Changeset 1184

Timestamp:

Nov 6, 2025, 7:03:02 PM (4 weeks ago)

Author:

sommeria

Message:

bed-scan updated and many updates

Location:

trunk/src

Files:

• command_launch_matlab.m (modified) (1 diff)
• get_file_index.m (modified) (1 diff)
• imadoc2struct.m (modified) (3 diffs)
• index2filename.m (modified) (2 diffs)
• keyboard_callback.m (modified) (1 diff)
• phys_XYZ.m (modified) (4 diffs)
• read_GUI.m (modified) (1 diff)
• read_field.m (modified) (1 diff)
• read_multimadoc.m (modified) (1 diff)
• rename_indexing.m (modified) (1 diff)
• series.m (modified) (31 diffs)
• series/beam_forming.m (modified) (1 diff)
• series/bed_scan.m (modified) (7 diffs)
• series/bed_scan_init.m (added)
• uvmat.fig (modified) (previous)
• uvmat.m (modified) (55 diffs)

trunk/src/command_launch_matlab.m

@@ -36 +36 @@
     'matlab -nodisplay -nosplash -nojvm ''' ThreadOption ''' -logfile ''' filelog ''' <<END_MATLAB\n'...%launch the new Matlab session  without display
     'addpath(''' path_uvmat ''');\n'...
-    'addpath(''' ActionPath ''');\n'];
+    'current_dir=pwd;\n'... % current working dir
+    'cd(''' ActionPath ''');\n'...
+'h_fun=str2func(''' ActionName ''');\n'...% create the function handle for the function ActionName
+'cd(current_dir);\n'];
+ %   'addpath(''' ActionPath ''');\n'];
 for iprocess=1:numel(inputxml)
-    cmd=[cmd '' ActionName  '(''' inputxml{iprocess} ''');\n'];
+%    cmd=[cmd '' ActionName  '(''' inputxml{iprocess} ''');\n'];
+cmd=[cmd ' h_fun  (''' inputxml{iprocess} ''');\n'];
 end
 cmd=[cmd  'exit\n' 'END_MATLAB\n'];

trunk/src/get_file_index.m

@@ -46 +46 @@
     switch r.mode
         case 'Di='  %  case 'series(Di)')
-            i1=ref_i-str2num(r.num1);
-            i2=ref_i+str2num(r.num2);
+            i1=ref_i-str2double(r.num1);
+            i2=ref_i+str2double(r.num2);
         case 'Dj='  %  case 'series(Dj)'
-            j1=ref_j-str2num(r.num1);
-            j2=ref_j+str2num(r.num2);
+            j1=ref_j-str2double(r.num1);
+            j2=ref_j+str2double(r.num2);
         case '-'  % case 'bursts'
-            j1=str2num(r.num1)*ones(size(ref_i));
-            j2=str2num(r.num2)*ones(size(ref_i));
+            j1=str2double(r.num1)*ones(size(ref_i));
+            j2=str2double(r.num2)*ones(size(ref_i));
     end
 end

trunk/src/imadoc2struct.m

@@ -34 +34 @@
 
 function [s,errormsg]=imadoc2struct(ImaDoc,varargin) 
-%% default input and output
-errormsg='';%default
-s=[];
+
+s=[]; %default output
 
 %% opening the xml file
-[tild,tild,FileExt]=fileparts(ImaDoc);
-
 if nargin ==1% no additional input variable beyond 'ImaDoc'
     [s,Heading,errormsg]=xml2struct(ImaDoc);% convert the whole xml file in a structure s
@@ -56 +53 @@
     return
 end
+
 %% reading timing
 if isfield(s,'Camera')
@@ -67 +65 @@
 end
 
-
-function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
-%--------------------------------------------------
-s=[];%default
-errormsg='';
-head_element=get(subt,1,'name');
-    cont=get(subt,1,'contents');
-    if ~isempty(cont)
-        for ilist=1:length(Data)
-            uid_key=find(subt,[head_element '/' Data{ilist}]);
-            if ~isequal(length(uid_key),NbOccur(ilist))
-                errormsg=['wrong number of occurence for ' Data{ilist}];
-                return
-            end
-            for ival=1:length(uid_key)
-                val=get(subt,children(subt,uid_key(ival)),'value');
-                if ~NumTest(ilist)
-                    eval(['s.' Data{ilist} '=val;']);
-                else
-                    eval(['s.' Data{ilist} '=str2double(val);'])
-                end
-            end
-        end
-    end
-
-
-%--------------------------------------------------
-%  read an xml element
-function val=get_value(t,label,default)
-%--------------------------------------------------
-val=default;
-uid=find(t,label);%find the element iud(s)
-if ~isempty(uid) %if the element named label exists
-   uid_child=children(t,uid);%find the children 
-   if ~isempty(uid_child)
-       data=get(t,uid_child,'type');%get the type of child
-       if iscell(data)% case of multiple element
-           for icell=1:numel(data)
-               val_read=str2num(get(t,uid_child(icell),'value'));
-               if ~isempty(val_read)
-                   val(icell,:)=val_read;
-               end
-           end
-%           val=val';
-       else % case of unique element value
-           val_read=str2num(get(t,uid_child,'value'));
-           if ~isempty(val_read)
-               val=val_read;
-           else
-              val=get(t,uid_child,'value');%char string data
-           end
-       end
-   end
-end
-
-%------------------------------------------------------------------------
-%'read_imatext': reads the .civ file for image documentation (obsolete)
-% fileinput: name of the documentation file 
-% time: matrix of times for the set of images
-%pxcmx: scale along x in pixels/cm
-%pxcmy: scale along y in pixels/cm
-function [error,time,TimeUnit,mode,npx,npy,GeometryCalib]=read_imatext(fileinput)
-%------------------------------------------------------------------------
-error='';%default
-time=[]; %default
-TimeUnit='s';
-mode='pairs';
-npx=[]; %default
-npy=[]; %default
-GeometryCalib=[];
-if ~exist(fileinput,'file'), error=['image doc file ' fileinput ' does not exist']; return;end;%input file does not exist
-dotciv=textread(fileinput);
-sizdot=size(dotciv);
-if ~isequal(sizdot(1)-8,dotciv(1,1));
-    error=1; %inconsistent number of bursts
-end
-nbfield=sizdot(1)-8;
-npx=(dotciv(2,1));
-npy=(dotciv(2,2));
-pxcmx=(dotciv(6,1));% pixels/cm in the .civ file 
-pxcmy=(dotciv(6,2));
-% nburst=dotciv(3,1); % nbre of bursts
-abs_time1=dotciv([9:nbfield+8],2);
-dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1);
-timeshift=[abs_time1 dtime];
-time=cumsum(timeshift,2);
-GeometryCalib.CalibrationType='rescale';
-GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
-GeometryCalib.Tx=0;
-GeometryCalib.Ty=0;
-GeometryCalib.Tz=1;
-GeometryCalib.dpx=1;
-GeometryCalib.dpy=1;
-GeometryCalib.sx=1;
-GeometryCalib.Cx=0;
-GeometryCalib.Cy=0;
-GeometryCalib.f=1;
-GeometryCalib.kappa1=0;
-GeometryCalib.CoordUnit='cm';

trunk/src/index2filename.m

@@ -1 @@
-% get the file name and frame index from a set of multimage files (e.g. from PCO camera)
+% translate logical indices i1, j1, into file name and frame index in a set of multimage files (e.g. from PCO camera)
 %------------------------------------------------------------------------
-% [RootFile,FileIndexString,FrameIndex]=index2filename(FileSeries,i1,j1,NbField_j)
+% [RootFile,FrameIndex]=index2filename(FileSeries,i1,j1,NbField_j)
 %
 % OUTPUT:
-% RootFile, FileIndexString: name of the multimage file = [RootFile FileIndexString FileExt]
-% FrameIndex: index in the multimage file     
+% FileName: name of the multimage file = [RootFile FileIndexString FileExt]
+% FrameIndex: index in the multimage file FileName    
 %
 % INPUT:
-% FileSeries: structure read from the xml file, defining the the multifile organisation of images  
-% i1: global frame index i, or  single concatenated index vector (then no further input j1 and NbField_j
+% FileSeries: structure read from the xml file, defining the  multifile organisation of images  
+% i1: global frame index i, or  single concatenated index vector (then no  input j1 and NbField_j
 % j1: j index
 % NbField_j: nbre of j indices in the index matrix
@@ -55 +55 @@
         FileName=FileSeries.FileName{FileIndex};
     end
-
-    % switch FileSeries.Convention
-    %     case 'PCO'
-    %         RootFile=FileSeries.RootName;
-    %         FileIndex=floor(i_vector/FileSeries.NbFramePerFile);
-    %         if FileIndex>0
-    %             RootFile=[RootFile '@'];
-    %            FileIndexString=num2str(FileIndex,'%04d');
-    %         end
     FrameIndex=mod(i_vector-1,FileSeries.NbFramePerFile)+1;
 end

trunk/src/keyboard_callback.m

@@ -90 +90 @@
                                 set(handleshaxes.movie_pair,'value',0);
                                 set(handleshaxes.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
-                                set(handleshaxes.i2,'String','')% the second i index display is suppressed
-                                set(handleshaxes.j2,'String','')% the second j index display is suppressed
+                                set(handleshaxes.num_i2,'String','')% the second i index display is suppressed
+                                set(handleshaxes.num_j2,'String','')% the second j index display is suppressed
                                 set(handleshaxes.Dt_txt,'String','')% the time interval indication is suppressed
                             end

trunk/src/phys_XYZ.m

@@ -1 +1 @@
 %------------------------------------------------------------------------
 %'phys_XYZ':transforms image (px) to real world (phys) coordinates using geometric calibration parameters
-% function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Zindex)
+% function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,Slice,X,Y,Zindex)
 %
 %OUTPUT:
@@ -7 +7 @@
 %INPUT:
 % Calib: Matlab structure containing the calibration parameters (pinhole camera model, see 
-% http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#GeometryCalib) and the
-%    parameters describing the illumination plane(s)
+% http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#GeometryCalib) 
 %    .Tx_Ty_Tz: translation (3 phys coordinates) defining the origine of the camera frame
 %    .R : rotation matrix from phys to camera frame
 %    .fx_fy: focal length along each direction of the image
+% Slice: Matlab structure containing the parameters describing the position and inclination of the illumination plane
 % X, Y: vectors of X and Y image coordinates
-% ZIndex: index defining the current illumination plane in a volume scan
+% ZIndex (if needed): index defining the current illumination plane in a volume scan,=1 by default
 
 %=======================================================================
@@ -37 +37 @@
 testangle=0;% =1 if the illumination plane is tilted with respect to the horizontal plane Xphys Yphys
 test_refraction=0;% =1 if the considered points are viewed through an horizontal interface (located at z=Calib.InterfaceCoord(3)') 
+if ~exist('X','var')||~exist('Y','var')
+    Xphys=[];
+    Yphys=[];%default
+    return
+end
 Zphys=0; %default output
+
 if isempty(Slice)
     Slice=Calib;%old convention < 2022
+elseif ~isfield(Slice,'SliceCoord')% bad input
+    Xphys=[];
+    Yphys=[];% bad input
+    return
 end
 if exist('Zindex','var')&& isequal(Zindex,round(Zindex))&& Zindex>0 && isfield(Slice,'SliceCoord')&&size(Slice.SliceCoord,1)>=Zindex
@@ -59 +69 @@
     Z0virt=0;
 end
-if ~exist('X','var')||~exist('Y','var')
-    Xphys=[];
-    Yphys=[];%default
-    return
-end
+
 %coordinate transform
 if ~isfield(Calib,'fx_fy')

trunk/src/read_GUI.m

@@ -43 +43 @@
         switch object_type
             case 'uipanel'
-                eval(['struct.' tag '=read_GUI(hchild(ichild));'])
+                struct.(tag)= read_GUI(hchild(ichild));
             case 'uicontrol'
                 object_style=get(hchild(ichild),'Style');

trunk/src/read_field.m

@@ -58 +58 @@
 errormsg='';
 if isempty(regexp(FileName,'^http://', 'once'))&& ~exist(FileName,'file')
-    errormsg=['input file ' FileName ' does not exist'];
+    errormsg='input file does not exist';
     return
 end

trunk/src/read_multimadoc.m

@@ -35 +35 @@
 warnmsg='';
 if ischar(RootPath)
-    RootPath={RootPath};SubDir={SubDir};RootFile={RootFile};FileExt={FileExt};
+    RootPath={RootPath};SubDir={SubDir};%RootFile={RootFile};FileExt={FileExt};
 end
 nbview=numel(RootPath);

trunk/src/rename_indexing.m

@@ -11 +11 @@
             NewName=[NewName '_1'];%add the index 1
         else
-            newindex=str2num(NewName(rr:end))+1; %increment the index by 1
+            newindex=str2double(NewName(rr:end))+1; %increment the index by 1
             NewName=[NewName(1:rr-1) num2str(newindex)];
         end

trunk/src/series.m

@@ -134 +134 @@
 %% Read the parameter file series.xml, or created from series.xml.default if it does not exist
 SeriesData=[];
-[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
+path_series=fileparts(which('series'));% path to the GUI series
 xmlfile=fullfile(path_series,'series.xml');
 if ~exist(xmlfile,'file')
@@ -157 +157 @@
 NbBuiltinAction=numel(ActionList);
 set(handles.Action,'UserData',NbBuiltinAction)
-path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
-[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
+%path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
+[path_series]=fileparts(which('series')); % path to the GUI series
 path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
 ActionExtList={'.m';'.sh';'fluidimage'}; % default choice of extensions (Matlab fct .m or compiled version .sh
@@ -166 +166 @@
 if isfield(SeriesData.ClusterParam, 'ExistenceTest')
     oarcommand=SeriesData.ClusterParam.ExistenceTest;
-    [s,w]=system(oarcommand); % look for cluster system presence
+    s=system(oarcommand); % look for cluster system presence
     if isequal(s,0)% cluster detected
         RunModeList=[RunModeList;{'cluster'}];
@@ -275 +275 @@
     %% fill the list of input file series
     InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
-    if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info
+    if isempty(find(cellfun('isempty',InputTable)==0,1)) % if there is no input file, do not introduce input info
         set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
         return
     end
-    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
+   % TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
     if isfield(Param.InputFile,'RootPath_1')
         InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
-        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
+       % TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
     end
     set(handles.InputTable,'Data',InputTable)
@@ -291 +291 @@
     set(handles.Device,'String',[Device DeviceExt])
     set(handles.Experiment,'String',[Experiment ExperimentExt])
-    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
+    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)','once'))
     set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
     end
@@ -308 +308 @@
     %% determine the selected reference field indices for pair display
 
-    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
-    if isempty(i1)
-        i1=1;
-    end
-    if isempty(i2)
-        i2=i1;
-    end
+  %  [~,~,~,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
+  i1=1;j1=1;%default
+    if isfield(Param,'i1')
+        i1=Param.i1;
+    end
+    if isfield(Param,'j1')
+        j1=Param.j1;
+    end
+    if isfield(Param,'i2')
+        i2=Param.i2;
+    end
+    if isfield(Param,'j2')
+        j2=Param.j2;
+    end
+    
     ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
     % set(handles.num_ref_i,'String',num2str(ref_i));
@@ -609 +617 @@
 %% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
 MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MinIndex_i_table)
 set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
-end
 MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MinIndex_j_table)
 set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
-end
 MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MaxIndex_i_table)
+
 set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
-end
 MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MaxIndex_j_table)
 set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
-end
 PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(PairString)
 set(handles.PairString,'Data',PairString(1:nbview,:));
-end
 TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(TimeTable)
 set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
-end
 
 %% set length of waitbar
@@ -861 +858 @@
 
 %% display the min and max indices for the whole file series
-if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
+if isempty(i1_series)
+    MinIndex_j=1;MaxIndex_j=1;MinIndex_i=1;MaxIndex_i=1;
+elseif size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
     MinIndex_j=1; % index j set to 1 by default
     MaxIndex_j=1;
@@ -988 +987 @@
 XmlData=[];
 check_calib=0;
-
 XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2});
 if ~isempty(XmlFileName)
@@ -996 +994 @@
     end
     % read time if available
-    if isfield(XmlData,'Time') && strcmp(FileInfo.FieldType,'image')
+    if isfield(XmlData,'Time')
         Time=XmlData.Time;
         TimeName='xml';
@@ -1310 +1308 @@
 end
 PairString=get(handles.PairString,'Data');
-ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
-ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
-ref_j_1=[];ref_j_2=[];
+ref_i_1=str2double(get(handles.num_first_i,'String')); % first reference index
+if isnan(ref_i_1)
+ref_i_1=1;
+end
+ref_i_2=str2double(get(handles.num_last_i,'String')); % last reference index
+if isnan(ref_i_2)
+ref_i_2=1;
+end
+ref_j_1=NaN;ref_j_2=NaN;
 if strcmp(get(handles.num_first_j,'Visible'),'on')
-ref_j_1=str2num(get(handles.num_first_j,'String'));
-ref_j_2=str2num(get(handles.num_last_j,'String'));
+    ref_j_1=str2double(get(handles.num_first_j,'String'));
+    ref_j_2=str2double(get(handles.num_last_j,'String'));
 end
 [i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
@@ -1429 +1433 @@
 
 function errormsg=launch_action(handles)
-errormsg=''; % default
+%errormsg=''; % default
 
 %% read the data on the GUI series
@@ -1637 +1641 @@
         end
     end
-    [xx,ExpName]=fileparts(Param.InputTable{1,1});
-    Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
-    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
+    [~,ExpName]=fileparts(Param.InputTable{1,1});
+    Param.IndexRange.first_i=str2double(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
+    Param.IndexRange.last_i=str2double(get(handles.num_last_i,'String'));
 
     %% create the output data directory if needed, after checking its existence
@@ -1655 +1659 @@
         else
             PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
-            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
+            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'));
         end
         if ~exist(PathExpOut,'dir')
-            [tild,msg1]=mkdir(PathExpOut);
+            [~,msg1]=mkdir(PathExpOut);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
@@ -1665 +1669 @@
         end
         if ~exist(PathExpDeviceOut,'dir')
-            [tild,msg1]=mkdir(PathExpDeviceOut);
+            [~,msg1]=mkdir(PathExpDeviceOut);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
@@ -1710 +1714 @@
         OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
         if check_create    % create output directory if it does not exist
-            [tild,msg1]=mkdir(OutputDir);
+            [~,msg1]=mkdir(OutputDir);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
@@ -1784 +1788 @@
         else
             ref_j=first_j:incr_j:last_j;
-            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
+            [~,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
             ref_i=ref_i-1;
             ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
@@ -1792 +1796 @@
         ref_i=first_i:incr_i:last_i;
         if isempty(incr_j)% automatic finding of the existing j indices
-            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
+            ref_j=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
             ref_j=ref_j-1;
             ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
@@ -1809 +1813 @@
             else
                 answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
-                CPUTime=str2num(answer);
+                CPUTime=str2double(answer);
                 set(handles.num_CPUTime,'String',answer)
                 Param.Action.CPUTime=CPUTime;
@@ -2091 +2095 @@
                 cd(curdir)
             else
-                [tild,msg1]=mkdir(DIR_CLUSTER);
+                [~,msg1]=mkdir(DIR_CLUSTER);
                 if ~strcmp(msg1,'')
                     errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
@@ -2186 +2190 @@
                 cd(curdir)
             else
-                [tild,msg1]=mkdir(DirSGE);
+                [~,msg1]=mkdir(DirSGE);
                 if ~strcmp(msg1,'')
                     errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
@@ -2211 +2215 @@
                         cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
                     end
-                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
+                    fid = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
                     fprintf(fid, cmd);
                     fclose(fid);
@@ -2221 +2225 @@
                         fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
                     fprintf(sge_command); % display in command line
-                    [status, result] = system(sge_command);
+                    [~, result] = system(sge_command);
                     fprintf(result);
                     currJobIndex = currJobIndex + 1;
@@ -2235 +2239 @@
             command = ['python -m fluidimage.run_from_xml ' filexml{iprocess}];
             fprintf(['command:\n' command '\n\n'])
-            [status, result] = call_command_clean(command);
+          %  [status, result] = call_command_clean(command);
     end
     if exist(OutputDir,'dir')
-        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
+        [~,MESSAGE] = fileattrib (OutputDir);
         if MESSAGE.GroupWrite~=1
             [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
@@ -2393 +2397 @@
 %% Put the first line of the selected Action fct as tooltip help
 try
-    [fid,errormsg] =fopen([fullfile(ActionPath,ActionName) '.m']);
+    fid=fopen([fullfile(ActionPath,ActionName) '.m']);
     InputText=textscan(fid,'%s',1,'delimiter','\n');
     fclose(fid);
@@ -2877 +2881 @@
         set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
         if ~strcmp(GetFieldData.FieldOption,'civdata...')
-           if ~isempty(regexp(FieldList{1},'^vec'))
+           if ~isempty(regexp(FieldList{1},'^vec', 'once'))
                 set(handles.FieldName,'Value',1)
            else
@@ -3031 +3035 @@
             datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
         end
-        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
+        [~,indsort2]=sort(datepair); % sort the multiplet by creation date
         ind_s=indsort2(1:end-1); %
         ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
@@ -3058 +3062 @@
     num_j1=meshgrid(num_j,ones(size(num_i1_line)));
     num_j2=meshgrid(num_j,ones(size(num_i1_line)));
-    [xx,num_i1]=meshgrid(num_j,num_i1_line);
-    [xx,num_i2]=meshgrid(num_j,num_i2_line);
+    [~,num_i1]=meshgrid(num_j,num_i1_line);
+    [~,num_i2]=meshgrid(num_j,num_i2_line);
 elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
     if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
@@ -3200 +3204 @@
     MaskTable=cell(NbView,2);
     
-    RootPath=Param.InputTable{1,1};
+    %RootPath=Param.InputTable{1,1};
     first_j=[];% note that the function will propose to cover the whole range of indices
     if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
-    last_j=[];
+   %last_j=[];
     if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
     PairString='';
@@ -3214 +3218 @@
             Param.InputTable{iview,5},Param.InputTable{iview,4},i1,i2,j1,j2);
         
-        [FileInfo,VideoObject]=get_file_info(FirstFileName);
+       % [FileInfo,VideoObject]=get_file_info(FirstFileName);
         
         
@@ -3422 +3426 @@
 %% use a browser to choose the xml file containing the processing config
 InputTable=get(handles.InputTable,'Data');
-oldfile='';
-if isempty(InputTable)
-    oldfile='';
-else
 oldfile=InputTable{1,1}; % current path in InputTable
-end
 if isempty(oldfile)
     % use a file name stored in prefdir

trunk/src/series/beam_forming.m

@@ +1 @@
+%'beam_forming': create images from multi-array acoustic signal (cf. project Philippe Roux)
+%------------------------------------------------------------------------
+% function ParamOut=beam_forming(Param)
+%------------------------------------------------------------------------
+%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%OUTPUT
+% ParamOut: sets options in the GUI series.fig needed for the function
+%
+%INPUT:
+% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
+% In batch mode, Param is the name of the corresponding xml file containing the same information
+% when Param.Action.RUN=0 (as activated when the current Action is selected
+% in series), the function ouput paramOut set the activation of the needed GUI elements
+%
+% Param contains the elements:(use the menu bar command 'export/GUI config' in series to 
+% see the current structure Param)
+%    .InputTable: cell of input file names, (several lines for multiple input)
+%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
+%    .OutputSubDir: name of the subdirectory for data outputs
+%    .OutputDirExt: directory extension for data outputs
+%    .Action: .ActionName: name of the current activated function
+%             .ActionPath:   path of the current activated function
+%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
+%             .RUN =0 for GUI input, =1 for function activation
+%             .RunMode='local','background', 'cluster': type of function  use
+%             
+%    .IndexRange: set the file or frame indices on which the action must be performed
+%    .FieldTransform: .TransformName: name of the selected transform function
+%                     .TransformPath:   path  of the selected transform function
+%    .InputFields: sub structure describing the input fields withfields
+%              .FieldName: name(s) of the field
+%              .VelType: velocity type
+%              .FieldName_1: name of the second field in case of two input series
+%              .VelType_1: velocity type of the second field in case of two input series
+%              .Coord_y: name of y coordinate variable
+%              .Coord_x: name of x coordinate variable
+%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
 %=======================================================================
 % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France

trunk/src/series/bed_scan.m

@@ -61 +61 @@
 %=======================================================================
 
-function ParamOut=bed_scan (Param)
+function ParamOut=bed_scan(Param)
 
 %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
@@ -67 +67 @@
     ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation)
     ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
-    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
-    ParamOut.NbSlice=1; %nbre of slices ('off' by default)
+    ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
+    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
     ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
     ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
@@ -75 +75 @@
     ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
     ParamOut.OutputDirExt='.bed';%set the output dir extension
-    ParamOut.OutputFileMode='NbSlice';% ='=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
-    %check the type of the existence and type of the first input file:
-    Param.IndexRange.last_i=Param.IndexRange.first_i;%keep only the first index in the series
-    if isfield(Param.IndexRange,'first_j')
-    Param.IndexRange.last_j=Param.IndexRange.first_j;
-    end
-    filecell=get_file_series(Param);
-    if ~exist(filecell{1,1},'file')
-        msgbox_uvmat('WARNING','the first input file does not exist')
-    else
-        FileInfo=get_file_info(filecell{1,1});
-        FileType=FileInfo.FileType;
-        if isempty(find(strcmp(FileType,{'image','multimage','mmreader','video'})))% =1 for images
-            msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image is needed'])
-        end
-    end
-return
+    ParamOut.OutputFileMode='NbInput_i';% ='=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice   
+    return
 end
 
@@ -111 +96 @@
 %% root input file names and nomenclature type (cell arrays with one element)
 RootPath=Param.InputTable{1,1};
-
+SubDir=Param.InputTable{1,2};
+RootFile=Param.InputTable{1,3};
+NomType=Param.InputTable{1,4};
+FileExt=Param.InputTable{1,5};
+i_series=Param.IndexRange.first_i:Param.IndexRange.incr_i:Param.IndexRange.last_i;
+j_series=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
+nbfield_i=numel(i_series);
+nbfield_j=numel(j_series);
 
 %% directory for output files
@@ -117 +109 @@
 
 %% get the set of input file names (cell array filecell), and file indices
-[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
+%[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
 % filecell{iview,fileindex}: cell array representing the list of file names
 %        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 
+%        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
-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
-
-%% set of y positions  
-ycalib=[-51 -1 49];% calibration planes
-y_scan=-51+(100/400)*(i1_series{1}-1);% transverse position given by the translating system: first view at y=-51, view 400 at y=+49
+%nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
+% nbfield_i=size(i1_series{1},2); %nb of fields for the i index
+% 
+% nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
+CheckVirtual=false;
+if isfield(Param,'FileSeries')% virtual file indexing used (e.g. multitif images)
+    CheckVirtual=true;
+end
+
+%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%fullfile(
+% EDIT FROM HERE
+%% load the initial scan
+[RootRoot,CamName]=fileparts(RootPath);
+RootRoot=fileparts(RootRoot);
+CalibFolder=fullfile(RootRoot,'EXP_INIT',CamName);
+File_init=fullfile(CalibFolder,'images.png.bed','Z_init.nc');
+Data_init=nc2struct(File_init);
+%% set of y positions
+
+nb_scan=400;% nbre of planes for a scan
+if nbfield_j<400
+    nb_scan=nbfield_j;
+end
+%ycalib=[-51 -1 49];% calibration planes
+y_scan=-51+0.25*(1:nb_scan);% transverse position given by the translating system: first view at y=-51, view 400 at y=+49
+coord_x=0.25:0.25:450;%% coord x in phys coordinates for final projection
+
 Mfiltre=ones(2,10)/20;%filter matrix for imnages
 
 %% calibration data and timing: read the ImaDoc files
-XmlData_A=xml2struct(fullfile(RootPath,'planeA.xml'));
-XmlData_B=xml2struct(fullfile(RootPath,'planeB.xml'));
-XmlData_C=xml2struct(fullfile(RootPath,'planeC.xml'));
-ycalib=[-51 -1 49];% the three y positions for calibration
-fx(1)=XmlData_A.GeometryCalib.fx_fy(1);
+
+XmlData_A=xml2struct(fullfile(CalibFolder,'planeA.xml'));
+XmlData_B=xml2struct(fullfile(CalibFolder,'planeB.xml'));
+XmlData_C=xml2struct(fullfile(CalibFolder,'planeC.xml'));
+ycalib=[-51 -1 49];% the three y positions for calibration=
+fx(1)=XmlData_C.GeometryCalib.fx_fy(1);
 fx(2)=XmlData_B.GeometryCalib.fx_fy(1);
-fx(3)=XmlData_C.GeometryCalib.fx_fy(1);
-fy(1)=XmlData_A.GeometryCalib.fx_fy(2);
+fx(3)=XmlData_A.GeometryCalib.fx_fy(1);
+fy(1)=XmlData_C.GeometryCalib.fx_fy(2);
 fy(2)=XmlData_B.GeometryCalib.fx_fy(2);
-fy(3)=XmlData_C.GeometryCalib.fx_fy(2);
-Tx(1)=XmlData_A.GeometryCalib.Tx_Ty_Tz(1);
+fy(3)=XmlData_A.GeometryCalib.fx_fy(2);
+Tx(1)=XmlData_C.GeometryCalib.Tx_Ty_Tz(1);
 Tx(2)=XmlData_B.GeometryCalib.Tx_Ty_Tz(1);
-Tx(3)=XmlData_C.GeometryCalib.Tx_Ty_Tz(1);
-Ty(1)=XmlData_A.GeometryCalib.Tx_Ty_Tz(2);
+Tx(3)=XmlData_A.GeometryCalib.Tx_Ty_Tz(1);
+Ty(1)=XmlData_C.GeometryCalib.Tx_Ty_Tz(2);
 Ty(2)=XmlData_B.GeometryCalib.Tx_Ty_Tz(2);
-Ty(3)=XmlData_C.GeometryCalib.Tx_Ty_Tz(2);
-R11(1)=XmlData_A.GeometryCalib.R(1,1);
+Ty(3)=XmlData_A.GeometryCalib.Tx_Ty_Tz(2);
+R11(1)=XmlData_C.GeometryCalib.R(1,1);
 R11(2)=XmlData_B.GeometryCalib.R(1,1);
-R11(3)=XmlData_C.GeometryCalib.R(1,1);
-R12(1)=XmlData_A.GeometryCalib.R(1,2);
+R11(3)=XmlData_A.GeometryCalib.R(1,1);
+R12(1)=XmlData_C.GeometryCalib.R(1,2);
 R12(2)=XmlData_B.GeometryCalib.R(1,2);
-R12(3)=XmlData_C.GeometryCalib.R(1,2);
-R21(1)=XmlData_A.GeometryCalib.R(2,1);
+R12(3)=XmlData_A.GeometryCalib.R(1,2);
+R21(1)=XmlData_C.GeometryCalib.R(2,1);
 R21(2)=XmlData_B.GeometryCalib.R(2,1);
-R21(3)=XmlData_C.GeometryCalib.R(2,1);
-R22(1)=XmlData_A.GeometryCalib.R(2,2);
+R21(3)=XmlData_A.GeometryCalib.R(2,1);
+R22(1)=XmlData_C.GeometryCalib.R(2,2);
 R22(2)=XmlData_B.GeometryCalib.R(2,2);
-R22(3)=XmlData_C.GeometryCalib.R(2,2);
-pfx=polyfit(ycalib,fx,1);%get the linear interpolation of each parameter of the three calibrations
+R22(3)=XmlData_A.GeometryCalib.R(2,2);
+pfx=polyfit(ycalib,fx,1);%get thfield_ie linear interpolation of each parameter of the three calibrations
 pfy=polyfit(ycalib,fy,1);
 pTx=polyfit(ycalib,Tx,1);
@@ -169 +183 @@
 p22=polyfit(ycalib,R22,1);
 %get the calibration parameters at each position y by interpolation of the 3 calibration parameters
-for img=1:nbfield_i
+for img=1:nb_scan
     Calib(img).fx_fy(1)=pfx(1)*y_scan(img)+pfx(2);
     Calib(img).fx_fy(2)=pfy(1)*y_scan(img)+pfy(2);
@@ -184 +198 @@
 end
 
-%% check coincdence in time for several input file series
-%not relevant for this function
-
-%% coordinate transform or other user defined transform
-%not relevant for this function
-
-%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
- % EDIT FROM HERE
+
+
 
 %% Load the init bed scan
 tic
-nb_scan=10;
-for img=1:nb_scan
-     img
-    a=flipud(imread(filecell{1,img}));%image of the initial bed
-    if img==1
-        x=1:size(a,2);%image absissa in pixel coordinates
+%filecell=reshape(filecell,nbfield_j,nbfield_i)
+% main loop
+for ifield=1:nbfield_i
+    for img=1:nbfield_j% loop on positions
+        if CheckVirtual
+            [FileName,FrameIndex]=index2filename(Param.FileSeries,i_series(ifield),j_series(img),nbfield_j);
+            InputFile=fullfile(RootPath,SubDir,FileName);
+        else
+            InputFile=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,FileIndex,ifield,[],img);
+            FrameIndex=1;
+        end
+        a=flipud(read_image(InputFile,'multimage',[],FrameIndex));
+        %a=flipud(imread(InputFile));%image of the initial bed  [X_b_new(img,:),Z_b_new(img,:)]=phys_XYZ(Calib(img),[],x,Z_sb(img,:))
+        if img==1
+            [nby,nbx]=size(a);
+            x_ima=1:nbx;%image absissa in pixel coordinates
+            X_phys=zeros(nb_scan,nbx);
+            Z_phys=zeros(nb_scan,nbx);
+        end
+        % filtering
+            a=filter2(Mfiltre,a);%smoothed image
+        amean=mean(a,2);
+     [~,ind_max]=max(amean);% get the max of the image averaged along x, to restrict the search region
+    ind_range=max(1,ind_max-30):min(nby,ind_max+30);% search band to find the line
+    z_ima=get_max(a(ind_range,:))+ind_range(1)-1;% get the max in the search band and shift to express it in indices of the original image
+
+ %       [~,iy]=max(a);% find the max along the first coordinate     Z_s_new=zeros(nb_scan,size(Z_s,2)); y, max values imax and the corresponding  y index iy along the first coordinate y
+        z_ima=smooth(z_ima,20,'rloess');%smooth Z, the image index of max luminosity (dependning on x)
+        [X_phys(img,:),Z_phys(img,:)]=phys_XYZ(Calib(img),[],x_ima,z_ima');
     end
-    % filtering
-    a=filter2(Mfiltre,a);%smoothed image
-    [imax,iy]=max(a);% find the max along the first coordinate y, max values imax and the corresponding  y index iy along the first coordinate y
-    Z_s(img,:)=smooth(iy,40,'rloess');%smooth Z, the image index of max luminosity (dependning on x)
-    Yima=y_scan(img)*ones(size(x));%positions Y transformed into a vector
-    X_new(img,:)=phys_XYZ(Calib(img),x,Yima,1);
-    %X_new(:,img)=phys_scan(x,y(img));
-end
-
-toc
-
-[X,Y]=meshgrid(x,y_scan);
-
-
-%% Load the current bed scan
-for img=1:nb_scan
-   b=flipud(imread(filecell{2,img}));%image of the current bed
-    b=filter2(Mfiltre,b); % filtering
-    [imaxb,iyb]=max(b);
-    Z_sb(img,:)=smooth(iyb,20,'rloess');
-end
-
-%% bed change
-dZ=Z_s-Z_sb;% displacement between current position and initial
-dZ_new=zeros(nb_scan,size(dZ,2));
-for img=1:nb_scan  
-    Yima=y_scan(img)*ones(1,size(dZ,2));
-    [~,dZ_new(img,:)]=phys_XYZ(Calib(img),dZ(img,:),Yima,1);
-   % dZ_new(:,img)=phys_scanz(dZ(:,img),y(img));
-end
-
-
-%% PLOTS
-coord_x=X_new(end,1):0.1:X_new(end,end);
-[Y_m,X_m]=meshgrid(y_scan,coord_x);
-%Y_new=Y';
-dZ_mesh=griddata(X_new,Y,dZ_new,X_m,Y_m);
-
-if checkrun
-    figure(1)
-    hold on
-    plot(x,Z_s+700)
-    % xlim([0 4096])
-    % ylim([0 3000])
-    
-    figure(2)
-    hold on
-    plot(x,Z_sb+700)
-    xlim([0 4096])
-    ylim([0 3000])
-    
-    figure(3)
-    surfc(X_m,Y_m,dZ_mesh)
-    shading interp;
-    colorbar;
-    caxis([0 3]);
-    
-    figure
-    pcolor(X_m,Y_m,dZ_mesh);
-    colormap;
-    set(gca,'Xdir','reverse');
-    caxis([0 3]);
-    shading flat
-    hold on
-    colorbar
-    title('Dz')
-end
-
-%save(fullfile(DirOut,'18OS_f.mat'),'dZ','dZ_new','X','Y','Z_s','Z_sb','y')
-
-% save netcdf
-Data.ListVarName={'coord_x','coord_y','dZ'};
-Data.VarDimName={'coord_x','coord_y',{'coord_y','coord_x'}};
-Data.VarAttribute{1}.Role='coord_x';
-Data.VarAttribute{1}.unit='cm';
-Data.VarAttribute{2}.Role='coord_y';
-Data.VarAttribute{2}.unit='cm';
-Data.VarAttribute{3}.Role='scalar';
-Data.VarAttribute{3}.unit='cm';
-Data.coord_x=[coord_x(1) coord_x(end)];
-Data.coord_y=[y(1) y(end)];
-Data.dZ=dZ_mesh';
-struct2nc(fullfile(DirOut,'dZ.nc'),Data)
-
-%% gives the physical position x from the image position X and the physical position y of the laser plane
-function F=phys_scan(X,y)
-% linear fct of X whose coefficient depend on y in a quadratic way
-F=(9.4*10^(-7)*y.^2-3.09*10^(-4)*y+0.07).*X +(-0.001023*y.^2+0.469*y+186.9);
-
-%% gives the physical position z from the image position Z and the physical position y of the laser plane
-function Fz=phys_scanz(Z,y)
-% scale factor applied to Z depending on the physical position y of the laser plane
-Fz=(-1.4587*10^(-5)*y.^2 + 0.001072*y+0.0833).*Z; %+(-2.1*10^(-6)*x.^2+5.1*10^(-4)*x+0.0735).*Z;
-
- 
+    disp(['last file of ' num2str(ifield)])
+     disp(FileName)
+     disp(FrameIndex)
+
+    %% interpolate on a regular grid
+    %coord_x=X_phys(end,1):0.1:X_phys(end,end);%% coord x in phys coordinates based in the last view plane (the last)
+    [X_m,Y_m]=meshgrid(coord_x,y_scan);
+    Y=y_scan'*ones(1,nbx);%initialisation of X, Y final topography map
+
+    Data.Z=griddata(X_phys,Y,Z_phys,X_m,Y_m);% dZ interpolated on the regular ph1ys grid X_m,Y_m
+    size(Data.Z)
+    size(Data_init.Z_init)
+    Data.dZ=Data.Z-Data_init.Z_init;
+
+    toc
+
+    % save netcdf
+    Data.ListVarName={'coord_x','y_scan','Z','dZ'};
+    Data.VarDimName={'coord_x','y_scan',{'y_scan','coord_x'},{'y_scan','coord_x'}};
+    Data.VarAttribute{1}.Role='coord_x';
+    Data.VarAttribute{1}.unit='cm';
+    Data.VarAttribute{2}.Role='coord_y';
+    Data.VarAttribute{2}.unit='cm';
+    Data.VarAttribute{3}.Role='scalar';
+    Data.VarAttribute{3}.unit='cm';
+        Data.VarAttribute{4}.Role='scalar';
+    Data.VarAttribute{4}.unit='cm';
+    Data.coord_x=coord_x;
+    Data.y_scan=y_scan;
+    struct2nc(fullfile(DirOut,['dZ_' num2str(ifield) '.nc']),Data)
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function iy=get_max(a)% get the max with sub picel resolution
+[a_max,iy]=max(a);
+[Nby,Nbx]=size(a);
+for ind_x=1:Nbx
+    if iy(ind_x)>1 && iy(ind_x)<Nby
+        a_plus=a(iy(ind_x)+1,ind_x);
+        a_min=a(iy(ind_x)-1,ind_x);
+        denom=2*a_max(ind_x)-a_plus-a_min;
+        if denom >0
+            iy(ind_x)=iy(ind_x)+0.5*(a_plus-a_min)/denom;%adjust the position of the max with a quadratic fit of the three points around the max
+        end
+    end
+end

trunk/src/uvmat.m

@@ -40 +40 @@
 %          .FileName_1: name of the current second field (used to detect a  constant field during file scanning)
 %          .FileType: current file type, as defined by the fct  get_file_type.m)
-%          .i1_series,.i2_series,.j1_series,.j1_series: series of i1,i2,j1,j2 indices detected in the input dir,set by  the fct find_file_series
+%          .i1_series,.i2_series,.j1_series,.j1_series: series of num_i1,num_i2,num_j1,num_j2 indices detected in the input dir,set by  the fct find_file_series
 %          .MovieObject: current movie object
 %          .TimeUnit: unit for time
@@ -280 +280 @@
         end
         if isfield(input,'TimeIndex')
-            set(handles.i1,num2str(input.TimeIndex))
+            set(handles.num_i1,num2str(input.TimeIndex))
         end
         if isfield(input,'FieldsString')
@@ -2124 +2124 @@
                 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
+            set(handles.num_i1,'String',num2str(i1_mod));%update the counters
+            set(handles.num_j1,'String',num2str(j1));%update the counters
             check_index=true;
         end
@@ -2131 +2131 @@
 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));
+set(handles.num_i1,'String',num2str(i1));%update the counters
+set(handles.num_i2,'String',num2str(i2));
+set(handles.num_j1,'String',num2str(j1));
+set(handles.num_j2,'String',num2str(j2));
 end
 
@@ -2141 +2141 @@
 function NomType_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
-i1=str2double(get(handles.i1,'String'));
-i2=str2double(get(handles.i2,'String'));
-j1=str2double(get(handles.j1,'String'));
-j2=str2double(get(handles.j2,'String'));
+i1=str2double(get(handles.num_i1,'String'));
+i2=str2double(get(handles.num_i2,'String'));
+j1=str2double(get(handles.num_j1,'String'));
+j2=str2double(get(handles.num_j2,'String'));
 NomType=get(hObject,'String');
 if strcmp(NomType,'level')
-    FileIndex=str2double(get(handles.i1,'String'));
+    FileIndex=str2double(get(handles.num_i1,'String'));
 else
 FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
@@ -2159 +2159 @@
 function NomType_1_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
-i1=str2double(get(handles.i1,'String'));
-i2=str2double(get(handles.i2,'String'));
-j1=str2double(get(handles.j1,'String'));
-j2=str2double(get(handles.j2,'String'));
+i1=str2double(get(handles.num_i1,'String'));
+i2=str2double(get(handles.num_i2,'String'));
+j1=str2double(get(handles.num_j1,'String'));
+j2=str2double(get(handles.num_j2,'String'));
 NomType=get(hObject,'String');
 if strcmp(NomType,'level')
-    FileIndex=str2double(get(handles.i1,'String'));
+    FileIndex=str2double(get(handles.num_i1,'String'));
 else
 FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
@@ -2174 +2174 @@
 
 %------------------------------------------------------------------------
-% --- Executes on button press in InputFileREFRESH.
+% --- Executes on press in button tagged 'InputFileREFRESH'.
 function InputFileREFRESH_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
@@ -2180 +2180 @@
 set(handles.uvmat,'Pointer','watch') % set the mouse pointer to 'watch'
 drawnow
-% get the current input file name:
-[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,FileIndices,FileExt]=read_file_boxes(handles);% get the current input file name:
 errormsg='';
-if isempty(RootFile)
+if isempty(RootFile)% open the file browser if the input file is not defined
     fileinput=uigetfile_uvmat('pick an input file',fullfile(RootPath,SubDir));
     hh=dir(fileinput);
@@ -2198 +2195 @@
         end
     end
-else
-    % initiate the input file series and refresh the current field view:
+else      % initiate the input file series and refresh the current field view:
     [FileInfo,VideoObject]=get_file_info(fullfile(RootPath,SubDir,[RootFile FileIndices FileExt]));
     errormsg=update_rootinfo(handles,RootPath,SubDir,[RootFile FileIndices FileExt],FileInfo,VideoObject,1);
@@ -2208 +2204 @@
     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
     % detect the file type, get the movie object if relevant, and look for the corresponding file series:
-    [RootPath,SubDir,~,i1_series,i2_series,j1_series,j2_series,~,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
+    [RootPath,SubDir,~,i1_series,~,~,~,~,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
     if isempty(i1_series)
         fileinput=uigetfile_uvmat('pick an input file for the second line',fullfile(RootPath,SubDir));
@@ -2311 +2307 @@
 %[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
+% the root name and indices may be corrected by including the first index num_i1 if a corresponding xml file exists
 
 set(handles_RootPath,'String',RootPath);
@@ -2328 +2324 @@
 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));
+    set(handles.num_i1,'String',num2str(i1));
+    set(handles.num_i2,'String',num2str(i2));
+    set(handles.num_j1,'String',num2stra(j1,NomType));
+    set(handles.num_j2,'String',num2stra(j2,NomType));
     if isfield(FileInfo,'MaskFile')
         if exist(FileInfo.MaskFile,'file')
@@ -2350 +2346 @@
     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'));
+    i1_s=str2double(get(handles.num_i1,'String'));
+    i2_0=str2double(get(handles.num_i2,'String'));
     if ~isempty(i2_0)
         i2_s=i2_0;
@@ -2357 +2353 @@
         i2_s=i2;
     end
-    j1_0=stra2num(get(handles.j1,'String'));
+    j1_0=stra2num(get(handles.num_j1,'String'));
     if ~isempty(j1_0)
         j1_s=j1_0;
@@ -2363 +2359 @@
         j1_s=j1;
     end
-    j2_0=stra2num(get(handles.j2,'String'));
+    j2_0=stra2num(get(handles.num_j2,'String'));
     if ~isempty(j2_0)
         j2_s=j2_0;
@@ -2444 +2440 @@
 XmlFileName=find_imadoc(RootPath,SubDir);% search the appropriate ImaDoc xml file 
 [~,XmlName]=fileparts(XmlFileName);
-
 CheckIndexing=false;% test for virtual indexing of frames different from the file name index, false by default
 if isempty(XmlFileName) %no ImaDoc xml file detected
@@ -2453 +2448 @@
     set(handles.view_xml,'String','view xml')
     drawnow
-    [XmlData,warntext]=imadoc2struct(XmlFileName);
+    [XmlData,warntext]=imadoc2struct(XmlFileName);% open xml file ImaDoc
     if ~isempty(warntext)
         msgbox_uvmat('WARNING',warntext)
@@ -2474 +2469 @@
 end
 if CheckIndexing
-set(handles.MenuRelabelFrames,'checked','on')% activate the relabel tool by default
+    set(handles.MenuRelabelFrames,'checked','on')% activate the relabel tool by default
 else
     set(handles.MenuRelabelFrames,'checked','off')
@@ -2488 +2483 @@
 TimeUnit='';%default
 TimeName='';%default
+state_j='off'; % no visualisation of the j index by default
 
 %% get the file series
@@ -2497 +2493 @@
     j1_series=[];
     j2_series=[];
-    nbfield=[];
+    nbfield_i=[];
     nbfield_j=[];
     FileInfo=XmlData.FileInfo;
-    %     if iscell(XmlData.FileSeries.FileName)(handles.i1,'String','1')
-    set(handles.i1,'String','1')% the index does not correspond to file name index anymore
-    set(handles.j1,'String','1')
+    set(handles.num_i1,'String','1')% the index does not correspond to file name index anymore, set i=1, j=1 by default as s start
+    set(handles.num_j1,'String','1')
 else % scan the input folder to get the list of existing files and NomType
     [~,~,~,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject]=...
         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)));
+    nbfield_i=max(max(max(i2_series)));% total number of fields (i index)
+    if isempty(nbfield_i)
+        nbfield_i=max(max(max(i1_series)));
     end
     nbfield_j=max(max(max(j2_series)));% number of fields along j index
@@ -2515 +2510 @@
     end
     if ~isempty(j1_series)&& ~strcmp(NomType,'*')% the j index is used to label the frame in multimage series
-        set(handles.j1,'String','1')
+        set(handles.num_j1,'String','1')
+             state_j='on';
     elseif strcmp(FileInfo.FieldType,'image') && ~isequal(FileInfo.NumberOfFrames,1)
-        set(handles.i1,'String','1')
+        set(handles.num_i1,'String','1')
     end
 end
@@ -2525 +2521 @@
     set(handles.NomType_1,'String',NomType)
 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
 
 
@@ -2562 +2543 @@
             TimeName='xml';%Time possibly documented by the xml file (but priority to the opened file if available)
 end
-
-if ~CheckIndexing && isfield(FileInfo,'FrameRate')% frame rate given in the file (case of video data)
-    TimeUnit='s';
-    if isempty(j1_series) %frame index along i
-        XmlData.Time=zeros(FileInfo.NumberOfFrames+1,2);
-        XmlData.Time(:,2)=(0:1/FileInfo.FrameRate:(FileInfo.NumberOfFrames)/FileInfo.FrameRate)';
-        set(handles.i1,'String','1')% set the frame index to 1 to start the movie
+if CheckIndexing
+    i1=str2double(get(handles.FileIndex,'String'));
+    if isnan(i1)
+        i1=1;
     else
-        XmlData.Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/FileInfo.FrameRate:(FileInfo.NumberOfFrames)/FileInfo.FrameRate);
+        FirstFileIndex=1;
+        if isfield(XmlData.FileSeries,'FirstFileIndex')
+            FirstFileIndex=XmlData.FileSeries.FirstFileIndex;
+        end
+        i1=(i1-FirstFileIndex)*XmlData.FileSeries.NbFramePerFile+1;%frame index deduced from input file index
+    end
+    if isfield(XmlData,'Time') && size(XmlData.Time,2)>1%
+        nbfield_j=size(XmlData.Time,2)-1;
+        nbfield_i=size(XmlData.Time,1)-1;
+        j1=mod(i1-1,nbfield_j)+1;
+        i1=floor((i1-1)/nbfield_j)+1;
+        set(handles.num_j1,'String',num2str(j1))
+        state_j='on';
+    end
+    set(handles.num_i1,'String',num2str(i1))
+else
+    if isfield(FileInfo,'FrameRate')% frame rate given in the file (case of video data)
+        TimeUnit='s';
+        if isempty(j1_series) %frame index along i
+            XmlData.Time=zeros(FileInfo.NumberOfFrames+1,2);
+            XmlData.Time(:,2)=(0:1/FileInfo.FrameRate:(FileInfo.NumberOfFrames)/FileInfo.FrameRate)';
+            set(handles.num_i1,'String','1')% set the frame index to 1 to start the movie
+        else
+            XmlData.Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/FileInfo.FrameRate:(FileInfo.NumberOfFrames)/FileInfo.FrameRate);
+            state_j='on';
+        end
     end
 end
@@ -2618 +2621 @@
 %% store last index in handles.MaxIndex_i and .MaxIndex_j
 last_i_cell=get(handles.MaxIndex_i,'String');
-if isempty(nbfield)
+if isempty(nbfield_i)
     last_i_cell{input_line}='';
 else
-    last_i_cell{input_line}=num2str(nbfield);
+    last_i_cell{input_line}=num2str(nbfield_i);
 end
 set(handles.MaxIndex_i,'String',last_i_cell)
@@ -2629 +2632 @@
 else
      last_j_cell{input_line}=num2str(nbfield_j);
+
 end
 set(handles.MaxIndex_j,'String',last_j_cell);
@@ -2745 +2749 @@
         end
     otherwise
-        set(handles_Fields,'Value',1) % set menu to 'image'
+        set(handles_Fields,'Value',1) % set menu to 'image'j1_series
         set(handles_Fields,'String',{'image'})
         %set(handles.Coord_x,'Value',1);
@@ -2757 +2761 @@
 %% set index navigation options
 scan_option='i';%default
-state_j='off'; %default
+%state_j='off'; %default
 if input_line==2
     if get(handles.scan_j,'Value')
         scan_option='j'; %keep the scan option for the second file series
     end
-    if strcmp(get(handles.j1,'Visible'),'on')
+    if strcmp(get(handles.num_j1,'Visible'),'on')
         state_j='on';
     end
@@ -2799 +2803 @@
 end
 set(handles.scan_j,'Visible',state_j)
-set(handles.j1,'Visible',state_j)
-set(handles.j2,'Visible',state_j)
+set(handles.num_j1,'Visible',state_j)
+set(handles.num_j2,'Visible',state_j)
 set(handles.MaxIndex_j,'Visible',state_j);
 set(handles.j_text,'Visible',state_j);
@@ -2850 +2854 @@
 
 %------------------------------------------------------------------------
-function i1_Callback(hObject, eventdata, handles)
+function num_i1_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
 update_ij(handles,1)
 
 %------------------------------------------------------------------------
-function i2_Callback(hObject, eventdata, handles)
+function num_i2_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
 update_ij(handles,2)
 
 %------------------------------------------------------------------------
-function j1_Callback(hObject, eventdata, handles)
+function num_j1_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
 update_ij(handles,3)
 
 %------------------------------------------------------------------------
-function j2_Callback(hObject, eventdata, handles)
+function num_j2_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
 update_ij(handles,4)
 
 %------------------------------------------------------------------------
-%--- update the index display after action on edit boxes i1, i2, j1 or j2
+%--- update the index display after action on edit boxes num_i1, num_i2, num_j1 or num_j2
 %------------------------------------------------------------------------
 function update_ij(handles,index_rank)
@@ -2878 +2882 @@
 
 if strcmp(NomType,'level')
-    index_string=get(handles.i1,'String');
+    index_string=get(handles.num_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'));
+        i1=str2double(get(handles.num_i1,'String'));
+        j1=str2double(get(handles.num_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);
+        RootFile=index2filename(UvData.XmlData{1}.FileSeries,i1,j1,NbField_j);
+        index_string='';
         set(handles.RootFile,'String',RootFile)
     else
@@ -2892 +2897 @@
         switch index_rank
             case 1
-                index_string=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
+                index_string=fullfile_uvmat('','','','',NomType,stra2num(get(handles.num_i1,'String')),i2,j1,j2);
             case 2
-                index_string=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
+                index_string=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.num_i2,'String')),j1,j2);
             case 3
-                index_string=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
+                index_string=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.num_j1,'String')),j2);
             case 4
-                index_string=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
+                index_string=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.num_j2,'String')));
         end
     end
@@ -2908 +2913 @@
     NomType_1=get(handles.NomType_1,'String');
     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
+    [~,~,~,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
-            index_string_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.num_i1,'String')),i2_1,j1_1,j2_1);
         case 2
-            index_string_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.num_i2,'String')),j1_1,j2_1);
         case 3
-            index_string_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.num_j1,'String')),j2_1);
         case 4
-            index_string_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
+            index_string_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.num_j2,'String')));
     end
     set(handles.FileIndex_1,'String',index_string_1)
@@ -2947 +2952 @@
 %------------------------------------------------------------------------
 mode=get(handles.slices,'String');
-nb_slice_str=get(handles.num_NbSlice,'String');
 if strcmp(mode,'volume')
-    z=stra2num(get(handles.j1,'String'));
-else
-    num=str2double(get(handles.i1,'String'));
+    z=stra2num(get(handles.num_j1,'String'));
+else
+    num=str2double(get(handles.num_i1,'String'));
     nbslice=str2double(get(handles.num_NbSlice,'String'));
     z=mod(num-1,nbslice)+1;
@@ -2980 +2984 @@
         FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
     end
-    heditxml=editxml(FileXml);
+    editxml(FileXml);
 end
 
@@ -2990 +2994 @@
 if isequal(get(handles.CheckMask,'Value'),1)
     [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
-    if isempty(regexp(RootPath,'^http://'))
+    if isempty(regexp(RootPath,'^http://', 'once'))% not opendap input file
         fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line)
     else
@@ -3029 +3033 @@
         [MaskPath,FileName,FileExt]=fileparts(filemask);
         Mask.File=filemask;
-        [RootPath,SubDir,RootFile,i1_series,i2,j1,j2,NomType]=find_file_series(MaskPath,[FileName FileExt]);
+        [~,~,~,i1_series,~,~,~,NomType]=find_file_series(MaskPath,[FileName FileExt]);
         Mask.NbSlice=[];%default
         Mask.VolumeScan=0;% TO UPDATE ***
@@ -3045 +3049 @@
             msgbox_uvmat(['ERROR','error in displaying mask, ' errormsg]);
         end
-        testmask=1;
     end
 else % desactivate mask display
@@ -3073 +3076 @@
     if isfield(MaskInfo,'NbSlice')&& ~isempty(MaskInfo.NbSlice)
         if isfield(MaskInfo,'VolumeScan') &&  MaskInfo.VolumeScan
-            MaskIndex_i=str2double(get(handles.j1,'String'));
+            MaskIndex_i=str2double(get(handles.num_j1,'String'));
         else
-            MaskIndex_i=mod(str2double(get(handles.i1,'String'))-1,MaskInfo.NbSlice)+1;
+            MaskIndex_i=mod(str2double(get(handles.num_i1,'String'))-1,MaskInfo.NbSlice)+1;
         end
         MaskName=[MaskInfo.File '_' num2str(MaskIndex_i) '.png'];
@@ -3274 +3277 @@
 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)
+    i1=str2double(get(handles.num_i1,'String'));
+    j1=str2double(get(handles.num_j1,'String'));%read the field indices (for movie, it is not given by the file name)
     i2=[];j2=[];
 else
     [~,~,~,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
+        i1=str2double(get(handles.num_i1,'String'));%read the field indices (for movie, it is not given by the file name)
+    elseif isempty(j1) && strcmp(get(handles.num_j1,'Visible'),'on')
+        j1=str2double(get(handles.num_j1,'String'));%case of indexed movie
     end
 end
@@ -3290 +3293 @@
     [~,~,~,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=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=str2double(get(handles.j1,'String'));%case of indexed movie
+        i1_1=str2double(get(handles.num_i1,'String'));%read the field indices (for movie, it is not given by the file name)
+    elseif isempty(j1_1) && strcmp(get(handles.num_j1,'Visible'),'on')
+        j1_1=str2double(get(handles.num_j1,'String'));%case of indexed movie
     end
 else
@@ -3302 +3305 @@
     set(handles.CheckFixPair,'Value',0)
 end
-%CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&& isempty(j2));
-
-% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
+%CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(num_i2)&& isempty(num_j2));
+
+% the pair num_i1-num_i2 or num_j1-num_j2 is imposed (check box CheckFixPair selected)
 if isnumeric(increment)
     if get(handles.scan_i,'Value')==1  % case of scanning along index i
@@ -3322 +3325 @@
     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
+    % the pair num_i1-num_i2 or num_j1-num_j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
 else
     ref_i=i1;
@@ -3465 +3468 @@
 
 %% update the index counters if the index move is successfull
-
 if isempty(errormsg)
-    set(handles.i1,'String',num2stra(i1,NomType,1));
+    set(handles.num_i1,'String',num2stra(i1,NomType,1));
     if isequal(i2,i1)
-        set(handles.i2,'String','');
+        set(handles.num_i2,'String','');
     else
-        set(handles.i2,'String',num2stra(i2,NomType,1));
-    end
-    set(handles.j1,'String',num2stra(j1,NomType,2));
+        set(handles.num_i2,'String',num2stra(i2,NomType,1));
+    end
+    set(handles.num_j1,'String',num2stra(j1,NomType,2));
     if isequal(j2,j1)
-        set(handles.j2,'String','');
+        set(handles.num_j2,'String','');
     else
-        set(handles.j2,'String',num2stra(j2,NomType,2));
+        set(handles.num_j2,'String',num2stra(j2,NomType,2));
     end
     if strcmp(NomType,'level')
@@ -3496 +3498 @@
         set(handles.FileIndex_1,'String',indices_1);
     end
-    if isempty(i2), set(handles.i2,'String',''); end % suppress the second index display if not used
-    if isempty(j2), set(handles.j2,'String',''); end
+    if isempty(i2), set(handles.num_i2,'String',''); end % suppress the second index display if not used
+    if isempty(j2), set(handles.num_j2,'String',''); end
 end
 
@@ -3508 +3510 @@
 if ~get(handles.movie_pair,'value')
     set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
-    set(handles.i2,'String','')% the second i index display is suppressed
-    set(handles.j2,'String','')% the second j index display is suppressed
+    set(handles.num_i2,'String','')% the second i index display is suppressed
+    set(handles.num_j2,'String','')% the second j index display is suppressed
     set(handles.Dt_txt,'String','')% the time interval indication is suppressed
     return
@@ -3523 +3525 @@
 
 %% make movie until movie speed is set to 0 or STOP is activated
-hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
 set(handles.STOP,'Visible','on')
 set(handles.speed,'Visible','on')
@@ -3541 +3542 @@
     end
     pause(1.02-get(handles.speed,'Value'));% wait for next image
-    get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')
 end
 set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
 set(handles.movie_pair,'Value',0)
 set(handles.Dt_txt,'String','')
-
 set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back in red
 
 
 %------------------------------------------------------------------------
-% --- Executes on button press in InputFileREFRESH. 
+% --- Executes on press in button tagged 'REFRESH'. 
 function REFRESH_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
@@ -3558 +3557 @@
 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);%read the features of the input file name (first line)
 [~,~,~,~,i2,~,j2]=fileparts_uvmat(FileIndex);% check back the indices used
-if isempty(i2), set(handles.i2,'String',''); end % suppress the second i index display if not used
-if isempty(j2), set(handles.j2,'String',''); end % suppress the second j index display if not used
-if isempty(regexp(RootPath,'^http://','once'))
+if isempty(i2), set(handles.num_i2,'String',''); end % suppress the second i index display if not used
+if isempty(j2), set(handles.num_j2,'String',''); end % suppress the second j index display if not used
+if isempty(regexp(RootPath,'^http://','once'))% if the input is not opendap 
     filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line)
 else
@@ -3571 +3570 @@
     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1]; %build the input file name (second line)
 end
-num_i1=stra2num(get(handles.i1,'String'));
-num_i2=stra2num(get(handles.i2,'String'));
-num_j1=stra2num(get(handles.j1,'String'));
-num_j2=stra2num(get(handles.j2,'String'));
-[tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);% get the indices of the second series from the string FileIndex_1
+num_i1=stra2num(get(handles.num_i1,'String'));
+num_i2=stra2num(get(handles.num_i2,'String'));
+num_j1=stra2num(get(handles.num_j1,'String'));
+num_j2=stra2num(get(handles.num_j2,'String'));
+[~,~,~,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);% get the indices of the second series from the string FileIndex_1
 if isempty(j1_1)% case of movies, the index is not given by file index
     j1_1=num_j1;
 end
-% in case of movies the index is set by edit boxes i1 or j1 (case of movies indexed by index i)
+% in case of movies the index is set by edit boxes num_i1 or num_j1 (case of movies indexed by index i)
 errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
 ResizeFcn(handles.uvmat,[],handles)
@@ -3661 +3660 @@
     frame_index=1;%default
     if UvData.FileInfo{1}.NumberOfFrames>1
+        % if strcmp(NomType,'*')
+        %     if num_i1>UvData.FileInfo{1}.NumberOfFrames
+        %         errormsg='specified frame index exceeds file content';
+        %         return
+        %     else
+        %         frame_index=num_i1;%frame index from a single movies or multimage
+        %     end
+        % else
+        %     if num_j1>UvData.FileInfo{1}.NumberOfFrames
+        %         errormsg='specified frame index exceeds file content';
+        %         return
+        %     else
+        %         frame_index=num_j1;% frame index from a set of indexed movies
+        %     end
+        % end
         if strcmp(NomType,'*')
-            if num_i1>UvData.FileInfo{1}.NumberOfFrames
-                errormsg='specified frame index exceeds file content';
-                return
-            else
-                frame_index=num_i1;%frame index from a single movies or multimage
-            end
+             frame_index=num_i1;%frame index from a single movies or multimage
         else
-            if num_j1>UvData.FileInfo{1}.NumberOfFrames
-                errormsg='specified frame index exceeds file content';
-                return
-            else
-                frame_index=num_j1;% frame index from a set of indexed movies
-            end
+              frame_index=num_j1;% frame index from a set of indexed movies
         end
     end
@@ -3988 +3992 @@
             % TODO: look for time unit attribute
         elseif ~isempty(regexp(TimeName,'^dim:', 'once'))
-            abstime=str2double(get(handles.i1,'String'));
+            abstime=str2double(get(handles.num_i1,'String'));
             TimeUnit='index';
         end
@@ -4873 +4877 @@
                     set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% put file index in the root name
                     set(handles.NomType,'String','')
-                    set(handles.i1,'String','1')% set counter to 1 (now the time index in the input matrix)
+                    set(handles.num_i1,'String','1')% set counter to 1 (now the time index in the input matrix)
                     MaxIndex_i=get(handles.MaxIndex_i,'String');
                     MaxIndex_i{1}=num2str(GetFieldData.Time.TimeDimension);
@@ -4885 +4889 @@
                     set(handles.NomType,'String','*')
                     set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
-                    set(handles.i1,'String','1')% set counter to 1 (now the time index in the input matrix)
+                    set(handles.num_i1,'String','1')% set counter to 1 (now the time index in the input matrix)
                     MaxIndex_i=get(handles.MaxIndex_i,'String');
                     MaxIndex_i{1}=num2str(GetFieldData.Time.TimeDimension);
@@ -5208 +5212 @@
     UvData.FileName_1='';% desactivate the use of a constant second file
     set(handles.uvmat,'UserData',UvData)
-    num_i1=stra2num(get(handles.i1,'String'));
-    num_i2=stra2num(get(handles.i2,'String'));
-    num_j1=stra2num(get(handles.j1,'String'));
-    num_j2=stra2num(get(handles.j2,'String'));
+    num_i1=stra2num(get(handles.num_i1,'String'));
+    num_i2=stra2num(get(handles.num_i2,'String'));
+    num_j1=stra2num(get(handles.num_j1,'String'));
+    num_j2=stra2num(get(handles.num_j2,'String'));
     [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
     errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
@@ -6297 +6301 @@
 % Hints: contents = cellstr(get(hObject,'String')) returns LogLinHisto contents as cell array
 %        contents{get(hObject,'Value')} returns selected item from LogLinHisto
-
-
-
-