SSF drawTracks and leversc impad

leversc/src/MATLAB/@leversc/leversc.m

@@ -30,6 +30,7 @@ classdef leversc <handle
                 optional_figNumber=1;
             end
             [im,imD,figNumber]=parseArgs(optional_im,optional_imD,optional_figNumber);
+            im = imPad4(im);
             obj.figNumber=figNumber;
             if isfield(imD,'imageData')
                 CONSTANTS=imD;
@@ -122,3 +123,19 @@ end
 
 end
 
+function im = imPad4(im)
+
+pad = [0,0,0];
+for d = 1:3
+    if 0~=mod(size(im,d),4)
+        pad(d) = size(im,d) + 4-mod(size(im,d),4);
+    end
+end
+if any(pad)
+    sz = size(im);
+    sz = sz(1:3);
+    pad = max(pad,sz);
+    im(pad(1),pad(2),pad(3),:) = 0;
+end
+
+end
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matlab/+Batch/batchProc.m

 
 function batchProc(ROOT,nproc,nthread)
 
-parpool(nproc)
+ljsStartParallel(nproc);
 
 flist = dir(fullfile(ROOT,'*.LEVER'));
 parfor ff=1:length(flist)

matlab/+SSF/drawSSFtracks.m

 % strDB = '/g/leverjs/Olivier/Agne/march_2023_20x/2022-04-05_steady_state_48h_deprived_13_ori.LEVER';
 
-function drawSSFtracks(ROOT,cache, kymo_channel, channel_description)
+function drawSSFtracks(ROOT,cache, kymo_channel, channel_description,fnames)
 
 [~,dsName,ext] = fileparts(ROOT);
+if ~exist('fnames','var')
+    fnames = [];
+end
 
-outfile = [dsName ' [0,1] ' channel_description ' SSF projection_y_t.pdf'];
+outfile = [dsName ' ' channel_description ' SSF projection_y_t.pdf'];
 if isempty(ext)
     flist = dir(fullfile(ROOT,'*.LEVER'));
 else
@@ -13,6 +16,8 @@ end
 f=figure(1);
 f.WindowState = 'maximized';
 pause(1)
+
+kymoPixels = {};
 for ff=1:length(flist)
     strDB = fullfile(flist(ff).folder,flist(ff).name);
     [ROOT,lf] = fileparts(strDB);
@@ -21,22 +26,35 @@ for ff = 1:length(flist)
         continue
     end
     imKymo = SSF.loadImage(strKymoDB,kymo_channel);
-    kymoPixels = imKymo(find(imKymo));
+    kymoPixels{ff} = imKymo(find(imKymo));
+end 
+kymoPixels = vertcat(kymoPixels{:});
 erkClipLimits = [prctile(kymoPixels,2.5),prctile(kymoPixels,97.5)];
-    % erkClipLimits = [0,prctile(kymoPixels,95)];
+
+for ff = 1:length(flist)
+    strDB = fullfile(flist(ff).folder,flist(ff).name);
+    [ROOT,lf] = fileparts(strDB);
+    strKymoDB = fullfile(ROOT,cache,[lf '.LEVER_ssf_cache.LEVER']);
+    if ~exist(strKymoDB,'file')
+        continue
+    end
+    imKymo = SSF.loadImage(strKymoDB,kymo_channel);
+    % 
     imp = squeeze(max(imKymo,[],2));
     imn = squeeze(min(imKymo,[],2));
     imn = abs(imn);
     idx = find(imn>imp);
     imp(idx) = -1 .* imn(idx);
-    imp(imp<-0.5) = 0;
+%     imp(imp<-0.5) = 0;
     impq = SSF.quantize8(imp,erkClipLimits);
-    impq(imp==0 & imn==0) = 0;
+%     impq(imp==0 & imn==0) = 0;
     
-    % keep just [0,1] SSF
+%     % keep just [0,1] SSF
+%     imp = squeeze(max(imKymo,[],2));
+%     erkClipLimits = [0,prctile(kymoPixels,99.9)];
 %     impq = SSF.quantize8(imp,erkClipLimits);
 %     impq(imp==0) = 0; % set the background
-    
+%     
     
     clf;imagesc(impq)
     cm = colormap('parula');
@@ -47,10 +65,18 @@ for ff = 1:length(flist)
     cticks = [clim(1)+1, mean([clim(1),mean(clim)]), mean(clim), mean([clim(2),mean(clim)]),clim(2)];
     c.Ticks = cticks;
     % c.TickLabels = {'-1','-0.5','0','0.5','1'}
-    c.TickLabels = {'0.0','0.25','0.5','0.75','1.0'};
-    c.Label.String = [channel_description ' SSF (dataset reference)'];
 
-    title([lf ' ' channel_description ' SSF [0,1] projection to (Y,time)'],'interpreter','none')
+    ticksSSF = linspace(erkClipLimits(1),erkClipLimits(2),5);
+    ticksSSF = arrayfun(@(x) num2str(x,2),ticksSSF,'UniformOutput',false);
+    c.TickLabels = ticksSSF;
+    c.Label.String = [channel_description ' SSF (dataset reference)'];
+    if ~isempty(fnames)
+        lf = fnames{ff};
+    end
+    hold on
+    yl = ylim();
+    plot([62,62],[yl(1),yl(2)],'--r','linewidth',2)
+    title([lf ' ' channel_description ' SSF projection to (Y/2,time)'],'interpreter','none')
     xlabel('time (frames)')
     ylabel('Y (max intensity projection along X)')
     bAppend = ff>1;

matlab/+SSF/quantize8.m

@@ -11,3 +11,4 @@ im = (im - clipLimits(1)) ./ (clipLimits(2) - clipLimits(1));
 
 im = im2uint8(im);
 im = max(im,1); % exclude 0 -- only for background
+im(1,1) = 0; % make sure at least 1 pixel hits background
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