Change function from

params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
to
params_acq = gtLoadAcquisitionXML(acq, list_acq, xmlfname, interactive)

General commenting for the other functions

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@393 4c865b51-4357-4376-afb4-474e03ccb993

1_preprocessing/gtSetup_Utils/gtLoadAcquisitionXML.m

-function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
+function params_acq = gtLoadAcquisitionXML(acq, list_acq, xmlfname, interactive)
 % FUNCTION gtLoadAcquisitionXML
-%     params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
-%     ----------------------------------------------------------------------
+%     params_acq = gtLoadAcquisitionXML(acq, list_acq, xmlfname, interactive)
+%     -----------------------------------------------------------------------
 %
 %     Version 002 02/05/2012 by LNervo
 %       Add acq.beamchroma default value to 'mono'
@@ -17,24 +17,22 @@ function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
         tmpxml = xml_read(xmlfname);
         tmpxml = tmpxml.acquisition;
 
-        parameters.acq.name       = tmpxml.scanName; % shouldn't change!
-        parameters.acq.date       = tmpxml.date;
-        parameters.acq.xdet       = tmpxml.projectionSize.DIM_2;
-        parameters.acq.ydet       = tmpxml.projectionSize.DIM_1;
-        parameters.acq.nproj      = tmpxml.tomo_N/2;
-        parameters.acq.refon      = tmpxml.ref_On;
-        parameters.acq.nref       = tmpxml.ref_N;
-        parameters.acq.ndark      = tmpxml.dark_N;
-        parameters.acq.pixelsize  = tmpxml.pixelSize/1000; % mm
-        parameters.acq.count_time = tmpxml.ccdtime;
-        parameters.acq.energy     = tmpxml.energy;
-        parameters.acq.dist       = tmpxml.distance; % mm
-        parameters.acq.sensortype = tmpxml.cameraName;
-        parameters.acq.type       = [num2str(tmpxml.scanRange) 'degree'];
-        parameters.acq.orig_xdet  = 2048;
-        parameters.acq.orig_ydet  = 2048;
-        parameters.acq.roi_x_off  = tmpxml.projectionSize.ROW_BEG;
-        parameters.acq.roi_y_off  = tmpxml.projectionSize.COL_BEG;
+        acq.name       = tmpxml.scanName; % shouldn't change!
+        acq.date       = tmpxml.date;
+        acq.xdet       = tmpxml.projectionSize.DIM_2;
+        acq.ydet       = tmpxml.projectionSize.DIM_1;
+        acq.nproj      = tmpxml.tomo_N/2;
+        acq.refon      = tmpxml.ref_On;
+        acq.nref       = tmpxml.ref_N;
+        acq.ndark      = tmpxml.dark_N;
+        acq.pixelsize  = tmpxml.pixelSize/1000; % mm
+        acq.count_time = tmpxml.ccdtime;
+        acq.energy     = tmpxml.energy;
+        acq.dist       = tmpxml.distance; % mm
+        acq.sensortype = tmpxml.cameraName;
+        acq.type       = [num2str(tmpxml.scanRange) 'degree'];
+        acq.roi_x_off  = tmpxml.projectionSize.ROW_BEG;
+        acq.roi_y_off  = tmpxml.projectionSize.COL_BEG;
     else %if .xml not found
         if interactive
             disp('No .xml file found!  Are you sure you are correctly in the acquistion directory?')
@@ -46,61 +44,62 @@ function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
             end
         end
         % guess some default values
-        parameters.acq.date       = date();
-        parameters.acq.xdet       = 2048;
-        parameters.acq.ydet       = 2048;
-        parameters.acq.nproj      = 7200;
-        parameters.acq.refon      = 200;
-        parameters.acq.nref       = 5;
-        parameters.acq.ndark      = 11;
-        parameters.acq.pixelsize  = 0.0014;
-        parameters.acq.count_time = 2;
-        parameters.acq.energy     = 20;
-        parameters.acq.dist       = 5;
-        parameters.acq.sensortype = 'frelon';
-        parameters.acq.type       = '360degree';
-        parameters.acq.orig_xdet  = 2048;
-        parameters.acq.orig_ydet  = 2048;
-        parameters.acq.roi_x_off  = 0;
-        parameters.acq.roi_y_off  = 0;
+        acq.date       = date();
+        acq.xdet       = 2048;
+        acq.ydet       = 2048;
+        acq.nproj      = 7200;
+        acq.refon      = 200;
+        acq.nref       = 5;
+        acq.ndark      = 11;
+        acq.pixelsize  = 0.0014;
+        acq.count_time = 2;
+        acq.energy     = 20;
+        acq.dist       = 5;
+        acq.sensortype = 'frelon';
+        acq.type       = '360degree';
+        acq.roi_x_off  = 0;
+        acq.roi_y_off  = 0;
         
         clear check
     end
-
+    
+    
+    acq.orig_xdet  = 2048;
+    acq.orig_ydet  = 2048;
     % interlacing parameters
     % try to guess whether the scan is interlaced
-    if exist([parameters.acq.name '0_0000.edf'], 'file')
-        parameters.acq.interlaced_turns = true; % assume one extra turn is reasonable guess
+    if exist([acq.name '0_0000.edf'], 'file')
+        acq.interlaced_turns = true; % assume one extra turn is reasonable guess
         disp('This looks like an interlaced scan! Doubling nproj...')
-        parameters.acq.nproj            = parameters.acq.nproj*2;
+        acq.nproj            = acq.nproj*2;
     else
-        parameters.acq.interlaced_turns = false;
+        acq.interlaced_turns = false;
     end
 
     % mono tuned during scan?
-    parameters.acq.mono_tune      = false;
+    acq.mono_tune      = false;
     % if we have a horizontal rotation axis we turn the images during the copying process
-    parameters.acq.rotation_axis  = 'vertical';
-    parameters.acq.distortion     = 'none';
+    acq.rotation_axis  = 'vertical';
+    acq.distortion     = 'none';
 
     %   deal with flips and rotations
     % subsequently, deal with flips and rotations, scans without direct beam
-    parameters.acq.flip_images    = false;
-    parameters.acq.no_direct_beam = false;
+    acq.flip_images    = false;
+    acq.no_direct_beam = false;
 
     % rotate images to the gt coordinate system !!! Help !!!
-    parameters.acq.rotation_direction = 'clockwise';
+    acq.rotation_direction = 'clockwise';
     
-    parameters.acq.rotu        = parameters.acq.xdet/2+0.5;   % Images will be shifted in gtCreateFullLive to have rotation axis in center...
-    parameters.acq.rotx        = parameters.acq.rotu;
-    parameters.acq.maxradius   = max(parameters.acq.xdet,parameters.acq.ydet)/2*sqrt(2);
-    parameters.acq.beamchroma  = 'mono';
+    acq.rotu        = acq.xdet/2+0.5;   % Images will be shifted in gtCreateFullLive to have rotation axis in center...
+    acq.rotx        = acq.rotu;
+    acq.maxradius   = max(acq.xdet,acq.ydet)/2*sqrt(2);
+    acq.beamchroma  = 'mono';
 
     % if it is 360degree data, we need a pair table
-    if strcmpi(parameters.acq.type, '360degree')
+    if strcmpi(acq.type, '360degree')
         % pair tablename can be derived from the scan name
-        parameters.acq.pair_tablename  = [parameters.acq.name 'spotpairs'];
-        parameters.acq.calib_tablename = [parameters.acq.name 'paircalib'];
+        acq.pair_tablename  = [acq.name 'spotpairs'];
+        acq.calib_tablename = [acq.name 'paircalib'];
     end
 
     if interactive
@@ -111,10 +110,10 @@ function params = gtLoadAcquisitionXML(parameters, list, xmlfname, interactive)
         else
             header='Check all values.  All "(?)" should be removed:';
         end
-        parameters.acq = gtModifyStructure(parameters.acq, list.acq(:,1:2), header);
+        acq = gtModifyStructure(acq, list_acq(:,1:2), header);
     end
 
-    params = parameters;
+    params_acq = acq;
     
 end % end of function
 

3_pairmatchingGUI/gtMatchDefaultParametersGUI.m

-% 
-% FUNCTION par_match = gtMatchDefaultParametersGUI()
-%
-% Stores and provides the default parameters for Friedel pair matching.
-%
-%
-
 function par_match = gtMatchDefaultParametersGUI()
+% GTMATCHDEFAULTPARAMETERSGUI  Stores and provides the default parameters for Friedel pair matching.
+%     par_match = gtMatchDefaultParametersGUI()
+%     -----------------------------------------
+%
 
 par_match.thr_theta        = 0.2;
 par_match.thr_theta_scale  = 0;
@@ -26,4 +23,4 @@ par_match.thr_meanerror    = Inf;
 par_match.thetalimits      = [0 90];
 
 
-end
+end % end of function
\ No newline at end of file

zUtil_Cryst/gtLoadReflections.m

@@ -125,16 +125,12 @@ if isreflections
         title = lower(title);
         title = strrep(title,'.','');
         title = regexprep(title,'[^a-zA-Z]','');
-        %title = regexprep(title,'theta','tt');
         title = regexprep(title,'theta','twotheta');
         if length(title)==1
             title = regexprep(title,'m','mult');
-            %title = regexprep(title,'^f','F');
             title = regexprep(title,'^f','formfactor');
         end
         title = strtrim(title);
-        %title = strrep(title,'dspacing','d0');
-        %title = strrep(title,'dspc','d0');
         title = strrep(title,'dspc','dspacing');
         if ~strcmpi(title,'no')
             reflections.(title)=C{i};
@@ -142,9 +138,7 @@ if isreflections
     end
 
     reflections.hkl=[reflections.h reflections.k reflections.l];
-    reflections=rmfield(reflections,'h');
-    reflections=rmfield(reflections,'k');
-    reflections=rmfield(reflections,'l');
+    reflections=rmfield(reflections,{'h','k','l'});
 
     xop = reflections;
     ind=strfind(file,filesep);

zUtil_Parameters/build_list_v2.m

@@ -265,9 +265,9 @@ list.labgeo{23,1} = 'reflabY';                         list.labgeo{23,2} = '';
                                                        list.labgeo{23,3} = 'char';
 list.labgeo{24,1} = 'reflabZ';                         list.labgeo{24,2} = '';                                
                                                        list.labgeo{24,3} = 'char';
-list.labgeo{25,1} = 'detsizeu';                        list.labgeo{25,2} = '';
+list.labgeo{25,1} = 'detsizeu';                        list.labgeo{25,2} = 'Number of pixels along the u direction';
                                                        list.labgeo{25,3} = 'double'; % scalar
-list.labgeo{26,1} = 'detsizev';                        list.labgeo{26,2} = '';                               
+list.labgeo{26,1} = 'detsizev';                        list.labgeo{26,2} = 'Number of pixels along the v direction';                               
                                                        list.labgeo{26,3} = 'double'; % scalar
 list.labgeo{27,1} = 'rotcomp';                         list.labgeo{27,2} = 'Rotation matrix components [computed]';                               
                                                        list.labgeo{27,3} = 'struct';