Changeset 618 for trunk/src/series

Timestamp:

Apr 24, 2013, 4:22:52 PM (11 years ago)

Author:

sommeria

Message:

particle_tracking updated

File:

• trunk/src/series/particle_tracking.m (modified) (10 diffs)

trunk/src/series/particle_tracking.m

@@ -16 +16 @@
 %
 % Method: 
-   dexing
 %       Series.NbSlice: %number of slices defined on the interface
 % global A rangx0 rangy0 minA maxA; % make current image A accessible in workspace
@@ -78 +77 @@
         msgbox_uvmat('WARNING','the first input file does not exist') 
     end
-    return
     % parameters specific to the function 'particle_tracking'
     %Par.Nblock=25;%size of image subblocks for analysis
@@ -89 +87 @@
     Par.ThreshLum=-2000;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles
     ParamOut.ActionInput=Par;
+    return
 end
 
@@ -125 +124 @@
 if ~isempty(errormsg),display(errormsg),return,end
 
+%% frame index for movie or multimage file input  
+if ~isempty(j1_series{1})
+    frame_index=j1_series{1};
+else
+    frame_index=i1_series{1};
+end
+
 %% check the input file type  
-[FileType,FileInfo,MovieObject]=get_file_type(filecell{1,1});
+[FileType,FileInfo,VideoObject]=get_file_type(filecell{1,1});
 ImageTypeOptions={'image','multimage','mmreader','video'};
 if isempty(find(strcmp(FileType,ImageTypeOptions)))
@@ -138 +144 @@
 %%%%%%%%%%%%   SPECIFIC PART (to edit) %%%%%%%%%%%%
 %filter for particle center of mass(luminosity)
-Nblock=Param.InputAction.Nblock;
-ThreshLum=Param.InputAction.ThreshLum;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles
+Nblock=Param.ActionInput.Nblock;
+ThreshLum=Param.ActionInput.ThreshLum;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles
 
 hh=ones(5,5);
@@ -206 +212 @@
 %     errordlg('number of images in a slice smaller than the proposed number of images for the sliding average')
 %     return
-% end
-A=[];
-      
-
-% [A,time,dt,rangx0,rangy0]=view_ima(handles,filename,[],1,1,1,1);
-% pxcm=str2num(get(handles.pxcm,'String')); %scales pixels per cm
-% pycm=str2num(get(handles.pycm,'String'));
-% np=size(A);
-
-%BACKGROUND LEVEL
-% Backg=zeros(size(A));
-% nburst(1)=1;
+
 for ifile=1:nbfield
     if checkrun
@@ -226 +221 @@
         end
     end
-    filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series(ifile),[],j1);
+    if ~isempty(j1_series)&&~isequal(j1_series,{[]})
+        j1=j1_series{1}(ifile);
+    end
+    filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series{1}(ifile),[],j1);
     A=read_image(filename,FileType,VideoObject,frame_index(ifile));
     if ndims(A)==3;%color images
-        A=sum(double(Aread),3);% take the sum of color components
+        A=sum(double(A),3);% take the sum of color components
     end
     if ThreshLum<0
         A=max(max(A))-A;%take the negative
     end
-    if TestMask
+    if CheckMask
         A=A.*Mask;
     end
@@ -251 +249 @@
         A=A-imresize(Backg/nburst(1),size(A),'bilinear');% interpolate to the initial size image and substract
     end
-    Aflagmax=sparse(imregionalmax(Ap));%find local maxima
-    Plum=imfilter(Ap,hh);% sum A on 5x% domains
+    Aflagmax=sparse(imregionalmax(A));%find local maxima
+    Plum=imfilter(A,hh);% sum A on 5x% domains
     Plum=Aflagmax.*Plum;% Plum gives the particle luminosity at each particle location, 0 elsewhere
     %make statistics on particles,restricted to a subdomain Sub
@@ -262 +260 @@
     nbtotal=nbtotal(1);
     %particle size
-    Parea=Aflagmax.*(Plum./Ap); %particle luminosity/max luminosity=area
+    Parea=Aflagmax.*(Plum./A); %particle luminosity/max luminosity=area
     Pdiam=sqrt(Parea);
     [Js,Is,diam]=find(Pdiam);%particle location
@@ -276 +274 @@
     
     % get the particle centre of mass
-    dx=imfilter(Ap,hdX);
-    dy=imfilter(Ap,-hdY);
+    dx=imfilter(A,hdX);
+    dy=imfilter(A,-hdY);
     dx=Aflagmax.*(dx./Plum);
     dy=Aflagmax.*(dy./Plum);