MATLAB scripted tracking and plotConnect improvements

matlab/GoSegmentIt.m

+function [rgDetect, rgMotionBlur, imKymo, LKymo, iPath, jPath, totalDetections] = GoSegmentIt(movieroot, moviefilename, tracefilename, kymofilename, alpha, extMaxH)
+rgDetect = [];
+rgMotionBlur = [];
+LKymo = [];
+iPath = [];
+jPath = [];
+
+bCheckMotionBlur = 1;
+if ( nargout < 2 )
+    bCheckMotionBlur = 0;
+end 
+
+Movie_Name = fullfile(movieroot, moviefilename);
+load(tracefilename);
+imKymo=imread(kymofilename);
+
+nKymo=0*imKymo;
+hold off; imagesc(imKymo);hold on;colormap gray
+RADIUS_DILATE=12;
+RADIUS=10;
+NFRAMES=120;
+
+sed = strel('disk',RADIUS_DILATE);
+se = strel('disk',RADIUS);
+
+stats=[0 Inf];
+rcFG={};
+rcPKS={};
+for t=1: NFRAMES
+    im=(imread(Movie_Name,t));
+    if max(im(:))<stats(2)
+        stats(2)=max(im(:));
+    end
+    if min(im(:))>stats(1)
+        stats(1)= min(im(:));
+    end
+end
+
+nbdsize = 5;
+nbdoffset = floor(nbdsize / 2);
+nbdsize = 2*nbdoffset+1;
+rgDetect = [];
+
+totalDetections = 0;
+
+for t=1: NFRAMES
+    im=(imread(Movie_Name,t));
+    im(im>stats(2))=stats(2);
+    im=mat2gray(im);
+%
+    bw=logical(0*im);
+    idx=sub2ind(size(im),round(iPath), round(jPath));
+    bw(idx)=1;
+    bwd=imdilate(bw,sed);
+    bw=imdilate(bw,se);
+
+%
+    level=alpha*graythresh(im(bwd));
+    bwi=im2bw(im,level);
+    bwi(~bw)=0;
+
+    bwMax=imextendedmax(im,extMaxH,4)& bwi;
+    bwMax=bwmorph(bwMax,'shrink',Inf);
+
+    [rfg cfg]=find(bwi);
+    rcFG{t}=[rfg cfg];
+    %[rpk cpk]=find(bwMax & bwi);
+    %rcPKS{t}=[rpk cpk];
+
+    [L num]=bwlabel(bwi,4);
+% 
+% 
+%     bwp=bwboundaries(bwi);
+%     hold off;imagesc(im);hold on
+%     if 1==t brighten(0.33),end
+%     for i=1:length(bwp)
+%         plot(bwp{i}(:,2),bwp{i}(:,1),'-r')
+%     end
+%     [r c]=find(bwi);
+%     plot(c,r,'.g')
+% 
+%     % plot all pts
+%     for n=1:num
+%         [r c]=find(L==n);
+%         for i=1:length(r)
+%             pKymo=LKymo(r(i),c(i));
+%             if 0==pKymo
+%                 dd=(jPath-c(i)).^2+(iPath-r(i)).^2;
+%                 [m pKymo]=min(dd);
+%             end
+%             plot(t,pKymo,'.b')
+%         end
+%     end
+    % plot maxima
+    j = 1;
+    for n=1:num
+        [r c]=find(L==n);
+        if length(r)>10,ccc='.m';
+        elseif length(r)>6,ccc='.r';
+        elseif length(r)>3,ccc='.g';
+        else ccc='.y';
+        end
+        ccc='.r';
+        for i=1:length(r)
+            if ~bwMax (r(i),c(i)),continue,end
+            pKymo=LKymo(r(i),c(i));
+            if 0==pKymo
+                dd=(jPath-c(i)).^2+(iPath-r(i)).^2;
+                [m pKymo]=min(dd);
+            end
+            plot(t,pKymo,ccc)
+            
+            yl = max(r(i)-nbdoffset,1);
+            xl = max(c(i)-nbdoffset,1);
+            yh = min(size(im,1),r(i)+nbdoffset);
+            xh = min(size(im,2),c(i)+nbdoffset);
+
+            yoffmin = yl - (r(i)-nbdoffset);
+            yoffmax = yh - (r(i)+nbdoffset);
+            xoffmin = xl - (c(i)-nbdoffset);
+            xoffmax = xh - (c(i)+nbdoffset);
+
+            peaknbd = -ones(2*nbdoffset+1, 2*nbdoffset+1);
+            peaknbd((yoffmin+1):(nbdsize+yoffmax),(xoffmin+1):(nbdsize+xoffmax)) = im(yl:yh,xl:xh);
+
+            rgDetect{t}(j,:) = [r(i) c(i) peaknbd(:)'];
+            rcPKS{t}(j,:) = [r(i) c(i)];
+            j = j + 1;
+            
+            totalDetections = totalDetections + 1;
+        end
+%         pix=find(L==n);
+%         if  ~any(bwMax(pix))
+%             rmean=round(mean(r));
+%             cmean=round(mean(c));
+%             bwMax (rmean,cmean)=1;
+%             pKymo=LKymo(rmean,cmean);
+%             if 0==pKymo
+%                 dd=(jPath-cmean).^2+(iPath-rmean).^2;
+%                 [m pKymo]=min(dd);
+%             end
+%             plot(t,pKymo,'xg')
+%         end
+     end
+
+    drawnow
+end
+
+if ( ~bCheckMotionBlur )
+    rgMotionBlur = [];
+    return;
+end
+
+lenpix = size(imKymo,1);
+if ( (totalDetections / (lenpix*120)) > 0.3 )
+    disp(['Too many detections ' moviefilename]);
+    rgDetect = [];
+    rgMotionBlur = [];
+    return;
+end
+
+VMAX=20;
+rgMotionBlur = cell(1,length(rgDetect)-1);
+for t=1: NFRAMES-1
+    
+    bwtFG=logical(0*im);
+    idx=sub2ind(size(im),rcFG{t}(:,1),rcFG{t}(:,2));
+    bwtFG(idx)=1;
+    
+    bwt1FG=logical(0*im);
+    idx=sub2ind(size(im),rcFG{t+1}(:,1),rcFG{t+1}(:,2));
+    bwt1FG(idx)=1;
+    
+    [L num]=bwlabel(bwtFG,8);
+    [L1 num1]=bwlabel(bwt1FG,8);
+    for i=1:size(rcPKS{t},1)
+        [r c]=find(L==L(rcPKS{t}(i,1),rcPKS{t}(i,2)));
+        rgMotionBlur{t}{i} = [];
+        for j=1:size(rcPKS{t+1},1)
+            vij=norm([rcPKS{t+1}(j,:)-rcPKS{t}(i,:)]);
+            if vij>VMAX,continue,end
+            [r1 c1]=find(L1==L1(rcPKS{t+1}(j,1),rcPKS{t+1}(j,2)));
+            dmin=Inf;
+            for k=1:length(r1)
+                d=sqrt( (r1(k)-r).^2 + (c1(k)-c).^2);
+                dd=min(d);
+                if dd<dmin
+                    dmin=dd;
+                end
+            end
+            
+            p1=LKymo(rcPKS{t}(i,1),rcPKS{t}(i,2));
+            if 0==p1
+                dd=(jPath-rcPKS{t}(i,2)).^2+(iPath-rcPKS{t}(i,1)).^2;
+                [m p1]=min(dd);
+            end
+            
+            p2=LKymo(rcPKS{t+1}(j,1),rcPKS{t+1}(j,2));
+            if 0==p2
+                dd=(jPath-rcPKS{t+1}(j,2)).^2+(iPath-rcPKS{t+1}(j,1)).^2;
+                [m p2]=min(dd);
+            end
+            if dmin< (1-150/650)*vij+2
+                plot([t t+1],[p1 p2],'-y')
+                %rgMotionBlur{t}{i}(1:2,end+1) = [j;1];
+            else
+                plot([t t+1],[p1 p2],'-b')
+                %rgMotionBlur{t}{i}(1:2,end+1) = [j;0];
+            end
+            rgMotionBlur{t}{i}(1:2,end+1) = [j;dmin];
+            
+            plot(t,p1,'.r')
+            plot(t+1,p2,'.r')
+        end
+    end
+    
+    drawnow
+end
\ No newline at end of file

matlab/GoTrack43.m

+inputroot = 'C:\Users\mwinter\Documents\MATLAB\KymoTrackingData\Movies';
+
+if ( ~exist('mvlist', 'var') )
+    mvlist = Make43MovieList(inputroot);
+end
+
+if ( ~exist('alphalist', 'var') )
+    alphalist = ones(size(mvlist));
+end
+
+if ( ~exist('exthlist', 'var') )
+    exthlist = 0.025*ones(size(mvlist));
+end
+
+if ( ~exist('startidx', 'var') )
+    startidx = 1;
+end
+
+if ( ~exist('endidx', 'var') )
+    endidx = length(mvlist);
+end
+
+if ( ~exist('errlist', 'var') )
+    errlist = [];
+end
+
+successlist = [];
+
+results = struct([]);
+
+for i=startidx:endidx
+    if ( ~isempty(find(errlist == i, 1)) )
+        continue;
+    end
+    
+    results(i).movieroot = mvlist(i).movieroot;
+    results(i).moviename = mvlist(i).moviename;
+    results(i).alpha = alphalist(i);
+    results(i).extH = exthlist(i);
+    
+    [rgDetect, rgMotionBlur, imKymo, LKymo, iPath, jPath] = GoSegmentIt(mvlist(i).movieroot, mvlist(i).moviename, mvlist(i).tracefilename, mvlist(i).kymofilename, alphalist(i), exthlist(i));
+    %results(i) = GoSegmentIt(results(i), mvlist(i).tracefilename, mvlist(i).kymofilename);
+%     if ( isempty(rgDetect) )
+%         disp(['Error segmenting ' mvlist(i).root ': ' mvlist(i).cellname]);
+%         errlist(end+1) = i;
+%         continue;
+%     end
+
+    outdatname = [mvlist(i).root '_' mvlist(i).cellname];
+    save([outdatname '.mat'], 'rgDetect', 'rgMotionBlur', 'imKymo', 'LKymo', 'iPath', 'jPath');
+    successlist(end+1) = i;
+
+    segdatname = [outdatname '_seg.dat'];
+    mbdatname = [outdatname '_mb.dat'];
+
+    writeSegData(segdatname, rgDetect);
+    %writeTraceData([outdatname '_trace.dat'], [jPath';iPath']);
+    writeMotionBlurData(mbdatname, rgMotionBlur);
+
+    system(['C:\Users\mwinter\Documents\Projects\KymoTracker\trunk\Release\KymoTracker.exe "' segdatname '" "' mbdatname '" "' outdatname '" &']);
+end
+
+save('finalstate.mat', 'mvlist', 'errlist', 'successlist', 'alphalist');
\ No newline at end of file

matlab/Make43MovieList.m

+function movielist = Make43MovieList(inputroot)
+    movielist = [];
+    
+    folders = {'HD5 BDNF middle', 'HD6 BDNF MIDDLE', 'HD9 BDNF MIDDLE', 'HD10 BDNF MIDDLE'};
+    
+    maxmovies = 20;
+    for i=1:length(folders)
+        ROOT = folders{i};
+        for j=1:maxmovies
+            cellname = ['cell ' num2str(j) ' middle'];
+            moviename = [cellname ' BDNF.tif'];
+            movieroot = fullfile(inputroot, ROOT);
+            moviefilename = fullfile(movieroot, moviename);
+            tracefilename = fullfile(inputroot, 'OutputKymos', [ROOT '_' cellname '_path.mat']);
+            kymofilename = fullfile(inputroot, 'OutputKymos', [ROOT '_' cellname '_kymo.tif']);
+            if ( exist(moviefilename, 'file') && exist(tracefilename, 'file') && exist(kymofilename, 'file') )
+                movielist(end+1).root = ROOT;
+                movielist(end).cellname = cellname;
+                movielist(end).moviename = moviename;
+                movielist(end).movieroot = movieroot;
+                movielist(end).tracefilename = tracefilename;
+                movielist(end).kymofilename = kymofilename;
+            end
+        end
+    end
+end
\ No newline at end of file

matlab/plotConnect.m

@@ -25,10 +25,25 @@ function plotConnect(trackList, gConnect, gCellData, hashNodes, rgDetect, imKymo
         
         plot(trkt(1), trkpts(1), 'o', 'Color', trackColors(i,:));
         h = plot(trkt, trkpts, 'Color', trackColors(i,:), 'LineWidth',1, 'LineStyle','-');
-        set(h, 'ButtonDownFcn',@PlotButtonClickFunc, 'UserData', i);
+        set(h, 'ButtonDownFcn',@PlotSegmentClickFunc, 'UserData', i);
     end
     
-    function PlotButtonClickFunc(src, evt)
+%     function PlotDetectionClickFunc(src, evt)
+%         clktype = get(gcf, 'SelectionType');
+%         
+%         if ( strcmpi(clktype,'normal') )
+%         elseif ( strcmpi(clktype,'alt') )
+%             if ( ~isempty(branchPaths) )
+%                 for j=1:length(branchPaths)
+%                     delete(branchPaths(j));
+%                 end
+%                 branchPaths = [];
+%                 highlightedBranch = [];
+%             end
+%         end
+%     end
+    
+    function PlotSegmentClickFunc(src, evt)
         clktype = get(gcf, 'SelectionType');
         if ( ~isempty(highlightedObj) )
             set(highlightedObj, 'LineWidth',1);
@@ -81,6 +96,6 @@ function plotConnect(trackList, gConnect, gCellData, hashNodes, rgDetect, imKymo
         highlightedBranch = src;
         set(src, 'LineWidth',2);
         cidx = get(src, 'UserData');
-        disp(['Path Cost: ' num2str(gCellData(cidx).cost)]);
+        disp(['Segment (' num2str(gCellData(cidx).path(1)) ',' num2str(gCellData(cidx).path(2)) ') Cost: ' num2str(gCellData(cidx).cost)]);
     end
 end
\ No newline at end of file