= SE.M =

MATLAB toolbox for plotting, processing and fitting 7NMR files.
The whole toolbox consists of two m files, SE.M and FIKUS.M.
Most of the toolbox features can be accessed from an easy to use GUI.
In addition, all data and functions are easily accessed from MATLAB command line
and from MATLAB programs.

''WARNING:'' about 2% of this manual is written as of <<DateTime(2011-01-19T18:43:03+0200)>>

This documentation is available at http://www.ijs.si/ijsw/TomazApih/Software/SE .

Send comments, feature requests and bug reports to tomaz.apih@ijs.si.

== Usage ==

=== Initialization ===
To initialize some local variables, start with '''se ini''' or '''se('ini')'''.
At that that point, two global variables are created: 
 *  '''FID''' holds all mesurement data (FIDS and spectrums)
 * '''SEP''' holds all settings data

== Command list ==
{{{
only a short bit is written here, so far
}}}

=== Initialization ===
||<tablewidth="98%" rowbgcolor="#FFFFE0">'''COMMAND'''||<75%> '''DESCRIPTION'''               ||
||`SE INI   `|| initialize SE session, a "FileOpen" dialog to load a FID will open (./) ||
||`SE INI filename.dat  `|| initialize SE session and load filename.dat (not yet) {i} ||
||`SE HELP`|| show short help {*} ||
||`SE DOC`|| open this documentation {o} ||

=== File reading command ===
||<tablewidth="98%" rowbgcolor="#FFFFE0">'''COMMAND'''||<75%> '''DESCRIPTION'''               ||
||`SE RE filename.dat`|| read FID stored in filename.dat||
||`SE RE file*.dat`|| - {X} ||
||`SE REZ file*.#`|| - {X} ||
||`SE RET file#-K-*.dat`|| - {X} ||
||`SE RESDF file.sdf`|| Read Stelar field cycling SDF files||
||`SE SAVE data.mat`|| Save all loaded signals (all zones) in a single file||
||`SE LOAD data.mat`|| Load previously saved dataset||


 SE etc etc many more


=== Plotting ===
To show one FID signal and corresponding spectrum, use `SE DR` command.
The main SE window will be opened with signal, spectrum and parameters displayed.
||<tablewidth="98%" rowbgcolor="#FFFFE0">'''COMMAND'''||<75%> '''DESCRIPTION'''               ||
||`SE DR 1   `|| draw first FID signal||
||`SE DR 5   `|| draw fifth FID signal||
||`SE DR +   `|| draw next signal||
||`SE DR -   `|| draw previous signal||
||`SE CLOSE  `|| close DR window||

=== Working with ZONEs ===
Like in twilight zone, this adds another dimension to our data.
A nice description comes here.
||<tablewidth="98%" rowbgcolor="#FFFFE0">'''COMMAND'''||<75%> '''DESCRIPTION'''               ||
||`SE ZONE 1   `|| Select first Zone||
||`SE ZONE +   `|| Select next Zone||
||`SE ZONE -   `|| Select previous Zone||





=== (temporary) ===
 SE FT:: do FT
 SE PH ph0 ph1:: input phase correction constant ph0  and ph1 (0th and 1st order)
 SE SORT TAU:: sort data on TAU parameter
 SE SORTM ITC_R0:: sort data on ITC_R0 (usually set temperature) parameter, highest T first
 SE SET:: ... set DIR etc
 SE OPT:: ... show or modify options
 SE DI:: ... dir
 SE DIR:: ... open side DIR list, interactive loading
 SE USER:: ... I forgot
 SE GETINT:: ... integrate
 SE SYM:: symmetrize spectra
 SE SHIFT:: shift something, obviously
 SE FITSPC:: fit spectra
 SE FITSORE:: etc
 SE FIT*G:: funny
 SE FIT*L:: funny
 SE FIT**:: funny
 SE FT*A:: funny
 SE FT*E:: funny
 SE FT*R:: funny
 SE PHASE:: phase, obviously









== Examples ==
Par primerorov, kako avtomatiziramo obdelavo signalov, etc
{{{#!highlight matlab
% naloži vse
% OBDELAVA SPEKTROV, Naloži v vse zone
    se ret LZBH-tdep-Li-T1-#K-*.DAT
    
%% Obdelaj vse FT
    for i = 1:SEP.Zones
        se('ZONE',i);   % izberi zono
        se('dr',100);   % izberi najdaljsi TAU
        se FT*A         % phase correction for the selected zone
        se getint       % integriraj
        fikus t1        % fitaj s funkcijo T1
        fikus plot      % nariši rezultat
        fikus t1_1:1    % fitaj z dvokomponentno funkcijo
        fikus plot 3    % doriši še ta rezultat
        print('-dpng', ['.\R-001\Li_T111-' int2str(i) '.png']) % shrani sliko fita
    end
}}}

== SE Parameters ==
SE parameter are stored in SEP global variable.
it has the following structure
{{{
SEP = 
         sename: 'se'
             se: @se
        Version: 'SE v0.16j'
    Initialized: 1
           Mode: 'none'
       FileType: '7NMR'
    FileOpenErr: 0
             FT: [1x1 struct]
            CUR: [1x1 struct]
            OPT: [1x1 struct]
           OptB: [1x1 struct]
              h: [1x1 struct]
            Fit: [1x1 struct]
        DataDir: 'C:\Users\Tomaz\Documents\MATLAB\tmp-data\'
             NN: 31
              i: 1
          Zones: 35
           Zone: 35
        ZoneNew: 0
       FileMask: 'LZBH-tdep-Li-T1-400K-*.DAT'
       Files_RE: 0
       ZoneMask: 'LZBH-tdep-Li-T1-#K-*.DAT'

SEP.FT
ans = 
      SI: 2048
     SHL: 48
    SHLA: 0
     HPP: 0.4883
      BC: 512
      LB: 0.2000
     PHA: 0
    PHAA: 0
     PH0: 130.4079
     PH1: 0
     PIV: 0
    PH1s: 1
     FRI: 1
     mBC: 0.0013 + 0.0009i
      SW: 1000
     Frq: [1x2048 double]
     Spc: [2048x1 double]
       i: 31
}}}