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<a NAME=Up></a>
<H3>Alignment plug-in Documentation</H3>
<H4>
Contents
</H4>
<br>
<a href=#Description>1. Usage and Description</a><br>
<a href=#Methods>2. Methods used by the plug-in</a><br>
<br>
<H4>
Synopsis
</H4>
Due to uncertainties in the experimental set-up, recorded data might be shifted unrelated
to physical effects probed in the experiment. The present plug-in calculates this shift and
corrects the data using a variety of different methods.
<H3><a NAME=Description>
1. Usage and Description
</a></H3>
<div class='main'>
Data that is subject to a shift must be loaded into the plot window of the main application.
The plug-in offers two ways to treat the data: a shortcut options called 'Perform FFT Shift'
calculates the shift and directly corrects the data and the 'Show Alignment Window' option
showing a window that allows for specification of the shift and alignment methods as well as
offering the possibility to safe calculated shifts respectively load previously calculated
shifts from a file. It is also possible to enter shift values by hand.</br>
</br>
Once the Alignment Window is opened, the alignment method and the shift method must be specified.
The alignment method specifies how the shift is calculated while the shift method determines
how the shift is applied to the data.</br>
</br>
The table shows three columns: The first one shows the plot legend of the data that will be
corrected by the shift method. The second column shows the plot legend from which the shift
is calculated. The third column shows the shift values calculated by the alignment method in
units of the plot windows x-axis. While columns one and two can not be edited, shift values
can be entered by hand. Another way of setting the shift values is to load them from a existing
*.shift file using the Load button.</br>
</br>
Once the shift values are set, they can either be directly applied to the data present in the
plot window using the Apply button or the data can be stored in memory. The latter options allow
to use a reference signal recorded during the experiment to determine the shift and then apply
the shift values to a different set of data.</br>
</br>
Notice: In order to match different sets of data to another, as necessary in the case of a
reference signal, the order in which the data is added to the plot window is crucial. If one
switches between two sets of data where one set aligns the other one it is highly encouraged
to consult the table in the Alignment window to check if every element in the two different
sets of data is assigned to its correct counterpart before applying the shift.</br>
</br>
If the data in the plot window is zoomed in to a distinct feature, only the visible data range
is used to calculate the shift.
</div>
<br><a href=#Up>up</a>
<H3><a NAME=Methods>
2. Methods used by the plug-in
</a></H3>
<div class='main'>
Alignment methods are used to calculate the shift. Present methods include FFT, MAX, FIT and
FIT DRV.
</div>
<div class=elem><i>FFT</i></div>
<div class='indent'>
Uses the Fourier Transform of the curves to calculate their cross-correlation. The maximum
of the correlation is determined and yields the shift value. This method is the default option.
Since it is not affected by the peak shape, it is fast and numerically robust. Notice: the shifts
are given in real space values.
</div>
<div class=elem><i>MAX</i></div>
<div class='indent'>
Determines the maximum of each curve. The shift is given by the differences in the x-position
of the maxima. Notice that this method is highly vulnerable to noise in the data and spikes.
</div>
<div class=elem><i>FIT</i></div>
<div class='indent'>
This method subtracts a background from the data using the SNIP algorithm (c.f. plug-in section,
Background subtraction tools) and searches for peaks in the data. For every curve, the single
most pronounced feature is selected. The peak is fitted by a Gaussian model. The shifts are then
given by differences in the x-offsets of the fitted Gaussians.
</div>
<div class=elem><i>FIT DRV</i></div>
<div class='indent'>
Uses the same procedure as the FIT method. However the fit is applied to the first derivative of
the data. This method is only recommended for X-ray absorption data.
</div>
<div class='main'>
Shift methods are used to apply the calculated shift to the data. Present methods include 'Shift x-range'
and 'Inverse FFT shift'.
</div>
<div class=elem><i>Shift x-range</i></div>
<div class='indent'>
This method takes the x-range of the respective curve and adds the calculated shift value to every
point.
</div>
<div class=elem><i>Inverse FFT shift</i></div>
<div class='indent'>
Takes the Fourier Transform of a curve and multiplies the shift as a phase factor. The multiplication
of a phase factor in Fourier space translates to a shift in the x-range in real space. The shifted data
is given by the inverse Fourier transform.
Notice: In the process, the data needs to have a equidistant x-range. If this is not the case, the data
will be interpolated on a equidistant x-range. Due to the cyclic nature of the Fourier transform, this
method is recommended for data that has linear background.
</div>
<br><a href=#Up>up</a>
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