Boundaries : commenting and formatting

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

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@581 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_Boundaries/gtMakeBoundariesStructure.m

@@ -2,12 +2,12 @@
 
 function boundaries_structure = gtMakeBoundariesStructure(boundaries, grains)
 
-% from the boundaries and grains volumes, start to build the
+% from the boundaries and grains volume, start to build the
 % boundaries_structure.
 
 nbounds=max(boundaries(:));
 
-for i=1:max(boundaries(:))
+for i=1:nbounds
     list=find(boundaries(:,1)==i);
     list=[list;find(boundaries(:,2)==i)];
     boundaries_structure(i).count=length(list);
@@ -19,12 +19,10 @@ for i=1:max(boundaries(:))
         disp('one voxel only')
         boundaries_structure(i).grain1=list(1);
         boundaries_structure(i).grain2=[];
-    else
-        keyboard
     end
     
     if mod(i, 100)==0
-        disp(sprintf('done %d percent', round(100*i/nbounds)))
+        fprintf('done %d percent\n', round(100*i/nbounds))
     end
     
 end

zUtil_Boundaries/gtReadBoundariesStructure.m

@@ -41,12 +41,11 @@ load('parameters.mat');
 spacegroup=parameters.cryst.spacegroup;
 
 if spacegroup==225 || spacegroup==229
-    sym = gtGetCubicSymOp;
+    sym = gtGetCubicSymOp();
 elseif spacegroup==663 || spacegroup==194
-    sym= gtGetHexagonalSymOp_sab;
+    sym= gtGetHexagonalSymOp_sab();
 elseif spacegroup==167
-    %  sym= gtGetHexagonalSymOp_sab;
-    sym=gtGetAluminaSymOp_sab;
+    sym=gtGetAluminaSymOp_sab();
     disp('alumina sym ops testing...')
 else
     disp('spacegroup not supported! cant do symmetry operations!')
@@ -117,6 +116,9 @@ if 1 % if using boundaries_structure
     weights=[weights; weights];
     output=poles;
     output2=weights;
+    
+    save poles poles
+    save weights weights
 end
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -162,3 +164,4 @@ if 0
     count
 end
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+end % end function
\ No newline at end of file

zUtil_Boundaries/gt_find_grain_boundaries.m

-function [vol_out, boundaries, boundaries_count]=gt_find_grain_boundaries(vol)
-%     [vol_out, boundaries, boundaries_count]=gt_find_grain_boundaries(vol)
-%     ---------------------------------------------------------------------
-%     Starts writing the boundaries_structure.mat file
+function [vol_out, boundaries, boundaries_count] = gt_find_grain_boundaries(vol)
+% GT_FIND_GRAIN_BOUNDARIES  Starts writing the boundaries_structure.mat file
+%     [vol_out, boundaries, boundaries_count] = gt_find_grain_boundaries(vol)
+%     -----------------------------------------------------------------------
 %     now need to read the grain boundaries from the stack with dilated grains
 %     Saves boundaries_structure as tmp.mat file
 %
@@ -15,7 +15,8 @@ function [vol_out, boundaries, boundaries_count]=gt_find_grain_boundaries(vol)
 %
 %     this actually shares functionality with gtMakeBoundariesStructure, which
 %     also suppresses single voxel "boundaries".  Should merge...
-
+% 
+%     Version 002 by LNervo
 
 boundaries=[];
 boundaries_count=0;
@@ -24,8 +25,8 @@ boundary_number=1;
 [size_x, size_y, size_z]=size(vol);
 vol_out=zeros(size(vol));
 
-%find the voxels that need to be studied
-%dilates colours
+% find the voxels that need to be studied
+% dilates colours
 vol_dilated = imdilate(vol, ones(3,3,3));
 vol_eroded  = imerode(vol,ones(3,3,3));
 dif         = vol_dilated-vol_eroded;
@@ -34,10 +35,9 @@ todo_voxels = find(dif~=0);
 
 for i=1:length(todo_voxels)
     
-    
     [x,y,z]=ind2sub(size(vol), todo_voxels(i));
     
-    %look at voxel neighbourhood
+    % look at voxel neighbourhood
     xstart=x-1;
     xend=x+1;
     ystart=y-1;
@@ -65,50 +65,52 @@ for i=1:length(todo_voxels)
     
     neighbours=vol(xstart:xend, ystart:yend, zstart:zend);
     neighbours=neighbours(:);
-    %neighbours(find(neighbours==0))=[];%don't consider boundaries to zeros
+    % neighbours(find(neighbours==0))=[]; % don't consider boundaries to zeros
     
     voxel_colour=vol(x,y,z);
-    %find any different coloured neighbours
+    % find any different coloured neighbours
     neighbours=neighbours(find(neighbours~=voxel_colour));
     if ~isempty(neighbours)
-        neighbour_colour=min(neighbours);%lowest non-zero neighbour colour
+        neighbour_colour=min(neighbours); % lowest non-zero neighbour colour
         
-        %has this combination of voxel_colour and neighbour_colour already been
-        %treated? look for rows in boundaries
+        % has this combination of voxel_colour and neighbour_colour already been
+        % treated? look for rows in boundaries
         dummy1=find(boundaries(:)==voxel_colour);
         [dummy1,a]=ind2sub(size(boundaries),dummy1);
         dummy2=find(boundaries(:)==neighbour_colour);
         [dummy2,a]=ind2sub(size(boundaries),dummy2);
         
-        %any common rows?
+        % any common rows?
         boundary_number=dummy1(find(ismember(dummy1,dummy2)));
         
-        if ~isempty(boundary_number) %a previously encountered boundary
+        if ~isempty(boundary_number) % a previously encountered boundary
             vol_out(x,y,z)=boundary_number;
             boundaries_count(boundary_number)=boundaries_count(boundary_number)+1;
-            %add to boundaries_structure
+            % add to boundaries_structure
             boundaries_structure(boundary_number).count=boundaries_structure(boundary_number).count+1;
             boundary_number=[];
-        else %a new boundary
+        else % a new boundary
             boundary_number=size(boundaries,1)+1;
-            disp(['now on boundary' num2str(boundary_number)])
+            disp(['now on boundary: ' num2str(boundary_number)])
             vol_out(x,y,z)=boundary_number;
             boundaries(boundary_number,:)=[voxel_colour, neighbour_colour];
             boundaries_count(boundary_number)=1;
-            %add to boundaries_structure
+            % add to boundaries_structure
             boundaries_structure(boundary_number).grain1=voxel_colour;
             boundaries_structure(boundary_number).grain2=neighbour_colour;
             boundaries_structure(boundary_number).count=1;
             boundary_number=[];
         end
         
-    end%if a boundary voxel
-    
-    
+    end % if a boundary voxel
     
-end %loop over todo voxels
 
-save tmp boundaries_structure
+end % loop over todo voxels
+
+save('tmp.mat','boundaries_structure');
+
+end % end of function
+
 % try
 %     if max(vol_out(:))<2^16
 % edf_write(vol_out, '5_reconstruction/boundaries_volume.edf', 'uint16')