gtMatchInitialize: removed resetting labgeo parameters (very bad to do it...

gtMatchInitialize: removed resetting labgeo parameters (very bad to do it within this function) and saving backup parameters file.
The labgeo.detrefpos values are now set in the preprocessing. Enabled parameters check again.

Signed-off-by: preischig <preischig@gmail.com>

3_pairmatchingGUI/gtMatchInitialize.m

 function handles = gtMatchInitialize(handles)
 
-% Set initial values for the main GUI's constants, handles, tables
+% Sets initial values for the main GUI's constants, handles, tables
 % and figures. Loads difspot data from database.
+%
+% It should not modify labgeo or any other parameter! All required 
+% parameters should be set upstream or from within the GUI.
 
 
 gtMatchSetBusy(handles,'on')
@@ -27,25 +30,20 @@ if strcmpi(check, 'y')
      parameters.match = gtMatchDefaultParametersGUI();
      parameters.match.thetalimits = 0.5*[parameters.labgeo.detanglemin, ...
                                          parameters.labgeo.detanglemax];
-     save('parameters.mat','parameters');
-     disp('Match parameters have been reset to default values')
-end
-
-% fix bounding box centering for the detector position along Z
-if ~isempty(parameters.acq.bb)
-    parameters.labgeo.detrefpos(3) = ((parameters.acq.bb(2)+parameters.acq.bb(4)/2)-parameters.labgeo.detrefv)*parameters.acq.pixelsize;
-    parameters.labgeo.detrefpos(2) = -((parameters.acq.bb(1)+parameters.acq.bb(3)/2)-parameters.labgeo.detrefu)*parameters.acq.pixelsize;
-    disp('corrected detrefpos with acq.bb')
+     % Do not change parameters file sneakily! (PR)
+     %save('parameters.mat','parameters');
+     disp('Match parameters have been reset to default values.')
 end
 
-if 0
-% checking parameters first
-parameters = gtCheckParameters(parameters, 'acq');
-parameters = gtCheckParameters(parameters, 'match');
-parameters = gtCheckParameters(parameters, 'labgeo');
-save('parameters.mat','parameters');
+if 1
+    % checking parameters first: adds missing parameters as new fields
+    parameters = gtCheckParameters(parameters, 'acq');
+    parameters = gtCheckParameters(parameters, 'match');
+    parameters = gtCheckParameters(parameters, 'labgeo');
+    % Do not change parameters file sneakily! (PR)
+    %save('parameters.mat','parameters');
 else
-    disp('skipping gtCheckParameters - very slow?')
+    disp('Skipping gtCheckParameters - very slow (!?)')
 end
 
 handles.parfilename = [];
@@ -365,7 +363,12 @@ for ip = 1:handles.nof_phases
     handles.CompPhaseThetas{ip} = asind(0.5*lambda_true./dsp_comp);
 
     handles.CompThetaIndices{ip} = 1:length(handles.CompPhaseThetas{ip});
+    
     % added by LNervo : keeping trace of used families
+    % !!! Notes by PReischig:
+    % This part is to be improved. The used families should be stored and read from  
+    % parameters.match only. Plus, double check the use of CompThetasTicked and others
+    % here when multiple phases have overlapping reflections! 
     filename = gtLastFileName(fullfile('3_pairmatching',['match_' date() '_']),'existing');
     if isempty(filename)
         list = dir(fullfile('3_pairmatching','match_*.mat'));
@@ -511,12 +514,10 @@ handles.fitsaved   = false;
 %% Save parameters backup file 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
 
-filename = gtLastFileName(sprintf('%s/3_pairmatching/parameters_old_%s_',...
-           handles.workingdir,date),'new');
-
-system(sprintf('cp parameters.mat %s',filename));
-
-
+% Disabled saving backup file; it's not needed anymore - PR
+%filename = gtLastFileName(sprintf('%s/3_pairmatching/parameters_old_%s_',...
+%           handles.workingdir,date),'new');
+%system(sprintf('cp parameters.mat %s',filename));
 
 set(handles.Text_Progress,'String','-');
 gtMatchSetBusy(handles,'off')
@@ -524,8 +525,3 @@ gtMatchSetBusy(handles,'off')
 
 end
 
-
-
-
-
-