diff --git a/MainScripts/findContour.m b/MainScripts/findContour.m
index 0304c9bdfed7434c38a31ff8a9307f2788fb2a1f..d154c28669a727a129a7e80175dc539300cb8819 100644
--- a/MainScripts/findContour.m
+++ b/MainScripts/findContour.m
@@ -1,20 +1,13 @@
%% finds the contour around a set of pixels originating from a previous segmentation
-function cellContour2D = findContour(contour2Dpos,bmethod,PARAMS)
-% find the correct order of the points defining the polygon contour of the
-% cell instead of sorted by XY position
-% Also create the connectivity pairs
+function boundaries = findContour( labelIm, PARAMS )
+% find the correct order of the points defining the polygon contour of each
+% individual cell in a CW order
+
% INPUT
-% - contour2Dpos: a cell array with N cells each representing the biological
-% cells each of dim = nx2 for the n pixels composing the segmented cell in
-% 2D.
-% - bmethod: 1 of 4 possibilities of boundary contour method
-% - msquare
-% - msquareImproved: method improved with dilatation and erosion
-% - bwboundary: default Matlab method
-% - mask2poly: fex boundary finding method, very close to bwboundary
-% although with more options
+% - dataSeg: a mask image of the segmentation ridges
+% - PARAMS: a structure containing image specs
% OUTPUT
% - cellContout2D: structure with 3 fields
% - cellContour2D.Line: paired vertices matrix to infer the pixel
@@ -26,85 +19,134 @@ fprintf('Recreating the cellular contours\n');
-%% Create a temporary binary image of each individual cell before applying a boundary finding method
-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)
+% %% Create a temporary binary image of each individual cell before
+% % 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
+
+%%
+
+tic
+% Find all the objects in the image
+cc = bwconncomp(labelIm, 4);
+
+% Prepare the morphological structuring element to recover the ridge element loss
+se =strel('disk', 1);
+
+% initialize output structure
+boundaries = cell( cc.NumObjects, 1 );
+
+% Extend each boundary to the center of the ridge
+for bioCell = 1 : cc.NumObjects
+
+ % Exclude cells touching the image border.
+ % TODO elsewhere?
- % Fill contour
- miniImg = imfill(miniImg,'holes');
+ emptyImage = zeros( cc.ImageSize, 'logical' );
+ emptyImage( cc.PixelIdxList{bioCell} ) = 1;
+ emptyImage = imdilate( emptyImage, se );
- 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');
- 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
+ b = bwboundaries( emptyImage, 8, 'noholes');
+ boundaries{ bioCell } = b{ 1 } * PARAMS.imSettings.latPixSize;
- 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
- cellContour2D{bioCell}.cellCt = cellContour2D{bioCell}.cellCt*PARAMS.imSettings.latPixSize; % scale back to µm
end
-cellContour2D = cellContour2D';
+toc
+% figure
+% imshow( labelIm, [] )
+% hold on
+% for bioCell = 1 : cc.NumObjects
+% line( boundaries{ bioCell }(:,2), boundaries{ bioCell }(:,1) , 'Marker', '.' )
+% end
+
+end
+
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-end
\ No newline at end of file