Merge branch 'develop' into 4pi

jries · Apr 6, 2022 · 46c5152 · 46c5152
2 parents c8ac70a + 30612c2
commit 46c5152
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Showing 27 changed files with 363 additions and 115 deletions.
diff --git a/+gui/GuiMainSMAP.m b/+gui/GuiMainSMAP.m
@@ -196,13 +196,16 @@ function makeGui(obj)
 
             gfile=obj.getGlobalSetting('guiPluginConfigFile');
             if ~exist(gfile,'file')
-                gfile=strrep(gfile,'settings', settingsdir);
+                ind = strfind(gfile,'settings');
+                gfile=[settingsdir gfile(ind+8:end)];
+%                 gfile=strrep(gfile,'settings', settingsdir);
             end
 
             if exist(gfile,'file')
                 guimodules=readstruct(gfile,[],true);
             else
-                guimodules=pmenu;
+%                 guimodules=pmenu;
+                guimodules=struct('File',[],'Analyze',[],'Process',[],'ROIManager',[]);
             end
             guimodulespure=myrmfield(guimodules,{'GuiParameters','globalGuiState'});
             obj.setPar('guimodules',guimodulespure);

diff --git a/+gui/SEExploreGui.m b/+gui/SEExploreGui.m
@@ -950,7 +950,10 @@ function keypress(a,event,obj,flag)
             removecell_callback(0,0,obj);
         else
             removesite_callback(0,0,obj);
-        end        
+        end    
+    case 'slash'
+            toggleuse_callback(0,0,obj)
+
 end
 
 end

diff --git a/+interfaces/SEEvaluationProcessor.m b/+interfaces/SEEvaluationProcessor.m
@@ -105,8 +105,12 @@ function redraw(obj)
                 parameters(inds:inds+1)=[];
             end
 
+            if ~isempty(obj.site.image)
                 sx=obj.site.image.rangex;
-                fovsize=(sx(2)-sx(1))*1000*[1,1];             
+                fovsize=(sx(2)-sx(1))*1000*[1,1];  
+            else
+                fovsize=obj.getPar('se_sitefov')*[1,1];
+            end
             if isempty(p.position) %no position specified, that is the usual case
 
                 pos=obj.site.pos;

diff --git a/+interfaces/SiteExplorer.m b/+interfaces/SiteExplorer.m
@@ -397,7 +397,20 @@ function addFile(obj,name,ID,info)
 
              %plot all site boxes
              if obj.locData.getPar('se_drawboxes')&&~isempty(obj.sites)&&~isempty(obj.sites(1).info)
-                 allsites=[obj.sites(:).info];
+                 try
+                    allsites=[obj.sites(:).info];
+                 catch err %fix connected sites
+                     err
+                     disp('fixing connected sites')
+                     for k=1:length(obj.sites)
+                        if ~isfield(obj.sites(k).info,'connectedsites')
+                            obj.sites(k).info.connectedsites=[];
+                        end
+                     end
+
+                     allsites=[obj.sites(:).info];
+                 end
+
                  ind=[allsites.cell]==cell.ID;
 
                  if sum(ind)>0

diff --git a/LocMoFit/@LocMoFit/rotCoordNMkImg.m b/LocMoFit/@LocMoFit/rotCoordNMkImg.m
@@ -185,7 +185,10 @@
                     imageo = drawerSMAP(imageo,p_render);
                 end
                 thisImg = imageo.image;
-                v = v + thisImg;
+
+                if ~isempty(thisImg) % XXXX added by Jonas
+                    v = v + thisImg;
+                end
             end
         end
         imagesc(ax, v);

diff --git a/LocMoFit/@LocMoFit/transModPoint.m b/LocMoFit/@LocMoFit/transModPoint.m
@@ -1,40 +1,19 @@
-function modPoint = transModPoint(obj, modPoint, varargin)
+function modPoint = transModPoint(obj, modPoint)
 % l stands for layer.
 % Variation is now controled by SMAP as linkage error
 
-p = inputParser;
-p.addParameter('lPars',[]);
-p.parse(varargin{:});
-p = p.Results;
 %% Transform the model
-if isempty(p.lPars)
-    lPars = obj.exportPars(1,'lPar');
-else
-    lPars = p.lPars;
-end
-if iscell(modPoint)
-    for l = 1:obj.numOfLayer
-        modPoint_.xnm = modPoint{l}.x; modPoint_.ynm = modPoint{l}.y;
-        if isfield(modPoint{l}, 'z')
-            modPoint_.znm = modPoint{l}.z;
-        end
-        modPoint_ = obj.locsHandler(modPoint_, lPars,0,'usedformalism', 'rotationMatrixRev','order_transform','RT');
-
-        modPoint{l}.x = modPoint_.xnm; modPoint{l}.y = modPoint_.ynm;
-        if isfield(modPoint{l}, 'z')
-            modPoint{l}.z = modPoint_.znm;
-        end
-    end
-else
-    modPoint_.xnm = modPoint.x; modPoint_.ynm = modPoint.y;
-    if isfield(modPoint, 'z')
-        modPoint_.znm = modPoint.z;
+lPar = obj.exportPars(1,'lPar');
+for l = 1:obj.numOfLayer
+    modPoint_.xnm = modPoint{l}.x; modPoint_.ynm = modPoint{l}.y;
+    if isfield(modPoint{l}, 'z')
+        modPoint_.znm = modPoint{l}.z;
     end
-    modPoint_ = obj.locsHandler(modPoint_, lPars,0,'usedformalism', 'rotationMatrixRev','order_transform','RT');
+    modPoint_ = obj.locsHandler(modPoint_, lPar,0,'usedformalism', 'rotationMatrixRev','order_transform','RT');
 
-    modPoint.x = modPoint_.xnm; modPoint.y = modPoint_.ynm;
-    if isfield(modPoint, 'z')
-        modPoint.z = modPoint_.znm;
+    modPoint{l}.x = modPoint_.xnm; modPoint{l}.y = modPoint_.ynm;
+    if isfield(modPoint{l}, 'z')
+        modPoint{l}.z = modPoint_.znm;
     end
 end
 end
diff --git a/LocMoFit/helperClass/SMLMModelFit_manager.m b/LocMoFit/helperClass/SMLMModelFit_manager.m
@@ -2,7 +2,7 @@
     % Please use LocMoFit_manager instead.
     methods
         function obj = SMLMModelFit_manager(varargin)
-            obj@LocMoFit_manager(varargin{:});
+            obj = LocMoFit_manager(varargin);
         end
     end
 end
diff --git a/fit3Dcspline/calibrate3D_GUI_g.m b/fit3Dcspline/calibrate3D_GUI_g.m
@@ -110,6 +110,8 @@
             obj.guihandles.dz=uicontrol('style','edit','String','10','Position',[xpos1+2*xw,top-9*vsep,xw*0.5,fieldheight],'FontSize',fontsize);
             obj.guihandles.dz.TooltipString=sprintf('Distance in nm between frames. By convention, these are objective positions (not corrected for refractive index mismatch). \n A spacing between 10 nm and 50 nm works well ');
             obj.guihandles.dzt.TooltipString=obj.guihandles.dz.TooltipString;
+            obj.guihandles.z0focus=uicontrol('style','checkbox','String','focus as z ref','Position',[xpos1+2.5*xw,top-9*vsep,xw*1.5,fieldheight],'FontSize',fontsize);
+
 
             obj.guihandles.modalityt=uicontrol('style','text','String','3D modality ','Position',[xpos1,top-8*vsep,xw*2,fieldheight],'FontSize',fontsize,'HorizontalAlignment',ha);
             obj.guihandles.modality=uicontrol('style','popupmenu','String',{'arbitrary','global 2 channel','4Pi'},'Value',1,'Position',[xpos1+2*xw,top-8*vsep,xw*1.3,fieldheight],'FontSize',fontsize,'Callback',@obj.modality_callback);
@@ -464,6 +466,7 @@ function selectroi_callback(obj,a,b)
             p.filelist=obj.guihandles.filelist.String;
             p.outputfile=obj.guihandles.outputfile.String;
             p.dz=str2double(obj.guihandles.dz.String);
+            p.z0focus=obj.guihandles.z0focus.Value;
             p.modality=obj.guihandles.modality.String{obj.guihandles.modality.Value};
             p.PSF2D=obj.guihandles.PSF2D.Value;
             p.zcorr=obj.guihandles.corrzselect.String{obj.guihandles.corrzselect.Value};

diff --git a/fit3Dcspline/calibrate_globalworkflow.m b/fit3Dcspline/calibrate_globalworkflow.m
@@ -274,7 +274,8 @@ function calibrate_globalworkflow(p)
 pt.xrange=pp.xrange1+camroi1(1); 
 pt.yrange=pp.yrange1+camroi1(2);
 pt.unit='pixel';
-pt.type='projective';
+%pt.type='projective'; %old
+pt.type=ph.Tform; %use from GUI
 transform.setTransform(1,pt)
 pt.mirror=pp.mirrorax;
 

diff --git a/fit3Dcspline/private/getfocusPSF.m b/fit3Dcspline/private/getfocusPSF.m
@@ -0,0 +1,11 @@
+function z0focus=getfocusPSF(PSF)
+for k=1:length(PSF)
+    [P,CRLB, LL] =mleFit_LM(PSF{k}*10000,4,100,1,0,1);
+    sx=P(:,5);
+    sy=P(:,6);
+    dsx=sx-sy;
+    [v,ind(k)]=min(dsx.^2);
+end
+z0focus=round(mean(ind));
+end
+
diff --git a/fit3Dcspline/private/getstackcal_g.m b/fit3Dcspline/private/getstackcal_g.m
@@ -235,7 +235,9 @@
         splinefit.PSFsmooth={single(corrPSFhdr)};   
         cspline.mirror=0;
     end
-
+    if p.z0focus
+        z0reference=getfocusPSF(splinefit.PSFsmooth);
+    end
 
         cspline.z0=z0reference;%round((b3_0.dataSize(3)+1)/2);
         cspline.dz=p.dz;

diff --git a/fit3Dcspline/private/getstackcal_gs.m b/fit3Dcspline/private/getstackcal_gs.m
@@ -194,6 +194,11 @@
     cspline.mirror=0;
 end
 
+%find focus z position
+if p.z0focus
+    z0reference=getfocusPSF(splinefit.PSFsmooth);
+end
+
 cspline.z0=z0reference;%round((b3_0.dataSize(3)+1)/2);
 cspline.dz=p.dz;
 cspline.x0=dRx+1;

diff --git a/other/CallBatchprocessorScript.m b/other/CallBatchprocessorScript.m
@@ -0,0 +1,18 @@
+SMAP %you need to start SMAP to add directories and set some variables
+smapobject=g;
+
+%main batch file:
+batchfile='/Volumes/Ries_Data/DataSSD/workingdirectory/GlobalFitPaper/Exampledata/NPC4C/191022_beads/003_beads_10nm_3D_2c_e_676_685_Z-stack_1_batch.mat';
+%list of data files:
+rawfiles={'/Volumes/Ries_Data/DataSSD/workingdirectory/GlobalFitPaper/Exampledata/NPC4C/191022_beads/001_beads_10nm_3D_2c_e_676_685_Z-stack_1/001_beads_10nm_3D_2c_e_676_685_Z-stack_1_MMStack_Pos0.ome.tif'};
+
+%make batch processor programmatically
+bp=WorkflowModules.Batchprocessor;
+bp.attachPar(smapobject.P)
+bp.makeGui;
+bp.guihandles.mainbatchfile.String=batchfile;
+bp.guihandles.filelist.String=rawfiles;
+bp.guihandles.filelist.Value=1;
+
+%run batch processor:
+bp.processb_callback(0,0);
diff --git a/plugins/+Analyze/+MINFLUX/MotorPAINT.m b/plugins/+Analyze/+MINFLUX/MotorPAINT.m
@@ -32,6 +32,14 @@
             end
             for k=1:length(gn)
                 indh=locs.groupindex==gn(k);
+
+                if p.skipfirst>0
+                    outn=find(indh,p.skipfirst,'first');
+                    indh(outn)=false;
+                end
+                if sum(indh)<p.minlen
+                    continue
+                end
 
                 x=locs.xnm(indh);
                 y=locs.ynm(indh);
@@ -83,16 +91,20 @@
                     t=tic;
                 end
             end
+            axis(axall,"ij")            
             axis(axall,"equal")
+
             [~, filename]=fileparts(obj.locData.files.file(1).name);
             obj.locData.addfile(['tracks_s' num2str(p.splitmergestep) '_' num2str(obj.locData.files.filenumberEnd) '_' filename]);
             % obj.locData.files.file(end).info.simulationParameters=obj.getGuiParameters;
+            if p.addtracks
             obj.locData.addLocData(locsout);
 
             obj.locData.filter
             %            try
             initGuiAfterLoad(obj);
             obj.locData.filter
+            end
 
             ax=obj.initaxis('tracks');
             hold(ax,'off')
@@ -101,6 +113,9 @@
                 hold(ax,'on')
             end
             axis(ax,"equal")
+            axis(ax,"ij")
+            ax.XLim=axall.XLim;
+            ax.YLim=axall.YLim;
 
             axc=obj.initaxis('angle');
             cmap=hsv(256);
@@ -111,6 +126,9 @@
                 hold(axc,'on')
             end
             axis(axc,"equal")
+            axis(axc,"ij")
+            axc.XLim=axall.XLim;
+            axc.YLim=axall.YLim;
 
         end
         function pard=guidef(obj)
@@ -165,6 +183,16 @@
 pard.stepfunctionm.position=[3,4.];
 pard.stepfunctionm.Width=1;
 
+pard.skipfirstt.object=struct('String','Skip first:','Style','text');
+pard.skipfirstt.position=[4,1];
+pard.skipfirstt.Width=1.5;
+pard.skipfirst.object=struct('String','0','Style','edit');
+pard.skipfirst.position=[4,2.5];
+pard.skipfirst.Width=0.5;
+
+pard.addtracks.object=struct('String','Add tracks','Style','checkbox','Value',1);
+pard.addtracks.position=[5,1];
+pard.addtracks.Width=2;
 
 pard.plugininfo.description=sprintf('');
 pard.plugininfo.type='ProcessorPlugin';

diff --git a/plugins/+Analyze/+calibrate/TrainDeepSMLM.m b/plugins/+Analyze/+calibrate/TrainDeepSMLM.m
@@ -30,17 +30,17 @@
         function pard=guidef(obj)
             pard=guidef(obj);
         end
-        function initGui(obj)
-            [email protected](obj);
-            obj.jsonfile=obj.jsondefault;
-            tt=uitable(obj.handle);
-            tt.Position=obj.guihandles.partablepos.Position;
-            tt.Position(4)=tt.Position(4)*7;
-            obj.guihandles.parttable=tt;
-            jsontxt=fileread(obj.jsondefault);
-            obj.jsonstruct=jsondecode(jsontxt);
-            makejsontable(obj);
-        end
+%         function initGui(obj)
+%             [email protected](obj);
+%             obj.jsonfile=obj.jsondefault;
+%             tt=uitable(obj.handle);
+%             tt.Position=obj.guihandles.partablepos.Position;
+%             tt.Position(4)=tt.Position(4)*7;
+%             obj.guihandles.parttable=tt;
+%             jsontxt=fileread(obj.jsondefault);
+%             obj.jsonstruct=jsondecode(jsontxt);
+%             makejsontable(obj);
+%         end
 
     end
 end

diff --git a/plugins/+Process/+Drift/private/applydriftcorrection.m b/plugins/+Process/+Drift/private/applydriftcorrection.m
@@ -11,7 +11,7 @@
                 poso.xnm(indg&indpos)=pos.xnm(indg&indpos)-drift.xy(1).x(pos.frame(indg&indpos));
                 poso.xnm(indg&~indpos)=pos.xnm(indg&~indpos)-drift.xy(2).x(pos.frame(indg&~indpos)); 
             else
-                poso.xnm(indg)=pos.xnm(indg)-drift.xy(1).x(pos.frame(indg));
+                poso.xnm(indg)=pos.xnm(indg)-drift.xy(1).x(round(pos.frame(indg)));
             end
         end
         if isfield(drift.xy(1),'y')
@@ -20,7 +20,7 @@
                 poso.ynm(indg&indpos)=pos.ynm(indg&indpos)-drift.xy(1).y(pos.frame(indg&indpos));
                 poso.ynm(indg&~indpos)=pos.ynm(indg&~indpos)-drift.xy(2).y(pos.frame(indg&~indpos)); 
             else
-                poso.ynm(indg)=pos.ynm(indg)-drift.xy(1).y(pos.frame(indg));
+                poso.ynm(indg)=pos.ynm(indg)-drift.xy(1).y(round(pos.frame(indg)));
             end
         end
 end

diff --git a/plugins/+Process/+Register/RegisterImages.m b/plugins/+Process/+Register/RegisterImages.m
@@ -51,10 +51,13 @@
 %             dxr=obj.getPar('shiftxy_min','layer',reflayer);
 %             dyr=obj.getPar('shiftxy_max','layer',reflayer);
             if p.correctcoordinates
-
-                tch=obj.locData.loc.channel==p.targetchannels(1);
-                for k=2:length(p.targetchannels)
-                    tch=tch|(obj.locData.loc.channel==p.targetchannels(k));
+                if isempty(p.targetchannels)
+                    tch=true(size(obj.locData.loc.channel));
+                else
+                    tch=obj.locData.loc.channel==p.targetchannels(1);
+                    for k=2:length(p.targetchannels)
+                        tch=tch|(obj.locData.loc.channel==p.targetchannels(k));
+                    end
                 end
                 tfile=p.dataselect.Value==obj.locData.loc.filenumber;
                 tch=tch&tfile;