Changeset 1178 for trunk

Timestamp:

Mar 21, 2025, 10:17:07 AM (4 weeks ago)

Author:

sommeria

Message:

virtual frame indexing introduced

Location:

trunk/src

Files:

• get_file_info.m (modified) (3 diffs)
• imadoc2struct.m (modified) (1 diff)
• index2filename.m (added)
• read_image.m (modified) (1 diff)
• read_rdvision.m (modified) (4 diffs)
• series.fig (modified) (previous)
• series.m (modified) (6 diffs)
• series/aver_spectral.m (modified) (1 diff)
• series/aver_stat.m (modified) (1 diff)
• series/civ_series.m (modified) (7 diffs)
• series/extract_rdvision_times.m (deleted)
• series/rdvision_check_time.m (added)
• series/sub_background.m (modified) (21 diffs)
• uvmat.m (modified) (43 diffs)
• xml_schemas (added)
• xml_schemas/ImaDoc.xsd (added)
• xml_schemas/ImaDoc_ancillary.xml (added)
• xml_schemas/ImaDoc_template_burst.xml (added)
• xml_schemas/ImaDoc_template_pairs.xml (added)
• xml_schemas/ImaDoc_template_series.xml (added)
• xml_schemas/ImaDoc_template_volume.xml (added)
• xml_shemas (deleted)

trunk/src/get_file_info.m

@@ -79 +79 @@
         FileInfo.FileType=regexprep(FileExt,'^.','');% eliminate the dot of the extension;
     case {'.seq','.sqb'}
-        [~,FileInfo,timestamps,errormsg]=read_rdvision(fileinput,[]);
+        [~,FileInfo]=read_rdvision(fileinput,[]);
     case '.im7'
         try
@@ -158 +158 @@
                         FileInfo=orderfields(FileInfo,[nbfield nbfield-1 nbfield-2 (1:nbfield-3)]); %reorder the fields of fileInfo for clarity
                     catch ME
-                        FileInfo.error=ME.message
+                        FileInfo.error=ME.message;
                     end
                 else
@@ -165 +165 @@
                         [Data,tild,tild,errormsg]=nc2struct(fileinput,[]);
                         if isempty(errormsg)
-                            %                             if isfield(Data,'absolut_time_T0') && isfield(Data,'hart') && ~isempty(Data.absolut_time_T0) && ~isempty(Data.hart)
-                            %                                 FileInfo.FileType='civx';%old civ data from the Fortran program
-                            %                                 if isfield(Data,'patch2') && isequal(Data.patch2,1)
-                            %                                     FileInfo.CivStage=6;
-                            %                                 elseif isfield(Data,'fix2') && isequal(Data.fix2,1)
-                            %                                     FileInfo.CivStage=5;
-                            %                                 elseif  isfield(Data,'civ2')&& isequal(Data.civ2,1)
-                            %                                     FileInfo.CivStage=4;
-                            %                                 elseif isfield(Data,'patch')&&isequal(Data.patch,1)
-                            %                                     FileInfo.CivStage=3;
-                            %                                 elseif isfield(Data,'fix')&&isequal(Data.fix,1)
-                            %                                     FileInfo.CivStage=2;
-                            %                                 else
-                            %                                     FileInfo.CivStage=1;
-                            %                                 end
-                            %                             else
                             if isfield(Data,'Conventions') && strcmp(Data.Conventions,'uvmat/civdata')
                                 FileInfo.FileType='civdata'; % test for civ velocity fields

trunk/src/imadoc2struct.m

@@ -40 +40 @@
 %% opening the xml file
 [tild,tild,FileExt]=fileparts(ImaDoc);
-%% case of .civ files (obsolete)
-if strcmp(FileExt,'.civ')
-    [errormsg,time,TimeUnit,mode,npx,npy,s.GeometryCalib]=read_imatext(ImaDoc);
-    return
-end
 
-%% case of xml files
 if nargin ==1
     [s,Heading,errormsg]=xml2struct(ImaDoc);% convert the whole xml file in a structure s

trunk/src/read_image.m

@@ -83 +83 @@
          A=(reshape(A,Header(1).Width,Header(1).Height))';
          A=flip(A,1);
+    case 'rdvision'
+         A=read_rdvision(FileName,num);
 end

trunk/src/read_rdvision.m

@@ -63 +63 @@
 s=ini2struct(filename_seq);
 FileInfo=s.sequenceSettings;
+FileInfo.Width=str2double(FileInfo.width);
+FileInfo.Height=str2double(FileInfo.height);
+if isequal(FileInfo.bytesperpixel,'2')
+    FileInfo.BitDepth=16;
+else
+    FileInfo.BitDepth=8;
+end
 if isfield(s.sequenceSettings,'numberoffiles')
     FileInfo.NumberOfFrames=str2double(s.sequenceSettings.numberoffiles);
@@ -119 +126 @@
             binrepertoire=regexprep(FileInfo.bindirectory,'\\$','');%tranform Windows notation to Linux
             binrepertoire=regexprep(binrepertoire,'\','/');
-            [tild,binrepertoire,DirExt]=fileparts(binrepertoire);
+            [~,binrepertoire,DirExt]=fileparts(binrepertoire);
             binrepertoire=[binrepertoire DirExt];     
         end 
@@ -144 +151 @@
     FileInfo.StartTime=regexprep(FileInfo.binrepertoire,'T',' ');
     FileInfo.EndTime=datestr(datenum(FileInfo.StartTime,'yyyy-mm-dd HH.MM.SS')+timestamps(end)/86400);
-    disp(FileInfo)
 end
 
@@ -238 +244 @@
     if isempty(s)
         continue;
-    end;
+    end
     if (s(1)==';')                      % ';' start comment lines
         continue;
-    end;
+    end
     if (s(1)=='#')                      % '#' start comment lines
         continue;
-    end;
+    end
     if ( s(1)=='[' ) && (s(end)==']' )
         % We found section

trunk/src/series.m

@@ -553 +553 @@
 set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
 set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
+set(handles.Relabel,'BackgroundColor',[0 1 0])
 drawnow
 empty_line=false(size(InputTable,1),1);
@@ -876 +877 @@
     MinIndex_j=0;
 end
+if isfield(FileInfo,'Software')&&~isempty(FileInfo.Software) && ~isempty(regexp(FileInfo.Software,'^pco.camware', 'once'))
+    MinIndex_i=0;
+end
+if strcmp(FileInfo.FileType,'rdvision')
+    set(handles.OutputSubDir,'String','/im')
+end
 MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
 MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
@@ -1035 +1042 @@
         TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
     end
+end
+
+%% case of possible index relabeling from xml info
+if isfield(XmlData,'FileSeries')&& strcmp(FileInfo.FileType,'multimage')
+    set(handles.Relabel,'Visible','on')
+    set(handles.Relabel,'Value',0)
+    SeriesData.FileSeries{iview}=XmlData.FileSeries;
+    TimeMin=Time(2,2);
+    TimeMax=Time(end,end);
+    TimeFirst=TimeMin;
+    TimeLast=TimeMax;
+elseif iview==1
+    set(handles.Relabel,'Visible','off')
 end
 
@@ -1407 +1427 @@
 if isfield(SeriesData,'ProjObject')
     Param.ProjObject=SeriesData.ProjObject;
+end
+if isfield(SeriesData,'FileSeries')
+    Param.FileSeries=SeriesData.FileSeries{1};
 end
 if ~isfield(SeriesData,'i1_series')
@@ -3936 +3959 @@
 
 
-
-
 function OutputPath_Callback(hObject, eventdata, handles)
 
@@ -3959 +3980 @@
 
 
-
 % --- Executes on button press in DeleteMask.
 function DeleteMask_Callback(hObject, eventdata, handles)
 set(handles.MaskTable,'Data',{})
+
+
+% --- Executes on button press in Relabel.
+function Relabel_Callback(hObject, eventdata, handles)
+if get(handles.Relabel,'Value')
+    SeriesData=get(handles.series,'UserData');
+    if isfield(SeriesData,'FileSeries')&& ~isempty(SeriesData.FileSeries{1})
+        [nbfield,nbfield_j]=size(SeriesData.Time{1});
+        nbfield=nbfield-1; %remove the possible index 0
+        nbfield_j=nbfield_j-1; %remove the possible index 0
+        MaxIndex_i=get(handles.MaxIndex_i,'Data');
+        MaxIndex_j=get(handles.MaxIndex_j,'Data');
+        MaxIndex_i(1,:)=nbfield;
+        MaxIndex_j(1,:)=nbfield_j;
+                MinIndex_i(1,:)=1;
+        MinIndex_j(1,:)=1;
+        set(handles.MaxIndex_i,'Data',MaxIndex_i)
+        set(handles.MaxIndex_j,'Data',MaxIndex_j)
+         set(handles.MinIndex_i,'Data',MinIndex_i)
+        set(handles.MinIndex_j,'Data',MinIndex_j)
+        first_i=str2double(get(handles.num_first_i,'String'));
+        first_j=str2double(get(handles.num_first_j,'String'));
+        i1=(first_i-SeriesData.FileSeries{1}.FirstFileIndex)*SeriesData.FileSeries{1}.NbFramePerFile+1;%frame index deduced from input file index
+        if strcmp(SeriesData.TimeName,'xml')% indices i and j
+            j1=mod(i1-1,nbfield_j)+first_j;
+            i1=floor((i1-1)/nbfield_j)+1;
+            set(handles.num_first_j,'String',num2str(j1))
+        end
+        set(handles.num_first_i,'String',num2str(i1))
+%         last_i=str2double(get(handles.num_last_i,'String'));
+%         last_j=str2double(get(handles.num_last_j,'String'));
+%         i1=(last_i-SeriesData.FileSeries{1}.FirstFileIndex)*SeriesData.FileSeries{1}.NbFramePerFile+1;%frame index deduced from input file index
+%         if strcmp(SeriesData.TimeName,'xml')% indices i and j
+%             j1=mod(i1-1,nbfield_j)+1;
+%             i1=floor((i1-1)/nbfield_j)+1;
+%         end
+        set(handles.num_last_i,'String',num2str(nbfield))
+         set(handles.num_last_j,'String',num2str(nbfield_j))
+    end
+else
+    check_input_file_series(handles)
+    ActionInput_Callback([],[], handles)
+end
+

trunk/src/series/aver_spectral.m

@@ -144 +144 @@
 transform_fct='';%default
 if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
-    addpath(Param.FieldTransform.TransformPath)
+            currentdir=pwd;
+    cd(Param.FieldTransform.TransformPath)
     transform_fct=str2func(Param.FieldTransform.TransformName);
-    rmpath(Param.FieldTransform.TransformPath)
+    cd (currentdir)
 end
 

trunk/src/series/aver_stat.m

@@ -198 +198 @@
 transform_fct='';%default
 if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
-    addpath(Param.FieldTransform.TransformPath)
+            currentdir=pwd;
+    cd(Param.FieldTransform.TransformPath)
     transform_fct=str2func(Param.FieldTransform.TransformName);
-    rmpath(Param.FieldTransform.TransformPath)
+    cd (currentdir)
     if isfield(Param,'TransformInput')
         XmlData{1}.TransformInput=Param.TransformInput;

trunk/src/series/civ_series.m

@@ -254 +254 @@
     end
 end
+CheckRelabel=isfield(Param,'FileSeries' );%=true for index relabeling (PCO)
 
 %% introduce input image transform
 transform_fct=[];%default, no transform
 if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
-       % addpath(Param.FieldTransform.TransformPath)
         currentdir=pwd;
     cd(Param.FieldTransform.TransformPath)
     transform_fct=str2func(Param.FieldTransform.TransformName);
     cd (currentdir)
-    %rmpath(Param.FieldTransform.TransformPath)
 end
 
@@ -289 +288 @@
     end
     OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
-
+    if CheckRelabel
+         RootFileOut=index2filename(Param.FileSeries,1,1,MaxIndex_j);
+    else
+        RootFileOut=RootFile_A;
+    end
     if strcmp(Param.ActionInput.ListCompareMode,'PIV')
-        ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
+        ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
             j1_series_Civ1(ifield),j2_series_Civ1(ifield));
     else
-        ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
+        ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
             j1_series_Civ1(ifield),j2_series_Civ1(ifield));
     end
@@ -314 +317 @@
         end
         if strcmp(Param.ActionInput.ListCompareMode,'PIV')
-            ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2);
+            ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2);
         else % displacement
-            ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2);
+            ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeNc,i2_civ2,[],j2_civ2);
         end
     end
@@ -336 +339 @@
             if strcmp(Param.ActionInput.ListCompareMode,'displacement')
                 ImageName_A=Param.ActionInput.RefFile;
+            elseif CheckRelabel
+            [RootFile,FileIndexString,FrameIndex_A]=index2filename(Param.FileSeries,i1_series_Civ1(ifield),j1_series_Civ1(ifield),MaxIndex_j);
+            ImageName_A=fullfile(RootPath_A,SubDir_A,[RootFile FileIndexString FileExt_A]);
             else
                 ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
+                FrameIndex_A=FrameIndex_A_Civ1(ifield);
             end
             if strcmp(FileExt_A,'.nc')% case of input images in format netcdf
@@ -368 +375 @@
                 end
                 tsart_input=tic;
-                [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
+                [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A);
                 time_input=toc(tsart_input);
             end
+if CheckRelabel
+            [RootFile,FileIndexString,FrameIndex_B]=index2filename(Param.FileSeries,i1_series_Civ1(ifield),j1_series_Civ1(ifield),MaxIndex_j);
+            ImageName_B=fullfile(RootPath_B,SubDir_B,[RootFile FileIndexString FileExt_B]);
+else
             ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
+            FrameIndex_B=FrameIndex_B_Civ1(ifield);
+end
             if isempty(FileType_B)% determine the image type for the first field
                 [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
@@ -380 +393 @@
                 continue
             end
-            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
+            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B);
             
         catch ME % display errors in reading input images
@@ -613 +626 @@
         if strcmp(Param.ActionInput.ListCompareMode,'displacement')
             ImageName_A_Civ2=Param.ActionInput.RefFile;
-        else
+        elseif CheckRelabel
+              [RootFile,FileIndexString,FrameIndex_A_2]=index2filename(Param.FileSeries,i1_series_Civ2(ifield),j1_series_Civ2(ifield),MaxIndex_j);
+            ImageName_A_Civ2=fullfile(RootPath_A,SubDir_A,[RootFile FileIndexString FileExt_A]);
+            else
             ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2);
-        end
-        if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
+            FrameIndex_A_2=FrameIndex_A_Civ2(ifield);
+        end
+        if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A,FrameIndex_A_2)
             par_civ2.ImageA=par_civ1.ImageA;
         else
-            [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
-        end
+            [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_2);
+        end
+        if CheckRelabel
+              [RootFile,FileIndexString,FrameIndex_B_2]=index2filename(Param.FileSeries,i2_civ2,j2_civ2,MaxIndex_j);
+            ImageName_B_Civ2=fullfile(RootPath_B,SubDir_B,[RootFile FileIndexString FileExt_B]);
+            else
+
+
         ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2);
-        if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
+        FrameIndex_B_2=FrameIndex_B_Civ2(ifield);
+        end
+        if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_2,FrameIndex_B)
             par_civ2.ImageB=par_civ1.ImageB;
         else
-            [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
+            [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_2);
         end
         %  [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2);

trunk/src/series/sub_background.m

@@ -10 +10 @@
 % Organization of image indices:
     % The program is working on a series of images, 
-    % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=nbfield_j)
-    % Else nbfield2=nbfield_j =nbre of images in a burst (j index)
+    % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=NbField_j)
+    % Else nbfield2=NbField_j =nbre of images in a burst (j index)
     
 % function GUI_config=sub_background(Param)
@@ -83 +83 @@
     ParamOut.OutputDirExt='.sback';%set the output dir extension
     ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
-    
-    %% root input file(s) and type
-    % check the existence of the first file in the series
-        first_j=[];% note that the function will propose to cover the whole range of indices
-    if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end
-    last_j=[];
-    if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end
-    PairString='';
-    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
-    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
-    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
-        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
-    if ~exist(FirstFileName,'file')
-        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
-    else
-        [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
-        LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
-        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
-        if ~exist(FirstFileName,'file')
-             msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
-        end
-    end
 
     %% check the validity of  input file types
-    FileInfo=get_file_info(FirstFileName);
-    FileType=FileInfo.FileType;
-    CheckImage=strcmp(FileInfo.FieldType,'image');% =1 for images
-    if ~CheckImage
-        msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image'])
+    if isfield(Param,'SeriesData')&& isfield(Param.SeriesData,'FileInfo')
+    if ~strcmp(Param.SeriesData.FileInfo{1}.FieldType,'image')
+        msgbox_uvmat('ERROR','invalid file type input: not an image series')
         return
     end
-    
+    end
+
     %% numbers of fields
     NbSlice_i=1;%default
@@ -124 +101 @@
         incr_j=Param.IndexRange.incr_j;
     end
-    if isempty(first_j)||isempty(last_j)
-        nbfield_j=1;
+    if isfield(Param.IndexRange,'first_j')&&~isempty(Param.IndexRange.first_j)
+        NbField_j=numel(Param.IndexRange.first_j:incr_j:Param.IndexRange.last_j);%nb of fields for the j index (bursts or volume slices)
     else
-        nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices)
+        NbField_j=1;
     end
     first_i=1;last_i=1;incr_i=1;%default
@@ -136 +113 @@
     end
     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=NbField_j*nbfield_i; %total number of fields
     nbfield_i=floor(nbfield/NbSlice_i);%total number of  indexes in a slice (adjusted to an integer number of slices)
     
@@ -143 +120 @@
     nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts 
     SaturationValue=0;
-     if nbfield_i~=1 && nbfield_j<=nbaver_init
-        nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background,
+     if nbfield_i~=1 && NbField_j<=nbaver_init
+        nbaver=floor(nbaver_init/NbField_j); % number of bursts used for the sliding background,
         if isequal(mod(nbaver,2),0)% if nbaver is even
             nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
         end
-        nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts
+        nbaver_init=nbaver*NbField_j;%propose by default an integer number of bursts
     end
     BrightnessRankThreshold=0.1;
@@ -161 +138 @@
           BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold;
         end
-%         if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian
-%         CheckSubmedian='Yes';
-%         end
         if isfield(Param.ActionInput,'SaturationValue') 
             SaturationValue=Param.ActionInput.SaturationValue;
@@ -190 +164 @@
         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
-    end
-    ParamOut.ActionInput.SlidingSequenceLength=adjust_slidinglength(str2num(answer{2}),step);
+        step=NbField_j;%case of bursts: the sliding background is shifted by the length of one burst
+    end
+    ParamOut.ActionInput.SlidingSequenceLength=adjust_slidinglength(str2double(answer{2}),step);
     ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
     ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3});
@@ -205 +179 @@
 
 %% read input parameters from an xml file if input is a file name (batch mode)
-checkrun=1;
+% checkrun=1;
 RUNHandle=[];
-WaitbarHandle=[];
+% WaitbarHandle=[];
 if ischar(Param)
     Param=xml2struct(Param);% read Param as input file (batch case)
-    checkrun=0;
-else
-hseries=findobj(allchild(0),'Tag','series');
+else
+ hseries=findobj(allchild(0),'Tag','series');
 RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
-WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
+% WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
 end
 
@@ -220 +193 @@
 NbSlice_i=Param.IndexRange.NbSlice;
 if ~isequal(NbSlice_i,1)
-    display(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
-end
-RootPath=Param.InputTable(:,1);
-RootFile=Param.InputTable(:,3);
-SubDir=Param.InputTable(:,2);
-NomType=Param.InputTable(:,4);
-FileExt=Param.InputTable(:,5);
-[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);%series of file names organised as a single array
-
-%%%%%%%%%%%%
-    % The cell array filecell is the list of input file names, while
-    % filecell{iview,fileindex}:
-    %        iview: line in the table corresponding to a given file series
-    %        fileindex: file index within  the file series,
-    % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
-    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
-%%%%%%%%%%%%
-[FileInfo{1},MovieObject{1}]=get_file_info(filecell{1,1});
-FileType{1}=FileInfo{1}.FileType;
-    if ~isempty(j1_series{1})
-        frame_index{1}=j1_series{1};
-    else
-        frame_index{1}=i1_series{1};
-    end
-
-
-%% output file naming
-FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
-if strcmp(FileInfo{1}.FileType,'image')
-    NomTypeOut=NomType{1};
-elseif isempty(j1_series{1})
-    NomTypeOut='_1';
-else
-    NomTypeOut='_1_1';% caseof purely numerical indexing
-end
-OutputDir=[Param.OutputSubDir Param.OutputDirExt];
-OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
+    disp(['multi-level splitting into ' num2str(NbSlice_i) ' slices']);
+end
+RootPath=Param.InputTable{1,1};
+RootFile=Param.InputTable{1,3};
+SubDir=Param.InputTable{1,2};
+NomType=Param.InputTable{1,4};
+FileExt=Param.InputTable{1,5};
+%[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);%series of file names organised as a single array
+
 
 %% file index parameters
@@ -267 +212 @@
 % 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
+i_indices=Param.IndexRange.first_i:Param.IndexRange.incr_i:Param.IndexRange.last_i;
+if isfield(Param.IndexRange,'first_j')
+j_indices=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
+else
+    j_indices=1;
+end
+nbfield_i=numel(i_indices); %nb of fields for the i index (bursts or volume slices)
+NbField_j=numel(j_indices); %nb of fields for the j index
+j_indices=j_indices'*ones(1,nbfield_i);
+i_indices=ones(NbField_j,1)*i_indices;
 
 if Param.ActionInput.CheckVolume% case of volume scan: the background images must be determined for each index j
     step=2;% we assume the burst contains only one image pair
-    NbSlice_j=nbfield_j;
+    NbSlice_j=NbField_j;
     nbfield_series=nbfield_i;
 else 
-    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
+    if Param.ActionInput.SlidingSequenceLength<NbField_j
+        step=1;
+    else
+    step=NbField_j;%case of bursts: the sliding background is shifted by the length of one burst
+    end
     NbSlice_j=1;
-    nbfield_series=nbfield_i*nbfield_j;
-end
-nbfield=nbfield_j*nbfield_i; %total number of fields
+    nbfield_series=nbfield_i*NbField_j;
+end
+nbfield=NbField_j*nbfield_i; %total number of fields
 [nbaver_ima,nbaver,step]=adjust_slidinglength(Param.ActionInput.SlidingSequenceLength,step);
 if nbaver_ima > nbfield
-    display('number of images in a slice smaller than the proposed number of images for the sliding average')
+    disp('number of images in a slice smaller than the proposed number of images for the sliding average')
     return
 end
 halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background 
+
+
+%% File relabeling documented by the xml file
+CheckRelabel=isfield(Param,'FileSeries' );
+
+%% Input file info
+if CheckRelabel
+      [RootFileOut,FileIndexString]=index2filename(Param.FileSeries,Param.IndexRange.first_i,j_indices(1),NbField_j);
+       FirstFileName=fullfile(RootPath,SubDir,[RootFileOut FileIndexString FileExt]);
+else
+FirstFileName=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,Param.IndexRange.first_i,[],j_indices(1));%get first file name
+RootFileOut=RootFile;
+end
+[FileInfo,MovieObject]=get_file_info(FirstFileName);
+FileType=FileInfo.FileType;
+if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
+    if isempty(regexp(NomType,'1$', 'once'))% no file indexing
+        frame_index=i_indices;% the index i denotes the frame number in a movie, no index j
+    else
+        frame_index=j_indices;% the index j denotes the frame number in a movie
+        MovieObject=[]; %not a single video object
+    end
+else
+    frame_index=ones(1,nbfield);
+end
+
+%% output file naming
+FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image'
+if strcmp(FileInfo.FileType,'image')
+    NomTypeOut=NomType;
+elseif NbField_j==1
+    NomTypeOut='_1';
+else
+    NomTypeOut='_1_1';% case of purely numerical indexing
+end
+OutputDir=[Param.OutputSubDir Param.OutputDirExt];
+OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
 
 %% calculate absolute brightness rank
@@ -294 +288 @@
 
 %% prealocate memory for the sliding background
-try
-    Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1));
-    [npy,npx,nbcolor]=size(Afirst);% the argument nbcolor is important to get npx right for color images
-    if strcmp(class(Afirst),'uint8') % case of 8bit images
-        Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
-        Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
-    else
-        Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
-        Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
-    end
-catch ME
-    msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message])
-    return
-end
-
-%selection of frame indices
+Ak=zeros(FileInfo.Height,FileInfo.Width,nbaver_ima,['uint' num2str(FileInfo.BitDepth)]); %prealocate memory    
+
+%% selection of frame indices
 if Param.ActionInput.CheckVolume 
     nbfield=floor(nbfield/NbSlice_j)*NbSlice_j;% truncate the total number of frames in case of incomplete series
@@ -326 +307 @@
 %%%%%%%  LOOP ON SLICES %%%%%%%
 for j_slice=1:NbSlice
-    %% 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];
-%     end
-    
+
     %% read the first series of nbaver_ima images and sort by luminosity at each pixel
     for ifield = 1:nbaver_ima
-        ifile=indselect(jslice,ifield);
-        filename=filecell{1,ifile};
-        Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
+        ifile=indselect(j_slice,ifield);
+        %filename=filecell{1,ifile};
+        if CheckRelabel
+            [RootFile,FileIndexString,FrameIndex]=index2filename(Param.FileSeries,i_indices(ifile),j_indices(ifile),NbField_j);
+            filename=fullfile(RootPath,SubDir,[RootFile FileIndexString FileExt]);
+        else
+            filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i_indices(ifile),[],j_indices(ifile));
+            FrameIndex=frame_index(ifile);
+        end
+        Aread=read_image(filename,FileType,MovieObject,FrameIndex);
         if ndims(Aread)==3%color images
             Aread=sum(double(Aread),3);% take the sum of color components
@@ -344 +327 @@
     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')
+    disp( '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(jslice,ifield);
-        j1=1;
-        if ~isempty(j1_series{1})
-            j1=j1_series{1}(ifile);
-        end
-        newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
-        
+        ifile=indselect(j_slice,ifield);
+        newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile));
+
         %write result file
         if ~isequal(Param.ActionInput.SaturationValue,0)
@@ -362 +341 @@
             imwrite(C,newname,'BitDepth',16); % save the new image
         else
-            if ~isfield(FileInfo{1},'BitDepth')
-                FileInfo{1}.BitDepth=16;
-            end
-            if isequal(FileInfo{1}.BitDepth,16)
+            if isequal(FileInfo.BitDepth,16)
                 C=uint16(Acor);
                 imwrite(C,newname,'BitDepth',16); % save the new image
@@ -373 +349 @@
             end
         end
-        display([newname ' written'])
-    end
-    
+        disp([newname ' written'])
+    end
+
     %% repeat the operation on a sliding series of images
-    display('sliding background image will be substracted')
+    disp('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)
+            %             update_waitbar(WaitbarHandle,ifield/nbfield_series)
             if  ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue')
                 disp('program stopped by user')
@@ -386 +362 @@
             end
             if nbaver_ima>step
-            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (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(jslice,ifield+iburst+step*halfnbaver);
-                j1=1;
-                if ~isempty(j1_series{1})
-                    j1=j1_series{1}(ifile);
+                ifile=indselect(j_slice,ifield+iburst+step*halfnbaver);
+                if CheckRelabel
+                    [RootFile,FileIndexString,FrameIndex]=index2filename(Param.FileSeries,i_indices(ifile),j_indices(ifile),NbField_j);
+                    filename=fullfile(RootPath,SubDir,[RootFile FileIndexString FileExt]);
+                else
+                    filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i_indices(ifile),[],j_indices(ifile));
+                    FrameIndex=frame_index(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},frame_index{1}(ifile));
+                Aread=read_image(filename,FileType,MovieObject,FrameIndex);
                 if ndims(Aread)==3%case of color images
                     Aread=sum(double(Aread),3);% take the sum of color components
@@ -409 +386 @@
                 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(jslice,ifield+iburst);
-                if ~isempty(j1_series{1})
-                    j1=j1_series{1}(ifile);
-                end
-                newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
+                ifile=indselect(j_slice,ifield+iburst);
+                newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile));
                 %write result file
                 if ~isequal(Param.ActionInput.SaturationValue,0)
@@ -419 +393 @@
                     imwrite(C,newname,'BitDepth',16); % save the new image
                 else
-                    if isequal(FileInfo{1}.BitDepth,16)
+                    if isequal(FileInfo.BitDepth,16)
                         C=uint16(Acor);
                         imwrite(C,newname,'BitDepth',16); % save the new image
@@ -427 +401 @@
                     end
                 end
-                display([newname ' written'])
-            end
-        end
-    end
-    
+                disp([newname ' written'])
+            end
+        end
+    end
+
     %% substract the background from the last images
-    display('last background image will be substracted')
+    disp('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(jslice,ifield);
-        if ~isempty(j1_series{1})
-            j1=j1_series{1}(ifile);
-        end
-        newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
+        ifile=indselect(j_slice,ifield);
+        newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile));
         %write result file
         if ~isequal(Param.ActionInput.SaturationValue,0)
@@ -447 +418 @@
             imwrite(C,newname,'BitDepth',16); % save the new image
         else
-            if isequal(FileInfo{1}.BitDepth,16)
+            if isequal(FileInfo.BitDepth,16)
                 C=uint16(Acor);
                 imwrite(C,newname,'BitDepth',16); % save the new image
@@ -455 +426 @@
             end
         end
-        display([newname ' written'])
+        disp([newname ' written'])
     end
 end

trunk/src/uvmat.m

@@ -221 +221 @@
 %% EXPORT menu
 export_menu={'as field in workspace';'in new figure';'on existing axis';'make movie';'more...'};
-export_path=fullfile(path_uvmat,'export_fct');
+%export_path=fullfile(path_uvmat,'export_fct');
 
 %% load the list of previously browsed files in menus Open, Open_1 and TransformName
@@ -625 +625 @@
         hveccolor=axes('Position',[0.93 0.1 0.02 0.5]);
         ima=permute(get(handles.VecColBar,'CData'),[2 1 3]);
-        ymin=str2num(get(handles.num_MinVec,'String'));
-        ymax=str2num(get(handles.num_MaxVec,'String'));
+        ymin=str2double(get(handles.num_MinVec,'String'));
+        ymax=str2double(get(handles.num_MaxVec,'String'));
         set(hveccolor,'YLim',[ymin ymax])
         imagesc([0 1],[ymin ymax],ima)
@@ -862 +862 @@
 huvmat=findobj(allchild(0),'Tag','uvmat');
 hhuvmat=guidata(huvmat);
-increment=str2num(get(hhuvmat.num_IndexIncrement,'String')); %get the field increment from uvmat
+increment=str2double(get(hhuvmat.num_IndexIncrement,'String')); %get the field increment from uvmat
 set(hhuvmat.STOP,'Visible','on')
 set(hhuvmat.speed,'Visible','on')
@@ -1409 +1409 @@
 hset_slice=get(hObject, 'parent');
 hZ=findobj(hset_slice,'Tag','num_Z_1');
-Z_plane=str2num(get(hZ,'String'));% set of Z positions explicitly entered as a Matlab vector
+Z_plane=str2double(get(hZ,'String'));% set of Z positions explicitly entered as a Matlab vector
 SliceData=read_GUI(hset_slice);
 Slice.NbSlice=SliceData.NbSlice;
@@ -2066 +2066 @@
 end
 
-% %------------------------------------------------------------------------
-% % -- open the GUI civ.fig for PIV
-% function MenuCIVx_Callback(hObject, eventdata, handles)
-% %------------------------------------------------------------------------
-%  [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
-%  FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
-% civ(FileName);% interface de civ(not in the uvmat file)
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % MenuHelp Callback
@@ -2083 +2075 @@
 
 
-
-
-
-
-
-
-
-
 %------------------------------------------------------------------------
 % --- Called by action in FileIndex edit box
@@ -2096 +2080 @@
 %------------------------------------------------------------------------
 [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
+UvData=get(handles.uvmat,'UserData');
+check_index=false;
+if isfield(UvData,'XmlData')&& ~isempty(UvData.XmlData)
+    if isfield(UvData.XmlData{1},'FileSeries')% case of frame indexing documented by the xml file (PCO)
+        if strcmp(UvData.XmlData{1}.FileSeries.Convention,'PCO')
+            i1_mod=i1*UvData.XmlData{1}.FileSeries.NbFramePerFile+1;
+            if isfield(UvData.XmlData{1},'Time')
+                [NbField,NbField_j]=size(UvData.XmlData{1}.Time);
+                j1=mod(i1_mod,NbField_j-1)+1;
+                i1_mod=floor(i1_mod/(NbField_j -1))+1;
+            end
+            set(handles.i1,'String',num2str(i1_mod));%update the counters
+            set(handles.j1,'String',num2str(j1));%update the counters
+            check_index=true;
+        end
+    end
+end
+if ~check_index
 set(handles.i1,'String',num2str(i1));%update the counters
 set(handles.i2,'String',num2str(i2));
 set(handles.j1,'String',num2str(j1));
 set(handles.j2,'String',num2str(j2));
-
+end
 
 %------------------------------------------------------------------------
@@ -2106 +2108 @@
 function NomType_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
-i1=str2num(get(handles.i1,'String'));
-i2=str2num(get(handles.i2,'String'));
-j1=str2num(get(handles.j1,'String'));
-j2=str2num(get(handles.j2,'String'));
+i1=str2double(get(handles.i1,'String'));
+i2=str2double(get(handles.i2,'String'));
+j1=str2double(get(handles.j1,'String'));
+j2=str2double(get(handles.j2,'String'));
 NomType=get(hObject,'String');
 if strcmp(NomType,'level')
-    FileIndex=str2num(get(handles.i1,'String'));
+    FileIndex=str2double(get(handles.i1,'String'));
 else
 FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
@@ -2124 +2126 @@
 function NomType_1_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
-i1=str2num(get(handles.i1,'String'));
-i2=str2num(get(handles.i2,'String'));
-j1=str2num(get(handles.j1,'String'));
-j2=str2num(get(handles.j2,'String'));
+i1=str2double(get(handles.i1,'String'));
+i2=str2double(get(handles.i2,'String'));
+j1=str2double(get(handles.j1,'String'));
+j2=str2double(get(handles.j2,'String'));
 NomType=get(hObject,'String');
 if strcmp(NomType,'level')
-    FileIndex=str2num(get(handles.i1,'String'));
+    FileIndex=str2double(get(handles.i1,'String'));
 else
 FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
@@ -2148 +2150 @@
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
-[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
+%[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
 errormsg='';
 if isempty(RootFile)
@@ -2165 +2167 @@
 else
     % initiate the input file series and refresh the current field view:
-    errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,1);
+    [FileInfo,VideoObject]=get_file_info(fullfile(RootPath,SubDir,[RootFile FileIndices FileExt]));
+    errormsg=update_rootinfo(handles,RootPath,SubDir,[RootFile FileIndices FileExt],FileInfo,VideoObject,1);
 end
 
@@ -2188 +2191 @@
     else
         % initiate the input file series and refresh the current field view:
-        errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,2);
+        errormsg=update_rootinfo(handles,RootPath,SubDir,FileName,FileInfo,MovieObject,2);
     end
 end
@@ -2200 +2203 @@
 function errormsg=display_file_name(handles,fileinput,input_line)
 %------------------------------------------------------------------------
-%% look for the input file existence
+%% look for the input file existence and properties in the structure FileInfo
 errormsg='';%default
 if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file')
@@ -2206 +2209 @@
     msgbox_uvmat('ERROR',errormsg)
     return
+end
+[FileInfo,MovieObject]=get_file_info(fileinput);
+FieldType=FileInfo.FieldType;
+
+%% case of isolated input files without series
+switch FieldType
+    case ''
+        msgbox_uvmat('ERROR','invalid input file type')
+        return
+    case 'txt'
+        edit(fileinput)
+        return
+    case 'figure'                           %display matlab figure
+        hfig=open(fileinput);
+        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
+        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
+        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
+        return
+    case 'xml'                % edit xml files
+        t=xmltree(fileinput);
+        % the xml file marks a project or project link, open datatree_browser
+        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
+            datatree_browser(fileinput)
+        else % other xml file, open the xml editor
+            editxml(fileinput);
+        end
+        return
+    case 'xls'% Excel file opended by editxml
+        editxml(fileinput);
+        return
 end
 
@@ -2239 +2272 @@
 drawnow
 
+[RootPath,SubDir,RootFile,i1,i2,j1,j2,~,NomType]=fileparts_uvmat(fileinput);
+[~,FileName,FileExt]=fileparts(fileinput);
+
+
 %% detect root name, nomenclature and indices in the input file name:
-[FilePath,FileName,FileExt]=fileparts(fileinput);
+%[FilePath,FileName,FileExt]=fileparts(fileinput);
 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
 % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
-[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=...
-    find_file_series(FilePath,[FileName FileExt]);
-
-%% open the file or fill the GUI uvmat according to the detected file type
-FieldType=FileInfo.FieldType;
-switch FieldType
-    case ''
-        msgbox_uvmat('ERROR','invalid input file type')
-        return
-    case 'txt'
-        edit(fileinput)
-        return
-    case 'figure'                           %display matlab figure
-        hfig=open(fileinput);
-        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
-        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
-        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
-        return
-    case 'xml'                % edit xml files
-        t=xmltree(fileinput);
-        % the xml file marks a project or project link, open datatree_browser
-        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
-            datatree_browser(fileinput)
-        else % other xml file, open the xml editor
-            editxml(fileinput);
-        end
-        return
-    case 'xls'% Excel file opended by editxml
-        editxml(fileinput);
-        return
-    otherwise
-        set(handles_RootPath,'String',RootPath);
-        set(handles_SubDir,'String',['/' SubDir]);
-        set(handles_RootFile,'String',['/' RootFile]); %display the separator
-        if isempty(regexp(RootPath,'^http://', 'once'))
-            rootname=fullfile(RootPath,SubDir,RootFile);
+
+set(handles_RootPath,'String',RootPath);
+set(handles_SubDir,'String',['/' SubDir]);
+set(handles_RootFile,'String',['/' RootFile]); %display the separator
+if isempty(regexp(RootPath,'^http://', 'once'))
+    rootname=fullfile(RootPath,SubDir,RootFile);
+else
+    rootname=[RootPath '/' SubDir '/' RootFile];
+end
+indices=fileinput(length(rootname)+1:end);
+indices(end-length(FileExt)+1:end)=[]; %remove extension
+set(handles_FileIndex,'String',indices);
+set(handles_NomType,'String',NomType);
+set(handles_FileExt,'String',FileExt);
+if input_line==1
+    % fill file index counters if the first file series is opened
+    set(handles.i1,'String',num2str(i1));
+    set(handles.i2,'String',num2str(i2));
+    set(handles.j1,'String',num2stra(j1,NomType));
+    set(handles.j2,'String',num2stra(j2,NomType));
+    if isfield(FileInfo,'MaskFile')
+        if exist(FileInfo.MaskFile)
+            set(handles.CheckMask,'Value',1)
         else
-            rootname=[RootPath '/' SubDir '/' RootFile];
-        end
-        indices=fileinput(length(rootname)+1:end);
-        indices(end-length(FileExt)+1:end)=[]; %remove extension
-        set(handles_FileIndex,'String',indices);
-        set(handles_NomType,'String',NomType);
-        set(handles_FileExt,'String',FileExt);
-        if input_line==1
-            % fill file index counters if the first file series is opened
-            set(handles.i1,'String',num2str(i1));
-            set(handles.i2,'String',num2str(i2));
-            set(handles.j1,'String',num2stra(j1,NomType));
-            set(handles.j2,'String',num2stra(j2,NomType));
-            if isfield(FileInfo,'MaskFile')
-                if exist(FileInfo.MaskFile)
-                set(handles.CheckMask,'Value',1)
-                else
-                    set(handles.CheckMask,'Value',0)
-                end
-                 Mask.File=FileInfo.MaskFile;
-                 if isfield(FileInfo,'MaskNbSlice')
-                     Mask.NbSlice=FileInfo.MaskNbSlice;
-                 elseif isfield(FileInfo,'VolumeScan')
-                     Mask.VolumeScan=FileInfo.VolumeScan;
-                 end  
-                 set(handles.CheckMask,'UserData', Mask)
-            else
-                set(handles.CheckMask,'Value',0)
-                CheckMask_Callback(handles.CheckMask, [], handles) 
-            end                         
-        else %read the current field index to synchronise with the first series
-            i1_s=str2num(get(handles.i1,'String'));
-            i2_0=str2num(get(handles.i2,'String'));
-            if ~isempty(i2_0)
-                i2_s=i2_0;
-            else
-                i2_s=i2;
-            end
-            j1_0=stra2num(get(handles.j1,'String'));
-            if ~isempty(j1_0)
-                j1_s=j1_0;
-            else
-                j1_s=j1;
-            end
-            j2_0=stra2num(get(handles.j2,'String'));
-            if ~isempty(j2_0)
-                j2_s=j2_0;
-            else
-                j2_s=j2;
-            end
-        end
-        
-        % synchronise indices of the second  input file if it exists
-        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
-            Input=read_GUI(handles.InputFile);
-            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
-                Input.RootPath_1=Input.RootPath;
-            end
-            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
-                Input.SubDir_1=Input.SubDir;
-            end
-            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
-                Input.RootFile_1=Input.RootFile;
-            end
-            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
-                Input.FileExt_1=Input.FileExt;
-            end
-            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
-                Input.NomType_1=Input.NomType;
-            end
-            %updtate the indices of the second field series to correspond to the newly opened one
-            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
-            if exist(FileName_1,'file')
-                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
-            else
-                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
-%                 msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
-            end
-            set(handles.FileIndex_1,'String',FileIndex_1)
-        end
-        
-        %enable other menus
-        set(handles.MenuExport,'Enable','on')
-        set(handles.MenuExportFigure,'Enable','on')
-        set(handles.MenuExportMovie,'Enable','on')
-        set(handles.MenuTools,'Enable','on')
-        
-        % initiate input file series and inputfilerefresh the current field view:
-        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,input_line);
-end
+            set(handles.CheckMask,'Value',0)
+        end
+        Mask.File=FileInfo.MaskFile;
+        if isfield(FileInfo,'MaskNbSlice')
+            Mask.NbSlice=FileInfo.MaskNbSlice;
+        elseif isfield(FileInfo,'VolumeScan')
+            Mask.VolumeScan=FileInfo.VolumeScan;
+end
+set(handles.CheckMask,'UserData', Mask)
+    else
+        set(handles.CheckMask,'Value',0)
+        CheckMask_Callback(handles.CheckMask, [], handles)
+end
+else %read the current field index to synchronise with the first series
+    i1_s=str2double(get(handles.i1,'String'));
+    i2_0=str2double(get(handles.i2,'String'));
+    if ~isempty(i2_0)
+        i2_s=i2_0;
+    else
+        i2_s=i2;
+    end
+    j1_0=stra2num(get(handles.j1,'String'));
+    if ~isempty(j1_0)
+        j1_s=j1_0;
+    else
+        j1_s=j1;
+    end
+    j2_0=stra2num(get(handles.j2,'String'));
+    if ~isempty(j2_0)
+        j2_s=j2_0;
+    else
+        j2_s=j2;
+    end
+end
+
+% synchronise indices of the second  input file if it exists
+if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
+    Input=read_GUI(handles.InputFile);
+    if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
+        Input.RootPath_1=Input.RootPath;
+    end
+    if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
+        Input.SubDir_1=Input.SubDir;
+    end
+    if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
+        Input.RootFile_1=Input.RootFile;
+    end
+    if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
+        Input.FileExt_1=Input.FileExt;
+    end
+    if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
+        Input.NomType_1=Input.NomType;
+    end
+    %updtate the indices of the second field series to correspond to the newly opened one
+    FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
+    if exist(FileName_1,'file')
+        FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
+    else
+        FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
+        %                 msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
+    end
+    set(handles.FileIndex_1,'String',FileIndex_1)
+end
+
+%enable other menus
+set(handles.MenuExport,'Enable','on')
+set(handles.MenuExportFigure,'Enable','on')
+set(handles.MenuExportMovie,'Enable','on')
+set(handles.MenuTools,'Enable','on')
+
+% initiate input file series and inputfilerefresh the current field view:
+update_rootinfo(handles,RootPath,SubDir,[FileName FileExt],FileInfo, MovieObject,input_line);
+
 
 %% update list of recent files in the menubar and save it for future opening
@@ -2396 +2403 @@
 % --- Update information about a new field series (indices to scan, timing,
 %     calibration from an xml file, then inputfilerefresh current plots
-function errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,input_line)
+%function errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,input_line)
+function errormsg=update_rootinfo(handles,RootPath,SubDir,FileName,FileInfo,VideoObject,input_line)
 %------------------------------------------------------------------------
 errormsg=''; %default error msg
@@ -2410 +2418 @@
 end
 set(handles.FixVelType,'Value',0); %desactivate fixed veltype by default
+
+%% look for the xml file and read it
+XmlFileName=find_imadoc(RootPath,SubDir);
+[~,XmlName]=fileparts(XmlFileName);
+warntext='';%default warning message
+NbSlice=1;%default
+%CheckImaDoc=false;
+TimeUnit='';%default
+TimeName='';%default
+CheckIndexing=false;%default
+if isempty(XmlFileName)
+    set(handles.view_xml,'Visible','off')
+else
+    set(handles.view_xml,'Visible','on')
+    set(handles.view_xml,'BackgroundColor',[1 1 0])% paint  to yellow color to indicate reading of the xml file
+    set(handles.view_xml,'String','view xml')
+    drawnow
+    [XmlData,warntext]=imadoc2struct(XmlFileName);
+    if ~isempty(warntext)
+        msgbox_uvmat('WARNING',warntext)
+    end
+    if ~isempty(XmlData)
+        %CheckImaDoc=true;
+        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
+            TimeUnit=XmlData.TimeUnit;
+        end
+        if isfield(XmlData,'Time')&& ~isempty(XmlData.Time)
+            TimeName='xml';%
+            if XmlData.Time(1,:)==XmlData.Time(2,:)% case starting with index 1
+                sizDti=size(XmlData.Time,1)-1;%size of the time vector explicitly defined in the xml file
+                ind_start=1;
+            else
+                sizDti=size(XmlData.Time,1);% case starting with index 0
+                ind_start=0;
+            end
+            if isfield(XmlData,'FileSeries')
+                if strcmp(XmlName,SubDir)% frame indexing documented from the xml file (case PCO)
+                    CheckIndexing=true;
+                else
+                    XmlData=rmfield(XmlData,'FileSeries');%desactivate file indexing option for derived file series
+                end
+            end
+        end
+    end
+    set(handles.view_xml,'BackgroundColor',[1 1 1])% paint back to white
+    set(handles.view_xml,'String','view xml')% indicate that a xml file has been detected
+    drawnow
+    if isfield(XmlData,'Slice') && isfield(XmlData.Slice,'CheckVolumeScan') && isequal(XmlData.Slice.CheckVolumeScan,1)
+        set (handles.slices,'String','volume')
+    end
+end
+
+%% get the file series
+MovieObject=[];
+if strcmp(TimeName,'xml') && strcmp(XmlName,SubDir)% get the image series info from the xml file
+    [nbfield,nbfield_j]=size(XmlData.Time);
+    nbfield=nbfield-1; %remove the possible index 0
+    nbfield_j=nbfield_j-1; %remove the possible index 0
+        i1_series=zeros(nbfield,nbfield_j,1);
+    i1_series(:,:,1)=(1:nbfield)'*ones(1,nbfield_j);
+    i2_series=i1_series;
+    if nbfield_j==1
+        j1_series=[];
+    else
+    j1_series(:,:,1)=ones(nbfield,1)*(1:nbfield_j);
+    end
+    j2_series=j1_series;
+else % scan the input folder to get the list of existing files
+    [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=...
+        find_file_series(fullfile(RootPath,SubDir),FileName);
+    nbfield=max(max(max(i2_series)));% total number of fields (i index)
+    if isempty(nbfield)
+        nbfield=max(max(max(i1_series)));
+    end
+    nbfield_j=max(max(max(j2_series)));% number of fields along j index
+    if isempty(nbfield_j)
+        nbfield_j=max(max(max(j1_series)));
+    end
+    if input_line==1
+    set(handles.NomType,'String',NomType)
+    else
+         set(handles.NomType_1,'String',NomType)
+    end
+end
+if CheckIndexing
+    i1=str2double(get(handles.FileIndex,'String'));
+    if isnan(i1)
+        i1=1;
+    else
+    i1=(i1-XmlData.FileSeries.FirstFileIndex)*XmlData.FileSeries.NbFramePerFile+1;%frame index deduced from input file index
+    end
+    if strcmp(TimeName,'xml')% indices i and j
+                j1=mod(i1-1,nbfield_j)+1;
+                i1=floor((i1-1)/nbfield_j)+1;
+                set(handles.j1,'String',num2str(j1))
+    end
+    set(handles.i1,'String',num2str(i1))
+end
+
 
 %% record info in UserData of the figure uvmat
@@ -2417 +2524 @@
 %UvData.FileType{input_line}=FileInfo.FileType;
 UvData.FileInfo{input_line}=FileInfo;
-UvData.MovieObject{input_line}=VideoObject;
+UvData.MovieObject{input_line}=MovieObject;
 UvData.i1_series{input_line}=i1_series;
 UvData.i2_series{input_line}=i2_series;
 UvData.j1_series{input_line}=j1_series;
 UvData.j2_series{input_line}=j2_series;
-nbfield=max(max(max(i2_series)));% total number of fields (i index)
-if isempty(nbfield)
-    nbfield=max(max(max(i1_series)));
-end
-nbfield_j=max(max(max(j2_series)));% number of fields along j index
-if isempty(nbfield_j)
-    nbfield_j=max(max(max(j1_series)));
-end
+
 
 %% read timing and total frame number from the current file (e.g. movie files)
-TimeUnit='';%default
-TimeName='';%default
-XmlData.Time=[];%default
 ColorType='falsecolor'; %default
 if isfield(FileInfo,'FrameRate')% frame rate given in the file (case of video data)
@@ -2468 +2565 @@
 else
     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
-end
-XmlFileName=find_imadoc(RootPath,SubDir);
-[tild,tild,DocExt]=fileparts(XmlFileName);
-warntext='';%default warning message
-NbSlice=1;%default
-ImaDoc_str='';
-if ~isempty(XmlFileName)
-    set(handles.view_xml,'Visible','on')
-    set(handles.view_xml,'BackgroundColor',[1 1 0])% paint  to yellow color to indicate reading of the xml file
-    set(handles.view_xml,'String','view .xml')
-    drawnow
-    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
-    if ~isempty(warntext)
-        msgbox_uvmat('WARNING',warntext)
-    end
-    if ~isempty(XmlDataRead)
-        ImaDoc_str=['view ' DocExt];  % DocExt= '.xml' or .civ (obsolete case)
-        if isfield(XmlDataRead,'TimeUnit')&& ~isempty(XmlDataRead.TimeUnit)
-            TimeUnit=XmlDataRead.TimeUnit;
-        end
-        if isfield(XmlDataRead,'Time')&& ~isempty(XmlDataRead.Time)
-            XmlData.Time=XmlDataRead.Time;
-            if XmlDataRead.Time(1,:)==XmlDataRead.Time(2,:)% case starting with index 1
-                sizDti=size(XmlDataRead.Time,1)-1;%size of the time vector explicitly defined in the xml file
-                ind_start=1;
-            else
-                sizDti=size(XmlDataRead.Time,1);% case starting with index 0
-                ind_start=0;
-            end
-        end
-        set(handles.view_xml,'BackgroundColor',[1 1 1])% paint back to white
-        drawnow
-        if isfield(XmlDataRead, 'GeometryCalib') && ~isempty(XmlDataRead.GeometryCalib)
-            XmlData.GeometryCalib=XmlDataRead.GeometryCalib;      
-        end
-        XmlData.Slice=XmlData.GeometryCalib;%default
-        if isfield(XmlDataRead, 'Slice') && ~isempty(XmlDataRead.Slice)
-            XmlData.Slice=XmlDataRead.Slice;
-        end
-        if isfield(XmlData.Slice,'CheckVolumeScan') && isequal(XmlData.Slice.CheckVolumeScan,1)
-                set (handles.slices,'String','volume')
-            end
-        if isfield(XmlDataRead, 'LIFCalib')
-            XmlData.LIFCalib=XmlDataRead.LIFCalib;
-        end
-    end
-end
-if isempty(ImaDoc_str)
-    set(handles.view_xml,'Visible','off') % no .xml (or .civ) file detected
-else
-    set(handles.view_xml,'String',ImaDoc_str)% indicate that a xml file has been detected
 end
 
@@ -2540 +2586 @@
 
 %% store last index in handles.MaxIndex_i and .MaxIndex_j
-if isfield(XmlData,'Time')&& ~isempty(XmlData.Time)
-    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
-    if isequal(size(XmlData.Time,1),1)
-        XmlData.Time=(XmlData.Time)';
-    end
-end
 last_i_cell=get(handles.MaxIndex_i,'String');
 if isempty(nbfield)
@@ -2794 +2834 @@
 
 NomType=get(handles.NomType,'String');
+UvData=get(handles.uvmat,'UserData');
 
 if strcmp(NomType,'level')
-    indices=get(handles.i1,'String');
-else
-    indices=get(handles.FileIndex,'String');
-    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex
-    switch index_rank
-        case 1
-            indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
-        case 2
-            indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
-        case 3
-            indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
-        case 4
-            indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
-    end
-end
-set(handles.FileIndex,'String',indices)
+    index_string=get(handles.i1,'String');
+else
+    index_string=get(handles.FileIndex,'String');
+    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'FileSeries')
+        i1=str2double(get(handles.i1,'String'));
+        j1=str2double(get(handles.j1,'String'));
+        NbField_j_cell=get(handles.MaxIndex_j,'String');
+        NbField_j=str2double(NbField_j_cell{1});
+        [RootFile,index_string,FrameIndex]=index2filename(UvData.XmlData{1}.FileSeries,i1,j1,NbField_j);
+        set(handles.RootFile,'String',RootFile)
+    else
+        [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(index_string);% the index_string for the second series taken from FileIndex
+        switch index_rank
+            case 1
+                index_string=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
+            case 2
+                index_string=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
+            case 3
+                index_string=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
+            case 4
+                index_string=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
+        end
+    end
+end
+set(handles.FileIndex,'String',index_string)
 
 % update the second index if relevant
 if strcmp(get(handles.FileIndex_1,'Visible'),'on')
     NomType_1=get(handles.NomType_1,'String');
-    indices_1=get(handles.FileIndex_1,'String');
-    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(indices_1);% the indices for the second series taken from FileIndex_1
+    index_string_1=get(handles.FileIndex_1,'String');
+    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(index_string_1);% the index_string for the second series taken from FileIndex_1
     switch index_rank
         case 1
-            indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
+            index_string_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
         case 2
-            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
+            index_string_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
         case 3
-            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
+            index_string_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
         case 4
-            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
-    end
-    set(handles.FileIndex_1,'String',indices_1)
+            index_string_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
+    end
+    set(handles.FileIndex_1,'String',index_string_1)
     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
 end
@@ -2884 +2934 @@
 end
 option=get(handles.view_xml,'String');
-if isequal(option,'view .xml')
+if isequal(option,'view xml')
     FileXml=fullfile(RootPath,[SubDir '.xml']);
     if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
@@ -2982 +3032 @@
     if isfield(MaskInfo,'NbSlice')&& ~isempty(MaskInfo.NbSlice)
         if isfield(MaskInfo,'VolumeScan') &&  MaskInfo.VolumeScan
-            MaskIndex_i=str2num(get(handles.j1,'String'));
+            MaskIndex_i=str2double(get(handles.j1,'String'));
         else
-            MaskIndex_i=mod(str2num(get(handles.i1,'String'))-1,MaskInfo.NbSlice)+1;
+            MaskIndex_i=mod(str2double(get(handles.i1,'String'))-1,MaskInfo.NbSlice)+1;
         end
         MaskName=[MaskInfo.File '_' num2str(MaskIndex_i) '.png'];
@@ -3174 +3224 @@
 %------------------------------------------------------------------------
 errormsg='';%default
-%% check for movie pair status
-% movie_status=get(handles.movie_pair,'Value');
-% if movie_status
-%     STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
-% end
 
 %% read the current input file name(s) and field indices
@@ -3186 +3231 @@
 FileExt=InputFile.FileExt;
 NomType=InputFile.NomType;
-[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(InputFile.FileIndex);% check back the indices used
-if isempty(i1)% no i index set by the input file name
-    i1=str2double(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
-elseif isempty(j1) && strcmp(get(handles.j1,'Visible'),'on')
-    j1=str2double(get(handles.j1,'String'));%case of indexed movie
-end
-% if movie_status% we read the second index from the edit box
-%     i2=str2num(get(handles.i2,'String'));%read the field indices (for movie, it is not given by the file name)
-%     if strcmp(get(handles.j2,'Visible'),'on')
-%     j2=str2num(get(handles.j2,'String'));%
-%     end
-% end
+UvData=get(handles.uvmat,'UserData');
+if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'FileSeries')% case of indexing documented by the xml file
+    i1=str2double(get(handles.i1,'String'));
+    j1=str2double(get(handles.j1,'String'));%read the field indices (for movie, it is not given by the file name)
+    i2=[];j2=[];
+else
+    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(InputFile.FileIndex);% check back the indices used
+    if isempty(i1)% no i index set by the input file name
+        i1=str2double(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
+    elseif isempty(j1) && strcmp(get(handles.j1,'Visible'),'on')
+        j1=str2double(get(handles.j1,'String'));%case of indexed movie
+    end
+end
 sub_value= get(handles.SubField,'Value');
 if sub_value % a second input file has been entered
@@ -3203 +3249 @@
     [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);% the indices for the second series taken from FileIndex_1
     if isempty(i1_1)
-        i1_1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
+        i1_1=str2double(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
     elseif isempty(j1_1) && strcmp(get(handles.j1,'Visible'),'on')
-        j1_1=str2num(get(handles.j1,'String'));%case of indexed movie
+        j1_1=str2double(get(handles.j1,'String'));%case of indexed movie
     end
 else
@@ -3234 +3280 @@
         end
     end
-    
+
     % the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
 else
-    UvData=get(handles.uvmat,'UserData');
     ref_i=i1;
     if ~isempty(i2)
@@ -3249 +3294 @@
         end
     end
-    if isnumeric(increment)
-        if get(handles.scan_i,'Value')==1% case of scanning along index i
-            ref_i=ref_i+increment;% increment the current reference index i
-        else % case of scanning along index j (burst numbers)
-            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
-        end
-    else % free increment
-        if strcmp(increment,'+')% if runplus or movie is activated
-            step=1;
-        else
-            step=-1;
-        end
-        if get(handles.scan_i,'Value')==1% case of scanning along index i
+
+    if strcmp(increment,'+')% if runplus or movie is activated
+        step=1;
+    else
+        step=-1;
+    end
+    if get(handles.scan_i,'Value')==1% case of scanning along index i
+        ref_i=ref_i+step;
+        while ref_i>=0  && size(UvData.i1_series{1},3)>=ref_i+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
             ref_i=ref_i+step;
-            while ref_i>=0  && size(UvData.i1_series{1},3)>=ref_i+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
-                ref_i=ref_i+step;
-            end
-        else % case of scanning along index j (burst numbers)
+        end
+    else % case of scanning along index j (burst numbers)
+        ref_j=ref_j+step;
+        while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
             ref_j=ref_j+step;
-            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
-                ref_j=ref_j+step;
-            end
         end
     end
@@ -3304 +3342 @@
         j2=UvData.j2_series{1}(ref_indices(end));
     end
-    
+
     % case of a second file series
     if sub_value
@@ -3340 +3378 @@
         elseif ref_i_1+1>size(UvData.i1_series{2},3)&&~isempty(InputFile.NomType_1)
             errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
-        %elseif ref_j_1+1>size(UvData.i1_series{2},2)&&~isempty(InputFile.NomType_1)
-         %   errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
+            %elseif ref_j_1+1>size(UvData.i1_series{2},2)&&~isempty(InputFile.NomType_1)
+            %   errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
         end
         if ~isempty(errormsg),return,end
@@ -3402 +3440 @@
     if strcmp(NomType,'level')
         indices=num2str(i1);
+    elseif isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'FileSeries')
+        NbField_j_cell=get(handles.MaxIndex_j,'String');
+        NbField_j=str2double(NbField_j_cell{1});
+        [RootFile,indices,FrameIndex]=index2filename(UvData.XmlData{1}.FileSeries,i1,j1,NbField_j);
+        set(handles.RootFile,'String',RootFile)
     else
         indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
@@ -3534 +3577 @@
 
 %% determine the main input file information for action
-if isempty(regexp(FileName,'^http://', 'once')) &&~exist(FileName,'file')
-    errormsg=['input file ' FileName ' does not exist'];
-    return
-end
+% if isempty(regexp(FileName,'^http://', 'once')) &&~exist(FileName,'file')
+%     errormsg=['input file ' FileName ' does not exist'];
+%     return
+% end
 NomType=get(handles.NomType,'String');
-% NomType_1='';
-% if strcmp(get(handles.NomType_1,'Visible'),'on')
-%     NomType_1=get(handles.NomType_1,'String');
-% end
 %update the z position index
 mode_slice=get(handles.slices,'String');
@@ -3564 +3603 @@
     for iobj=1:numel(UvData.ProjObject)
         if isfield(UvData.ProjObject{iobj},'ProjMode')&& strcmp(UvData.ProjObject{iobj}.ProjMode,'interp_tps')
-            check_proj_tps=1;% tps projection proposed
+            check_proj_tps=1;% tps projection proposedUvData.XmlData
             break
         end
@@ -3598 +3637 @@
         ParamIn=UvData.MovieObject{1};
     end
+end
+%% case of special file series (PCO)
+if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'FileSeries')
+    [RootName,~,Ext]=fileparts(FileName);
+    NbField_j_cell=get(handles.MaxIndex_j,'String');
+    NbField_j=str2double(NbField_j_cell{1});
+    if num_j1>NbField_j
+       errormsg=['index j exceeds upper bound ' num2str(NbField_j)];
+       return
+    elseif num_j1<1
+         errormsg='index j smaller that 1';
+        return
+    end
+    [FNameMulti,FileIndexString,frame_index]=index2filename(UvData.XmlData{1}.FileSeries,num_i1,num_j1,NbField_j);
+    FileName=fullfile(RootName,[FNameMulti FileIndexString Ext]);
 end
 switch UvData.FileInfo{1}.FieldType
@@ -3885 +3939 @@
         % TODO: look for time unit attribute
     elseif ~isempty(regexp(TimeName,'^dim:'))
-        abstime=str2num(get(handles.i1,'String'));
+        abstime=str2double(get(handles.i1,'String'));
         TimeUnit='index';
     end
@@ -5111 +5165 @@
     if ~isempty(errormsg)
         msgbox_uvmat('ERROR',errormsg);
-    else
-%         set(handles.i1,'BackgroundColor',[1 1 1])
-%         set(handles.i2,'BackgroundColor',[1 1 1])
-%         set(handles.j1,'BackgroundColor',[1 1 1])
-%         set(handles.j2,'BackgroundColor',[1 1 1])
-%         set(handles.FileIndex,'BackgroundColor',[1 1 1])
-%         set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
     end
     set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])
@@ -5139 +5186 @@
 function VOLUME_Callback(hObject, eventdata, handles)
 %-----------------------------------------------------------------------
-%errordlg('command VOL not implemented yet')
 if ishandle(handles.UVMAT_title)
     delete(handles.UVMAT_title)
@@ -5150 +5196 @@
     edit_vect_Callback(hObject, eventdata, handles)
     set(handles.CheckEditObject,'Value',0)
-%     set(handles.CheckEditObject,'BackgroundColor',[0.7 0.7 0.7])
-%     set(handles.cal,'Value',0)
-%     set(handles.cal,'BackgroundColor',[0 1 0])
     set(handles.edit_vect,'Value',0)
     edit_vect_Callback(hObject, eventdata, handles)
@@ -5441 +5484 @@
 drawnow
 
-%% inputfilerefresh the current plot
+%% inputfile refresh the current plot
 if isempty(list_path{ichoice}) || nargin(transform_handle)<3
     set(handles.SubField,'Value',0)
@@ -5682 +5725 @@
 %------------------------------------------------------------------
 slider1=get(handles.Slider1,'Value');
-min_val=str2num(get(handles.num_MinVec,'String'));
-max_val=str2num(get(handles.num_MaxVec,'String'));
+min_val=str2double(get(handles.num_MinVec,'String'));
+max_val=str2double(get(handles.num_MaxVec,'String'));
 col=min_val+(max_val-min_val)*slider1;
 set(handles.num_ColCode1,'String',num2str(col))
@@ -5698 +5741 @@
 function Slider2_Callback(hObject, eventdata, handles)
 slider2=get(handles.Slider2,'Value');
-min_val=str2num(get(handles.num_MinVec,'String'));
-max_val=str2num(get(handles.num_MaxVec,'String'));
+min_val=str2double(get(handles.num_MinVec,'String'));
+max_val=str2double(get(handles.num_MaxVec,'String'));
 col=min_val+(max_val-min_val)*slider2;
 set(handles.num_ColCode2,'String',num2str(col))
@@ -5749 +5792 @@
 set(handles.CheckFixVecColor,'Value',1)
 CheckFixVecColor_Callback(hObject, eventdata, handles)
-min_val=str2num(get(handles.num_MinVec,'String'));
-max_val=str2num(get(handles.num_MaxVec,'String'));
+min_val=str2double(get(handles.num_MinVec,'String'));
+max_val=str2double(get(handles.num_MaxVec,'String'));
 slider1=get(handles.Slider1,'Value');
 slider2=get(handles.Slider2,'Value');
@@ -5774 +5817 @@
 ichoice=get(handles.ColorCode,'Value');
 colcode.ColorCode=list{ichoice};
-colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
-colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
+colcode.MinVec=str2double(get(handles.num_MinVec,'String'));
+colcode.MaxVec=str2double(get(handles.num_MaxVec,'String'));
 test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
 if test3color
-    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
-    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
+    colcode.ColCode1=str2double(get(handles.num_ColCode1,'String'));
+    colcode.ColCode2=str2double(get(handles.num_ColCode2,'String'));
 end
 vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max