Deleting old code

MainScripts/findContour.m

@@ -18,87 +18,6 @@ function [boundaries, cellIdx] = findContour( labelIm, PARAMS )
 
 fprintf('Recreating the cellular contours\n');
 
-%% %% Create a temporary binary image of each individual cell before => Old version from Bellaiche data
-% % applying a boundary finding method == OLD VERSION
-% for bioCell = 1:length(contour2Dpos) % for all cells
-%     clear miniContour miniImg
-%     contour2Dpos{bioCell} = round(contour2Dpos{bioCell}/PARAMS.imSettings.latPixSize); % rescale from µm to pix for image creation
-%     miniContour=[contour2Dpos{bioCell}(:,1) contour2Dpos{bioCell}(:,2)]-(min(contour2Dpos{bioCell})-1);
-%     miniImg = zeros(max(miniContour(:,1)),max(miniContour(:,2))); % columns and lines are switched
-%     for i = 1:size(miniContour,1)
-%         miniImg(miniContour(i,1),miniContour(i,2))=1;
-%     end
-%     
-%     % append 1 layer in all directions to avoid border effect
-%     % could be merged with the previous paragraph drawing the contour but simpler like this
-%     miniImg = [zeros(1,size(miniImg,2)) ; miniImg ; zeros(1,size(miniImg,2))];
-%     miniImg = [zeros(size(miniImg,1),1) , miniImg , zeros(size(miniImg,1),1)];
-%     %     figure;imshow(testIm)
-%     
-%     % Fill contour
-%     miniImg = imfill(miniImg,'holes');
-%     
-%     switch bmethod
-%         
-%         case 'msquare'
-%             % Find contour
-%             [cellContour2D{bioCell}.Lines,cellContour2D{bioCell}.Vertices]=isocontour(miniImg,0.5);
-%             % Replace in full image % -1 for start table at 1 and -1 for
-%             % appened lines
-%             cellContour2D{bioCell}.Vertices = cellContour2D{bioCell}.Vertices+...
-%                 min(contour2Dpos{bioCell})-2; % replace in full image % -1 for start table at 1 and -1 for appened lines
-%             
-%         case 'msquareImproved'
-%             % Enlarge and erode
-%             miniImg = imresize(miniImg, 2);
-%             selem = ones(3,3); %// square, 8-Negihbours
-%             miniImg = imerode(miniImg, selem);
-%             % Find contour
-%             [cellContour2D{bioCell}.Lines,cellContour2D{bioCell}.Vertices]=isocontour(miniImg,0.5);
-%             % Replace in full image % -1 for start table at 1 and -1 for
-%             % appened lines and /2 for the enlargment             
-%             cellContour2D.Vertices = (cellContour2D{bioCell}.Vertices)/2-2+...
-%                 min(contour2Dpos{bioCell});
-%             
-%         case 'bwboundary'
-%             [boundaries,~] = bwboundaries(miniImg,'noholes'); % simpler call is boundaries = bwboundaries(miniImg,'noholes');
-%             cellContour2D{bioCell}.cellCt = boundaries{1}+...
-%                 min(contour2Dpos{bioCell})-2; % replace in full image % -1 for start table at 1 and -1 for appened lines
-%             
-%         case 'mask2poly'
-%             polyCell=mask2poly(miniImg,'Inner','MINDIST');
-%             % switch columns 1 and 2
-%             polyCell(:,3) = polyCell(:,1);
-%             polyCell(:,1) = polyCell(:,2);
-%             polyCell(:,2) = polyCell(:,3);
-%             polyCell(:,3) = [];
-%             cellContour2D{bioCell}.cellCt = polyCell+...
-%                 min(contour2Dpos{bioCell})-2; % replace in full image % -1 for start table at 1 and -1 for appened lines
-%         
-%         otherwise
-%             fprintf('Error: Unknown contour method: %s\n', bmethod);
-%     end
-%     
-%     switch bmethod % this step to reorganize the msquare output
-%         case {'msquare','msquareImproved'}
-%             Ori = 1;
-%             tempVert = zeros(length(cellContour2D{bioCell}.Lines),2);
-%             for lines = 1:length(cellContour2D{bioCell}.Lines)
-%                 tempVert(lines,:) = cellContour2D{bioCell}.Vertices(cellContour2D{bioCell}.Lines(Ori,1),:);
-%                 Dest = cellContour2D{bioCell}.Lines(Ori,2);
-%                 if length(find(cellContour2D{bioCell}.Lines(:,1)==Dest))~=1
-%                     fprintf('Error: a contour line is open. Check cell %d at Origin = %d\n',...
-%                         bioCell,Dest);
-%                     break
-%                 end
-%                 Ori = find(cellContour2D{bioCell}.Lines(:,1)==Dest);
-%             end
-%             cellContour2D{bioCell}.cellCt = tempVert;
-%             clear tempVert
-%     end
-
-%%
-
 % Find all the objects in the image
 cc = bwconncomp(labelIm, 4);