Changeset 1152 for trunk

Timestamp:

Jul 4, 2024, 4:23:43 PM (6 months ago)

Author:

sommeria

Message:

update_xml simlified, bug on civ_series corrected

Location:

trunk/src

Files:

• filter_tps.m (modified) (2 diffs)
• find_imadoc.m (modified) (3 diffs)
• geometry_calib.m (modified) (7 diffs)
• plot_field.m (modified) (1 diff)
• read_multimadoc.m (modified) (1 diff)
• series.m (modified) (1 diff)
• series/civ_3D.m (modified) (1 diff)
• series/civ_input.fig (modified) (previous)
• series/civ_input.m (modified) (1 diff)
• series/civ_series.m (modified) (2 diffs)
• series/merge_proj.m (modified) (1 diff)
• series/stereo_civ.m (modified) (1 diff)
• update_imadoc.m (modified) (5 diffs)
• uvmat.m (modified) (7 diffs)

trunk/src/filter_tps.m

@@ -106 +106 @@
             ind_ind_sel=1:numel(ind_sel);%default
             if exist('Threshold','var')&&~isempty(Threshold)
-                FF(ind_sel)=2*(NormDiff>Threshold);%put FF value to 2 to identify the criterium of elimmination
+                FF(ind_sel)=4*(NormDiff>Threshold);%put FF value to 4 to identify the criterium of elimmination
                 ind_ind_sel=find(FF(ind_sel)==0); % select the indices of remaining vectors in the subset of ind_sel vectors 
             end
@@ -166 +166 @@
 U_smooth=U_smooth./nb_select;% take the average at the intersection of several subdomains
 V_smooth=V_smooth./nb_select;
-U_smooth(FF==2)=U(FF==2);% set to the initial values the eliminated vectors (flagged as false)
-V_smooth(FF==2)=V(FF==2);
+U_smooth(FF==4)=U(FF==4);% set to the initial values the eliminated vectors (flagged as false)
+V_smooth(FF==4)=V(FF==4);
 fill=zeros(NbCoord+1,NbCoord,size(SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage)
 Coord_tps=cat(1,Coord_tps,fill);

trunk/src/find_imadoc.m

@@ -2 +2 @@
 % take into account the old conventions
 %-----------------------------------------------------------------------
-% function XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt)
+% function XmlFileName=find_imadoc(RootPath,SubDir)
 %
 % OUTPUT:
@@ -8 +8 @@
 %
 % INPUT:
-% RootPath,SubDir,RootFile,FileExt, as given from the input file name by fileparts_uvmat
+% RootPath: path to the folder containing the image series,
+% SubDir: name of the folder containing the image series
 
 %=======================================================================
@@ -28 +29 @@
 %=======================================================================
 
-function XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt)
-SubDirBase=SubDir;
-XmlFileName=fullfile(RootPath,[SubDir '.xml']);
-if ~exist (XmlFileName,'file')
-    dotchar=regexp(SubDir,'\.');
+function XmlFileName=find_imadoc(RootPath,SubDir)
+
+dotchar=regexp(SubDir,'\.');%detect the dots in the folder name
+if isempty(dotchar)
+    XmlFileName=fullfile(RootPath,[SubDir '.xml']);
+else %go upward to the root name, stop if an xml file already exists
     for idot=1:numel(dotchar)
-        XmlFileName=fullfile(RootPath,[SubDir(1:dotchar(end-idot+1)-1) '.xml']);
+        SubDir=SubDir(1:dotchar(end-idot+1)-1);
+        XmlFileName=fullfile(RootPath,[SubDir '.xml']);
         if exist(XmlFileName,'file')
-            SubDirBase=fullfile(RootPath,SubDir(1:dotchar(end-idot+1)-1));
             break
-        end
-    end   
-end
-if ~exist(XmlFileName,'file')
-    XmlFileName=[fullfile(RootPath,SubDirBase,RootFile) '.xml']; % old convention: xml inside the image folder, case of images or new civ files
-    if ~exist(XmlFileName,'file')
-        XmlFileName=[fullfile(RootPath,SubDirBase,RootFile) '.civ']; % very old convention: .civ file
-        if ~exist(XmlFileName,'file') && strcmp(FileExt,'.nc')
-            XmlFileName=[fullfile(RootPath,RootFile) '.xml'] ; % old convention: xml inside the image folder, old civ file opened
-            if ~exist(XmlFileName,'file')
-                XmlFileName=[fullfile(RootPath,RootFile) '.civ']; % very old convention: .civ file
-            end
         end
     end
 end
-if ~exist(XmlFileName,'file')% convention Pierre Augier for 3D images
-    check3D=find(~isempty(regexp(SubDirBase,'^level')));
-    if check3D
-        [RootRootPath,RootDir]=fileparts(RootPath);
-        XmlFileName=fullfile(RootRootPath,[RootDir '.xml']);
-        dotchar=regexp(RootDir,'\.');
-        for idot=1:numel(dotchar)
-            XmlFileName=fullfile(RootRootPath,[RootDir(1:dotchar(end-idot+1)-1) '.xml']);
-            if exist(XmlFileName,'file')
-                break
-            end
-        end
-    end
-end
-if exist(XmlFileName,'file')~=2
+if ~exist(XmlFileName,'file')
     XmlFileName='';
 end
+
+
+

trunk/src/geometry_calib.m

@@ -125 +125 @@
 if exist('inputfile','var')&& ~isempty(inputfile)
     [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(inputfile);
-    struct.XmlInputFile=find_imadoc(RootPath,SubDir,RootFile,FileExt);
+    struct.XmlInputFile=find_imadoc(RootPath,SubDir);
     set(handles.ListCoord,'Data',[])
     if exist(struct.XmlInputFile,'file')
@@ -305 +305 @@
             end
             if find(~cellfun('isempty',strfind(ListDataSeries,'.')))
-                msgbox_uvmat('ERROR','select only folders at the root, without dot (.) in the name');
-                return
+                msgbox_uvmat('WARNING','select folders at the root, without dot (.) in the name');
             end
             NbExp=0; % counter of the number of experiments set by the GUI browse_data
@@ -332 +331 @@
             NbErrors=0;
             for iexp=1:NbExp
-                XmlName=fullfile(ListPath{iexp},[ListSubdir{iexp} '.xml']);
-                if exist(XmlName,'file')
-                    check_update=1;
-                else
-                    check_update=0;
-                end
-                errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file
+                [check_update,xmlfile,errormsg]=update_imadoc(ListPath{iexp},ListSubdir{iexp},'GeometryCalib',GeometryCalib);% introduce the calibration data in the xml file
                 dispmessage='';
                 if checkslice
-                    errormsg=update_imadoc(Slice,XmlName,'Slice');% introduce the slice position in the xml file
+                   [~,~,errormsg]=update_imadoc(ListPath{iexp},ListSubdir{iexp},'Slice',Slice,0);% introduce the slice position in the xml file
                     dispmessage=' and slice position';
                 end
@@ -349 +342 @@
                 else
                     if check_update
-                        disp([XmlName ' updated with calibration parameters' dispmessage]);
+                        disp([xmlfile ' updated with calibration parameters' dispmessage]);
                     else
-                        disp([XmlName ' created with calibration parameters: no timing defined' dispmessage]);
+                        disp([xmlfile ' created with calibration parameters: no timing defined' dispmessage]);
                     end
                 end
@@ -363 +356 @@
     else
         %% update the calibration parameters in the currently opened uvmat GUI
-        if ~exist(outputfile,'file') && ~isempty(SubDirBase) %copy the xml file from the old location if appropriate
-            oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
-            if exist(oldxml,'file')
-                [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
-            end
-        end
-        errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file
+        % if ~exist(outputfile,'file') && ~isempty(SubDirBase) %copy the xml file from the old location if appropriate
+        %     oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
+        %     if exist(oldxml,'file')
+        %         [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
+        %     end
+        % endSlice,
+        [~,~,errormsg]=update_imadoc(RootPath,get(hhuvmat.SubDir,'String'),'GeometryCalib',GeometryCalib);% introduce the calibration data in the xml file
         if checkslice
-            errormsg=update_imadoc(Slice,outputfile,'Slice');% introduce the slice position in the xml file
+          [~,~,errormsg]=update_imadoc(RootPath,get(hhuvmat.SubDir,'String'),'Slice',Slice,0);% introduce the slice position in the xml file
         end
         if ~strcmp(errormsg,'')
@@ -839 +832 @@
 
 %------------------------------------------------------------------------
-% --- Executes on button press in STORE.
+% --- Executes on button press in STORE: store the current points
 function STORE_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
 Coord=get(handles.ListCoord,'Data');
-%Object=read_geometry_calib(Coord_cell);
 unitlist=get(handles.CoordUnit,'String');
 unit=unitlist{get(handles.CoordUnit,'value')};
@@ -850 +842 @@
 huvmat=findobj(allchild(0),'Name','uvmat');
 hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
-% RootPath='';
-% RootFile='';
-if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
-    %     testhandle=1;
+if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.SubDir)
     RootPath=get(hhuvmat.RootPath,'String');
-    RootFile=get(hhuvmat.RootFile,'String');
-    filebase=[fullfile(RootPath,RootFile) '~'];
+    SubDir=get(hhuvmat.SubDir,'String');
+    filebase=[fullfile(RootPath,SubDir) '~'];
     while exist([filebase '.xml'],'file')
         filebase=[filebase '~'];
     end
     outputfile=[filebase '.xml'];
-    errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');
+    [~,RootFile]=fileparts(filebase);
+    [~,~,errormsg]=update_imadoc(RootPath,SubDir,'GeometryCalib',GeometryCalib,0);
     if ~strcmp(errormsg,'')
         msgbox_uvmat('ERROR',errormsg);

trunk/src/plot_field.m

@@ -1219 +1219 @@
     if ~isempty(ivar_FF_vec)
         if isfield(PlotParam.Vectors,'CheckShowFalse') && PlotParam.Vectors.CheckShowFalse==1
-           % colorlist(nbcolor,:)=[1 0 1];% magenta color
-            colorlist(nbcolor,:)=[0 0 0];% blackcolor
+            colorlist(nbcolor,:)=[1 0 1];% magenta color
+            %colorlist(nbcolor,:)=[0 0 0];% blackcolor
             if strcmp(PlotParam.Vectors.FalseCriteria,'ALL')
                 col_vec(vec_FF~=0)=nbcolor;

trunk/src/read_multimadoc.m

@@ -42 +42 @@
 timecell=cell(1,nbview);
 for iview=1:nbview%Loop on views
-    XmlFileName=find_imadoc(RootPath{iview},SubDir{iview},RootFile{iview},FileExt{iview});
+    XmlFileName=find_imadoc(RootPath{iview},SubDir{iview});
     if ~isempty(XmlFileName)
         [XmlData{iview},warnmsg]=imadoc2struct(XmlFileName);% read the ImaDoc xml file

trunk/src/series.m

@@ -949 +949 @@
 XmlData=[];
 check_calib=0;
-XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
+XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2});
 if ~isempty(XmlFileName)
     [XmlData,errormsg]=imadoc2struct(XmlFileName);

trunk/src/series/civ_3D.m

@@ -189 +189 @@
 %% get timing from the ImaDoc file or input video
 if iview_A~=0
-    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
+    XmlFileName=find_imadoc(RootPath_A,SubDir_A);
     Time=[];
     if ~isempty(XmlFileName)

trunk/src/series/civ_input.m

@@ -2362 +2362 @@
 % --- Executes on selection change in field_ref2.
 function field_ref2_Callback(hObject, eventdata, handles)
-
-
-

trunk/src/series/civ_series.m

@@ -256 +256 @@
 %% get timing from the ImaDoc file or input video
 if iview_A~=0
-    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
+    XmlFileName=find_imadoc(RootPath_A,SubDir_A);
     Time=[];
     if ~isempty(XmlFileName)
@@ -488 +488 @@
         end
         if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
-            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
-            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
-            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];
-            for ivol=1:NbSlice
-                % caluclate velocity data (y and v in indices, reverse to y component)
-                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
-                if ~isempty(errormsg)
-                    disp_uvmat('ERROR',errormsg,checkrun)
-                    return
-                end
-                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
-                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
-                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
-                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
-                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
-                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
-                Data.Civ1_FF=[Data.Civ1_FF reshape(F,[],1)];
-            end
+            % Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
+            % Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
+            % Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];
+            % for ivol=1:NbSlice
+            %     % caluclate velocity data (y and v in indices, reverse to y component)
+            %     [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
+            %     if ~isempty(errormsg)
+            %         disp_uvmat('ERROR',errormsg,checkrun)
+            %         return
+            %     end
+            %     Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
+            %     Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
+            %     Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
+            %     Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
+            %     Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
+            %     Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
+            %     Data.Civ1_FF=[Data.Civ1_FF reshape(F,[],1)];
+            % end
         else %usual PIV
             % caluclate velocity data (y and v in indices, reverse to y component)

trunk/src/series/merge_proj.m

@@ -338 +338 @@
             end
             [MaskData,~,errormsg] = read_field(maskname,'image');
+            if ~isempty(NbSlice_calib)
+            MaskData.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
+        end
             if ~isempty(transform_fct) && nargin(transform_fct)>=2
                 MaskData=transform_fct(MaskData,XmlData{iview});

trunk/src/series/stereo_civ.m

@@ -95 +95 @@
 time=[];
 for iview=1:size(Param.InputTable,1)
-    XmlFileName=find_imadoc(Param.InputTable{iview,1},Param.InputTable{iview,2},Param.InputTable{iview,3},Param.InputTable{iview,5});
+    XmlFileName=find_imadoc(Param.InputTable{iview,1},Param.InputTable{iview,2});
     if isempty(XmlFileName)
         disp_uvmat('ERROR', [XmlFileName ' not found'],checkrun)

trunk/src/update_imadoc.m

@@ -1 +1 @@
 %'update_imadoc': update an xml file with geometric calibration parameters
 %--------------------------------------------------------------------------
-%  function update_imadoc(Struct,outputfile)
+%  function [checkcreate,xmlfile,errormsg]=update_imadoc(Struct,RootPath,SubDir,StructName)
 %
-%INPUT:
-% Struct: structure containing the calibration parameters
-% outputfile: xml file to modify
+% OUTPUT:
+% checkupdate= 1 if the xml file (containing timing)already exist, =0 when it has to be created
+% xmlfile: name of the xmlfile containing the the calibration data
+% errormsg: error message, ='' if OK
+
+% INPUT:
+
+% RootPath: path to the folder containing the image series to calibrate
+% SubDir: folder contaiting the image series to calibrate
 % StructName : Name of the field in the xml file
+% Struct: Matlab structure containing the calibration parameters
+% checkbackup=1 (default): backup of existing xml file as .xml~, 
 %-------------------------------------------------------------
 
@@ -27 +35 @@
 %=======================================================================
 
-function errormsg=update_imadoc(Struct,outputfile,StructName)
+function [checkupdate,xmlfile,errormsg]=update_imadoc(RootPath,SubDir,StructName,Struct,checkbackup)
+
 errormsg='';
-testappend=0;
+if ~exist('checkbackup','var')
+    checkbackup=1;
+end
 
 %% set the output xml file at the root, hide other existing  xml files
-dotchar=regexp(outputfile,'\.');
-for idot=1:numel(dotchar)
-    outputfile=[outputfile(1:dotchar(end-idot+1)-1) '.xml'];
-    if exist(outputfile,'file')
-         backupfile=outputfile;
-         testexist=2;
+xmlfile=find_imadoc(RootPath,SubDir);
+if isempty(xmlfile)
+    checkupdate=0;
+else
+    checkupdate=1;
+end
+
+%% backup the existing xml file, adding a ~ to its name
+if checkupdate
+    if checkbackup
+        backupfile=xmlfile;
+        testexist=2;
         while testexist==2
             backupfile=[backupfile '~'];
             testexist=exist(backupfile,'file');
         end
-        [success,message]=movefile(outputfile,backupfile);%make backup
+        [success,message]=copyfile(xmlfile,backupfile);%make backup
         if success~=1
             errormsg=['errror in xml file backup: ' message];
@@ -48 +65 @@
         end
     end
-end
-
-
-%% backup the output file if it already exist, and read it
-if exist(outputfile,'file')%=1 if the output file already exists, 0 else
-    testappend=1;
-    t=xmltree(outputfile); %read the file
+    t=xmltree(xmlfile); %read the file
     title=get(t,1,'name');
     if ~strcmp(title,'ImaDoc')
-        errormsg=[outputfile ' not appropriate for calibration'];
+        errormsg=[xmlfile ' not appropriate for calibration'];
         return
     end
@@ -67 +78 @@
         t=delete(t,uid_child);
     end
-end
-
-%% create a new xml file
-if ~testappend
+else   % create a new xml file
     t=xmltree;
     t=set(t,1,'name','ImaDoc');
-    % in case of movie (avi file), copy timing info in the new xml file
-    [pp,outputroot]=fileparts(outputfile);
-    %     imainfo=[];
-    if exist(fullfile(pp,[outputroot '.avi']),'file')
-        FileName=fullfile(pp,[outputroot '.avi']);
-        hhh=which('videoreader');
-        if isempty(hhh)%use old video function of matlab
-            imainfo=aviinfo(FileName);
-            imainfo.FrameRate=imainfo.FramesPerSecond;
-            imainfo.NumberOfFrames=imainfo.NumFrames;
-        else %use video function videoreader of matlab
-            imainfo=get(videoreader(FileName));
-        end
-        if ~isempty(imainfo)
-            [t,uid_camera]=add(t,1,'element','Camera');
-            Camera.TimeUnit='s';
-            Camera.BurstTiming.Time=0;
-            Camera.BurstTiming.Dti=1/imainfo.FrameRate;
-            Camera.BurstTiming.NbDti=imainfo.NumberOfFrames-1;
-            t=struct2xml(Camera,t,uid_camera);
-        end
-    end
     [t,uid_calib]=add(t,1,'element',StructName);
 end
@@ -101 +87 @@
 t=struct2xml(Struct,t,uid_calib);
 try
-    save(t,outputfile);
+    save(t,xmlfile);
 catch ME
-    errormsg=['error in saving ' outputfile ': ' ME.message];
+    errormsg=['error in saving ' xmlfile ': ' ME.message];
 end

trunk/src/uvmat.m

@@ -1399 +1399 @@
 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%name of the current input file
 [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(FileName);
-XmlFile=find_imadoc(RootPath,SubDir,RootFile,FileExt);%find name of the relevant xml file
+XmlFile=find_imadoc(RootPath,SubDir);%find name of the relevant xml file
 if isempty(XmlFile)
     msgbox_uvmat('ERROR','an xml file with calibration parameters must be first created, use Tools/geometric calibration');
@@ -1474 +1474 @@
         end
         for iexp=1:NbExp
-            XmlName=fullfile(ListPath{iexp},[ListSubdir{iexp} '.xml']);
-            if exist(XmlName,'file')
-                check_update=1;
-            else
-                check_update=0;
-            end
-            errormsg=update_imadoc(Slice,XmlName,'Slice');% introduce the calibration data in the xml file
+            % XmlName=fullfile(ListPath{iexp},[ListSubdir{iexp} '.xml']);
+            % if exist(XmlName,'file')
+            %     check_update=1;
+            % else
+            %     check_update=0;
+            % end
+            [check_update,xmlfile,errormsg]=update_imadoc(ListPath{iexp},ListSubdir{iexp},'Slice',Slice);% introduce the calibration data in the xml file
             if ~strcmp(errormsg,'')
                 msgbox_uvmat('ERROR',errormsg);
             else
                 if check_update
-                    display([XmlName ' updated with slice positions'])
+                    disp([xmlfile ' updated with slice positions'])
                 else
-                    display([XmlName ' created with slice positions'])
+                    disp([xmlfile ' created with slice positions'])
                 end
             end
@@ -1496 +1496 @@
     
     %% store the result in the xml file used for calibration
-    errormsg=update_imadoc(Slice,XmlFile,'Slice');% introduce the calibration data in the xml file
+    [~,xmlfile,errormsg]=update_imadoc(RootPath,SubDir,'Slice',Slice);% introduce the calibration data in the xml file
     if strcmp(errormsg,'')
-        msgbox_uvmat('CONFIRMATION',['slice positions saved in ' XmlFile]);
+        msgbox_uvmat('CONFIRMATION',['slice positions saved in ' xmlfile]);
     else
         msgbox_uvmat('ERROR',errormsg);
@@ -1779 +1779 @@
 answer = questdlg('Where','record the LIF parameters','Current series', 'Replicate', 'Cancel', 'Cancel');
 if strcmp(answer,'Current series')
-    XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String'));
-    update_imadoc(XmlData.LIFCalib,XmlFileName,'LIFCalib');% introduce the calibration data in the xml file
+    %XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String'));
+    update_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),'LIFCalib',XmlData.LIFCalib);% introduce the calibration data in the xml file
     % display the concentration in uvmat
     InputFileREFRESH_Callback(hObject, eventdata, handles);% refresh the current xml file to apply 'ima2concentration'
@@ -1827 +1827 @@
     end
     for iexp=1:NbExp
-        XmlName=fullfile(ListPath{iexp},[ListSubdir{iexp} '.xml']);
-        if exist(XmlName,'file')
-            check_update=1;
-        else
-            check_update=0;
-        end
-        errormsg=update_imadoc(XmlData.LIFCalib,XmlName,'LIFCalib');% introduce the calibration data in the xml file
+        % XmlName=fullfile(ListPath{iexp},[ListSubdir{iexp} '.xml']);
+        % if exist(XmlName,'file')
+        %     check_update=1;
+        % else
+        %     check_update=0;
+        % end
+        [check_update,xmlfile,errormsg]=update_imadoc(ListPath{iexp},ListSubdir{iexp},'LIFCalib',XmlData.LIFCalib);% introduce the calibration data in the xml file
         if ~strcmp(errormsg,'')
             msgbox_uvmat('ERROR',errormsg);
         else
             if check_update
-                display([XmlName ' updated with calibration parameters'])
+                display([xmlfile ' updated with calibration parameters'])
             else
-                display([XmlName ' created with calibration parameters'])
+                display([xmlfile ' created with calibration parameters'])
             end
         end
@@ -1846 +1846 @@
     msgbox_uvmat('CONFIMATION',['LIF calibration replicated for ' num2str(NbExp) ' experiments']);
 end
-
-
-
-%     
-%     
-%     t=xmltree(XmlFileName); %read the file
-%     title_str=get(t,1,'name');
-%     if ~strcmp(title_str,'ImaDoc')
-%         msgbox_uvmat('ERROR','wrong xml file');
-%         return
-%     end
-%     % backup the output file if it already exist, and read it
-%     backupfile=XmlFileName;
-%     testexist=2;
-%     while testexist==2
-%         backupfile=[backupfile '~'];
-%         testexist=exist(backupfile,'file');
-%     end
-%     [success,message]=copyfile(XmlFileName,backupfile);%make backup
-%     if success~=1
-%         errormsg=['errror in xml file backup: ' message];
-%         return
-%     end
-%     uid_illumination=find(t,'ImaDoc/LIFCalib');
-%     if isempty(uid_illumination)  %if GeometryCalib does not already exists, create it
-%         [t,uid_illumination]=add(t,1,'element','LIFCalib');
-%     end
-%     uid_origin=find(t,'ImaDoc/LIFCalib/LightOrigin');
-%     if ~isempty(uid_origin)  %if LightOrigin already exists, delete it
-%         t=delete(t,uid_origin);
-%     end
-%     uid_line=find(t,'ImaDoc/LIFCalib/Ray1Coord');
-%     if ~isempty(uid_line)  %if Ray1Coord already exists, delete it
-%         t=delete(t,uid_line);
-%     end
-%     uid_line=find(t,'ImaDoc/LIFCalib/Ray2Coord');
-%     if ~isempty(uid_line)  %if Ray2Coord already exists, delete it
-%         t=delete(t,uid_line);
-%     end
-%     uid_line=find(t,'ImaDoc/LIFCalib/RefLineCoord');
-%     if ~isempty(uid_line)  %if RefLineCoord already exists, delete it
-%         t=delete(t,uid_line);
-%     end
-%     uid_mask=find(t,'ImaDoc/LIFCalib/MaskPolygonCoord');
-%     if ~isempty(uid_mask) %if MaskPolygonCoord already exists, delete it
-%         t=delete(t,uid_mask);
-%     end
-%     uid_BlackOffset=find(t,'ImaDoc/LIFCalib/BlackOffset');
-%     if ~isempty(uid_BlackOffset)  %if BlackOffset already exists, delete it
-%         t=delete(t,uid_BlackOffset);
-%     end
-%     uid_RefLineWidth=find(t,'ImaDoc/LIFCalib/RefLineWidth');
-%     if ~isempty(uid_RefLineWidth)  %if RefLineWidth already exists, delete it
-%         t=delete(t,uid_RefLineWidth);
-%     end
-%     uid_DecayRate=find(t,'ImaDoc/LIFCalib/DecayRate');
-%     if ~isempty(uid_DecayRate)  %if DecayRate already exists, delete it
-%         t=delete(t,uid_DecayRate);
-%     end
-%     uid_RefLineRadius=find(t,'ImaDoc/LIFCalib/RefLineRadius');
-%     if ~isempty(uid_RefLineRadius)  %if RefLineLum already exists, delete it
-%         t=delete(t,uid_RefLineRadius);
-%     end
-%     uid_RefLineLum=find(t,'ImaDoc/LIFCalib/RefLineLum');
-%     if ~isempty(uid_RefLineLum)  %if RefLineLum already exists, delete it
-%         t=delete(t,uid_RefLineLum);
-%     end
-%     uid_RefLineAzimuth=find(t,'ImaDoc/LIFCalib/RefLineAzimuth');
-%     if ~isempty(uid_RefLineAzimuth)  %if RefLineLum already exists, delete it
-%         t=delete(t,uid_RefLineAzimuth);
-%     end
-%     
-%     % save the LIF calibration data
-%     t=struct2xml(XmlData.LIFCalib,t,uid_illumination);
-%     save(t,XmlFileName);
-    
-
 
 
@@ -2504 +2427 @@
     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
 end
-XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
+XmlFileName=find_imadoc(RootPath,SubDir);
 [tild,tild,DocExt]=fileparts(XmlFileName);
 warntext='';%default warning message