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Commit 9b3d67e8 authored by Mark Winter's avatar Mark Winter Committed by Mark Winter
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Various fixes and improvements to matlab scripts

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matlab/GenerateStats43.m
+ 50
− 11
View file @ 9b3d67e8
%inputroot = 'C:\Users\mwinter\Documents\MATLAB\KymoTrackingData\Movies';
%outputroot = 'C:\Users\mwinter\Documents\MATLAB\KymoTrackingResults';
inputroot = 'C:\Users\mwinter\Documents\Data\OHSU\ssNPY';
%inputroot = 'C:\Users\mwinter\Documents\Data\OHSU\ssNPY';
%outputroot = fullfile(inputroot, 'OutputTrackingResults');
inputroot = 'C:\Users\mwinter\Documents\Data\OHSU\BDNF';
outputroot = fullfile(inputroot, 'OutputTrackingResults');
if ( ~exist('movielist', 'var') )
if ( exist(fullfile(inputroot, 'movielist.mat'), 'file') )
load(fullfile(inputroot, 'movielist.mat'));
else
movielist = Make43MovieList(inputroot);
movielist = MakeBDNFMovieList(inputroot);
end
end
......@@ -27,13 +29,46 @@ ps = {};
ds = {};
ts = {};
j=1;
for i=startidx:endidx
alpha = 0.0;
bNameWithAlpha = 0;
if ( ~exist(fullfile(outputroot,[movielist(i).root movielist(i).cellname '.mat']),'file') )
for alpha=0.05:0.01:2.0
if ( exist(fullfile(outputroot,[movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '.mat']),'file') )
bNameWithAlpha = 1;
break;
end
end
if ( ~bNameWithAlpha )
continue;
end
end
if ( bNameWithAlpha )
load(fullfile(outputroot,[movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '.mat']));
else
load(fullfile(outputroot,[movielist(i).root movielist(i).cellname '.mat']));
outdatname = [movielist(i).root movielist(i).cellname '_tracks.txt'];
dbgdatname = [movielist(i).root movielist(i).cellname '_dbginfo.txt'];
segdatname = [movielist(i).root movielist(i).cellname '_seg.dat'];
mbdatname = [movielist(i).root movielist(i).cellname '_mb.dat'];
alpha = trackingStruct.alpha;
system(['copy "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '.mat']) '" "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '.mat']) '"']);
delete(fullfile(outputroot,[movielist(i).root movielist(i).cellname '.mat']));
system(['copy "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_tracks.txt']) '" "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_tracks.txt']) '"']);
delete(fullfile(outputroot,[movielist(i).root movielist(i).cellname '_tracks.txt']));
system(['copy "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_dbginfo.txt']) '" "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_dbginfo.txt']) '"']);
delete(fullfile(outputroot,[movielist(i).root movielist(i).cellname '_dbginfo.txt']));
system(['copy "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_seg.dat']) '" "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_seg.dat']) '"']);
delete(fullfile(outputroot,[movielist(i).root movielist(i).cellname '_seg.dat']));
system(['copy "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_mb.dat']) '" "' fullfile(outputroot,[movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_mb.dat']) '"']);
delete(fullfile(outputroot,[movielist(i).root movielist(i).cellname '_mb.dat']));
end
outdatname = [movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_tracks.txt'];
dbgdatname = [movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_dbginfo.txt'];
segdatname = [movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_seg.dat'];
mbdatname = [movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_mb.dat'];
trackingStruct.fullname = [movielist(i).root movielist(i).cellname];
......@@ -43,15 +78,19 @@ for i=startidx:endidx
trackingStruct = readConnectData(trackingStruct, fullfile(outputroot,outdatname), fullfile(outputroot,dbgdatname));
trackingStruct.umppix = 0.18;
trackingStruct.spfrm = 0.575;
trackingStruct.spfrm = 0.650;
plotConnect(trackingStruct,5,5);
%axis([0 (numframes-1)*trackingStruct.spfrm 0 kymoArcLength*trackingStruct.umppix]);
print('-dtiff','-r300',['Z:\Prints\' movielist(i).root movielist(i).cellname '_interestingtracks.tiff']);
print('-dtiff','-r300',['Z:\Prints\allbdnf\' movielist(i).root movielist(i).cellname '_a' mkalphastr(alpha) '_interestingtracks.tiff']);
close all;
[stats{i,1} vs{i,1} ps{i,1} ds{i,1} ts{i,1} vtrkidx{i,1}] = GenerateStats(trackingStruct);
names{i,1} = [movielist(i).root movielist(i).cellname];
[stats{j,1} vs{j,1} ps{j,1} ds{j,1} ts{j,1} vtrkidx{j,1}] = GenerateStats(trackingStruct);
names{j,1} = [movielist(i).root movielist(i).cellname];
dsetnum(j,1) = movielist(i).datasetnum;
dsetmap(j,1) = i;
j=j+1;
end
\ No newline at end of file
matlab/GoSegmentIt.m
+ 3
− 1
View file @ 9b3d67e8
......@@ -78,6 +78,7 @@ for t=1: NFRAMES
%
level=alpha*graythresh(im(bwd));
level = min(level,0.95);
bwi=im2bw(im,level);
bwi(~bw)=0;
......@@ -115,6 +116,7 @@ for t=1: NFRAMES
% end
% plot maxima
j = 1;
rcPKS{t} = [];
for n=1:num
[r c]=find(L==n);
if length(r)>10,ccc='.m';
......@@ -179,7 +181,7 @@ if ( ~bCheckMotionBlur )
end
lenpix = size(imKymo,1);
if ( (totalDetections / (lenpix*120)) > 0.3 )
if ( (totalDetections / (lenpix*NFRAMES)) > 0.20 )
disp(['Too many detections ' inResultStruct.moviename]);
rgDetect = [];
rgMotionBlur = [];
......
matlab/GoTrackMovies.m
+ 65
− 51
View file @ 9b3d67e8
inputroot = 'C:\Users\mwinter\Documents\Data\OHSU\BDNF';
outputroot = fullfile(inputroot, 'OutputTrackingResults');
%inputroot = 'C:\Users\mwinter\Documents\Data\OHSU\BDNF';
%outputroot = fullfile(inputroot, 'OutputTrackingResults');
%inputroot = 'C:\Users\mwinter\Documents\Data\OHSU\ssNPY';
%outputroot = fullfile(inputroot, 'OutputTrackingResults');
inputroot = 'C:\Users\mwinter\Documents\Data\OHSU\newbdnf';
outputroot = fullfile(inputroot, 'OutputTrackingResults');
if ( ~exist(outputroot, 'dir') )
mkdir(outputroot);
......@@ -11,7 +13,8 @@ if ( ~exist('movielist', 'var') )
if ( exist(fullfile(inputroot, 'movielist.mat'), 'file') )
load(fullfile(inputroot, 'movielist.mat'));
else
movielist = Make43MovieList(inputroot);
movielist = MakeBDNFMovieList(inputroot);
save(fullfile(inputroot, 'movielist.mat'), 'movielist');
end
end
......@@ -49,6 +52,7 @@ end
disp(['Start time: ' datestr(clock())]);
goodsegs = [];
for i=startidx:endidx
trackingStruct.moviepath = movielist(i).moviepath;
......@@ -71,26 +75,29 @@ for i=startidx:endidx
trackingStruct.trackList = [];
trackingStruct.tracerange = tracelist{i};
if ( exist(fullfile(outputroot, [trackingStruct.fullname '.mat']), 'file') )
%for tryalpha = 0.4:0.3:1.6
if ( exist(fullfile(outputroot, [trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '.mat']), 'file') )
continue;
end
%[rgDetect, rgMotionBlur, imKymo, LKymo, iPath, jPath] = GoSegmentIt(mvlist(i).movieroot, mvlist(i).moviename, mvlist(i).tracefilename, mvlist(i).kymofilename, alphalist(i), exthlist(i));
%trackingStruct.alpha = tryalpha;
trackingStruct = GoSegmentIt(trackingStruct, movielist(i).tracefilename, movielist(i).kymofilename);
if ( isempty(trackingStruct.rgDetect) )
disp(['Error segmenting ' movielist(i).root movielist(i).cellname]);
disp(['Error segmenting ' movielist(i).root movielist(i).cellname ' with alpha=' num2str(trackingStruct.alpha)]);
continue;
end
outdatname = [trackingStruct.fullname '_tracks.txt'];
dbgdatname = [trackingStruct.fullname '_dbginfo.txt'];
segdatname = [trackingStruct.fullname '_seg.dat'];
mbdatname = [trackingStruct.fullname '_mb.dat'];
goodsegs(end+1,:) = [i trackingStruct.alpha];
outdatname = [trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '_tracks.txt'];
dbgdatname = [trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '_dbginfo.txt'];
segdatname = [trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '_seg.dat'];
mbdatname = [trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '_mb.dat'];
trackingStruct.outdatname = outdatname;
trackingStruct.dbgdatname = dbgdatname;
results(i) = trackingStruct;
save(fullfile(outputroot, [trackingStruct.fullname '.mat']), 'trackingStruct');
save(fullfile(outputroot, [trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '.mat']), 'trackingStruct');
writeSegData(fullfile(outputroot, segdatname), results(i).rgDetect, results(i).rgCC);
%writeTraceData([outdatname '_trace.dat'], [jPath';iPath']);
......@@ -101,36 +108,43 @@ for i=startidx:endidx
system(['C:\Users\mwinter\Documents\Projects\KymoTracker_v2\Release\KymoTracker_v2.exe "' fullfile(outputroot, segdatname) '" "' fullfile(outputroot, mbdatname) '" "' fullfile(outputroot, outdatname) '" "' fullfile(outputroot, dbgdatname) '" &']);
end
disp(['Finished ' trackingStruct.fullname ': ' datestr(clock())]);
%end
end
lastidx = startidx;
for i=startidx:endidx
if ( exist(fullfile(outputroot, [movielist(i).root movielist(i).cellname '.mat']), 'file') )
lastidx = i;
end
end
lastidx = goodsegs(end,1);
lastalpha = goodsegs(end,2);
while ( ~exist(fullfile(outputroot, [movielist(lastidx).root movielist(lastidx).cellname '_tracks.txt']), 'file')...
|| ~exist(fullfile(outputroot,[movielist(lastidx).root movielist(lastidx).cellname '_dbginfo.txt']), 'file') )
while ( ~exist(fullfile(outputroot, [movielist(lastidx).root movielist(lastidx).cellname '_a' mkalphastr(trackingStruct.alpha) '_tracks.txt']), 'file')...
|| ~exist(fullfile(outputroot,[movielist(lastidx).root movielist(lastidx).cellname '_a' mkalphastr(trackingStruct.alpha) '_dbginfo.txt']), 'file') )
pause(30);
end
close all;
for i=startidx:endidx
while ( ~exist(fullfile(outputroot, [movielist(i).root movielist(i).cellname '_tracks.txt']), 'file')...
|| ~exist(fullfile(outputroot,[movielist(i).root movielist(i).cellname '_dbginfo.txt']), 'file') )
pause(30);
if ( ~exist(fullfile(outputroot,'Prints'), 'dir') )
mkdir(fullfile(outputroot,'Prints'));
end
for i=1:size(goodsegs,1)
mvidx = goodsegs(i,1);
alpha = goodsegs(i,2);
if ( ~exist(fullfile(outputroot, [movielist(mvidx).root movielist(mvidx).cellname '_a' mkalphastr(alpha) '_tracks.txt']), 'file')...
|| ~exist(fullfile(outputroot,[movielist(mvidx).root movielist(mvidx).cellname '_a' mkalphastr(alpha) '_dbginfo.txt']), 'file') )
continue;
end
outdatname = [movielist(i).root movielist(i).cellname '_tracks.txt'];
dbgdatname = [movielist(i).root movielist(i).cellname '_dbginfo.txt'];
load(fullfile(outputroot, [movielist(i).root movielist(i).cellname '.mat']));
outdatname = [movielist(mvidx).root movielist(mvidx).cellname '_a' mkalphastr(alpha) '_tracks.txt'];
dbgdatname = [movielist(mvidx).root movielist(mvidx).cellname '_a' mkalphastr(alpha) '_dbginfo.txt'];
load(fullfile(outputroot, [movielist(mvidx).root movielist(mvidx).cellname '_a' mkalphastr(alpha) '.mat']));
trackingStruct = readConnectData(trackingStruct, fullfile(outputroot, outdatname), fullfile(outputroot, dbgdatname));
save(fullfile(outputroot, [trackingStruct.fullname '.mat']), 'trackingStruct');
save(fullfile(outputroot, [trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '.mat']), 'trackingStruct');
try
plotConnect(trackingStruct,5);
print('-r300', '-dtiffn', ['Z:\Prints\' trackingStruct.fullname '_tracks.tiff']);
print('-r300', '-dtiffn', [fullfile(outputroot,'Prints') filesep trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '_tracks.tiff']);
catch(me)
disp(['Problem plotting: ' fullfile(outputroot,'Prints') filesep trackingStruct.fullname '_a' mkalphastr(trackingStruct.alpha) '_tracks.tiff']);
disp([' :' me.message]);
end
close all;
end
......
matlab/makeTrackingMovie.m
+ 34
− 13
View file @ 9b3d67e8
......@@ -46,11 +46,11 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
imfig = figure();
kymofig = figure();
bFlipKymo = (trackingStruct.iPath(end) - trackingStruct.iPath(1)) < 0;
bFlipKymo = (trackingStruct.iPath(end) - trackingStruct.iPath(1)) > 0;
movfile = [];
try
movfile = avifile(fname, 'Compression','None', 'fps',fps);
%movfile = avifile(fname, 'Compression','None', 'fps',fps);
for t=1:N
kymoFrame = drawKymo();
......@@ -59,7 +59,7 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
fullFrame = kymoFrame;
fullFrame.cdata = [kymoFrame.cdata imFrame.cdata];
movfile = addframe(movfile,fullFrame);
%movfile = addframe(movfile,fullFrame);
end
catch excp
......@@ -69,7 +69,7 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
rethrow (excp);
end
movfile = close(movfile);
%movfile = close(movfile);
function frm = drawKymo()
......@@ -78,7 +78,7 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
if ( bFlipKymo )
kymoimg = kymoimg(end:-1:1,:);
end
imagesc(kymoimg);colormap(gray);hold on;
imagesc(kymoimg);colormap(gray);axis xy;hold on;
for i=1:length(fullTrackList)
if ( any(i == selectTracks) )
continue;
......@@ -91,7 +91,8 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
continue;
end
plotidx = find(trkt <= t);
%plotidx = find(trkt <= t);
plotidx = 1:length(trkt);
if ( length(plotidx) < 2 )
continue
......@@ -109,9 +110,10 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
trkt = trackingStruct.globNodeLUT(fullTrackList{selectTracks(i)},1)';
trkidx = trackingStruct.globNodeLUT(fullTrackList{selectTracks(i)},2)';
plotidx = find(trkt <= t);
%plotidx = find(trkt <= t);
plotidx = 1:length(trkt);
if ( isempty(plotidx) )
if ( length(plotidx) < 2 )
continue
end
......@@ -121,12 +123,20 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
end
%plot(trkt(1), trkpts(1), 'o', 'Color', trackColors(i,:));
plot(trkt(plotidx), trkpts(plotidx), 'Color', [1 0 0], 'LineWidth',2, 'LineStyle','-');
plot(trkt(plotidx(end)), trkpts(plotidx(end)), 'or', 'LineWidth',2);
markeridx = find(trkt == t,1);
if ( isempty(markeridx) )
if ( t < trkt(1) )
markeridx = plotidx(1);
else
markeridx = plotidx(end);
end
end
plot(trkt(markeridx), trkpts(markeridx), 'or', 'LineWidth',2);
text(trkt(plotidx(end))-3, trkpts(plotidx(end)), [num2str(selectTracks(i)) ' \rightarrow'], 'HorizontalAlign','Right', 'FontSize',8, 'Color', [1 0 0]);
%text(trkt(plotidx(end))-3, trkpts(plotidx(end)), [num2str(selectTracks(i)) ' \rightarrow'], 'HorizontalAlign','Right', 'FontSize',8, 'Color', [1 0 0]);
end
plot([t t], [1 size(trackingStruct.imKymo,1)], '-r', 'LineWidth',2);
%plot([t t], [1 size(trackingStruct.imKymo,1)], '-r', 'LineWidth',2);
hold off;
drawnow;
......@@ -197,8 +207,8 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
bwbound = bwboundaries(bwim);
plot(bwbound{1}(:,2),bwbound{1}(:,1), 'Color',[1 0 0], 'LineStyle','-');
n2 = length(trkt)/2;
if ( trackingStruct.jPath(round(trkpts(n2))) < trackingStruct.rgDetect{t}(trkidx(n2),2) )
n2 = round(length(trkt)/2);
if ( trackingStruct.jPath(trkpts(n2)) < trackingStruct.rgDetect{trkt(n2)}(trkidx(n2),2) )
text(x+5,y,['\leftarrow ' num2str(selectTracks(i))], 'FontSize',10, 'HorizontalAlignment','Left', 'Color',[1 0 0]);
else
text(x-5,y,[num2str(selectTracks(i)) ' \rightarrow'], 'FontSize',10, 'HorizontalAlignment','Right', 'Color',[1 0 0]);
......@@ -213,6 +223,17 @@ function makeTrackingMovie(trackingStruct, fname, fps, selectTracks, minlength)
hold off;
drawnow;
scllength = 10;
%upp = 0.18;
if ( ~isfield(trackingStruct,'umppix') )
trackingStruct.umppix = 0.18;
end
while ( scllength/trackingStruct.umppix > (0.5*(tracemax(1)-tracemin(1))) )
scllength = scllength / 10;
end
posx = min(tracemax(1)-(0.5*scllength/trackingStruct.umppix + 1),0.45*(tracemax(1)-tracemin(1))+tracemin(1));
plot_scale([posx,0.55*(tracemax(2)-tracemin(2))+tracemin(2)], trackingStruct.umppix, scllength, 'r', 'um', 'h');
truesize(imfig, imsize);
frm = getframe(gca);
end
......
matlab/plotConnect.m
+ 12
− 1
View file @ 9b3d67e8
......@@ -18,6 +18,13 @@ function plotConnect(inStruct, minlength, mintravel)
branchPaths = [];
highlightedBranch = [];
if ( ~isfield(inStruct,'umppix') )
inStruct.umppix = 0.18;
end
if ( ~isfield(inStruct,'spfrm') )
inStruct.spfrm = 0.575;
end
figure
[rgbKymo rgbmap] = gray2ind(inStruct.imKymo, 255);
hold off;imagesc(ind2rgb(rgbKymo, rgbmap));
......@@ -36,9 +43,13 @@ function plotConnect(inStruct, minlength, mintravel)
trkt = inStruct.globNodeLUT(inStruct.trackList{i},1)';
trkidx = inStruct.globNodeLUT(inStruct.trackList{i},2)';
if ( length(trkt) <= minlength )
continue;
end
lengthTraveled = norm(inStruct.rgDetect{trkt(end)}(trkidx(end),1:2) - inStruct.rgDetect{trkt(1)}(trkidx(1),1:2)) * inStruct.umppix;
if ( length(trkt) <= minlength || lengthTraveled < mintravel )
if ( lengthTraveled < mintravel )
continue;
end
......
matlab/plotVoronoi.m 0 → 100644
+ 77
− 0
View file @ 9b3d67e8
function [dist, dtst] = plotVoronoi(trackingStruct, dist, dtst)
iminfo = imfinfo(fullfile(trackingStruct.moviepath, trackingStruct.moviename));
immin = [-70 1];
immax = [iminfo(1).Height iminfo(1).Width];
gridx = immin(2):immax(2);
gridy = immin(1):immax(1);
[X,Y] = meshgrid(gridx, gridy);
path = [trackingStruct.jPath';trackingStruct.iPath'];
if ( ~exist('dist','var') || ~exist('dtst','var') )
[dist dtst] = distToPath(X,Y,path);
end
figure;
imagesc(gridx, gridy, label2rgb(dtst));
axis ij;
hold on;
plot(path(1,:)', path(2,:)', '-k');
hold off;
[XI,YI] = meshgrid((immin(2)*2:immax(2)*2)/2, (immin(1)*2:immax(1)*2)/2);
smoothdist = interp2(X,Y,dist,XI,YI);
[gradx,grady] = gradient(smoothdist,(immin(2)*2:immax(2)*2)/2,(immin(1)*2:immax(1)*2)/2);
N = 70;
NC = 1;
gridcolor = [0.75 0.75 0.75];
figure;
rdtst = dtst;
rdtst(dist>8) = 0;
%imagesc(gridx, gridy, label2rgb(rdtst));
imagesc(gridx, gridy, label2rgb(dtst));
%imagesc(gridx, gridy, dist);
hold on;
[C, hgrid] = contour(XI,YI,smoothdist, 10, 'b');
set(hgrid, 'Color', gridcolor);
%axis ij;
hold on;
endidx = 0;
for i=1:NC
nextidx = endidx + 1;
startidx = nextidx + 1;
endidx = C(2,nextidx) + nextidx;
end
cpts = C(:,startidx:endidx);
cvec = diff(cpts,1,2);
clens = sqrt((cvec(1,:).^2) + (cvec(2,:).^2));
cunit = cvec ./ (ones(2,1)*clens);
totallens = [0 cumsum(clens)];
inclen = totallens(end) / N;
streampts = [];
for i=1:N
curlength = (i-1)*inclen;
idx = find(totallens <= curlength,1,'last');
lninc = curlength - totallens(idx);
lnpt = cpts(:,idx) + lninc*cunit(:,idx);
streampts(:,i) = lnpt;
end
hgrid = streamline(stream2(XI,YI,-gradx,-grady,streampts(1,:),streampts(2,:)));
set(hgrid, 'Color', gridcolor);
hgrid = streamline(stream2(XI,YI,gradx,grady,streampts(1,:),streampts(2,:)));
set(hgrid, 'Color', gridcolor);
plot(path(1,:)', path(2,:)', '-k', 'LineWidth',2);
hold off;
end
\ No newline at end of file
matlab/scrollTrackingFigure.m 0 → 100644
+ 258
− 0
View file @ 9b3d67e8
function scrollTrackingFigure(trackingStruct, minlength)
if ( ~exist('minlength','var'))
minlength = 0;
end
fullTrackList = BuildFullTrackList(trackingStruct);
numtracks = length(fullTrackList);
cmap = [winter(512); summer(512)];
trackColors = cmap(round(rand(length(fullTrackList),1)*1023)+1,:);
iminfo = imfinfo(fullfile(trackingStruct.moviepath, trackingStruct.moviename));
kymoinfo = imfinfo(fullfile(trackingStruct.moviepath, trackingStruct.moviename));
N = length(iminfo);
istat=[]; stats=[0 Inf];
for t=1: N
im=(imread(fullfile(trackingStruct.moviepath, trackingStruct.moviename),t));
if max(im(:))<stats(2)
stats(2)=max(im(:));
end
if min(im(:))>stats(1)
stats(1)= min(im(:));
end
end
% 1. Trace Line
% 2. Trace Normals
% 3. Peaks
% 4. Connected Components
% 5. Connected Component Outlines(track colored)
% 6. Peaks(track colored)
% 7. Track Labels
bOverlays = boolean(zeros(7,1));
bOverlays(1) = 1;
bOldOverlays = [];
mvfig = figure();
clf(mvfig,'reset');
set(mvfig, 'WindowScrollWheelFcn', @scrollWheelCallback);
set(mvfig, 'KeyPressFcn', @keyPressFunction);
trace = [trackingStruct.jPath';trackingStruct.iPath'];
[tracemin, tracemax] = getTrackExtents(trackingStruct, N);
imsize = [iminfo(1).Height, iminfo(1).Width];
im = zeros(imsize);
imwght = (1.6)*mkHCAxon(im, trace, 1.0, 5) + 0.4;
%imwght = ones(size(im));
t = 1;
dispImage();
dispOverlays();
function dispImage(curxlim, curylim)
if ( ~exist('curxlim','var') || ~exist('curylim', 'var') )
curxlim = [1 imsize(2)];
curylim = [1 imsize(1)];
end
im=imread(fullfile(trackingStruct.moviepath, trackingStruct.moviename),t);
%im(im<stats(1))=stats(1);
im(im>stats(2))=stats(2);
im=mat2gray(im);
hold off;imagesc(im.*imwght);colormap(gray);hold on
%axis equal;
title(num2str(t));
xlim(curxlim);
ylim(curylim);
end
function dispOverlays(curxlim, curylim)
if ( ~exist('curxlim','var') || ~exist('curylim', 'var') )
curxlim = [1 imsize(2)];
curylim = [1 imsize(1)];
end
% 1. Plot scale bar
if ( bOverlays(1) )
scllength = 10;
%upp = 0.18;
if ( ~isfield(trackingStruct,'umppix') )
trackingStruct.umppix = 0.18;
end
while ( scllength/trackingStruct.umppix > (0.5*(curxlim(2)-curxlim(1))) )
scllength = scllength / 10;
end
posx = min(curxlim(2)-(0.5*scllength/trackingStruct.umppix + 1),0.9*(curxlim(2)-curxlim(1))+curxlim(1));
plot_scale([posx,0.9*(curylim(2)-curylim(1))+curylim(1)], trackingStruct.umppix, scllength, 'r', 'um', 'h');
end
% 1. Trace Line
if ( bOverlays(1) )
plot(trace(1,:),trace(2,:),'b')
end
% 2. Trace Normals
if ( bOverlays(2) )
nrmextent = 8;
ctrnrms = diff(trace,1,2);
lengths = sqrt((ctrnrms(1,:).^2) + (ctrnrms(2,:).^2));
ctrnrms = [-ctrnrms(2,:); ctrnrms(1,:)]./(ones(2,1)*lengths);
ptnrms = [ctrnrms(:,1) (ctrnrms(:,2:end) + ctrnrms(:,1:end-1))/2 ctrnrms(:,end)];
plot([trace(1,:)-nrmextent*ptnrms(1,:);trace(1,:)+nrmextent*ptnrms(1,:)],[trace(2,:)-nrmextent*ptnrms(2,:);trace(2,:)+nrmextent*ptnrms(2,:)], '-y');
end
% 4. Connected Components
if ( bOverlays(4) )
% for k=1:length(trackingStruct.rgCC{t})
% plot(trackingStruct.rgCC{t}{k}(:,2),trackingStruct.rgCC{t}{k}(:,1), '.g');
% end
end
% 3. Peaks
if ( bOverlays(3) )
r= trackingStruct.rgDetect{t}(:,1);
c= trackingStruct.rgDetect{t}(:,2);
plot(c,r,'.r');
end
for k=1:length(fullTrackList)
trkt = trackingStruct.globNodeLUT(fullTrackList{k},1)';
trkidx = trackingStruct.globNodeLUT(fullTrackList{k},2)';
if ( length(trkt) <= minlength )
continue;
end
trkpts = GetKymoPt(trackingStruct.rgDetect, trkidx', trkt', trackingStruct.LKymo, [trackingStruct.jPath';trackingStruct.iPath']);
umppix = 0.18;
lengthTraveled = norm(trackingStruct.rgDetect{trkt(end)}(trkidx(end),1:2) - trackingStruct.rgDetect{trkt(1)}(trkidx(1),1:2)) * umppix;
% if ( lengthTraveled <= 5 )
% continue;
% end
idx = find(trkt==t);
if ( ~isempty(idx) )
x=trackingStruct.rgDetect{t}(trkidx(idx),2);
y=trackingStruct.rgDetect{t}(trkidx(idx),1);
% 4. Connected Components
if ( bOverlays(4) )
plot(trackingStruct.rgCC{t}{trkidx(idx)}(:,2),trackingStruct.rgCC{t}{trkidx(idx)}(:,1), '.', 'Color',trackColors(k,:));
end
% 5. Connected Component Outlines(track colored)
if ( bOverlays(5) )
bwim = zeros(size(im));
r = trackingStruct.rgCC{t}{trkidx(idx)}(:,1);
c = trackingStruct.rgCC{t}{trkidx(idx)}(:,2);
linidx = sub2ind(size(bwim), r,c);
bwim(linidx) = 1;
bwbound = bwboundaries(bwim);
plot(bwbound{1}(:,2),bwbound{1}(:,1), 'Color',trackColors(k,:), 'LineStyle','-');
end
% 6. Peaks(track colored)
if ( bOverlays(6) )
plot(x,y,'o','color',trackColors(k,:));
plot(x,y,'.r');
end
% 7. Track Labels
if ( bOverlays(7) )
textoffset = 2;
n2 = round(length(trkt)/2);
if ( trackingStruct.jPath(trkpts(n2)) < trackingStruct.rgDetect{trkt(n2)}(trkidx(n2),2) )
text(x+textoffset,y, ['\leftarrow ' num2str(k)], 'FontSize',10, 'HorizontalAlignment','Left', 'Color','w', 'BackgroundColor',trackColors(k,:));
else
text(x-textoffset,y, [num2str(k) ' \rightarrow'], 'FontSize',10, 'HorizontalAlignment','Right', 'Color','w', 'BackgroundColor',trackColors(k,:));
end
end
end
end
end
function scrollWheelCallback(src, evt)
if ( evt.VerticalScrollCount < 0 )
t = t - 1;
else
t = t + 1;
end
if ( t > N-1 )
t = N-1;
elseif ( t < 1 )
t = 1;
end
curxlim = xlim;
curylim = ylim;
dispImage(curxlim, curylim);
dispOverlays(curxlim, curylim);
end
function keyPressFunction(src, evt)
key = str2num(evt.Key);
if ( ~isempty(key) )
if ( key <= 0 )
key = 10;
end
if ( key <= length(bOverlays) )
if ( ~isempty(bOldOverlays) )
bOverlays = bOldOverlays;
end
bOverlays(key) = ~bOverlays(key);
curxlim = xlim;
curylim = ylim;
dispImage(curxlim, curylim);
dispOverlays(curxlim, curylim);
end
elseif ( evt.Key == 't' )
if ( isempty(bOldOverlays) )
bOldOverlays = bOverlays;
bOverlays(2:end) = 0;
else
bOverlays = bOldOverlays;
bOldOverlays = [];
end
curxlim = xlim;
curylim = ylim;
dispImage(curxlim, curylim);
dispOverlays(curxlim, curylim);
end
end
end
function [tracemin, tracemax] = getTrackExtents(trackingStruct, N)
tracemin = [Inf Inf];
tracemax = [0 0];
for t=1:N
xmin = min(trackingStruct.rgDetect{t}(:,2));
xmax = max(trackingStruct.rgDetect{t}(:,2));
ymin = min(trackingStruct.rgDetect{t}(:,1));
ymax = max(trackingStruct.rgDetect{t}(:,1));
tracemin = [min(tracemin(1), xmin) min(tracemin(2), ymin)];
tracemax = [max(tracemax(1), xmax) max(tracemax(2), ymax)];
end
end
\ No newline at end of file
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