diff --git a/matlab/+SSF/drawKymosCondition.m b/matlab/+SSF/drawKymosCondition.m
index 45ad1431d0830388a0a22dce1cca806aa14349d6..5b330d04ac011fd0bd3677eae289084dfdac2f16 100644
--- a/matlab/+SSF/drawKymosCondition.m
+++ b/matlab/+SSF/drawKymosCondition.m
@@ -18,15 +18,22 @@
%
% cbLabel = 'ERK SSF';
% targetChannels = 1;
-function drawKymosCondition(flist,classList,labelNames,outfile,cbLabel,targetChannels,stride)
+function drawKymosCondition(flist,classList,labelNames,outfile,cbLabel,targetChannels,stride,framesPerHour)
+if ~exist('xticksLabels','var')
+ xticksLabels.xticks = [];
+ xticksLabels.xlabels = {};
+end
xClasses = unique(classList);
nKeep = 0;
clipRange = [2.5,97.5];
+% clipRange = [0.5,99.5];
clipLimits = SSF.getClipLimits(flist,targetChannels,clipRange,nKeep);
xyim = []; % one per flist
+xticks = [];
+xtickLabels = {};
for cc = 1:length(xClasses)
idxCC = find(strcmp(classList,xClasses(cc)));
flistCC = flist(idxCC);
@@ -74,29 +81,43 @@ for cc = 1:length(xClasses)
plot([x,x],[y,y+szim(ff,1)],'-k')
% don't draw to your right...
% plot([x+szim(ff,2),x+szim(ff,2)],[y,y+szim(ff,1)],'-k')
- text(x,y,ccLabels{ff},'Interpreter','none','FontSize',6,'BackgroundColor',[0.8,0.8,0.8,0.5],...
+ text(x,y,ccLabels{ff},'Interpreter','none','FontSize',6,'BackgroundColor',[0.9,0.5,0.7,0.5],...
'VerticalAlignment','top');
+
+ % label time
+ tHours = [24:24:szim(ff,2)-12];
+ for i = 1:length(tHours)
+ text(x+tHours(i),y+szim(ff,1),num2str(round(tHours(i)./framesPerHour)),'Interpreter','none','FontSize',6,...
+ 'VerticalAlignment','bottom');
+ end
+
+
+
+
x = x + szim(ff,2);
% date_movie = regexp(flistCC(ff).name,'(\d{4}-\d{2}-\d{2}).+_(\d{2})','tokens');
% text(x,y,[date_movie{1}{1} '_' date_movie{1}{2}],'Interpreter','none','FontSize',6,'BackgroundColor',[0.8,0.8,0.8,0.5]);
% plot([x+62,x+62],[y+5,y+size(imq,1)-5],'-r')
% treatment = regexp(tblCC.Treatment{ff},'(.*)\w*(','tokens');
% text(x+30,y+20,[date_movie{1}{1} '_' date_movie{1}{2} ' :: ' treatment{1}{1}],'Interpreter','none','FontSize',6,'BackgroundColor',[0.8,0.8,0.8,0.7]);
+
end
-
+
+
% set background (index 0, colormap(1)) to white
cm = parula();
cm(1,:) = [1,1,1];
colormap(cm);
axis on
- set(gca,'xtick',[]);
+ set(gca,'xtick',xticksLabels.xticks);
+ set(gca,'XTickLabel',xticksLabels.xlabels);
set(gca,'ytick',[]);
- ylabel('xy \Downarrow x');
+ ylabel('xyz \Downarrow x');
xlabel('time');
fx = strfind(flist(ff).name,'.LEVER');
fx = fx(1)-1;
- title(xClasses{cc},'Interpreter','none');
- tick_labels = round(linspace(clipLimits(1),clipLimits(2),5),2);
+% title(xClasses{cc},'Interpreter','none');
+ tick_labels = round(linspace(clipLimits(1),clipLimits(2),5),2,'significant');
cb = colorbar('Ticks',[1,64,128,192,255],'TickLabels',tick_labels);
cb.Label.String = cbLabel;
if 1 == cc
diff --git a/matlab/+SSF/draw_ssf_ncd.m b/matlab/+SSF/draw_ssf_ncd.m
index b4d49c1834c0cb95b1e9468064fa690e719ea440..6112032bae5f4ccaa8ed64bfdecb12f6834f8398 100644
--- a/matlab/+SSF/draw_ssf_ncd.m
+++ b/matlab/+SSF/draw_ssf_ncd.m
@@ -2,23 +2,20 @@
ROOT = '/g/leverjs/Olivier/Agne/march_2023_20x';
flist = dir(fullfile(ROOT,'*.LEVER'));
-className = {};
-for ff=1:length(flist)
- cn = regexp(flist(ff).name,'(\d+-\d+-\d+)_.*(\d\d)_ori*','tokens');
- cn = [cn{1}{1} '_' cn{1}{2}];
- className{ff} = classMap(cn);
-end
+classList = get_ssClasses(flist);
+[classUnique,ia,ic]= unique(classList);
+idxTrue = ic;
% targetClass = {'AKT1_E17K','WT','PIK3CA_E545K'}
% idx = find(cellfun(@(x) ~isempty(find(strcmp(targetClass,x))),className));
% A=d(idx,idx);
% className = className(idx);
A = d;
-K=3;
-
+K=6;
+[idx,Y] = Cluster.SpectralCluster(A,K);
+[csf_mean, csf_std] = CSF.csf_spatial(Y,idxTrue)
-[idx,Y] = Cluster.SpectralCluster(A,K);
% Y = tsne(Y,'Algorithm','exact','NumDimensions',3);
clf;hold off;
% if size(Y,2) == 3
@@ -26,21 +23,17 @@ clf;hold off;
% else
% plot(Y(:,1),Y(:,2),'.')
% end
-sym = {'ko','cv','m^','r*','gx','<k','b>','gs','bd'};
+sym = {'ko','cv','m^','r*','gx','gs','bd'};
-classList = unique(className);
-hx = zeros(size(classList));
+hx = zeros(size(classUnique));
hold on
for ff=1:size(Y,1)
- idxSym = find(strcmp(classList,className{ff}));
- if K==3
+ idxSym = find(strcmp(classUnique,classList{ff}));
+
h1 = plot3(Y(ff,1),Y(ff,2),Y(ff,3),sym{idxSym});
- else
- h1 = plot(Y(ff,1),Y(ff,2),sym{idxSym},'UserData',ff);
- end
if ~hx(idxSym)
hx(idxSym) = h1;
end
@@ -52,5 +45,8 @@ for ff=1:size(Y,1)
% end
end
set(gcf,'color','w')
-xlabel('u1');ylabel('u2'),zlabel('u3')
-legend(hx(find(hx)),classList(find(hx)),'interpreter','none');
\ No newline at end of file
+xlabel('k1');ylabel('k2'),zlabel('k3')
+legend(hx(find(hx)),classUnique(find(hx)),'interpreter','none');
+tstr = ['CSF^6_{Erk,Velocity} = ' mat2str([csf_mean, csf_std],2)];
+title(tstr)
+
diff --git a/matlab/+SSF/getClipLimits.m b/matlab/+SSF/getClipLimits.m
index e1303ec949c38bbe821bfc58e7374c31fabbfe1a..423e83296bbdca01b9575d4777b874e278f748a7 100644
--- a/matlab/+SSF/getClipLimits.m
+++ b/matlab/+SSF/getClipLimits.m
@@ -1,6 +1,6 @@
% map [-1,1] kymographs to color space [0,255]
%
-function clipLimits = getClipLimits(flist,targetChannelNumbers,clipRange,nKeep)
+function clipLimits = getClipLimits(flist,targetChannelNumbers,clipRange,nKeep,tClip)
if ~exist('clipRange','var')
clipRange= [2.5,97.5];
@@ -8,13 +8,16 @@ end
if ~exist('nKeep','var')
nKeep = 0;
end
+if ~exist('tClip','var')
+ tClip = [];
+end
p = ljsStartParallel();
kymoPixels = {};
parfor ff=1:length(flist)
kp = {};
for c = 1:length(targetChannelNumbers)
strDB_ff = fullfile(flist(ff).folder,flist(ff).name);
- im_ff = SSF.loadImage(strDB_ff,targetChannelNumbers(c));
+ im_ff = SSF.loadImage(strDB_ff,targetChannelNumbers(c), 0, tClip);
if nKeep>0
im_ff(im_ff<0)=0;
end
diff --git a/matlab/+SSF/go_ssf_ncd.m b/matlab/+SSF/go_ssf_ncd.m
index b7e82bec83cf6d5216830922423c1ddea3215ab4..e19aaf493800faf5a62c201cc9b2995adc248fe3 100644
--- a/matlab/+SSF/go_ssf_ncd.m
+++ b/matlab/+SSF/go_ssf_ncd.m
@@ -4,7 +4,7 @@
% AKT_CHANNEL = 2;
% H2B_CHANNEL = 3;
% targetChannels = [ERK_CHANNEL,AKT_CHANNEL];
-function d=go_ssf_ncd(kROOT,targetChannels,clipRange, nKeep)
+function d=go_ssf_ncd(kROOT,targetChannels,clipRange, nKeep, tClip)
tStart = tic();
@@ -15,7 +15,15 @@ end
if ~exist('clipRange','var')
clipRange = [2.5,97.5];
end
-flist = dir(fullfile(kROOT,'*.LEVER'));
+
+if ~exist('tClip','var')
+ tClip = [];
+end
+if isstring(kROOT) || ischar(kROOT)
+ flist = dir(fullfile(kROOT,'*.LEVER'));
+else
+ flist = kROOT;
+end
d = zeros(length(flist));
kymoPixels = {};
@@ -24,7 +32,7 @@ p = ljsStartParallel();
if iscell(clipRange)
clipLimits = clipRange;
else
- clipLimits = SSF.getClipLimits(flist,targetChannels,clipRange,nKeep);
+ clipLimits = SSF.getClipLimits(flist,targetChannels,clipRange,nKeep,tClip);
end
%
cmdList = NCD.dParallelCommandList(ones(length(flist)),p.NumWorkers);
@@ -44,7 +52,7 @@ parfor i=1:H
end
strDB_ff = fullfile(flist(ff).folder, flist(ff).name);
if ~strcmp(strDB_ff,str_ff_prev)
- im_ff = SSF.loadImage(strDB_ff, targetChannels, nKeep);
+ im_ff = SSF.loadImage(strDB_ff, targetChannels, nKeep, tClip);
if iscell(clipLimits)
cx = clipLimits{ff};
else
@@ -59,7 +67,7 @@ parfor i=1:H
dxx(i,j) = d1;
else
strDB_gg = fullfile(flist(gg).folder,flist(gg).name);
- im_gg = SSF.loadImage(strDB_gg,targetChannels, nKeep);
+ im_gg = SSF.loadImage(strDB_gg,targetChannels, nKeep, tClip);
if iscell(clipLimits)
cx = clipLimits{gg};
else
@@ -74,7 +82,7 @@ parfor i=1:H
dxx(i,j) = min(d1,d2);
end
tElapsed = toc(t0);
- fprintf('%s tElapsed = %0.2f\n',mat2str([ff,gg,dxx(i,j)]),tElapsed);
+% fprintf('%s tElapsed = %0.2f\n',mat2str([ff,gg,dxx(i,j)]),tElapsed);
end
end
% convert dxx to distance matrix d
diff --git a/matlab/+SSF/loadImage.m b/matlab/+SSF/loadImage.m
index 54b3f2db8a2deee7fccaed5a752f16801ef64ed6..827e1c330d99bb20e3b86dd49a3bd69cba401a64 100644
--- a/matlab/+SSF/loadImage.m
+++ b/matlab/+SSF/loadImage.m
@@ -1,5 +1,5 @@
-function im = loadImage(strDB, channelList, nKeep)
+function im = loadImage(strDB, channelList, nKeep, tClip)
if ~exist('bDouble','var')
bDouble = false;
@@ -9,6 +9,11 @@ time = 1; % kymo is single time point
for c=1:length(channelList)
im(:,:,:,c) = leversc.loadImage(strDB,time,channelList(c));
end
+% tClip
+if exist('tClip','var') && ~isempty(tClip)
+ tClip(tClip>size(im,3)) = [];
+ im = im(:,:,tClip,:);
+end
if ~exist('nKeep','var')
return
@@ -20,3 +25,4 @@ if nKeep < 0
im(im>0) = 0;
im = abs(im);
end
+
diff --git a/matlab/+Segment/frameSegment.m b/matlab/+Segment/frameSegment.m
index 58756230a73dbb0f87c25dd2734cd0cc6728d7bf..79c2bdece3aa27415e347a6391b9f0da59d0b04c 100644
--- a/matlab/+Segment/frameSegment.m
+++ b/matlab/+Segment/frameSegment.m
@@ -143,7 +143,7 @@ for n=1:max(L(:))
newCell.LoG = LoG.sampleCell(newCell,CONSTANTS,imLoG);
% check ecc
- v = eig(cov(newCell.pts));
+ v = eig(cov(double(newCell.pts)));
ecc = max(v)/min(v);
if ecc>50
continue