Cosmetics only.

(comments, indent, missing semi-colons, typos, useless whitespaces)

Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>

4_grains/gtCalculateGrain.m

@@ -45,15 +45,12 @@ function grain = gtCalculateGrain(grain, parameters, varargin)
 %
 % Simplified version of gtFedGenerateRandomGrain   15-03-2012  - WLudwig
 %
-%
-
 
 if ~exist('parameters','var') || isempty(parameters)
     parameters = load('parameters.mat');
     parameters = parameters.parameters;
 end
 
-
 % set default values for optional arguments
 app.color = false;
 app.showfigure = false;
@@ -68,13 +65,12 @@ app = parse_pv_pairs(app,varargin);
 %disp(app)
 
 if nargin < 1
-    disp('Usage:  grain =  gtCalculateGrain(grain, parameters, varargin)')
-    disp('                 grain      = grain{grainid}')
-    disp('                 parameters = parameters file')
+    disp('Usage:  grain =  gtCalculateGrain(grain, parameters, varargin)');
+    disp('                 grain      = grain{grainid}');
+    disp('                 parameters = parameters file');
     return
 end
 
-
 % If strain data is not available, disable strain
 if ~isfield(grain,'strain') || ~isfield(grain.strain,'strainT') || ...
    isnan(grain.strain.strainT(1,1))
@@ -109,7 +105,6 @@ detpos  = (labgeo.detrefpos./pixelsize)';
 
 detposcorner = detpos - detrefu*detdiru - detrefv*detdirv;  % the (0,0) corner of the detector in Lab system (edge of detector pixel)
 
-
 uvorig  = [labgeo.detrefu, labgeo.detrefv]';
 csam    = grain.center' ./ pixelsize';
 omstep  = 180/acq.nproj;
@@ -152,28 +147,26 @@ grain.allblobs.uvw   = [];
 grain.allblobs.srot  = [];
 grain.allblobs.proj_geom = [];
 
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Compute diffraction angles and detector intersection points
 rotcomp = gtFedRotationMatrixComp(rotdir);
 
 rotcomp_maths = gtMathsRotationMatrixComp(rotdir','row');
 
-for ii = 1:size(pl_sam,1)
+for ii = 1:size(pl_sam, 1)
 
     %hkl(i,:) = hklt(thetatypesp(i),:);
     hkl(:,ii) = hklt(:,thetatypesp(ii))';
-    
-    
+
     % Impose strain on grain
     if app.usestrain
-        
+
         % Deformation tensor (use strain tensor for now)
         defT = grain.strain.strainT;
-        
+
         % New deformed plane normal and relative elongation (relative d-spacing)
         [pl, drel] = gtStrainPlaneNormals(pl_sam(ii,:)', defT); % unit vector
-        
+
         % New sin(theta) in deformed state is inversely proportional to elongation
         sinth = sind(thetasp(ii))/drel;
         theta = asind(sinth);
@@ -182,8 +175,7 @@ for ii = 1:size(pl_sam,1)
         theta = thetasp(ii);
         sinth = sind(theta);
     end
-    
-    
+
     % Four omegas of the plane normal (1-3 and 2-4 are the two Friedel pairs):
     % pls is plus or minus pl
     [om,pllab,pls] = gtFedPredictOmega(pl, sinth, beamdir, rotdir, rotcomp);
@@ -197,7 +189,7 @@ for ii = 1:size(pl_sam,1)
 %         S3 = gtFedRotationTensor(om(3), rotcomp);
 %         S4 = gtFedRotationTensor(om(4), rotcomp);
         S = gtMathsRotationTensor(om, rotcomp_maths);
-        
+
         % Diffraction vectors
         d1 = gtFedPredictDiffVec(pllab(:,1), sinth, beamdir); % takes coloumn vectors
         d2 = gtFedPredictDiffVec(pllab(:,2), sinth, beamdir);
@@ -210,7 +202,7 @@ for ii = 1:size(pl_sam,1)
         d3 = d3/norm(d3);
         d4 = d4/norm(d4);
 
-        % Following the convention of the mathcing output, the omega value
+        % Following the convention of the matching output, the omega value
         % smaller than 180deg (spot "a") is used in the pair data.
         % The two Friedel pairs are 1a-1b and 2a-2b.
 
@@ -294,11 +286,10 @@ for ii = 1:size(pl_sam,1)
         if isempty(uv2b)
             uv2b = NaN(3,1);
         end
-        
+
         % add projection geometry for grain center of mass  (using Rottens'
         % instead Rottens in order to perfrom negative rotation)
-        
-        
+
         r_th1a      = s1a'*beamdir + 2*sinth*pl1a';
         r_th1b      = s1b'*beamdir + 2*sinth*pl1b';
         r_th2a      = s2a'*beamdir + 2*sinth*pl2a';
@@ -307,16 +298,12 @@ for ii = 1:size(pl_sam,1)
         detpos1b    = detposcorner + uv1b(1)*detdiru + uv1b(2)*detdirv;
         detpos2a    = detposcorner + uv2a(1)*detdiru + uv2a(2)*detdirv;
         detpos2b    = detposcorner + uv2b(1)*detdiru + uv2b(2)*detdirv;
-        
-        
+
         proj_geom1a = [r_th1a; s1a'*detpos1a - csam; s1a'*detdiru; s1a'*detdirv]';
         proj_geom1b = [r_th1b; s1b'*detpos1b - csam; s1b'*detdiru; s1b'*detdirv]';
         proj_geom2a = [r_th2a; s2a'*detpos2a - csam; s2a'*detdiru; s2a'*detdirv]';
         proj_geom2b = [r_th2b; s2b'*detpos2b - csam; s2b'*detdiru; s2b'*detdirv]';
-        
-        
-        
-        
+
         % fill the output structure with the two pairs
         grain.allblobs.pl    = [grain.allblobs.pl; pl1a; pl1b; pl2a; pl2b];
         grain.allblobs.pllab = [grain.allblobs.pllab; pllab1a; pllab1b; pllab2a; pllab2b];
@@ -336,8 +323,6 @@ for ii = 1:size(pl_sam,1)
 
 end % end for pl_sam
 
-
-
 if app.showfigure
 
     figure
@@ -405,9 +390,4 @@ if app.showfigure
 
 end % showfigure
 
-
-
-
-end
-
-
+end % end of function

6_rendering/gtPlotHexagon.m

@@ -118,35 +118,35 @@ for ii = 1:length(app.grainids)
     
     % reference hex
     if app.reference && ~app.overlap
-        patch('Vertices', corners3, 'Faces', hex_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4)
-        patch('Vertices', corners3, 'Faces', rec_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4)
+        patch('Vertices', corners3, 'Faces', hex_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4);
+        patch('Vertices', corners3, 'Faces', rec_faces, 'FaceColor', 'b', 'FaceAlpha', 0.4);
     end
     % if overlap the first grain is used as reference for the others
     if app.overlap && app.grainids(1) ~= grainID
         overlapID = app.grainids(1);
         kk = find(r_vectors(:, 1) == overlapID);
         corners3a = all_corners3(:, :, kk);
-        patch('Vertices', corners3a, 'Faces', hex_faces, 'FaceColor', app.cmap(overlapID,:), 'FaceAlpha', 0.4)
-        patch('Vertices', corners3a, 'Faces', rec_faces, 'FaceColor', app.cmap(overlapID,:), 'FaceAlpha', 0.4)
+        patch('Vertices', corners3a, 'Faces', hex_faces, 'FaceColor', app.cmap(overlapID,:), 'FaceAlpha', 0.4);
+        patch('Vertices', corners3a, 'Faces', rec_faces, 'FaceColor', app.cmap(overlapID,:), 'FaceAlpha', 0.4);
     end
     % reference background like the section plane
     if app.section
         pos=min(mean(corners3b(hex_faces(1,:), 1)), mean(corners3b(hex_faces(2,:), 1)));
         section_plane_vertices=[pos 1 1; pos 1 -1; pos -1 1; pos -1 -1];
         section_plane_face=[1 2 4 3];
-        patch('Vertices', section_plane_vertices, 'Faces', section_plane_face, 'FaceColor', 'k', 'FaceAlpha', 0.4)
+        patch('Vertices', section_plane_vertices, 'Faces', section_plane_face, 'FaceColor', 'k', 'FaceAlpha', 0.4);
     end
     % including the rotation for sectioning
-    patch('Vertices', corners3b, 'Faces', hex_faces, 'FaceColor', app.cmap(grainID,:), 'FaceAlpha', 1)
-    patch('Vertices', corners3b, 'Faces', rec_faces, 'FaceColor', app.cmap(grainID,:), 'FaceAlpha', 1)
+    patch('Vertices', corners3b, 'Faces', hex_faces, 'FaceColor', app.cmap(grainID,:), 'FaceAlpha', 1);
+    patch('Vertices', corners3b, 'Faces', rec_faces, 'FaceColor', app.cmap(grainID,:), 'FaceAlpha', 1);
 
     % a bit of labeling
-    set(get(get(gcf, 'CurrentAxes'), 'Title'), 'String', sprintf('grain %d unit cell', grainID))
-    set(get(get(gcf, 'CurrentAxes'), 'xLabel'),'String', 'x axis')
-    set(get(get(gcf, 'CurrentAxes'), 'yLabel'),'String', 'y axis')
-    set(get(get(gcf, 'CurrentAxes'), 'zLabel'),'String', 'z axis')
+    set(get(get(gcf, 'CurrentAxes'), 'Title'), 'String', sprintf('grain %d unit cell', grainID));
+    set(get(get(gcf, 'CurrentAxes'), 'xLabel'),'String', 'x axis');
+    set(get(get(gcf, 'CurrentAxes'), 'yLabel'),'String', 'y axis');
+    set(get(get(gcf, 'CurrentAxes'), 'zLabel'),'String', 'z axis');
     % view
-    set(get(gcf, 'CurrentAxes'), 'view', app.view)
+    set(get(gcf, 'CurrentAxes'), 'view', app.view);
 
     axis tight;
     axis equal;
@@ -160,7 +160,7 @@ for ii = 1:length(app.grainids)
     
 end % end for grains
 
-set(gcf,'UserData',vertices)
+set(gcf,'UserData',vertices);
 
 hf=gcf;
 

6_rendering/gtShowSampleSurface.m

@@ -27,7 +27,7 @@ outline_rot=sum(vol==lookID, 3);
 depth=depth_orig+find(sum(outline_rot, 1),1, 'first');
 if isempty(depth)
   depth=depth_orig;
-  disp('no outline found - designed for outline==800 - guessing')
+  disp('no outline found - designed for outline==800 - guessing');
 end
 %get section, transpose for correct orientation and view direction
 section=squeeze(vol(:,depth,:))';
@@ -54,7 +54,7 @@ else %more difficult...
     sample_dia=find(sum(outline_rot,1), 1, 'last')-find(sum(outline_rot,1), 1, 'first');
     if isempty(sample_dia)
       sample_dia=max(size(outline_rot));
-      disp('again, no outline (==800) found')
+      disp('again, no outline (==800) found');
     end
     
     
@@ -115,8 +115,8 @@ end
 dum=[];
 %plot basal plane traces on the grains of interest
 
-disp('note that the section plane that we look at is y (--> left to right) z (--> top to bottom')
-disp('~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~')
+disp('note that the section plane that we look at is y (--> left to right) z (--> top to bottom');
+disp('~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~');
 
 % Compute all orientation matrices g
 all_g = gtMathsRod2RotMat(r_vectors(:, 2:4));

7_fed/AndyFunctions/gtFedSpreadIntByVoxel.m

@@ -284,7 +284,7 @@ for i=1:nbl
                         blint(flu(1):clu(1),flu(2):clu(2),flu(3):clu(3)) + dint;
 
                 else % treating only 1 voxel in 27
-                    % 3x3x3 cube equivelent to 3.7 diameter sphere
+                    % 3x3x3 cube equivalent to 3.7 diameter sphere
                     % at each point of dint place a 5x5x1 image of
                     % projected sphere
                     %

7_fed/Ccode_SpreadInt/gtFedSpreadIntByVoxel.m

@@ -234,7 +234,7 @@ end
 					blint(flu(1):clu(1),flu(2):clu(2),flu(3):clu(3)) + dint;
 
                 else % treating only 1 voxel in 27
-                    % 3x3x3 cube equivelent to 3.7 diameter sphere
+                    % 3x3x3 cube equivalent to 3.7 diameter sphere
                     % at each point of dint place a 5x5x1 image of
                     % projected sphere
 %                     

zUtil_Boundaries/gtAnalyseBoundaryIndexPlane.m

@@ -24,24 +24,25 @@ function [voldev, volhkl, poles]=gtAnalyseBoundaryIndexPlane(bounds_vol, grain_v
 
 
 if isempty(list)
-  list=1:max(bounds_vol(:));
-disp('doing all boundaries...')
+    list=1:max(bounds_vol(:));
+    disp('doing all boundaries...');
 end
 
 voldev=zeros(size(bounds_vol));%output vol
 volhkl=zeros(size(bounds_vol));%output vol
 poles=[];
 
-%low index hkls to consider
+% Low index hkls to consider
 hkls=[1 0 0; 1 1 0; 1 1 1; 2 1 0; 2 1 1; 2 2 1; 3 1 0; 3 1 1; 3 2 0; 3 2 1; 3 2 2; 1 1 4];
-%expand to all variants
+% Expand to all variants
 all_hkls=[];
 hkl_type=[];
 for ii = 1:size(hkls,1)
     all_hkls = [all_hkls ; gtGetReflections(hkls(ii, :))];
     hkl_type = [hkl_type; repmat(ii, size( gtGetReflections(hkls(ii,:)), 1),1)]; %list of hkl type
 end
-%normalise hkl vectors
+
+% Normalise hkl vectors
 tmp = sqrt(sum((all_hkls.*all_hkls),2));
 normalised_hkls = all_hkls./(repmat(tmp,1,3));
 
@@ -123,7 +124,8 @@ poles2 = [];
 for ii = 1:length(symm)
     poles2 = [poles2; poles*symm(ii).g3];
 end
-%add this to correspond to line in gtMakePoleFigure
+
+% Add this to correspond to line in gtMakePoleFigure
 poles2=[poles2; -poles2];
 %poles=unique(poles2, 'rows');
 poles=poles2;

zUtil_Boundaries/gtAnalyseGrainBoundarySurface.m

@@ -95,7 +95,7 @@ for k = 1:length(bounds_list)
         for ii = 1:length(symm)
             poles2 = [poles2; poles*symm(ii).g3];
         end
-        %add this to correspond to line in gtMakePoleFigure
+        % Add this to correspond to line in gtMakePoleFigure
         poles2=[poles2; -poles2];
         poles=poles2;
 

zUtil_Boundaries/gtAnalyseGrainBoundarySurface2.m

@@ -58,7 +58,7 @@ f1=figure;
 
 %llop through the boundaries being considered, analysing the planes of the
 %facets
-for k=1:length(bounds_list)
+for k = 1:length(bounds_list)
 
     poles=[];
     poles_areas=[];
@@ -99,82 +99,81 @@ for k=1:length(bounds_list)
             poles_areas(end+1) = areas(ii); 
         end
 
-        %remove NaN faces from dum
+        % Remove NaN faces from dum
         dum(bad_faces)=[];
         poles(bad_faces, :)=[];
         poles_areas(bad_faces)=[];
         
         
-        %apply the symmetry operators
+        % Apply the symmetry operators
         poles2=[];
         poles_for_pole_fig=[]
         
-        for ii=1:length(symm)
+        for ii = 1:length(symm)
             % Deal with this in a 3d array
             poles2 = cat(3, poles2, poles*symm(ii).g);
             % Keep a 2d array for gtMakePoleFigure
             poles_for_pole_fig = [poles_for_pole_fig; poles*symm(ii).g];
         end
-        %add this to correspond to line in gtMakePoleFigure
+        % Add this to correspond to line in gtMakePoleFigure
         poles2=cat(3,poles2,-poles2);
         poles_for_pole_fig=[poles_for_pole_fig; -poles_for_pole_fig];
         poles_areas_for_pole_fig=repmat(poles_areas', 2*length(symm), 1);
      
-        %keep all pole data for the grain
+        % Keep all pole data for the grain
         poles_all=[poles_all; poles_for_pole_fig];
         poles_areas_all=[poles_areas_all; poles_areas_for_pole_fig];
         
-        %get those poles which lie in the SST
+        % Get those poles which lie in the SST
         a=find(poles2(:,2,:)>=0 & poles2(:,2,:)<=poles2(:,1,:) & poles2(:,3,:)>=poles2(:,1,:));
-        %a is effectively an index in an 2d array, size(poles2, 1) by size(poles2, 3) (48)
+        % a is effectively an index in an 2d array, size(poles2, 1) by size(poles2, 3) (48)
         [a1,a2]=ind2sub([size(poles2, 1), size(poles2, 3)], a);
-        %but - this scrambles the order (i think)  should sort by a1 to keep poles3 in
-        %orignal order
-        [a1,i]=sort(a1);
-        a2=a2(i);
-
-  %get the relevent poles back out of the 3d thing
-  %temp use poles3
-  poles3=zeros(size(poles));
-  for p=1:size(poles2, 1)
-      poles3(p,:)=poles2(a1(p),:,a2(p));
-  end
+        % But - this scrambles the order (i think)  should sort by a1 to keep poles3 in
+        % Orignal order
+        [a1, ii] = sort(a1);
+        a2 = a2(ii);
+
+        % Get the relevent poles back out of the 3d thing
+        % temp use poles3
+        poles3=zeros(size(poles));
+        for p=1:size(poles2, 1)
+            poles3(p,:)=poles2(a1(p),:,a2(p));
+        end
   
-  %get the colour
-  x=poles3(:,1);
-  y=poles3(:,2);
-  z=poles3(:,3);
+        % Get the colour
+        x=poles3(:,1);
+        y=poles3(:,2);
+        z=poles3(:,3);
 
-  alpha=atan(x./z); % in sst alpha 0->pi/4
-  phi=atan2(y,x);
+        alpha=atan(x./z); % in sst alpha 0->pi/4
+        phi=atan2(y,x);
 
-  rgb=[1-(alpha/(pi/4)) (alpha/(pi/4)).*(1-(phi/(pi/4))) (alpha/(pi/4)).*(phi/(pi/4))];
-  for i=1:size(rgb, 1)
-      rgb(i,:)=rgb(i,:)/max(rgb(i,:));
-  end
+        rgb=[1-(alpha/(pi/4)) (alpha/(pi/4)).*(1-(phi/(pi/4))) (alpha/(pi/4)).*(phi/(pi/4))];
+        for ii = 1:size(rgb, 1)
+            rgb(ii,:) = rgb(ii, :)/max(rgb(ii, :));
+        end
 
-  figure(f1)
-  fv_fig.vertices=fv.vertices;
-  fv_fig.faces=fv.faces(dum,:);
-  p=patch(fv_fig);
-  set(p, 'facevertexcdata', rgb)
-  shading faceted
+        figure(f1);
+        fv_fig.vertices=fv.vertices;
+        fv_fig.faces=fv.faces(dum,:);
+        p=patch(fv_fig);
+        set(p, 'facevertexcdata', rgb);
+        shading faceted;
 
 
-  %      poles=poles2;
-  %not really needed if 3d thing works
+        %poles=poles2;
+        % Not really needed if 3d thing works
         %poles_areas=repmat(poles_areas', 48, 1);
-        
-        %plot a pole figure of this boundary?
+
+        % Plot a pole figure of this boundary?
         if 0
-            
             gtMakePoleFigure(poles_for_pole_fig, 'weights', poles_areas_for_pole_fig, 'inc', 0.01, 'searchR', 0.03)
             title(sprintf('boundary %d - mesh reduced %f', bounds_list(k), reduce_factor))
         end
         
 %         %make some kind of fancy pants coloured 3d figure
 %         %grain figure with the individual boundaries coloured
-%        figure(f1)
+%         figure(f1);
 %         fv_fig.vertices=fv.vertices;
 %         fv_fig.faces=fv.faces(dum,:);
 %         p=patch(fv_fig)
@@ -183,25 +182,22 @@ for k=1:length(bounds_list)
 %         else
 %             set(p, 'facecolor', rand(3,1))
 %         end
-%         
-        
-
-
     end
 end
 
 %optional - add the facets that do not belong uniquely to one boundary,
 %coloured black.
 if 1
- dum=find(faces_bounds(:,1)~=faces_bounds(:,2) || faces_bounds(:,1)~=faces_bounds(:,3));
-  figure(f1)
-  fv_fig.vertices=fv.vertices;
-  fv_fig.faces=fv.faces(dum,:);
-  p=patch(fv_fig)
+    dum=find(faces_bounds(:,1)~=faces_bounds(:,2) || faces_bounds(:,1)~=faces_bounds(:,3));
+    figure(f1);
+    fv_fig.vertices=fv.vertices;
+    fv_fig.faces=fv.faces(dum,:);
+    p=patch(fv_fig);
 set(p, 'facevertexcdata', zeros(length(dum), 3))
 shading faceted
 end
 
-axis equal
-axis vis3d
+axis equal;
+axis vis3d;
 
+end % end of function

zUtil_Boundaries/gtBoundaryPoles.m

@@ -66,7 +66,7 @@ for k=1:length(list) %just look at the possible twin boundaries
 %   gb_normal1=boundaries_structure(i).gb_norm_grain1';
 %   gb_normal2=boundaries_structure(i).gb_norm_grain2';
  
-    %need to search symmetry equivelents for the pole in the SST
+    % Need to search symmetry equivalents for the pole in the SST
     tmp1=[];tmp2=[];
 
     for ii=1:length(symm)

zUtil_Boundaries/gtReadBoundariesStructure.m

@@ -21,7 +21,7 @@ function [output, output2] = gtReadBoundariesStructure(boundaries_structure, vTh
 % grain2_R_vector
 
 %therefore, can pull out the poles for a pole figure according to different
-%criteria, as well as producing symmetry equivelent (for xtallographic
+%criteria, as well as producing symmetry equivalent (for xtallographic
 %things) if required.
 
 % add - in a crude way - the stuff to read from the the

zUtil_Boundaries/gtReadBoundaryProperties.m

@@ -57,7 +57,7 @@ for ii=1:size(boundaries_structure, 2)
         % TODO: replace by a MISORIENTATION function
         if ~isempty(g1) && ~isempty(g2)
             % If we have both grains
-            % need to search symmetry equivelents for the minimum misorientation
+            % Need to search symmetry equivalents for the minimum misorientation
             rot_offset=[];
             % warning('g*symm maybe should be symm*g')
             for jj=1:length(symm)

zUtil_Indexter/gtINDEXMatchGrains.m

@@ -115,19 +115,19 @@ function [match, dev, dcm, drotm, conflicts, toBeChecked] = gtINDEXMatchGrains(.
 
 
 if ~exist('ph1','var') || isempty(ph1)
-  ph1 = 1;	
+  ph1 = 1;
 end
 
 if ~exist('dc','var') || isempty(dc)
-  dc = [0 0 0];	
+  dc = [0 0 0];
 end
 
 if ~exist('drot','var') || isempty(drot)
-  drot = [];	
+  drot = [];
 end
 
 if ~exist('cent','var') || isempty(cent)
-  cent = false;	
+  cent = false;
 end
 
 if ~exist('grain1','var') || isempty(grain1)
@@ -285,7 +285,7 @@ end
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 if isempty(drot)
-    rotmat = eye(3,3);
+    rotmat = eye(3);
 else
     rotmat = drot;   % for column vectors ! for row vectors, use transpose!
 end
@@ -308,7 +308,7 @@ all_g2 = gtMathsRod2RotMat(gr2.R_vector);
 
 if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
    
-    disp('Calculating Rodrigues coordinates ...')
+    disp('Calculating Rodrigues coordinates ...');
 
     % Generate a prime number larger than 3 for each grain to be used to 
     % generate distinct reflection id-s later 
@@ -339,7 +339,7 @@ if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
         if isempty(Rvec)
             disp('WARNING! Rodrigues vector could not be fitted. Possible bug.' )
             gr2.R_vector(ii,:) = NaN;
-            gr2_rot(:,:,ii)    = NaN;
+            gr2_rot(:, :, ii)  = NaN;
         else
             gr2.R_vector(ii,:) = Rvec;
             gr2_rot(:, :, ii)  = all_rot(:, :, ii);
@@ -347,7 +347,7 @@ if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
 
         % Rodrigues line and distinct line ID (Rid contains (1,2,3))
         gr2.Rlines{ii} = Rline;
-        gr2.Rids{ii}   = Rid*pr(ii); 
+        gr2.Rids{ii}   = Rid*pr(ii);
 
         % For debugging: 
         %   Rvec = gtCrystRodriguesTest(pl_sam1', [shkl1(:,1), shkl2(:,1), shkl3(:,1)]', spacegroup, Bmat, 0, 0, 0);
@@ -527,7 +527,7 @@ else
 end
 
 
-fprintf('\nRemaining median deviation of Rodrigues vectors:\n  [%s]',num2str(Rvec_med))
+fprintf('\nRemaining median deviation of Rodrigues vectors:\n  [%s]',num2str(Rvec_med));
 
 fprintf('\nRemaining median deviation of grain centers:\n  [%s]',num2str(dxyz_med));
 
@@ -540,10 +540,10 @@ fprintf('\nRemaining root mean square deviation of grain center distances:\n  %g
 
 fprintf('\n\nRecommended total displacement correction (dc):\n  [%s]\n',num2str(dcm));
 
-disp('Recommended total rotation correction (drot):')
-disp(drotm)
+disp('Recommended total rotation correction (drot):');
+disp(drotm);
 
-fprintf('Number of matching grains found:\n  %d \n\n',sum(~isnan(match(:,2))))
+fprintf('Number of matching grains found:\n  %d \n\n',sum(~isnan(match(:,2))));
 
 
 end % of main function
@@ -587,7 +587,7 @@ function tomatch = sfCheckMatching(act, cand, tol, fzone_acc, fzone_ext, pixsize
     tomatch(~cons) = [];
     
     if isempty(tomatch)
-        return
+        return;
     end
     
     % Rodriguez vector close enough?
@@ -637,7 +637,6 @@ function tomatch = sfCheckMatching(act, cand, tol, fzone_acc, fzone_ext, pixsize
 end
 
 
-
 function grk = sfSelectGrains(keeplist,gr)
 
     grk.ind      = gr.ind(keeplist);
@@ -652,14 +651,3 @@ function grk = sfSelectGrains(keeplist,gr)
  
 end
 
-
-
-
-
-
-
-
-
-
-
-

zUtil_Twins/gtTwinTest.m

@@ -50,8 +50,8 @@ end
 % calculate the misorientation angle and axis between these grains
 % TODO: replace by a MISORIENTATION function
 if ~isempty(g1) && ~isempty(g2)
-    %if we have both grains
-    %need to search symmetry equivelents for the minimum misorientation
+    % if we have both grains
+    % Need to search symmetry equivalents for the minimum misorientation
     rot_offset=[];
     % warning('g*symm.g maybe should be symm.g*g')
     for jj=1:length(symm)