==============
Peak Separator
==============


.. |pulldown| image:: ../images/pulldown.png
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.. |check| image:: ../images/check.png
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.. |radio| image:: ../images/radio.png
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.. |float| image:: ../images/float.png
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.. |int| image:: ../images/int.png
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.. |entry| image:: ../images/entry.png
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.. |button| image:: ../images/button.png
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.. |ramp| image:: ../images/ramp.png
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.. |selector| image:: ../images/selector.png
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**Separate Merged Peaks Using Peak Models**

The Peak Separator code uses a Markov Chain Monte Carlo search which, using
idealised peak shapes, attempts to deconvolve overlapped peak regions into
their separate constituent peaks.

This routine is also suitable for accurately fitting model shapes to single
peaks in order to calculate precise intensities.

**Options Peak Separator Parameters**
*Min. Number of peaks* is by default set to one, it is not possible to set
this to a value less than one.
*Max. Number of peaks* is by default set to one, increasing this value allows
the search routine to fit more models. The best fit may be found with fewer than
the maximum number models. Higher numbers slow the routine, and setting this
value to 0 allows the routine to (effectively) fit unlimited peaks.
*Only pick positive peaks*. If you are not interested in negative peaks, removing
the possibility of fitting negative peaks can reduce search time.
*Peak Model* fits the spectra with either a Gaussian peak model or a Lorentzian
peak model.

**Options Region**
*Peak List* choose which peak list newly picked peaks should be added to. Peaks
picked using this method will have their details appended with 'PeakSepartor'
so you know where they came from.
*Region Table* shows which area of the current spectrum is about to be searched.
*Add Region*. Once an area of spectra has been highlighted clicking this button
will pass it's details on to the Peak Separator.
*Reset All* will reset all search parameters.
*Separate Peaks* will run the Peak Separator code with your current settings. This
may take a few minutes to run, depending on the size of the spectral region being
searched, the number of peaks being fitted and the speed of your machine. Please
wait while this completes.

After a successful Peak Separation run, the found peaks will be added to the
selected peak list. These peaks intensties (volume) have been found using the
peak model selected.

**Advanced Settings Tab**
*Rate* affects the speed of the Markov Chain Monte Carlo routine. A smaller value
results in longer execution, but possibly higher quality results. The default
setting is deemed sensible for the majority of runs.
*Line Width* offers a finer degree of control over maximum and minimum peak widths
for each dimension. The default values are *very* stupid and could do with
re-checking for each experiment.
*Re-Pick Entire Peak List* if you would like to use the Peak Separator to repick
*every* peak in your peak list, try this option - but note that this may take
a very long time!



Main Panel
==========

|button| **Clone**: Clone popup window

|button| **Help**: Show popup help document

|button| **Close**: Close popup

Peak Separator
==============

*Documentation missing*

Peak Separator Parameters
~~~~~~~~~~~~~~~~~~~~~~~~~


|int| **Min. number of peaks**: Minimum number of peaks to find (must be > 0)

|int| **Max. number of peaks**: Maximum number of peaks to find (0 is unlimited - not recommended)


|radio| **False**: Search for both positive and negative intensity peaks

|radio| **True**: Limit search to only positive peaks


|radio| **Gaussian**: Choose a Gaussian model peak shape to fit to peaks

|radio| **Lorentzian**: Choose a Lorentzian model peak shape to fit to peaks

Region
~~~~~~

Region that search will limit itself to


|pulldown| **Peak List**: Select which peak list new peaks are to be added to

=============  =======================
**Table 1**
--------------------------------------
       *dim.*  *Documentation missing* 
*start (ppm)*  *Documentation missing* 
  *end (ppm)*  *Documentation missing* 
*actual size*  *Documentation missing* 
=============  =======================



|button| **Add Region**: Add selected specrtral region

|button| **Separate Peaks**: Run peak search now

Advanced Settings
=================

*Documentation missing*

Rate:
~~~~~


|float| **Rate of MCMC step size change**: Rate effects speed of run, smaller values take longer but may produce better results

Line Width (Hz):
~~~~~~~~~~~~~~~~


==============  =======================
**Table 2**
---------------------------------------
        *dim.*  *Documentation missing* 
*min. σ (Hz)*  *Documentation missing*  *(Editable)*
*max. σ (Hz)*  *Documentation missing*  *(Editable)*
==============  =======================



(optional - repick entire peak list)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


|pulldown| ***None***: Select which peak list to repick (new peaks will be put into a new peak list)

|button| **Repick Peak List**: Repick selected peak list into a new peak list.

|button| **Separate Peaks**: Run peak search now

