Changeset 1099 for trunk

Timestamp:

Apr 14, 2021, 4:02:22 PM (4 years ago)

Author:

sommeria

Message:

extrtact_multitif cleaned

Location:

trunk/src

Files:

• plot_object.m (modified) (7 diffs)
• series/extract_multitif.m (modified) (4 diffs)
• series/extract_multitif_special.m (deleted)
• series/ima_levels_batch.m (deleted)

trunk/src/plot_object.m

@@ -245 +245 @@
     end
 end
-if ismember(ObjectData.Type,{'line','polyline','polygon'})
+if ismember(ObjectData.Type,{'line','polyline','polygon'})&&...
+        ismember(ObjectData.ProjMode,{'projection','interp_lin','interp_tps'})
     if length(xline)<2
         theta=0;
@@ -357 +358 @@
                 end
             elseif length(PlotData.SubObject)==2
-                set(PlotData.SubObject(1),'XData',xinf);
-                set(PlotData.SubObject(1),'YData',yinf);
-                set(PlotData.SubObject(2),'XData',xsup);
-                set(PlotData.SubObject(2),'YData',ysup);
+                if ismember(ObjectData.ProjMode,{'projection','interp_lin','interp_tps'})
+                    set(PlotData.SubObject(1),'XData',xinf);
+                    set(PlotData.SubObject(1),'YData',yinf);
+                    set(PlotData.SubObject(2),'XData',xsup);
+                    set(PlotData.SubObject(2),'YData',ysup);
+                end
             elseif length(PlotData.SubObject)==1
-                set(PlotData.SubObject(1),'XData',xsup);
-                set(PlotData.SubObject(1),'YData',ysup);
+                if ismember(ObjectData.ProjMode,{'projection','interp_lin','interp_tps'})
+                    set(PlotData.SubObject(1),'XData',xsup);
+                    set(PlotData.SubObject(1),'YData',ysup);
+                end
+            end
+            if strcmp(ObjectData.ProjMode,'none')
+                delete(PlotData.SubObject)
+                PlotData=rmfield(PlotData,'SubObject');
             end
         end
@@ -398 +407 @@
     end
     if test_patch
+        createimage=1;
         if isfield(PlotData,'SubObject')
-        for iobj=1:length(PlotData.SubObject)
-            if ~ishandle(PlotData.SubObject(iobj))
-                hold on
-                hhh=image([xlim(1)+dx/2 xlim(2)-dx/2],[ylim(1)+dy/2 ylim(2)-dy/2],imflag,'Tag','proj_object','HitTest','off');
-                set(hhh,'AlphaData',(flag)*0.2)% set partial transparency to the filling color
-                PlotData.SubObject(iobj)=hhh;
-            else
+            for iobj=1:length(PlotData.SubObject)
                 objtype=get(PlotData.SubObject(iobj),'Type');
                 if isequal(objtype,'image')
@@ -411 +415 @@
                     set(PlotData.SubObject(iobj),'XData',[xlim(1)+dx/2 xlim(2)-dx/2])
                     set(PlotData.SubObject(iobj),'YData',[ylim(1)+dy/2 ylim(2)-dy/2])
-                end
-            end
-        end 
+                    createimage=0;
+                end
+            end
+        end
+        if createimage
+            hold on
+            hhh=image([xlim(1)+dx/2 xlim(2)-dx/2],[ylim(1)+dy/2 ylim(2)-dy/2],imflag,'Tag','proj_object','HitTest','off');
+            set(hhh,'AlphaData',(flag)*0.2)% set partial transparency to the filling color
+            PlotData.SubObject(1)=hhh;
         end
     else% no patch image requested, erase existing ones
@@ -420 +430 @@
                 if ishandle(PlotData.SubObject(iobj)) && strcmp(get(PlotData.SubObject(iobj),'Type'),'image')
                     delete(PlotData.SubObject(iobj))
+                    PlotData=rmfield(PlotData,SubObject(iobj));
                 end
             end
@@ -462 +473 @@
         case {'line','polyline','polygon'}
             hh=line(xline,yline,'Color',col);
+            if ismember(ObjectData.ProjMode,{'projection','interp_lin','interp_tps'})
                 PlotData.SubObject(1)=line(xinf,yinf,'Color',col,'LineStyle',SubLineStyle,'Tag','proj_object');%draw sub-lines
                 PlotData.SubObject(2)=line(xsup,ysup,'Color',col,'LineStyle',SubLineStyle,'Tag','proj_object');
+            end
                 for ipt=1:sizcoord(1)
                     PlotData.DeformPoint(ipt)=line(ObjectData.Coord(ipt,1),ObjectData.Coord(ipt,2),'Color',...
@@ -496 +509 @@
     end
 end
+%put the deformpoints to the front
+            listc=get(gca,'children');
+            checkdeform=strcmp(get(listc,'tag'),'DeformPoint');
+            [nn,Index]=sort(checkdeform,'descend');
+            set(gca,'children',listc(Index))
 set(hh,'UserData',PlotData)

trunk/src/series/extract_multitif.m

@@ -1 @@
-%'ima2netcdf': read image series and transform to netcdf
+%'extract_multitif': read image series from PCO cameras (tiff image series) and write .png images
 %------------------------------------------------------------------------
-
     
-% function ParamOut=ima2netcdf(Param)
+% function ParamOut=extract_multitif(Param)
 %
 %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -59 +58 @@
 %=======================================================================
 
-function ParamOut=extract_multitif_parallel(Param)
+function ParamOut=extract_multitif(Param)
 
 %%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
@@ -74 +73 @@
     ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
     ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
-    ParamOut.CPUTime=7;% expected time for writting one image ( in minute)
+    ParamOut.CPUTime=10;% expected time for writting the output of one source image ( in minute)
     %% root input file(s) and type
     % check the existence of the first file in the series
@@ -126 +125 @@
 ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices
 
-%% create the xml file of PCO camera if it does not exist
-Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']);
-if ~exist(Newxml,'file')
-XmlInput.Camera.CameraName='PCO';
-XmlInput=rmfield(XmlInput,'Time');
-XmlInput=rmfield(XmlInput,'TimeUnit');
-t=struct2xml(XmlInput);
-t=set(t,1,'name','ImaDoc');
-save(t,Newxml);
+%% create the xml file for timing if it does not exist : example to adapt
+TEST=0;
+if TEST
+    count0=14;
+    Dtj=0.05;% time interval between frames
+    ImagesPerLevel=455;% total number of images per position, ImagesPerLevel-Nbj images skiiped during motion between two positions
+    Nbj=390; %Nbre of images kept at a given position
+    Dti=Dtj*ImagesPerLevel;
+    NbLevel=11;
+    NbScan=3;
+    TimeReturn=268.5; %time needed to return back to the first position (in sec)
+    NbReturn=round(TimeReturn/Dtj);
+    NbSkipReturn=NbReturn+1-NbLevel*ImagesPerLevel;
+    
+    Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']);
+    if ~exist(Newxml,'file')
+        XmlInput.Camera.CameraName='PCO';
+        XmlInput.Camera.TimeUnit='s';
+        XmlInput.Camera.BurstTiming.FrameFrequency=1;
+        XmlInput.Camera.BurstTiming.Time=0;% for 200
+        XmlInput.Camera.BurstTiming.Dtj=Dtj;
+        XmlInput.Camera.BurstTiming.NbDtj=Nbj-1;
+        XmlInput.Camera.BurstTiming.Dti=Dti;
+        XmlInput.Camera.BurstTiming.NbDti=NbLevel-1;
+        XmlInput.Camera.BurstTiming.Dtk=TimeReturn;
+        XmlInput.Camera.BurstTiming.NbDtk=NbScan-1;
+        t=struct2xml(XmlInput);
+        t=set(t,1,'name','ImaDoc');
+        save(t,Newxml);
+    end
 end