Merge branch 'develop'

other/BP_Gauss_analysis.m

@@ -0,0 +1,56 @@
+
+% pixs=100;
+dz=10;
+zoff=750;
+
+%% BEADS: calibrate sx
+pixs=g.locData.files.file(1).info.cam_pixelsize_um(1)*1000;
+loc=g.locData.getloc({'PSFxnm','PSFynm','frame'},'layer',1,'position','roi');
+indg=loc.PSFxnm>0.1&loc.PSFynm>0.1;
+sx=loc.PSFxnm(indg)/pixs;
+sy=loc.PSFynm(indg)/pixs;
+
+
+frame=loc.frame(indg);
+z=frame*dz-zoff;
+figure(88);
+plot(frame,sx,'+',frame,sy,'.')
+
+ds=sx.^2-sy.^2;
+figure(89)
+plot(frame,ds,'.')
+
+range=[44,100];
+
+inr=frame>range(1)&frame<range(2);
+
+figure(89)
+hold off
+plot(ds(inr),z(inr),'.')
+
+calbead=fit(ds(inr),z(inr),'smoothingspline','SmoothingParam',.1);
+hold on
+nds=min(ds(inr)):0.1:max(ds(inr));
+plot(nds,calbead(nds))
+
+maxrangeds=[min(ds(inr)) max(ds(inr))];
+%%
+pfad=[fileparts(g.locData.files.file(1).name) filesep 'beadcal_Gauss_smoothingspline'];
+save(pfad,'calbead','maxrangeds')
+
+%% data: calculate z
+pixs=g.locData.files.file(1).info.cam_pixelsize_um(1)*1000;
+outz=1000;
+sx=g.locData.loc.PSFxnm/pixs;
+sy=g.locData.loc.PSFynm/pixs;
+ds=sx.^2-sy.^2;
+z=calbead(ds);
+g.locData.loc.znm=z;
+
+outofrange=ds<maxrangeds(1) | ds>maxrangeds(2) | sx==0 | sy==0;
+g.locData.loc.znm(outofrange)=outz;
+g.locData.regroup;
+
+
+%% data: average x,y
+%use combine channels plugin 

plugins/+Analyze/+cluster/ClusterStatistics.m

@@ -0,0 +1,93 @@
+classdef ClusterStatistics<interfaces.DialogProcessor
+%  pair correlation functions calculated according to:
+%  Sengupta, Prabuddha, Tijana Jovanovic-Talisman, Dunja Skoko, Malte Renz, 
+%  Sarah L Veatch, and Jennifer Lippincott-Schwartz. “Probing Protein Heterogeneity 
+%  in the Plasma Membrane Using PALM and Pair Correlation Analysis.” 
+%  Nature Methods 8 (September 18, 2011): 969.
+    properties
+        resultstable
+    end
+    methods
+        function obj=ClusterStatistics(varargin)    
+            obj@interfaces.DialogProcessor(varargin{:}) ;
+            obj.inputParameters={'sr_pixrec','numberOfLayers','sr_pos','sr_size','layers','sr_layerson'};
+%             obj.history=true;    
+            obj.showresults=true;
+        end
+
+        function out=run(obj,p)
+           out=[];          
+           layers=find(obj.getPar('sr_layerson'));
+           locs=obj.locData.getloc({'xnm','ynm','znm','clusterindex'},'layer',layers,'Position','roi');
+           clusterinds=unique(locs.clusterindex(locs.clusterindex>0));
+           cind=1;
+           ax=obj.initaxis('boundaries');
+           hold(ax,'off')
+           plot(ax,locs.xnm,locs.ynm,'b.');
+           for k=1:length(clusterinds)
+               inc=locs.clusterindex==clusterinds(k);
+               if sum(inc)<p.minloc
+                   continue
+               end
+               xh=double(locs.xnm(inc));yh=double(locs.ynm(inc));zh=double(locs.znm(inc));
+               numlocs(cind,1)=sum(inc);
+               xpos(cind,1)=mean(xh);
+               ypos(cind,1)=mean(yh);
+               zpos(cind,1)=mean(zh);
+               [kc3,volumeCHull(cind,1)]=convhull(xh,yh,zh);
+               [kc2,areaCHull(cind,1)]=convhull(xh,yh);
+               [kb3,volumeB(cind,1)]=boundary(xh,yh,zh);
+               [kb2,areaB(cind,1)]=boundary(xh,yh);
+               cID(cind,1)=clusterinds(k);
+               cind=cind+1;
+               hold(ax,'on')
+               plot(ax,xh,yh,'+')
+
+               plot(ax,xh(kc2),yh(kc2),'r')
+               plot(ax,xh(kb2),yh(kb2),'m')
+           end
+           obj.resultstable=table(cID,numlocs,areaCHull,volumeCHull,areaB,volumeB,xpos,ypos,zpos);
+
+        end
+        function pard=guidef(obj)
+            pard=guidef(obj);
+        end
+        function exportbutton(obj,a,b)
+            tableo=obj.resultstable;
+            fn=obj.getPar('lastSMLFile');
+            if ~isempty(fn)
+                fno=strrep(fn,'_sml.mat','_cluster.csv');
+            else
+                fno='*.csv';
+            end
+           [f,p]=uiputfile(fno);
+           if f
+               writetable(tableo,[p f])
+           end
+
+        end
+
+    end
+end
+
+
+
+
+function pard=guidef(obj)
+pard.minloct.object=struct('String','min number of locs per cluster','Style','text');
+pard.minloct.position=[1,1];
+pard.minloct.Width=2;
+pard.minloc.object=struct('String','10','Style','edit');
+pard.minloc.position=[1,3];
+pard.minloc.Width=0.5;
+
+pard.export.object=struct('String','export','Style','pushbutton','Callback',@obj.exportbutton);
+pard.export.position=[2,1];
+pard.export.Width=1;
+
+
+pard.plugininfo.name='Cluster Statistics';
+pard.plugininfo.description= 'Calculates spatial statistics based on pair correlation and Ripleys K function. pair correlation functions calculated according to: Sengupta, Prabuddha, Tijana Jovanovic-Talisman, Dunja Skoko, Malte Renz, Sarah L Veatch, and Jennifer Lippincott-Schwartz. “Probing Protein Heterogeneity  Nature Methods 8 (September 18, 2011): 969.';
+pard.plugininfo.type='ProcessorPlugin';
+
+end

plugins/+Analyze/+sr3D/Biplane_getPSFxy.m

@@ -17,9 +17,20 @@
                 out.error='selected transformation file does not have a valid transformation';
                 return
             end
-            file=obj.locData.files.file(p.dataselect.Value);
+
              p.datapart.selection='all';
-            loc=get2ClocPSF(obj.locData.loc,tload.transformation,file,p);
+             if p.allfiles
+                 loc=obj.locData.loc;
+                 keepold=true;
+                 for k=1:length(obj.locData.files.file)
+                     k
+                     loc=get2ClocPSF(loc,tload.transformation,obj.locData.files.file(k),p,keepold);
+                 end
+             else
+                 file=obj.locData.files.file(p.dataselect.Value);
+                 keepold=false;
+                loc=get2ClocPSF(obj.locData.loc,tload.transformation,file,p,keepold);
+             end
             obj.locData.loc=copyfields(obj.locData.loc,loc);
             obj.locData.regroup;
              obj.setPar('locFields',fieldnames(obj.locData.loc))
@@ -53,21 +64,43 @@ function loadbutton(obj,a,b)
 end
 
 
-function loco=get2ClocPSF(loc,transform,file,p)
+function loco=get2ClocPSF(loc,transform,file,p,keepold)
 
- p.datapart.selection='all (T->R)';
-loct=apply_transform_locs(loc,transform,file,p);
+p.datapart.selection='all (T->R)';
+% p.datapart.selection='target';
+infi=file.number==loc.filenumber;
+
+inref=transform.getRef(loc.xnm,loc.ynm);
+locref=copystructReduce(loc,infi&inref);
+locth=copystructReduce(loc,infi&~inref);
+loct=apply_transform_locs(locth,transform,file,p);
 
 % only valid parts?
-[iA,iB,uiA,uiB]=matchlocsall(renamefields(loc),renamefields(loct),0,0,1000);
+[iA,iB,uiA,uiB]=matchlocsall(renamefields(locref),renamefields(loct),0,0,1000);
 length(iA)/(length(uiA)+length(uiB))
-loco.PSFxnm_old=loc.PSFxnm;
-loco.PSFxnm=zeros(size(loc.xnm),'single');
-loco.PSFynm=zeros(size(loc.xnm),'single');
-loco.PSFxnm(iA)=loc.PSFxnm(iA);
-loco.PSFynm(iA)=loc.PSFxnm(iB);
-loco.PSFxnm(iB)=loc.PSFxnm(iA);
-loco.PSFynm(iB)=loc.PSFxnm(iB);
+inffr=find(infi&inref);
+infft=find(infi&~inref);
+
+
+if ~keepold
+    loco.PSFxnm_old=loc.PSFxnm;
+    loco.PSFxnm=zeros(size(loc.xnm),'single');
+    loco.PSFynm=zeros(size(loc.xnm),'single');
+else
+    loco=loc;
+    if ~isfield(loco,'PSFxnm')
+        loco.PSFxnm=zeros(size(loc.xnm),'single');
+    end
+    if ~isfield(loco,'PSFynm')
+        loco.PSFynm=zeros(size(loc.xnm),'single');
+    end
+end
+
+
+loco.PSFxnm(inffr(iA))=loc.PSFxnm(inffr(iA));
+loco.PSFynm(inffr(iA))=loc.PSFxnm(infft(iB));
+loco.PSFxnm(infft(iB))=loc.PSFxnm(inffr(iA));
+loco.PSFynm(infft(iB))=loc.PSFxnm(infft(iB));
 end
 
 function loco=renamefields(loci)
@@ -84,6 +117,8 @@ function loadbutton(obj,a,b)
 pard.dataselect.object=struct('Style','popupmenu','String','File');
 pard.dataselect.position=[2,1];
 
+pard.allfiles.object=struct('Style','checkbox','String','all files');
+pard.allfiles.position=[2,2];
 % pard.datapart.object=struct('Style','popupmenu','String','all|left|right|top|bottom');
 % pard.datapart.position=[3,1];
 

plugins/+Process/+Register/CombineChannels.m

@@ -45,13 +45,13 @@
                 unmatchedB=copystructReduce(loctt,uiB);
                 fn=fieldnames(loc);
                 if isfield(matchedA,'locprecnm')
-                    wA=1./matchedA.locprecnm;
-                    wB=1./matchedB.locprecnm;
+                    wA=1./matchedA.locprecnm.^2;
+                    wB=1./matchedB.locprecnm.^2;
                 else
                     photA=matchedA.phot;
                     photB=matchedB.phot;
-                    wA=sqrt(photA);
-                    wB=sqrt(photB);
+                    wA=(photA);
+                    wB=(photB);
                 end
                 for k=1:length(fn)
                     switch fn{k}

plugins/+WorkflowModules/+Fitters/MLE_global_spline.m

@@ -253,8 +253,8 @@ function loadscmos_callback(a,b,obj)
             switch fitpar.mainchannel
                 case 1
                     locs.([names{k} 'err'])=1./sqrt(1./ve(:,1).^2+1./ve(:,2).^2)*sqrt(2);
-                    ve(:,1)=ve(:,1)/errfactor(1);
-                    ve(:,2)=ve(:,2)/errfactor(2);
+                    ve(:,1)=(ve(:,1)/errfactor(1)).^2; %use as weights the correct 1/sigma^2
+                    ve(:,2)=(ve(:,2)/errfactor(2)).^2;
                     locs.(names{k})=sum(v./ve,2)./sum(1./ve,2); %average based on CRLB before weighting
                 case 2
                     locs.(names{k})=v(:,1);