channelLoG study

matlab/+Read/getAlgorithms.m

@@ -6,9 +6,11 @@ if isempty(Q)
         algorithms=[];
         return
 end
-algorithms=cellfun(@jsondecode,Q);
+algorithms=cellfun(@jsondecode,Q,'UniformOutput',false);
 for i=1:length(algorithms)
-    if isfield(algorithms(i),'function')
-        algorithms(i).function=str2func(algorithms(i).function(2:end-2));
+    if isfield(algorithms{i},'function')
+        algorithms{i}.function=str2func(algorithms{i}.function(2:end-2));
     end
 end
+
+algorithms=[algorithms{:}];
\ No newline at end of file

matlab/+Read/getSegmentationParams.m

@@ -2,6 +2,10 @@ function segParams=getSegmentationParams(conn)
 
 algs=Read.getAlgorithms(conn,'segment');
 if ~isempty(algs)
+    if length(algs)>1
+        fprintf(2,'WARNING %s found multiple segmentations -- picking first',conn.DataSource);
+        algs=algs(1);
+    end
     segParams=algs.params; % settings from db
 else
     segParams=[];

matlab/+Write/setChannelLoGfolder.m

+% add channel log to folder
+% ROOT = '/g/leverjs/mcf10a_3d_final'
+function setChannelLoGfolder(ROOT,featureParams)
+% 
+if ~exist('featureParams','var')
+    featureParams.name='erkLoG';
+    featureParams.radius_um=4;
+    featureParams.channel=2;
+    featureParams.color='#ff00ff';
+end
+flist = dir(fullfile(ROOT,'/**/*.LEVER')); 
+
+% extracted via processJSON.m
+logjs = ['{"name":"signalLoG","type":"feature","description":"dark nucleus detector",' ...
+    '"function":"+CellFeatures.channelLoG.m","commandHost":"matlab"}'];
+logAlg = jsondecode(logjs);
+logAlg.params=featureParams;
+logjs = jsonencode(logAlg); % with params
+targetChannel=2;
+for ff=1:length(flist)
+    strDB=fullfile(flist(ff).folder,flist(ff).name);
+    [conn,CONSTANTS,segParams]=openDB(strDB);    
+    nameCheck=strfind(lower({CONSTANTS.renderParams.name}),'erk');
+    if nameCheck{targetChannel}~=1
+        fprintf(2,'%s: erk name not set (%s)\n',strDB,CONSTANTS.renderParams(2).name);
+        continue
+    end
+    algs=Read.getAlgorithms(conn,'feature');
+    % already there?
+    parx={algs.params};
+    algCheck = cellfun(@(x) strcmp(x.name,'erkLoG'),parx);
+    if any(algCheck)
+        fprintf(1,'%s: found erkLoG algorithm, skipping insert\n',strDB);
+    else    
+        cmd=['insert into tblAlgorithms(fqn,type,jsAlgorithmInfo) values (' ...
+            '''' logAlg.name ''', ''' logAlg.type ''', ''' logjs ''')'];
+        exec(conn,cmd);
+    end
+    Batch.batchFeatures(conn,CONSTANTS,28);
+    close(conn)
+end
\ No newline at end of file

matlab/logStudy.m

@@ -10,7 +10,7 @@
 % if you're at the bottom of a bowl, 2nd derivative is +
 sz=200;
 center=round(sz/2);
-radius=10;
+radius=20;
 im=zeros([sz,sz]);
 
 for y=1:size(im,1)
@@ -18,24 +18,23 @@ for y=1:size(im,1)
         d = sqrt((y-center)^2 + (x-center)^2);
         if d<radius
             im(y,x)=1;
-%         elseif d<radius+2
-%             im(y,x)=1;  
         end
     end
 end
+im=imcomplement(im);
 
-% clf;
-strDB = '/f/leverjs/Olivier/Yannick/20210924/20210924_pos1.LEVER';
-t=187;channelERK=2;
-im=leversc.loadImage(strDB,t,channelERK);
-im=mat2gray(im);
-radius=3;
-% imagesc(im)
-
-rx = 1/sqrt(2) .* [radius,radius,0];
+rx = 1/2 .* [radius,radius,0];
 imf = HIP.LoG(im,rx,[]);
-imc = Segment.separateLoG(imf);
-figure;imagesc(imc);
-[conn,CONSTANTS,segParams]=openDB(strDB);
-cellList=Read.getCellsTime(conn,1,1,CONSTANTS);
-hold on;for i=1:length(cellList),plot(cellList(i).surface(:,1),cellList(i).surface(:,2),'color','m'),end
\ No newline at end of file
+
+clf;
+plot(imf(center,:));
+hold on
+plot(im(center,:))
+
+
+% 
+% imc = Segment.separateLoG(imf);
+% figure;imagesc(imc);
+% [conn,CONSTANTS,segParams]=openDB(strDB);
+% cellList=Read.getCellsTime(conn,1,1,CONSTANTS);
+% hold on;for i=1:length(cellList),plot(cellList(i).surface(:,1),cellList(i).surface(:,2),'color','m'),end
\ No newline at end of file