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\begin_body

\begin_layout Title
MuSRFit GUI Documentation
\end_layout

\begin_layout Author
Zaher Salman
\end_layout

\begin_layout Affiliation
Laboratory for Muon Spin Spectroscopy, Paul Scherrer Institut, CH-5232 Villigen,
 Switzerland 
\end_layout

\begin_layout Section
Introduction
\end_layout

\begin_layout Standard
This document gives a quick guide for using MuSRFit graphical user interface
 (GUI).
 The GUI is developed using Perl and PerlQT3, and provides a simple layer
 that utilises the musrfit package.
 MuSRFit allows the user to fit musr data without the need for any knowledge
 about musrfit itself.
 However, due to its simplicity, it is also limited in its applications.
 These limitations will be obvious once more complicated functions are required
 to fit the data, or when the user needs to fit the data to more than 3
 components.
 MuSRFit is extremely powerful when it comes to fitting multple data sets
 with or without shared parameters.
\end_layout

\begin_layout Section
Quick start
\end_layout

\begin_layout Standard
To star using MuSRFit follow these simple steps
\end_layout

\begin_layout Itemize
type in the RUN number in the 
\begin_inset Quotes eld
\end_inset

RUN Numbers
\begin_inset Quotes erd
\end_inset

 (RN) box (Fig.
 ).
\end_layout

\begin_layout Itemize
select the year and appropriate beamline from the dropdown menus.
\end_layout

\begin_layout Itemize
select the function that the data should be fit to.
 You may fit the data to a sum of up to 3 components, each with a different
 function.
\end_layout

\begin_layout Itemize
type in the 
\begin_inset Quotes eld
\end_inset

Initial Time
\begin_inset Quotes erd
\end_inset

 (Ti), 
\begin_inset Quotes eld
\end_inset

Final Time
\begin_inset Quotes erd
\end_inset

 (Tf) and 
\begin_inset Quotes eld
\end_inset

Binning Factor
\begin_inset Quotes erd
\end_inset

 (NB) in the appropriate boxes.
 The data will be fit within the range [Ti,Tf] using a binning factor NB,
 i.e.
 the data points within this range will represent NB points from the raw
 histograms.
 Note that Ti and Tf are in 
\begin_inset Formula $\mu$
\end_inset

s units.
\end_layout

\begin_layout Itemize
Finally, select the type of fit you want to do, either and 
\begin_inset Quotes eld
\end_inset

Asymmetry
\begin_inset Quotes erd
\end_inset

 or a 
\begin_inset Quotes eld
\end_inset

Single Histogram
\begin_inset Quotes erd
\end_inset

 fit.
 In the first case the user provides two groups of histogram numbers separated
 by comma, i.e.
 to fit the asymmetry between histograms (1+5) and (3+7) one types 
\begin_inset Quotes eld
\end_inset

1 5,3 7
\begin_inset Quotes erd
\end_inset

.
 In the case of 
\begin_inset Quotes eld
\end_inset

Single Histogram
\begin_inset Quotes erd
\end_inset

 fits, the histograms are fit individually.
 A list of histogram numbers separated by commas can be given, e.g.
 
\begin_inset Quotes eld
\end_inset

1,2,3,4
\begin_inset Quotes erd
\end_inset

.
\end_layout

\begin_layout Standard
Now we are ready to fit, you may click on the 
\begin_inset Quotes eld
\end_inset

FIT
\begin_inset Quotes erd
\end_inset

 button at the top pannel (or hit Ctrl+F or select 
\begin_inset Quotes eld
\end_inset

Fit and Plot
\begin_inset Quotes erd
\end_inset

 from the 
\begin_inset Quotes eld
\end_inset

Actions
\begin_inset Quotes erd
\end_inset

 menu).
 If you are lucky and that initial default parameters are close enough,
 Minuit will converge and give you the fit parameters.
 Other wise you may need to tweek the initial parameters from the 
\begin_inset Quotes eld
\end_inset

Initialization
\begin_inset Quotes erd
\end_inset

 tab and then try to fit again.
 Once the fit is done, a Root canvas will pop up with a plot of the data
 with the fit curve and summary of the fit.
\begin_inset Float figure
placement H
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename RUNS_Tab.png
	width 10cm

\end_inset


\begin_inset Caption

\begin_layout Plain Layout
A view of the RUNS tab.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Section
Fitting and Minimization
\end_layout

\begin_layout Standard
The user can choose the minimization and error estimation type during the
 fit by selecting the 
\begin_inset Quotes eld
\end_inset

Fitting
\begin_inset Quotes erd
\end_inset

 tab.
 The 
\begin_inset Quotes eld
\end_inset

Minimization type
\begin_inset Quotes erd
\end_inset

 can be 
\begin_inset Quotes eld
\end_inset

MINIMIZE
\begin_inset Quotes erd
\end_inset

, 
\begin_inset Quotes eld
\end_inset

MIGRAD
\begin_inset Quotes erd
\end_inset

 or 
\begin_inset Quotes eld
\end_inset

SIMPLEX
\begin_inset Quotes erd
\end_inset

, while the 
\begin_inset Quotes eld
\end_inset

Error estimation
\begin_inset Quotes erd
\end_inset

 can be either 
\begin_inset Quotes eld
\end_inset

HESSE
\begin_inset Quotes erd
\end_inset

 or 
\begin_inset Quotes eld
\end_inset

MINOS
\begin_inset Quotes erd
\end_inset

.
 Details of all these can be found in the MINUIT2 documentation.
\end_layout

\begin_layout Standard
In the same 
\begin_inset Quotes eld
\end_inset

Fitting
\begin_inset Quotes erd
\end_inset

 tab that user can also provide x and y ranges for the plot.
 The fit will still be done within the range [Ti,Tf].
 Note that you cannot limit x or y range separately, you must give the limits
 for both.
\end_layout

\begin_layout Standard
The 
\begin_inset Quotes eld
\end_inset

Life time correction
\begin_inset Quotes erd
\end_inset

 checkbox is only valid for single histogram fits, where the exponential
 relaxation due to the lifetime of the muon is removed.
\end_layout

\begin_layout Standard
The text box at the bottom of this tab provides the output of the msrfit
 that can be used to diagnose problems or bugs.
 However, it is essential to check this output to confitm whether or not
 the fit has converged.
\begin_inset Float figure
placement H
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename Fitting_Tab.png
	width 10cm
	rotateOrigin center

\end_inset


\begin_inset Caption

\begin_layout Plain Layout
A view of the Fitting tab.
\end_layout

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Section
Multiple RUN Fits and Common Parameters
\end_layout

\begin_layout Standard
In order to fit multiple data sets to the same theory function, the user
 should type in the RUN numbers in the RN box.
 The RUN numbers should be comma separated.
 MuSRFit will identify whether a multiple or a single RUN are being fit,
 and enables sharing accordingly.
 Next, you may click on the 
\begin_inset Quotes eld
\end_inset

Sharing
\begin_inset Quotes erd
\end_inset

 tab to select shared (common) and individual parameters.
 This dialogue issues 3 columns of check boxes, each column corresponds
 to a different theory function component, with a checkbox for each parameter
 in that component.
 By checking the box the user demands that the corresponding parameter is
 common to all data sets.
\begin_inset Float figure
placement H
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename Sharing_Tab.png
	width 10cm
	rotateOrigin center

\end_inset


\begin_inset Caption

\begin_layout Plain Layout
A view of the Sharing tab.
\end_layout

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Section
Initializing and Fixing Parameters
\end_layout

\begin_layout Standard
It is highly recommended to initialize the fit parameters before you actually
 start fitting.
 MuSRFit will start the fitting procedure with default values for the fit
 parameters.
 However, the user can usually provide a much better initial guess for these
 values.
 In order to do this, select the 
\begin_inset Quotes eld
\end_inset

Initialization
\begin_inset Quotes erd
\end_inset

 tab, which will issue a table with 5 columns.
 These columns are the name of the parameter, its initial value (Value),
 its initial steps size (Error), its minimum (Min) and maximum (Max) limits,
 respectively.
 These values will be updated after a fitting procedure is performed.
\begin_inset Float figure
placement H
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename Initialization_Tab.png
	width 10cm

\end_inset


\begin_inset Caption

\begin_layout Plain Layout
A view of the Initialization tab.
\end_layout

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Standard
In addition to providing the initial values of the fit parameters, the user
 can use this table to fix and/or limit the their values following these
 rules
\end_layout

\begin_layout Itemize
the value of the fit parameter will be fixed to the initial value if its
 Error is set to zero.
\end_layout

\begin_layout Itemize
If both Min and Max are set to zero, the corresponding fit parameter can
 vary from 
\begin_inset Formula $-\infty$
\end_inset

 up to 
\begin_inset Formula $+\infty$
\end_inset

.
 However, if either is different than zero, then the Min and Max will be
 taken as limits for the value of the fit parameter.
 
\end_layout

\end_body
\end_document
