Changeset 897 for trunk

Timestamp:

May 25, 2015, 8:48:58 PM (10 years ago)

Author:

sommeria

Message:

sub_background corrected for volume and multilevel cases

Location:

trunk/src

Files:

• series.fig (modified) (previous)
• series.m (modified) (17 diffs)
• series/civ_input.m (modified) (1 diff)
• series/civ_series.m (modified) (1 diff)
• series/sub_background.m (modified) (12 diffs)
• transform_field/ima_remove_background.m (modified) (1 diff)
• transform_field/ima_remove_particles.m (modified) (3 diffs)

trunk/src/series.m

@@ -1556 +1556 @@
 end
 
-%% set nbre of cluster cores and processes
+%% set nbre of cluster cores and processes: 
+% NbCore is the number of computer processors used 
+% NbProcess is the number of independent processes in which the required calculation is split
 switch RunMode
     case {'local','background'}
@@ -1598 +1600 @@
 end
 if isempty(Param.IndexRange.NbSlice)
-    NbProcess=NbCore;% choose one process per core
+    NbProcess=NbCore;% choose one process per core if NbSlice is not imposed
 else
-    NbProcess=Param.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices
-    NbCore=min(NbCore,NbProcess);% at least one process per core
+    NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes 
+    NbCore=min(NbCore,NbProcess);% reduces the number of cores if it exceeds the number of processes
 end
 
@@ -1662 +1664 @@
 OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
 
-%% get the set of reference field indices
-first_i=1;
-last_i=1;
-incr_i=1;
-first_j=1;
-last_j=1;
-incr_j=1;
+%% get the set of reference input field indices 
+first_i=1;% first i index to process
+last_i=1;% last i index to process
+incr_i=1;% increment step in i index
+first_j=1;% first j index to process
+last_j=1;% last j index to process
+incr_j=1;% increment step in j index
 if isfield(Param.IndexRange,'first_i')
     first_i=Param.IndexRange.first_i;
@@ -1688 +1690 @@
     set(handles.num_incr_i,'String','1')
 end
+% case of no increment i defined: processing is done on the available files found in i1_series
 if isempty(incr_i)
     if isempty(incr_j)
@@ -1701 +1704 @@
         ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
     end
+% increment i is defined: processing is done on first_i:incr_i:last_i;
 else
     ref_i=first_i:incr_i:last_i;
@@ -1711 +1715 @@
     end
 end
-BlockLength=ceil(numel(ref_i)/NbProcess);
-nbfield_j=numel(ref_j);
+BlockLength=ceil(numel(ref_i)/NbProcess);% nbre of input fields in each process 
+nbfield_j=numel(ref_j); % number of j indices
 
 %% record nbre of output files and starting time for computation for status
@@ -1729 +1733 @@
 set(handles.status,'UserData',StatusData)
 
-
+%% case of a function in Python
 if strcmp(ActionExt, '.py (in dev.)')
     fprintf([
@@ -1759 +1763 @@
             %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i);
         else %multislices (then incr_i is not empty)
-             Param.IndexRange.first_i= first_i+incr_i*(iprocess-1);
-             Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
+            Param.IndexRange.first_i= first_i+incr_i*(iprocess-1);
+            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
         end
         if isfield(Param,'OutputSubDir')
-        t=struct2xml(Param);
-        t=set(t,1,'name','Series');
-        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
-            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
-        save(t,filexml);
+            t=struct2xml(Param);
+            t=set(t,1,'name','Series');
+            filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
+                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
+            save(t,filexml);
         end
         switch ActionExt
@@ -1895 +1899 @@
         for iprocess=1:NbProcess
             system([batch_file_list{iprocess} ' &'])% directly execute the command file for each process
-            msgbox_uvmat('CONFIRMATION',[ActionName ' launched in background: press STATUS to see results'])
-        end
+        end
+        msgbox_uvmat('CONFIRMATION',[ActionName ' launched in background: press STATUS to see results'])
     case 'cluster_oar' % option 'oar-parexec' used
         %create subdirectory for oar command and log files
@@ -2041 +2045 @@
 drawnow
 
-%% check whether the input file(s) need to be refreshed
-% SeriesData=get(handles.series,'UserData');%hidden parameters
-% if ~isfield(SeriesData,'i1_series')
-%     msgbox_uvmat('ERROR','The input field series needs to be refreshed: press REFRESH');
-%     return
-% end
-
 %% get Action name and path
 NbBuiltinAction=get(handles.Action,'UserData'); %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
@@ -2106 +2103 @@
        set(handles.ActionName,'UserData',ActionPathList);
     set(handles.ActionExt,'Value',ActionExtIndex)
-%     ActionPathList{ActionIndex,ActionExtIndex}=PathName;
         
     %record the user defined menu additions in personal file profil_perso
@@ -2134 +2130 @@
 
 %% create the function handle for Action
-path_series=which('series');
-if ~isequal(ActionPath,path_series)
-    eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
-    if ~exist(ActionPath,'dir')
-        errormsg=['The prescribed function path ' ActionPath ' does not exist'];
-        return
-    end
-    if ~isequal(spath,ActionPath)
-        addpath(ActionPath)% add the prescribed path if not the current one
-    end
-end
-eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
-if ~isequal(ActionPath,path_series)
-        rmpath(ActionPath)% add the prescribed path if not the current one    
-end
+if ~exist(ActionPath,'dir')
+    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
+    return
+end
+current_dir=pwd;%current working dir
+cd(ActionPath)
+h_fun=str2func(ActionName);
+cd(current_dir)
+
+% 
+% checkaddpath=0;
+% path_series=which('series');
+% %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
+% spath=fileparts(which(ActionName)); %spath = current path of the selected function ACTION
+% if ~exist(ActionPath,'dir')
+%     msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
+%     return
+% end
+% if ~strcmp(spath,ActionPath)
+%     if strcmp(pwd,spath)
+%         msgbox_uvmat('ERROR',[ 'a function called ' ActionName ' on your working space oversets the selected one']);
+%         return
+%     else
+%         addpath(ActionPath)% add the prescribed path if not the current one
+%         checkaddpath=1;
+%     end
+% end
+% eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
+% if checkaddpath && ~isequal(ActionPath,path_series)
+%     rmpath(ActionPath)% add the prescribed path if not the current one
+% end
 
 %% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
@@ -2185 +2197 @@
 FieldList_1=get(handles.FieldName_1,'String');% previous list as default
 if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
-CheckList=0;% indicate whether FieldName has been updated
+%CheckList=0;% indicate whether FieldName has been updated
 CheckList_1=1;% indicate whether FieldName_1 has been updated
 handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
@@ -2195 +2207 @@
     set(handles.VelType_title,'Visible','on')
     FieldList=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
-    CheckList=1;
+    %CheckList=1;
     set(handles.FieldName,'Value',1); %velocity vector choice by default
     if  VelTypeRequest_1 && numel(iview_civ)>=2 
@@ -2347 +2359 @@
 
 %% NbSlice visibility
-NbSliceVisible='off';%default
-if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on')
-    NbSliceVisible='on';
-    set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
+%NbSliceVisible='off';%default
+if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
+    set(handles.num_NbSlice,'Visible','on')
+    set(handles.NbSlice_title,'Visible','on')
 else
-    set(handles.num_NbProcess,'String','')% free nbre of processes 
-end
-set(handles.num_NbSlice,'Visible',NbSliceVisible)
-set(handles.NbSlice_title,'Visible',NbSliceVisible)
+    set(handles.num_NbSlice,'Visible','off')
+    set(handles.NbSlice_title,'Visible','off')
+    %     set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
+    % else
+    %     set(handles.num_NbProcess,'String','')% free nbre of processes
+end
+if isnumeric(ParamOut.NbSlice)
+    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
+    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
+else
+    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
+end
+% set(handles.num_NbSlice,'Visible',NbSliceVisible)
+% set(handles.NbSlice_title,'Visible',NbSliceVisible)
 
 
@@ -3003 +3025 @@
 %% create the function handle of the selected fct
 if ~isempty(TransformName)
+    if ~exist(TransformPathList{TransformIndex},'dir')
+        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
+        return
+    end
     current_dir=pwd;%current working dir
     cd(TransformPathList{TransformIndex})
@@ -3294 +3320 @@
 end
 
-function num_NbProcess_Callback(hObject, eventdata, handles)
+%function num_NbProcess_Callback(hObject, eventdata, handles)
 
 
 function num_NbSlice_Callback(hObject, eventdata, handles)
 NbSlice=str2num(get(handles.num_NbSlice,'String'));
-set(handles.num_NbProcess,'String',num2str(NbSlice))
+%set(handles.num_NbProcess,'String',num2str(NbSlice))
 
 %------------------------------------------------------------------------

trunk/src/series/civ_input.m

@@ -1793 +1793 @@
      end
      Param.ActionInput.Civ1.CorrSmooth=0;% launch Civ1 with no data point (to get the image names for A and B)
+     Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
+     Param.IndexRange.last_i=str2num(get(handles.ref_i,'String'));
+     if strcmp(get(handles.ref_j,'Visible'),'on')
+         Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
+         Param.IndexRange.last_j=Param.IndexRange.first_j;
+     else
+         Param.IndexRange.first_j=1;
+         Param.IndexRange.last_j=1;
+     end
      [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results 
      if ~isempty(errormsg), return, end % rmq: error msg displayed in civ_series

trunk/src/series/civ_series.m

@@ -355 +355 @@
     % if Civ1 computation is requested
     if isfield (Param.ActionInput,'Civ1')
+        if CheckInputFile
         disp('civ1 started')
+        end
         par_civ1=Param.ActionInput.Civ1;
         if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)

trunk/src/series/sub_background.m

@@ -75 +75 @@
     ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
     ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
-    ParamOut.NbSlice='on'; %nbre of slices ('off' by default)
+    ParamOut.NbSlice='on'; % edit box nbre of slices made active
     ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
     ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
@@ -117 +117 @@
     
     %% numbers of fields
-    NbSlice=1;%default
+    NbSlice_i=1;%default
     if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
-        NbSlice=Param.IndexRange.NbSlice;
+        NbSlice_i=Param.IndexRange.NbSlice;
     end
     incr_j=1;%default
@@ -130 +130 @@
         nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices)
     end
-    incr_i=1;%default
-    first_i=1;last_i=1;incr_i;%default
+    first_i=1;last_i=1;incr_i=1;%default
     if isfield(Param.IndexRange,'first_i'); last_i=Param.IndexRange.first_i; end   
     if isfield(Param.IndexRange,'last_i'); last_i=Param.IndexRange.last_i; end
@@ -139 +138 @@
     nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices)
     nbfield=nbfield_j*nbfield_i; %total number of fields
-    nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
+    nbfield_i=floor(nbfield/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
     
     %% setting of  parameters specific to sub_background
@@ -159 +158 @@
     
     %check input consistency
-    if strcmp(answer{1},'No') && ~isequal(NbSlice,1)
-        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']);
+    if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1)
+        check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']);
         if ~strcmp(check,'Yes')
             return
@@ -166 +165 @@
     end
     if strcmp(answer{1},'Yes')
-        step=1;
+        step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume ;ode
+        ParamOut.NbSlice=1; %nbre of slices displayed 
     else
         step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
@@ -198 +198 @@
 
 %% input preparation
-NbSlice=Param.IndexRange.NbSlice;
-if ~isequal(NbSlice,1)
-    display(['multi-level splitting into ' num2str(NbSlice) ' slices']);
+NbSlice_i=Param.IndexRange.NbSlice;
+if ~isequal(NbSlice_i,1)
+    display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
 end
 RootPath=Param.InputTable(:,1);
@@ -207 +207 @@
 NomType=Param.InputTable(:,4);
 FileExt=Param.InputTable(:,5);
-hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
-[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
-if ~isempty(hdisp),delete(hdisp),end;
+%hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
+[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);
+% if ~isempty(hdisp),delete(hdisp),end;
 %%%%%%%%%%%%
     % The cell array filecell is the list of input file names, while
@@ -225 +225 @@
         frame_index{1}=i1_series{1};
     end
-nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
-nbfield_i=size(i1_series{1},2); %nb of fields for the i index
-nbfield=nbfield_j*nbfield_i; %total number of fields
-nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
-nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
-
-%% output
+
+
+%% output file naming
 FileExtOut='.png'; % write result as .png images for image inputs
 if strcmp(lower(NomType{1}(end)),'a')
@@ -240 +236 @@
     NomTypeOut='_1_1';% caseof purely numerical indexing
 end
-
 OutputDir=[Param.OutputSubDir Param.OutputDirExt];
 
-if isequal(Param.ActionInput.CheckVolume,1)
-    step=1;
-else
+%% file index parameters
+% NbSlice_i: nbre of slices for i index: different of of 1 for multi-level,
+% the function sub_background is then relaunched by the GUI series for each
+%      slice, incrementing the first index i by 1
+% NbSlice_j: nbre of slices in volume mode
+% nbfield : total number of images treated per slice
+% step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst)
+% nbaver_ima: nbre of the images in the sliding sequence used for the background
+% nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer
+nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
+nbfield_i=size(i1_series{1},2); %nb of fields for the i index
+nbfield=nbfield_j*nbfield_i; %total number of fields
+if Param.ActionInput.CheckVolume
+    step=2;% we assume the burst contains only one image pair
+    NbSlice_j=nbfield_j;
+    NbSlice=nbfield_j;
+    nbfield_series=nbfield_i;
+else 
     step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
+        NbSlice_j=1;
+        NbSlice=NbSlice_i;
+    nbfield_i=floor(nbfield/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
+    nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement
+    nbfield_series=nbfield;
 end
 nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background
@@ -258 +273 @@
     return
 end
-
-% calculate absolute brightness rank
+halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background 
+
+%% calculate absolute brightness rank
 rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima);
 if rank==0
@@ -281 +297 @@
 end
 
-%% summary of the parameters:
-% nbfield : total number of images treated (in case of multislices the function sub_background is repeated for each slice)
-% step: shift at each step of the sliding background (corresponding to the nbre of images in a burst)
-% nbaver_ima: length of the sequence used for the sliding background
-
-% nbaver=nbaver_ima/step: nbaver_ima has been adjusted so that nbaver is an odd integer
-halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background 
-
-%% select the series of image indices to process
-indselect=1:step:nbfield;% select file indices of the slice
-for ifield=1:step-1
-    indselect=[indselect;indselect(end,:)+1];
-end
-
-%% read the first series of nbaver_ima images and sort by luminosity at each pixel
-for ifield = 1:nbaver_ima
-    ifile=indselect(ifield);
-    filename=filecell{1,ifile};
-    Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
-    if ndims(Aread)==3;%color images
-        Aread=sum(double(Aread),3);% take the sum of color components
-    end
-    Ak(:,:,ifield)=Aread;
-end
-Asort=sort(Ak,3);%sort the luminosity of images at each point
-B=Asort(:,:,rank);%background image
-
-%% substract the first background image to the first images
-display( 'first background image will be substracted')
-for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image
-    Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
-    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
-    ifile=indselect(ifield);
-    j1=1;
-    if ~isempty(j1_series{1})
-        j1=j1_series{1}(ifile);
-    end
-    newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
-    
-    %write result file
-    if Param.ActionInput.CheckLevelTransform
-        C=levels(Acor);
-        imwrite(C,newname,'BitDepth',8); % save the new image
-    else
-        if isequal(FileInfo{1}.BitDepth,16)
-            C=uint16(Acor);
-            imwrite(C,newname,'BitDepth',16); % save the new image
+
+%%%%%%%  LOOP ON SLICES FOR VOLUME SCAN %%%%%%%
+for j_slice=1:NbSlice_j
+    %% select the series of i indices to process
+    indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice
+    for ifield=1:step-1
+        indselect=[indselect;indselect(end,:)+NbSlice_j];
+    end
+    
+    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
+    for ifield = 1:nbaver_ima
+        ifile=indselect(ifield);
+        filename=filecell{1,ifile};
+        Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
+        if ndims(Aread)==3;%color images
+            Aread=sum(double(Aread),3);% take the sum of color components
+        end
+        Ak(:,:,ifield)=Aread;
+    end
+    Asort=sort(Ak,3);%sort the luminosity of images at each point
+    B=Asort(:,:,rank);%background image
+    
+    %% substract the first background image to the first images
+    display( 'first background image will be substracted')
+    for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image
+        Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
+        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
+        ifile=indselect(ifield);
+        j1=1;
+        if ~isempty(j1_series{1})
+            j1=j1_series{1}(ifile);
+        end
+        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
+        
+        %write result file
+        if Param.ActionInput.CheckLevelTransform
+            C=levels(Acor);
+            imwrite(C,newname,'BitDepth',8); % save the new image
         else
-            C=uint8(Acor);
+            if isequal(FileInfo{1}.BitDepth,16)
+                C=uint16(Acor);
+                imwrite(C,newname,'BitDepth',16); % save the new image
+            else
+                C=uint8(Acor);
+                imwrite(C,newname,'BitDepth',8); % save the new image
+            end
+        end
+        display([newname ' written'])
+    end
+    
+    %% repeat the operation on a sliding series of images
+    display('sliding background image will be substracted')
+    if nbfield_series > nbaver_ima
+        for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
+            update_waitbar(WaitbarHandle,ifield/nbfield_series)
+            if  ~strcmp(get(RUNHandle,'BusyAction'),'queue')
+                disp('program stopped by user')
+                return
+            end
+            if nbaver_ima>step
+            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
+            end
+            %incorporate next burst in the current image series
+            for iburst=1:step
+                ifile=indselect(ifield+iburst+step*halfnbaver);
+                j1=1;
+                if ~isempty(j1_series{1})
+                    j1=j1_series{1}(ifile);
+                end
+                filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
+                Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile));
+                if ndims(Aread)==3;%color images
+                    Aread=sum(double(Aread),3);% take the sum of color components
+                end
+                Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
+            end
+            Asort=sort(Ak,3);%sort the new current image series by luminosity
+            B=Asort(:,:,rank);%current background image
+            %substract the background for the current burst
+            for iburst=1:step
+                Acor=double(Ak(:,:,step*halfnbaver+iburst))-double(B); %the current image has been already read ans stored as index step*halfnbaver+iburst in the current series
+                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
+                ifile=indselect(ifield+iburst);
+                if ~isempty(j1_series{1})
+                    j1=j1_series{1}(ifile);
+                end
+                newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
+                %write result file
+                if Param.ActionInput.CheckLevelTransform
+                    C=levels(Acor);
+                    imwrite(C,newname,'BitDepth',8); % save the new image
+                else
+                    if isequal(FileInfo{1}.BitDepth,16)
+                        C=uint16(Acor);
+                        imwrite(C,newname,'BitDepth',16); % save the new image
+                    else
+                        C=uint8(Acor);
+                        imwrite(C,newname,'BitDepth',8); % save the new image
+                    end
+                end
+                display([newname ' written'])
+            end
+        end
+    end
+    
+    %% substract the background from the last images
+    display('last background image will be substracted')
+    for  ifield=nbfield_series-step*halfnbaver+1:nbfield_series
+        Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B);
+        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
+        ifile=indselect(ifield);
+        if ~isempty(j1_series{1})
+            j1=j1_series{1}(ifile);
+        end
+        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
+        %write result file
+        if Param.ActionInput.CheckLevelTransform
+            C=levels(Acor);
             imwrite(C,newname,'BitDepth',8); % save the new image
-        end
-    end
-    display([newname ' written'])
-end
-
-%% repeat the operation on a sliding series of images
-display('sliding background image will be substracted')
-if nbfield_i > nbaver_ima
-    for ifield = step*(halfnbaver+1):step:nbfield_i-step*(halfnbaver+1)% ifield +iburst=index of the current processed image
-        update_waitbar(WaitbarHandle,ifield/nbfield_i)
-        if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
-            disp('program stopped by user')
-            return
-        end
-        Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
-        %incorporate next burst in the current image series
-        for iburst=1:step
-            ifile=indselect(ifield+iburst+step*halfnbaver);
-            j1=1;
-    if ~isempty(j1_series{1})
-        j1=j1_series{1}(ifile);
-    end
-            filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
-            Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile));
-            if ndims(Aread)==3;%color images
-                Aread=sum(double(Aread),3);% take the sum of color components
-            end
-            Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image
-        end
-        Asort=sort(Ak,3);%sort the new current image series by luminosity
-        B=Asort(:,:,rank);%current background image
-        %substract the background for the current burst
-        for iburst=1:step
-            Acor=double(Ak(:,:,step*halfnbaver+iburst))-double(B); %the current image has been already read ans stored as index step*halfnbaver+iburst in the current series
-            Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
-            ifile=indselect(ifield+iburst);
-            if ~isempty(j1_series{1})
-                j1=j1_series{1}(ifile);
-            end
-            newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
-            %write result file
-            if Param.ActionInput.CheckLevelTransform
-                C=levels(Acor);
+        else
+            if isequal(FileInfo{1}.BitDepth,16)
+                C=uint16(Acor);
+                imwrite(C,newname,'BitDepth',16); % save the new image
+            else
+                C=uint8(Acor);
                 imwrite(C,newname,'BitDepth',8); % save the new image
-            else
-                if isequal(FileInfo{1}.BitDepth,16)
-                    C=uint16(Acor);
-                    imwrite(C,newname,'BitDepth',16); % save the new image
-                else
-                    C=uint8(Acor);
-                    imwrite(C,newname,'BitDepth',8); % save the new image
-                end
-            end
-            display([newname ' written'])        
-        end
-    end
-end
-
-%% substract the background from the last images
-display('last background image will be substracted')
-for  ifield=nbfield_i-step*halfnbaver+1:nbfield_i
-    Acor=double(Ak(:,:,ifield-nbfield_i+step*(2*halfnbaver+1)))-double(B);
-    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
-    ifile=indselect(ifield);
-    if ~isempty(j1_series{1})
-        j1=j1_series{1}(ifile);
-    end
-    newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);  
-    %write result file
-    if Param.ActionInput.CheckLevelTransform
-        C=levels(Acor);
-        imwrite(C,newname,'BitDepth',8); % save the new image
-    else
-        if isequal(FileInfo{1}.BitDepth,16)
-            C=uint16(Acor);
-            imwrite(C,newname,'BitDepth',16); % save the new image
-        else
-            C=uint8(Acor);
-            imwrite(C,newname,'BitDepth',8); % save the new image
-        end
-    end
-    display([newname ' written'])
-end
-
+            end
+        end
+        display([newname ' written'])
+    end
+end
 
 

trunk/src/transform_field/ima_remove_background.m

@@ -54 +54 @@
 B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
 ImPart=(A-B);
-DataOut.A=ImPart.*(ImPart>threshold);
+DataOut.A=ImPart;
+%DataOut.A=ImPart.*(ImPart>threshold);
 DataOut.A=feval(Atype,DataOut.A);

trunk/src/transform_field/ima_remove_particles.m

@@ -32 +32 @@
 if strcmp(DataIn,'*')
     return
+    
 end
 
 %parameters
 threshold=200;
-nblock_x=30;%size of image subblocks for analysis
-nblock_y=30;
+nblock_x=10;%size of image subblocks for analysis
+nblock_y=10;
 %--------------------------------------------------------- 
 DataOut=DataIn;%default
@@ -49 +50 @@
 Atype=class(DataIn.A);
 A=double(DataIn.A);
-Backg=zeros(size(A));
+% Backg=zeros(size(A));
 Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
 Amin=A.*Aflagmin;%values of A at local minima
@@ -58 +59 @@
 Backg=Backg./Bmin; % find the average of minima in blocks
 B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
-ImPart=(A-B);
-ImPart=ImPart.*(ImPart>threshold);
-DataOut.A=A-ImPart;%
+DataOut.A=B;
+% ImPart=(A-B);
+% ImPart=ImPart.*(ImPart>threshold);
+% DataOut.A=A-ImPart;%
 DataOut.A=feval(Atype,DataOut.A);