     ('x%' uses a fraction of the smallest image dimension.)
--perturb-lower=x Perturbation lower bound pixels/arclength   (.125 is default)
                     ('x%' uses a fraction of the smallest image dimension.)
--rot-upper=x     Rotation-specific upper bound in degrees    (32.0 is default)
</ll>

</s><s><t>Barrel/pincushion distortion adjustment multiplier and rate</t>

<p>When using barrel/pincushion distortion parameters, any frame-to-frame
adjustments to these parameters are made in a manner dependent on the
perturbation size.  A multiplier, the barrel distortion adjustment multiplier,
is used to determine the perturbation of these parameters, based on the generic
perturbation size.  Additionally, the frame-to-frame rate of change of each
barrel distortion parameter can be limited to a specified maximum.  To disable
frame-to-frame adjustment of barrel/pincushion distortion parameters, set
bda-mult to zero.  Setting bda-rate to zero disables rate limitation.</p>

<ll>--bda-mult=x      Barrel distortion adjustment multiplier   (0.0001 is default)
--bda-rate=x      Barrel distortion rate of change maximum  (0.0004 is default)
</ll>

</s><s><t>Level of detail</t>

<p>Alignment at large perturbation sizes is usually carried out on
reduced-detail images.  To disable this, set lod-max to
log<sub>2</sub>(perturb-upper).</p>

<ll>--lod-max=x       LOD scale factor is max(1, (2^floor(x))/perturb)  (1 is def.)
</ll>

</s><s><t>Perturbation Types (experimental)</t>

<p>Perturbations are normally performed in output image coordinates.  To perform
perturbations in source image coordinates, specify <l>--perturb-source</l>.</p>

<ll>--perturb-output  Apply perturbations in output image coordinates. [default]
--perturb-source  Apply perturbations in source image coordinates.
</ll>

</s><s><t>Global Searching</t>

<p>In cases where important image features do not have sufficient overlap using
default alignment parameters (determined by <l>--identity</l> and
<l>--follow</l>), a number of translations can be applied to the default
parameters in order to find a new alignment starting point.  Since this process
searches the entire region of the alignment reference image, it is called a
global (as opposed to local) search.  To avoid misalignment, a minimum overlap
area can be specified.  In versions 0.8.1 and later, the search type 'points'
searches for a control point metric minimum.</p>

<ll>--gs &lt;type>       Set global search to &lt;type>, one of:
                     local     Local alignment only [default]
                     inner     Alignment reference image inner region
                     outer     Alignment reference image outer region
                     all       Union of inner and outer
                     central   inner if below threshold or better; else, outer.
		     points    Align by control points.  Ignores gs-mo.   [0.8.1 and later]

--gs-mo &lt;x>       Set &lt;x> pixel min. overlap for global search. (16 is default)
</ll>

</s>
</s>

</chapter>